@article{yaschenko_alonso_stepanova_2024, title={Arabidopsis as a model for translational research}, volume={2}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koae065}, DOI={10.1093/plcell/koae065}, abstractNote={Abstract}, journal={PLANT CELL}, author={Yaschenko, Anna E. and Alonso, Jose M. and Stepanova, Anna N.}, year={2024}, month={Feb} }
@misc{yaschenko_fenech_mazzoni-putman_alonso_stepanova_2022, title={Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?}, volume={68}, ISSN={["1879-0356"]}, url={https://doi.org/10.1016/j.pbi.2022.102241}, DOI={10.1016/j.pbi.2022.102241}, abstractNote={Gene expression differences between distinct cell types are orchestrated by specific sets of transcription factors and epigenetic regulators acting upon the genome. In plants, the mechanisms underlying tissue-specific gene activity remain largely unexplored. Although transcriptional and epigenetic profiling of individual organs, tissues, and more recently, of single cells can easily detect the molecular signatures of different biological samples, how these unique cell identities are established at the mechanistic level is only beginning to be decoded. Computational methods, including machine learning, used in combination with experimental approaches, enable the identification and validation of candidate cis-regulatory elements driving cell-specific expression. Synthetic biology shows great promise not only as a means of testing candidate DNA motifs but also for establishing the general rules of nature driving promoter architecture and for the rational design of genetic circuits in research and agriculture to confer tissue-specific expression to genes or molecular pathways of interest.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Yaschenko, Anna E. and Fenech, Mario and Mazzoni-Putman, Serina and Alonso, Jose M. and Stepanova, Anna N.}, year={2022}, month={Aug} }
@article{mallery_yanagisawa_zhang_lee_robles_alonso_szymanski_2022, title={Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor}, volume={135}, ISSN={["1477-9137"]}, url={https://doi.org/10.1242/jcs.259825}, DOI={10.1242/jcs.259825}, abstractNote={ABSTRACT}, number={7}, journal={JOURNAL OF CELL SCIENCE}, publisher={The Company of Biologists}, author={Mallery, Eileen L. and Yanagisawa, Makoto and Zhang, Chunhua and Lee, Youngwoo and Robles, Linda M. and Alonso, Jose M. and Szymanski, Daniel B.}, year={2022}, month={Apr} }
@article{chen_bullock_alonso_stepanova_2022, title={To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses}, volume={11}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants11010033}, DOI={10.3390/plants11010033}, abstractNote={Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses.}, number={1}, journal={PLANTS-BASEL}, author={Chen, Hao and Bullock, David A., Jr. and Alonso, Jose M. and Stepanova, Anna N.}, year={2022}, month={Jan} }
@article{mcfarlane_mutwil-anderwald_verbancic_picard_gookin_froehlich_chakravorty_trindade_alonso_assmann_et al._2021, title={A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis}, volume={56}, ISSN={["1878-1551"]}, DOI={10.1016/j.devcel.2021.03.031}, abstractNote={Cellulose is produced at the plasma membrane of plant cells by cellulose synthase (CESA) complexes (CSCs). CSCs are assembled in the endomembrane system and then trafficked to the plasma membrane. Because CESAs are only active in the plasma membrane, control of CSC secretion regulates cellulose synthesis. We identified members of a family of seven transmembrane domain-containing proteins (7TMs) that are important for cellulose production during cell wall integrity stress. 7TMs are often associated with guanine nucleotide-binding (G) protein signaling and we found that mutants affecting the Gβγ dimer phenocopied the 7tm mutants. Unexpectedly, the 7TMs localized to the Golgi/trans-Golgi network where they interacted with G protein components. Here, the 7TMs and Gβγ regulated CESA trafficking but did not affect general protein secretion. Our results outline how a G protein-coupled module regulates CESA trafficking and reveal that defects in this process lead to exacerbated responses to cell wall integrity stress.}, number={10}, journal={DEVELOPMENTAL CELL}, author={McFarlane, Heather E. and Mutwil-Anderwald, Daniela and Verbancic, Jana and Picard, Kelsey L. and Gookin, Timothy E. and Froehlich, Anja and Chakravorty, David and Trindade, Luisa M. and Alonso, Jose M. and Assmann, Sarah M. and et al.}, year={2021}, month={May}, pages={1484-+} }
@article{mazzoni-putman_brumos_zhao_alonso_stepanova_2021, title={Auxin Interactions with Other Hormones in Plant Development}, volume={13}, ISSN={1943-0264}, url={http://dx.doi.org/10.1101/cshperspect.a039990}, DOI={10.1101/cshperspect.a039990}, abstractNote={Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.}, number={10}, journal={Cold Spring Harbor Perspectives in Biology}, publisher={Cold Spring Harbor Laboratory}, author={Mazzoni-Putman, Serina M. and Brumos, Javier and Zhao, Chengsong and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr}, pages={a039990} }
@misc{zhao_yaschenko_alonso_stepanova_2021, title={Leveraging synthetic biology approaches in plant hormone research}, volume={60}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2020.10998}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Zhao, Chengsong and Yaschenko, Anna and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr} }
@article{brumos_zhao_gong_soriano_patel_perez-amador_stepanova_alonso_2020, title={An Improved Recombineering Toolset for Plants}, url={https://doi.org/10.1105/tpc.19.00431}, DOI={10.1105/tpc.19.00431}, abstractNote={Abstract}, journal={The Plant Cell}, author={Brumos, Javier and Zhao, Chengsong and Gong, Yan and Soriano, David and Patel, Arjun P. and Perez-Amador, Miguel A. and Stepanova, Anna N. and Alonso, Jose M.}, year={2020}, month={Jan} }
@article{bagley_stepanova_ekelof_alonso_muddiman_2020, title={Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings}, volume={34}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.8616}, abstractNote={RationaleMass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin‐related compounds using stable‐isotope‐labelled (SIL) indole‐3‐acetic acid (IAA) doped into agarose substrate.}, number={6}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Stepanova, Anna N. and Ekelof, Mans and Alonso, Jose M. and Muddiman, David C.}, year={2020}, month={Mar} }
@article{dolores gomez_barro-trastoy_fuster-almunia_tornero_alonso_perez-amador_2020, title={Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis}, volume={71}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/eraa395}, abstractNote={Abstract}, number={22}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Dolores Gomez, Maria and Barro-Trastoy, Daniela and Fuster-Almunia, Clara and Tornero, Pablo and Alonso, Jose M. and Perez-Amador, Miguel A.}, year={2020}, month={Dec}, pages={7059–7072} }
@article{barro‐trastoy_carrera_baños_palau‐rodríguez_ruiz‐rivero_tornero_alonso_lópez‐díaz_gómez_pérez‐amador_2020, title={Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms}, url={https://doi.org/10.1111/tpj.14684}, DOI={10.1111/tpj.14684}, abstractNote={Summary}, journal={The Plant Journal}, author={Barro‐Trastoy, Daniela and Carrera, Esther and Baños, Jorge and Palau‐Rodríguez, Julia and Ruiz‐Rivero, Omar and Tornero, Pablo and Alonso, José M. and López‐Díaz, Isabel and Gómez, María Dolores and Pérez‐Amador, Miguel A.}, year={2020}, month={Jun} }
@inbook{perkins_stepanova_alonso_heber_2020, place={Cham, Switzerland}, series={Lecture Notes in Computer Science}, title={RiboSimR: A Tool for Simulation and Power Analysis of Ribo-seq Data}, ISBN={9783030461645 9783030461652}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-030-46165-2_10}, DOI={10.1007/978-3-030-46165-2_10}, abstractNote={RNA-seq and Ribo-seq are widespread quantitative methods for assessing transcription and translation. They can be used to detect differential expression, differential translation, and differential translation efficiency between conditions. The statistical power to detect differential genes is affected by multiple factors, such as the number of replicates, sequencing depth, magnitude of differential expression and translation, distribution of gene counts, and method for estimating biological variance. As power estimation of translational efficiency involves the combination of both RNA-seq measurements and Ribo-seq measurements, this task is particularly challenging. Here we propose a power assessment tool, called RiboSimR, based purely on data simulation. RiboSimR, produces semi-parametric simulations that generate data based on real RNA and Ribo-seq experiments, with customizable choices on baseline parameters and tool configurations. We demonstrate the usefulness of our tool by simulating data based on two published Ribo-seq datasets and analyzing various aspects of experimental design.}, booktitle={Computational Advances in Bio and Medical Sciences}, publisher={Springer International Publishing}, author={Perkins, Patrick and Stepanova, Anna and Alonso, Jose and Heber, Steffen}, editor={Măndoiu, I. and Murali, T. and Narasimhan, G. and Rajasekaran, S. and Skums, P. and Zelikovsky, A.Editors}, year={2020}, pages={121–133}, collection={Lecture Notes in Computer Science} }
@article{brumos_bobay_clark_alonso_stepanova_2020, title={Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes}, volume={183}, url={https://doi.org/10.1104/pp.20.00310}, DOI={10.1104/pp.20.00310}, abstractNote={Structure–function modeling explores the basis of interallelic complementation in multiple combinations of rooty alleles. Auxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in genes involved in glucosinolate biosynthesis, a metabolically related route that produces defense compounds, result in auxin overproduction. We identified an allelic series of fertile, hypomorphic Arabidopsis (Arabidopsis thaliana) mutants for the essential glucosinolate biosynthetic gene ROOTY (RTY) that exhibit a range of phenotypic defects characteristic of enhanced auxin production. Genetic characterization of these lines uncovered phenotypic suppression by cyp79b2 cyp79b3, wei2, and wei7 mutations and revealed the phenomenon of interallelic complementation in several RTY transheterozygotes. Structural modeling of RTY elucidated the relationships between structure and function in the RTY homo- and heterodimers, and unveiled the likely structural basis of interallelic complementation. This work underscores the importance of employing true null mutants in genetic complementation studies.}, number={3}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Brumos, Javier and Bobay, Benjamin G. and Clark, Cierra A. and Alonso, Jose M. and Stepanova, Anna N.}, year={2020}, month={Jul}, pages={1110–1125} }
@article{brumos_zhao_gong_soriano_patel_perez-amador_stepanova_alonso_2019, title={An improved plant toolset for high-throughput recombineering}, volume={6}, url={https://doi.org/10.1101/659276}, DOI={10.1101/659276}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Brumos, J. and Zhao, C. and Gong, Y. and Soriano, D. and Patel, A.P. and Perez-Amador, M.A. and Stepanova, A.N. and Alonso, J.M}, year={2019}, month={Jun} }
@article{stepanova_alonso_2019, title={From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration}, volume={31}, ISSN={["1532-298X"]}, url={https://doi.org/10.1105/tpc.19.00339}, DOI={10.1105/tpc.19.00339}, abstractNote={The field of plant hormone biology, like many other research areas in plant sciences, has benefited tremendously from the adoption of Arabidopsis ( Arabidopsis thaliana ) as a model system. The development of a great genetic toolbox in this species led to the identification of many of the core}, number={7}, journal={PLANT CELL}, publisher={American Society of Plant Biologists (ASPB)}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2019}, month={Jul}, pages={1393–1394} }
@article{dolores gomez_fuster-almunia_ocana-cuesta_alonso_perez-amador_2019, title={RGL2 controls flower development, ovule number and fertility in Arabidopsis}, volume={281}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2019.01.014}, abstractNote={DELLA proteins are a group of plant specific GRAS proteins of transcriptional regulators that have a key role in gibberellin (GA) signaling. In Arabidopsis, the DELLA family is formed by five members. The complexity of this gene family raises the question on whether single DELLA proteins have specific or overlapping functions in the control of several GA-dependent developmental processes. To better understand the roles played by RGL2, one of the DELLA proteins in Arabidopsis, two transgenic lines that express fusion proteins of Venus-RGL2 and a dominant version of RGL2, YPet-rgl2Δ17, were generated by recombineering strategy using a genomic clone that contained the RGL2 gene. The dominant YPet-rgl2Δ17 protein is not degraded by GAs, and therefore it blocks the RGL2-dependent GA signaling and hence RGL2-dependent development. The RGL2 role in seed germination was further confirmed using these genetic tools, while new functions of RGL2 in plant development were uncovered. RGL2 has a clear function in the regulation of flower development, particularly stamen growth and anther dehiscence, which has a great impact in fertility. Moreover, the increased ovule number in the YPet-rgl2Δ17 line points out the role of RGL2 in the determination of ovule number.}, journal={PLANT SCIENCE}, author={Dolores Gomez, Maria and Fuster-Almunia, Clara and Ocana-Cuesta, Javier and Alonso, Jose M. and Perez-Amador, Miguel A.}, year={2019}, month={Apr}, pages={82–92} }
@article{perkins_mazzoni-putman_stepanova_alonso_heber_2019, title={RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data}, volume={20}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-019-5700-7}, abstractNote={Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell's transcriptome. In practice, Ribo-seq data analysis can be sensitive to quality issues such as read length variation, low read periodicities, and contaminations with ribosomal and transfer RNA. Various software tools for data preprocessing, quality assessment, analysis, and visualization of Ribo-seq data have been developed. However, many of these tools require considerable practical knowledge of software applications, and often multiple different tools have to be used in combination with each other.We present riboStreamR, a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application. RiboStreamR provides visualization and analysis tools for various Ribo-seq QC metrics, including read length distribution, read periodicity, and translational efficiency. Our platform is focused on providing a user-friendly experience, and includes various options for graphical customization, report generation, and anomaly detection within Ribo-seq datasets.RiboStreamR takes advantage of the vast resources provided by the R and Bioconductor environments, and utilizes the Shiny R package to ensure a high level of usability. Our goal is to develop a tool which facilitates in-depth quality assessment of Ribo-seq data by providing reference datasets and automatically highlighting quality issues and anomalies within datasets.}, journal={BMC GENOMICS}, author={Perkins, Patrick and Mazzoni-Putman, Serina and Stepanova, Anna and Alonso, Jose and Heber, Steffen}, year={2019}, month={Jun} }
@article{bhosale_giri_pandey_giehl_hartmann_traini_truskina_leftley_hanlon_swarup_et al._2018, title={A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/S41467-018-03851-3}, DOI={10.1038/S41467-018-03851-3}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and et al.}, year={2018}, month={Apr} }
@article{bhosale_giri_pandey_giehl_hartmann_traini_truskina_leftley_hanlon_swarup_et al._2018, title={Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/S41467-018-04281-X}, DOI={10.1038/S41467-018-04281-X}, abstractNote={The original version of this Article omitted the following from the Acknowledgements: ‘We also thank DBT-CREST BT/HRD/03/01/2002.’ This has been corrected in both the PDF and HTML versions of the Article.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and et al.}, year={2018}, month={May}, pages={1818} }
@article{gomez_barro-trastoy_escoms_saura-sánchez_sánchez_briones-moreno_vera-sirera_carrera_ripoll_yanofsky_et al._2018, title={Gibberellins negatively modulate ovule number in plants}, volume={145}, ISSN={1477-9129 0950-1991}, url={http://dx.doi.org/10.1242/dev.163865}, DOI={10.1242/dev.163865}, abstractNote={Ovule formation is a complex developmental process in plants with a strong impact on the production of seeds. Ovule primordia initiation is controlled by a gene network, including components of the signaling pathways of auxin, brassinosteroids and cytokinins. In contrast, gibberellins (GAs) and their signaling negative regulators DELLA proteins have never been shown to be involved in ovule initiation. Here we provide molecular and genetic evidences that point to DELLA proteins as novel players in the determination of ovule number in Arabidopsis and in species of agronomic interest like tomato and rapeseed, adding a new layer of complexity to this important developmental process. DELLA activity correlates positively with ovule number, acting as a positive factor for ovule initiation. In addition, ectopic expression of a dominant DELLA in the placenta is sufficient to increase ovule number. The role of DELLA proteins in ovule number seems not to be related to auxins transport or signaling in the ovule primordia. A possible crosstalk of DELLA proteins with the molecular and hormonal network controlling ovule initiation is discussed.}, number={13}, journal={Development}, publisher={The Company of Biologists}, author={Gomez, M. D. and Barro-Trastoy, D. and Escoms, E. and Saura-Sánchez, M. and Sánchez, I. and Briones-Moreno, A. and Vera-Sirera, F. and Carrera, E. and Ripoll, J. J. and Yanofsky, M. F. and et al.}, year={2018}, month={Jan}, pages={dev163865} }
@article{brumos_robles_yun_vu_jackson_alonso_stepanova_2018, title={Local Auxin Biosynthesis Is a Key Regulator of Plant Development}, volume={47}, ISSN={["1878-1551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055097260&partnerID=MN8TOARS}, DOI={10.1016/j.devcel.2018.09.022}, abstractNote={Auxin is a major phytohormone that controls numerous aspects of plant development and coordinates plant responses to the environment. Morphogenic gradients of auxin govern cell fate decisions and underlie plant phenotypic plasticity. Polar auxin transport plays a central role in auxin maxima generation. The discovery of the exquisite spatiotemporal expression patterns of auxin biosynthesis genes of the WEI8/TAR and YUC families suggested that local auxin production may contribute to the formation of auxin maxima. Herein, we systematically addressed the role of local auxin biosynthesis in plant development and responses to the stress phytohormone ethylene by manipulating spatiotemporal patterns of WEI8. Our study revealed that local auxin biosynthesis and transport act synergistically and are individually dispensable for root meristem maintenance. In contrast, flower fertility and root responses to ethylene require local auxin production that cannot be fully compensated for by transport in the generation of morphogenic auxin maxima.}, number={3}, journal={DEVELOPMENTAL CELL}, author={Brumos, Javier and Robles, Linda M. and Yun, Jeonga and Vu, Thien C. and Jackson, Savannah and Alonso, Jose M. and Stepanova, Anna N.}, year={2018}, month={Nov}, pages={306-+} }
@article{yanagisawa_alonso_szymanski_2018, title={Microtubule-Dependent Confinement of a Cell Signaling and Actin Polymerization Control Module Regulates Polarized Cell Growth}, volume={28}, ISSN={0960-9822}, url={http://dx.doi.org/10.1016/J.CUB.2018.05.076}, DOI={10.1016/J.CUB.2018.05.076}, abstractNote={Cell types with wildly varying shapes use many of the same signaling and cytoskeletal proteins to dynamically pattern their geometry [1-3]. Plant cells are encased in a tough outer cell wall, and growth patterns are indirectly controlled by the cytoskeleton and its ability to locally specify the material properties of the wall [4, 5]. Broad and non-overlapping domains of actin and microtubules are predicted to create sharp cell-wall boundaries with distinct mechanical properties [6] that are often proposed to direct growth patterns and cell shape [1, 6, 7]. However, mechanisms by which the cytoskeleton is patterned at the spatial and temporal scales that dictate cell morphology are not known. Here, we used combinations of live-cell imaging probes and unique morphology mutants in Arabidopsis to discover how the microtubule and actin systems are spatially coordinated to pattern polarized growth in leaf epidermal cells. The DOCK family guanine nucleotide exchange factor (GEF) SPIKE1 [8, 9] clusters and activates conserved heteromeric WAVE/SCAR and ARP2/3 complexes at the cell apex to generate organized actin networks that define general cytoplasmic flow patterns. Cortical microtubules corral punctate SPIKE1 signaling nodules and restrict actin polymerization within a broad microtubule-depletion zone at the cell apex. Our data provide a useful model for cell-shape control, in which a GEF, actin filament nucleation complexes, microtubules, and the cell wall function as interacting systems that dynamically pattern polarized growth.}, number={15}, journal={Current Biology}, publisher={Elsevier BV}, author={Yanagisawa, Makoto and Alonso, Jose M. and Szymanski, Daniel B.}, year={2018}, month={Aug}, pages={2459–2466.e4} }
@article{estrada-johnson_csukasi_pizarro_vallarino_kiryakova_vioque_merchante_brumos_medina-escobar_botella_et al._2017, title={Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017)}, volume={8}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2017.01305}, abstractNote={[This corrects the article on p. 889 in vol. 8, PMID: 28611805.].}, journal={FRONTIERS IN PLANT SCIENCE}, author={Estrada-Johnson, Elizabeth and Csukasi, Fabiana and Pizarro, Carmen M. and Vallarino, Jose G. and Kiryakova, Yulia and Vioque, Amalia and Merchante, Catharina and Brumos, Javier and Medina-Escobar, Nieves and Botella, Miguel A. and et al.}, year={2017}, month={Jul} }
@article{estrada-johnson_csukasi_pizarro_vallarino_kiryakova_vioque_brumos_medina-escobar_botella_alonso_et al._2017, title={Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle}, volume={8}, journal={Frontiers in Plant Science}, author={Estrada-Johnson, E. and Csukasi, F. and Pizarro, C. M. and Vallarino, J. G. and Kiryakova, Y. and Vioque, A. and Brumos, J. and Medina-Escobar, N. and Botella, M. A. and Alonso, J. M. and et al.}, year={2017} }
@article{merchante_stepanova_alonso_2017, title={Translation regulation in plants: an interesting past, an exciting present and a promising future}, volume={90}, ISSN={["1365-313X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85017002891&partnerID=MN8TOARS}, DOI={10.1111/tpj.13520}, abstractNote={Summary}, number={4}, journal={PLANT JOURNAL}, author={Merchante, Catharina and Stepanova, Anna N. and Alonso, Jose M.}, year={2017}, month={May}, pages={628–653} }
@book{merchante_yun_valpuesta-fernandez_stepanova_alonso_2017, title={Translation regulation of uORFs-containing genes in Arabidopsis}, author={Merchante, C. and Yun, J. and Valpuesta-Fernandez, V. and Stepanova, A. and Alonso, J.}, year={2017} }
@misc{provart_alonso_assmann_bergmann_brady_brkljacic_browse_chapple_colot_cutler_et al._2016, title={50 years of Arabidopsis research: Highlights and future directions}, volume={209}, number={3}, journal={New Phytologist}, author={Provart, N. J. and Alonso, J. and Assmann, S. M. and Bergmann, D. and Brady, S. M. and Brkljacic, J. and Browse, J. and Chapple, C. and Colot, V. and Cutler, S. and et al.}, year={2016}, pages={921–944} }
@article{merchante_hu_heber_alonso_stepanova_2016, title={A Ribosome Footprinting Protocol for Plants}, volume={6}, ISSN={2331-8325}, url={http://dx.doi.org/10.21769/bioprotoc.1985}, DOI={10.21769/bioprotoc.1985}, abstractNote={[Abstract] Ribosome footprinting, or Ribo-seq, has revolutionized the studies of translation. It was originally developed for yeast and mammalian cells in culture (Ingolia et al ., 2009). Herein, we describe a plant-optimized hands-on ribosome footprinting protocol derived from previously published procedures of polysome isolation (Ingolia et al ., 2009; Mustroph et al ., 2009) and ribosome footprinting (Ingolia et al ., 2009; Ingolia et al ., 2013). With this protocol, we have been able to successfully isolate and analyze high-quality ribosomal footprints from different stages of in vitro grown Arabidopsis thaliana plants (dark-grown seedlings [Merchante et al ., 2015] and 13-day-old plantlets in plates and plants grown in liquid culture [unpublished results]).}, number={21}, journal={BIO-PROTOCOL}, publisher={Bio-Protocol, LLC}, author={Merchante, Catharina and Hu, Qiwen and Heber, Steffen and Alonso, Jose and Stepanova, Anna}, year={2016} }
@article{stepanova_alonso_2016, title={Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis}, volume={113}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84989870534&partnerID=MN8TOARS}, DOI={10.1073/pnas.1613506113}, abstractNote={Plants rely on the levels and concentration gradients of the hormone auxin as crucial information cues to trigger and modulate almost every aspect of their life cycle, from establishing embryo polarity to promoting phototropic and gravitropic responses (1). Thus, it is critical for plants to finely control the levels of the bioactive form of this hormone, both at spatial and temporal levels. Local production, transport, conjugation, storage, and catabolism are all well-known processes participating in the dynamic regulation of auxin homeostasis (2). It is, however, unknown whether or how these different auxin homeostasis mechanisms talk to each other. In the past 30 y, the identification of the genes coding for the key components of the auxin biosynthetic, transport, and conjugation machineries has proven instrumental in assessing the contribution of each of these processes to concrete developmental pathways, as well as to specific plant responses to environmental changes. Although much less is known about the ways the predominant auxin, indole-3-acetic acid (IAA), is catabolized, classical labeling and metabolite quantification experiments indicate that the oxidation of IAA into 2-oxindole-3-acetic acid (oxIAA) is one of the most prevalent mechanisms to inactivate this hormone (3). Identifying the specific enzymes catalyzing this reaction in vivo has proved to be more challenging than anticipated, as different plant peroxidases and oxygenases, the original suspects for catalyzing this reaction, were found not to play a significant physiological role in the production of oxIAA (3). The recent identification of a rice 2-oxoglutarate-dependent-Fe(II) dioxygenase, DIOXYGENASE FOR AUXIN OXIDATION ( DAO ), originally linked to male fertility in rice and capable of oxidizing IAA into oxIAA (1⇓⇓–4), has opened new avenues for addressing the physiological significance of auxin catabolism in plant growth and development. In PNAS, Zhang et al. (5), Porco et al. (6), and Mellor et al. (7 …
[↵][1]1To whom correspondence should be addressed. Email: jmalonso{at}ncsu.edu.
[1]: #xref-corresp-1-1}, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2016}, month={Sep}, pages={10742–10744} }
@article{stepanova_alonso_2016, title={Cutting Out the Middle Man in Light-Hormone Interactions}, volume={39}, ISSN={["1878-1551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85000977812&partnerID=MN8TOARS}, DOI={10.1016/j.devcel.2016.11.013}, abstractNote={In this issue of Developmental Cell, Shi et al. (2016a) show that red-light-activated phytochrome B interacts with transcriptional regulators of ethylene signaling, EIN3/EIL1, triggering their degradation by bringing the F-box proteins EBF1 and 2 to the complex. These findings provide a paradigm for crosstalk between light and hormone signaling pathways.}, number={5}, journal={DEVELOPMENTAL CELL}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2016}, month={Dec}, pages={524–526} }
@article{hu_merchante_stepanova_alonso_heber_2016, title={Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana}, volume={15}, number={2}, journal={IEEE Transactions on Nanobioscience}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2016}, pages={150–159} }
@book{merchante_brumós_yun_stepanova_alonso_2016, title={Hormone-Mediated Gene-Specific Translation Regulation}, url={http://hdl.handle.net/10630/11885}, author={Merchante, C. and Brumós, J. and Yun, J. and Stepanova, A. and Alonso, J.}, year={2016} }
@article{alonso_stepanova_2015, title={A Recombineering-based gene tagging system for Arabidopsis}, volume={1227}, journal={Bacterial artificial chromosomes, 2nd edition}, author={Alonso, J. M. and Stepanova, A. N.}, year={2015}, pages={233–243} }
@inbook{hu_merchante_stepanova_alonso_heber_2015, title={A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana}, volume={9096}, ISBN={9783319190471 9783319190488}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-319-19048-8_12}, DOI={10.1007/978-3-319-19048-8_12}, abstractNote={Upstream open reading frames (uORFs) are open reading frames located within the 5’ UTR of an mRNA. It is believed that translated uORFs reduce the translational efficiency of the main coding region, and play an important role in gene regulation. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a stacking-based classification approach to identify translated uORFs in Arabidopsis thaliana. Our approach resulted in a set of 5360 potentially translated uORFs in 2051 genes. GO terms enriched in uORF-containing genes include gene regulation, signal transduction and metabolic pathway. The identified uORFs occur with a higher frequency in multi-isoform genes, and many uORFs are affected by alternative transcript start sites or alternative splicing events.}, booktitle={Bioinformatics Research and Applications}, publisher={Springer International Publishing}, author={Hu, Qiwen and Merchante, Catharina and Stepanova, Anna N. and Alonso, Jose M. and Heber, Steffen}, year={2015}, pages={138–149} }
@inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana}, volume={9096}, booktitle={Bioinformatics research and applications (isbra 2015)}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2015}, pages={138–149} }
@article{fabregas_formosa-jordan_confraria_siligato_alonso_swarup_bennett_mahonen_cano-delgado_ibanes_2015, title={Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana}, volume={11}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1005183}, abstractNote={Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants.}, number={4}, journal={PLOS GENETICS}, author={Fabregas, Norma and Formosa-Jordan, Pau and Confraria, Ana and Siligato, Riccardo and Alonso, Jose M. and Swarup, Ranjan and Bennett, Malcolm J. and Mahonen, Ari Pekka and Cano-Delgado, Ana I. and Ibanes, Marta}, year={2015}, month={Apr} }
@article{moreno-risueno_sozzani_yardimici_petricka_vernoux_blilou_alonso_winter_ohler_scheres_et al._2015, title={Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots}, volume={350}, ISSN={["1095-9203"]}, DOI={10.1126/science.aad1171}, abstractNote={Multifunctional root regulators}, number={6259}, journal={Science}, author={Moreno-Risueno, MA. and Sozzani, R. and Yardimici, GG. and Petricka, JJ. and Vernoux, T. and Blilou, I. and Alonso, J. and Winter, CM. and Ohler, U. and Scheres, B. and et al.}, year={2015}, pages={426–430} }
@article{worden_wilkop_esteve_jeannotte_lathe_vernhettes_weimer_hicks_alonso_labavitch_et al._2015, title={CESA TRAFFICKING INHIBITOR Inhibits Cellulose Deposition and Interferes with the Trafficking of Cellulose Synthase Complexes and Their Associated Proteins KORRIGAN1 and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN}, volume={167}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.114.249003}, DOI={10.1104/pp.114.249003}, abstractNote={The compound CESTRIN reduces cellulose content and inhibits the trafficking of CESA in Arabidopsis hypocotyls. Cellulose synthase complexes (CSCs) at the plasma membrane (PM) are aligned with cortical microtubules (MTs) and direct the biosynthesis of cellulose. The mechanism of the interaction between CSCs and MTs, and the cellular determinants that control the delivery of CSCs at the PM, are not yet well understood. We identified a unique small molecule, CESA TRAFFICKING INHIBITOR (CESTRIN), which reduces cellulose content and alters the anisotropic growth of Arabidopsis (Arabidopsis thaliana) hypocotyls. We monitored the distribution and mobility of fluorescently labeled cellulose synthases (CESAs) in live Arabidopsis cells under chemical exposure to characterize their subcellular effects. CESTRIN reduces the velocity of PM CSCs and causes their accumulation in the cell cortex. The CSC-associated proteins KORRIGAN1 (KOR1) and POM2/CELLULOSE SYNTHASE INTERACTIVE PROTEIN1 (CSI1) were differentially affected by CESTRIN treatment, indicating different forms of association with the PM CSCs. KOR1 accumulated in bodies similar to CESA; however, POM2/CSI1 dissociated into the cytoplasm. In addition, MT stability was altered without direct inhibition of MT polymerization, suggesting a feedback mechanism caused by cellulose interference. The selectivity of CESTRIN was assessed using a variety of subcellular markers for which no morphological effect was observed. The association of CESAs with vesicles decorated by the trans-Golgi network-localized protein SYNTAXIN OF PLANTS61 (SYP61) was increased under CESTRIN treatment, implicating SYP61 compartments in CESA trafficking. The properties of CESTRIN compared with known CESA inhibitors afford unique avenues to study and understand the mechanism under which PM-associated CSCs are maintained and interact with MTs and to dissect their trafficking routes in etiolated hypocotyls.}, number={2}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Worden, Natasha and Wilkop, Thomas E. and Esteve, Victor Esteva and Jeannotte, Richard and Lathe, Rahul and Vernhettes, Samantha and Weimer, Bart and Hicks, Glenn and Alonso, Jose and Labavitch, John and et al.}, year={2015}, month={Feb}, pages={381–393} }
@article{merchante_brumos_yun_hu_spencer_enriquez_binder_heber_stepanova_alonso_2015, title={Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2}, volume={163}, ISSN={["1097-4172"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84948814371&partnerID=MN8TOARS}, DOI={10.1016/j.cell.2015.09.036}, abstractNote={The central role of translation in modulating gene activity has long been recognized, yet the systematic exploration of quantitative changes in translation at a genome-wide scale in response to a specific stimulus has only recently become technically feasible. Using the well-characterized signaling pathway of the phytohormone ethylene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism linking this hormone's perception to the activation of a gene-specific translational control mechanism. Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsense-mediated decay proteins UPFs play a central role in this ethylene-induced translational response. Furthermore, the 3'UTR of EBF2 is sufficient to confer translational regulation and required for the proper activation of ethylene responses. These findings represent a mechanistic paradigm of gene-specific regulation of translation in response to a key growth regulator.}, number={3}, journal={CELL}, author={Merchante, Catharina and Brumos, Javier and Yun, Jeonga and Hu, Qiwen and Spencer, Kristina R. and Enriquez, Paul and Binder, Brad M. and Heber, Steffen and Stepanova, Anna N. and Alonso, Jose M.}, year={2015}, month={Oct}, pages={684–697} }
@inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={Mining transcript features related to translation in Arabidopsis using LASSO and random forest}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84960900444&partnerID=MN8TOARS}, DOI={10.1109/iccabs.2015.7344713}, abstractNote={Translation is an important process for all living organisms. During translation, messenger RNA is rewritten into protein. Multiple control mechanisms determine how much protein is generated during translation. In particular, several regulatory elements located on mRNA transcripts are known to affect translation. In this study, a genome-wide analysis was performed to mine features related to translation in the genome of Arabidopsis thaliana. We used ribosome footprinting data to measure translation and constructed a predictive model using LASSO and random forest to select features that likely affect translation. We identified multiple transcript features and measured their influence on translation in different transcript regions. We found that features related to different translation stages may have a different impact on translation; often, features relevant to the elongation step were playing a stronger role. Interestingly, we found that the contribution of features may be different for transcripts belonging to different functional groups, suggesting that transcripts might employ different mechanisms for the regulation of translation.}, booktitle={International conference on computational advances in bio and medical}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, Jose and Heber, S.}, year={2015} }
@article{alonso_stepanova_2015, title={Plant functional genomics methods and protocols second edition preface}, volume={1284}, journal={Plant functional genomics: methods and protocols, 2nd edition}, author={Alonso, J. M. and Stepanova, A. N.}, year={2015}, pages={V-} }
@book{alonso_stepanova_2015, place={Humana Press}, edition={2nd}, series={Methods in Molecular Biology}, title={Plant functional genomics: Methods and protocols}, ISBN={9781493924431 9781493924448}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84954619611&partnerID=MN8TOARS}, DOI={10.1007/978-1-4939-2444-8}, abstractNote={This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utili}, journal={Plant Functional Genomics: Methods and Protocols: Second Edition}, publisher={New York}, author={Alonso, Jose and STEPANOVA, ANNA}, editor={Alonso, J. M. and Stepanova, A. N.Editors}, year={2015}, pages={1–526}, collection={Methods in Molecular Biology} }
@article{han_alonso_rojas-pierce_2015, title={Regulator of bulb biogenesis1 (RBB1) is involved in vacuole bulb formation in arabidopsis}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84928576948&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0125621}, abstractNote={Vacuoles are dynamic compartments with constant fluctuations and transient structures such as trans-vacuolar strands and bulbs. Bulbs are highly dynamic spherical structures inside vacuoles that are formed by multiple layers of membranes and are continuous with the main tonoplast. We recently carried out a screen for mutants with abnormal trafficking to the vacuole or aberrant vacuole morphology. We characterized regulator of bulb biogenesis1-1 (rbb1-1), a mutant in Arabidopsis that contains increased numbers of bulbs when compared to the parental control. rbb1-1 mutants also contain fewer transvacuolar strands than the parental control, and we propose the hypothesis that the formation of transvacuolar strands and bulbs is functionally related. We propose that the bulbs may function transiently to accommodate membranes and proteins when transvacuolar strands fail to elongate. We show that RBB1 corresponds to a very large protein of unknown function that is specific to plants, is present in the cytosol, and may associate with cellular membranes. RBB1 is involved in the regulation of vacuole morphology and may be involved in the establishment or stability of trans-vacuolar strands and bulbs.}, number={4}, journal={PLoS One}, publisher={Public Library of Science (PLoS)}, author={Han, S. W. and Alonso, Jose and Rojas-Pierce, Marcela}, editor={Bassham, DianeEditor}, year={2015}, pages={e0125621} }
@inbook{alonso_stepanova_2014, title={Arabidopsis Transformation with Large Bacterial Artificial Chromosomes}, booktitle={Arabidopsis Protocols}, author={Alonso, Jose M. and Stepanova, Anna N.}, year={2014}, pages={271–283} }
@article{brumos_alonso_stepanova_2014, title={Genetic aspects of auxin biosynthesis and its regulation}, volume={151}, ISSN={["1399-3054"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84898468296&partnerID=MN8TOARS}, DOI={10.1111/ppl.12098}, abstractNote={Auxin is an essential plant hormone that controls nearly every aspect of a plant's life, from embryo development to organ senescence. In the last decade the key genes involved in auxin transport, perception, signaling and response have been identified and characterized, but the elucidation of auxin biosynthesis has proven to be especially challenging. In plants, a significant amount of indole‐3‐acetic acid (IAA), the predominant biologically active form of auxin, is synthesized via a simple two‐step route where indole‐3‐pyruvic acid (IPyA) produced from l‐tryptophan by tryptophan aminotransferases (TAA1/TAR) is converted to IAA by the YUC family of flavin monooxygenases. The TAA1/TAR and YUC gene families constitute the first complete auxin biosynthetic pathway described in plants. Detailed characterization of these genes' expression patterns suggested a key role of local auxin biosynthesis in plant development. This has prompted an active search for the molecular mechanisms that regulate the spatiotemporal activity of the IPyA route. In addition to the TAA1/TAR and YUC‐mediated auxin biosynthesis, several alternative routes of IAA production have been postulated to function in plants, but their biological significance is yet to be demonstrated. Herein, we take a genetic perspective to describe the current view of auxin biosynthesis and its regulation in plants, focusing primarily on Arabidopsis.}, number={1}, journal={PHYSIOLOGIA PLANTARUM}, author={Brumos, Javier and Alonso, Jose M. and Stepanova, Anna N.}, year={2014}, month={May}, pages={3–12} }
@article{band_wells_fozard_ghetiu_french_pound_wilson_yu_li_hijazi_et al._2014, title={Systems analysis of auxin transport in the arabidopsis root apex}, volume={26}, number={3}, journal={Plant Cell}, author={Band, L. R. and Wells, D. M. and Fozard, J. A. and Ghetiu, T. and French, A. P. and Pound, M. P. and Wilson, M. H. and Yu, L. and Li, W. D. and Hijazi, H. I. and et al.}, year={2014}, pages={862–875} }
@article{catalá_lópez-cobollo_mar castellano_angosto_alonso_ecker_salinas_2014, title={The Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation
}, volume={26}, ISSN={1532-298X 1040-4651}, url={http://dx.doi.org/10.1105/tpc.114.127605}, DOI={10.1105/tpc.114.127605}, abstractNote={Abstract}, number={8}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Catalá, Rafael and López-Cobollo, Rosa and Mar Castellano, M. and Angosto, Trinidad and Alonso, José M. and Ecker, Joseph R. and Salinas, Julio}, year={2014}, month={Aug}, pages={3326–3342} }
@article{pietra_gustavsson_kiefer_kalmbach_horstedt_ikeda_stepanova_alonso_grebe_2013, title={Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity}, volume={4}, ISSN={["2041-1723"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889562507&partnerID=MN8TOARS}, DOI={10.1038/ncomms3779}, abstractNote={The orientation of cell division and the coordination of cell polarity within the plane of the tissue layer (planar polarity) contribute to shape diverse multicellular organisms. The root of Arabidopsis thaliana displays regularly oriented cell divisions, cell elongation and planar polarity providing a plant model system to study these processes. Here we report that the SABRE protein, which shares similarity with proteins of unknown function throughout eukaryotes, has important roles in orienting cell division and planar polarity. SABRE localizes at the plasma membrane, endomembranes, mitotic spindle and cell plate. SABRE stabilizes the orientation of CLASP-labelled preprophase band microtubules predicting the cell division plane, and of cortical microtubules driving cell elongation. During planar polarity establishment, sabre is epistatic to clasp at directing polar membrane domains of Rho-of-plant GTPases. Our findings mechanistically link SABRE to CLASP-dependent microtubule organization, shedding new light on the function of SABRE-related proteins in eukaryotes. Cell and planar polarity are important for the organization of cells within organisms. Pietra et al. demonstrate in Arabidopsisthat the SABRE protein is important for mediating cell and planar polarity by stabilizing the orientation of microtubules during cell division and cell elongation.}, journal={NATURE COMMUNICATIONS}, author={Pietra, Stefano and Gustavsson, Anna and Kiefer, Christian and Kalmbach, Lothar and Horstedt, Per and Ikeda, Yoshihisa and Stepanova, Anna N. and Alonso, Jose M. and Grebe, Markus}, year={2013}, month={Nov} }
@misc{merchante_alonso_stepanova_2013, title={Ethylene signaling: simple ligand, complex regulation}, volume={16}, ISSN={["1879-0356"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84885368622&partnerID=MN8TOARS}, DOI={10.1016/j.pbi.2013.08.001}, abstractNote={The hormone ethylene plays numerous roles in plant development. In the last few years the model of ethylene signaling has evolved from an initially largely linear route to a much more complex pathway with multiple feedback loops. Identification of key transcriptional and post-transcriptional regulatory modules controlling expression and/or stability of the core pathway components revealed that ethylene perception and signaling are tightly regulated at multiple levels. This review describes the most current outlook on ethylene signal transduction and emphasizes the latest discoveries in the ethylene field that shed light on the mechanistic mode of action of the central pathway components CTR1 and EIN2, as well as on the post-transcriptional regulatory steps that modulate the signaling flow through the pathway.}, number={5}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Merchante, Catharina and Alonso, Jose M. and Stepanova, Anna N.}, year={2013}, month={Oct}, pages={554–560} }
@article{hill_mathews_kim_street_wildes_chiang_mason_alonso_ecker_kieber_et al._2013, title={Functional Characterization of Type-B Response Regulators in the Arabidopsis Cytokinin Response
}, volume={162}, ISSN={1532-2548}, url={http://dx.doi.org/10.1104/pp.112.208736}, DOI={10.1104/pp.112.208736}, abstractNote={Abstract}, number={1}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Hill, Kristine and Mathews, Dennis E. and Kim, Hyo Jung and Street, Ian H. and Wildes, Sarah L. and Chiang, Yi-Hsuan and Mason, Michael G. and Alonso, Jose M. and Ecker, Joseph R. and Kieber, Joseph J. and et al.}, year={2013}, month={May}, pages={212–224} }
@article{kopycki_wieduwild_kohlschmidt_brandt_stepanova_alonso_pedras_abel_grubb_2013, title={Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition}, volume={450}, ISSN={["1470-8728"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84873043425&partnerID=MN8TOARS}, DOI={10.1042/bj20121403}, abstractNote={Plant genomes encode numerous small molecule glycosyltransferases which modulate the solubility, activity, immunogenicity and/or reactivity of hormones, xenobiotics and natural products. The products of these enzymes can accumulate to very high concentrations, yet somehow avoid inhibiting their own biosynthesis. Glucosyltransferase UGT74B1 (UDP-glycosyltransferase 74B1) catalyses the penultimate step in the core biosynthetic pathway of glucosinolates, a group of natural products with important functions in plant defence against pests and pathogens. We found that mutation of the highly conserved Ser284 to leucine [wei9-1 (weak ethylene insensitive)] caused only very mild morphological and metabolic phenotypes, in dramatic contrast with knockout mutants, indicating that steady state glucosinolate levels are actively regulated even in unchallenged plants. Analysis of the effects of the mutation via a structural modelling approach indicated that the affected serine interacts directly with UDP-glucose, but also predicted alterations in acceptor substrate affinity and the kcat value, sparking an interest in the kinetic behaviour of the wild-type enzyme. Initial velocity and inhibition studies revealed that UGT74B1 is not inhibited by its glycoside product. Together with the effects of the missense mutation, these findings are most consistent with a partial rapid equilibrium ordered mechanism. This model explains the lack of product inhibition observed both in vitro and in vivo, illustrating a general mechanism whereby enzymes can continue to function even at very high product/precursor ratios.}, number={1}, journal={BIOCHEMICAL JOURNAL}, author={Kopycki, Jakub and Wieduwild, Elizabeth and Kohlschmidt, Janine and Brandt, Wolfgang and Stepanova, Anna N. and Alonso, Jose M. and Pedras, M. Soledade C. and Abel, Steffen and Grubb, C. Douglas}, year={2013}, month={Feb}, pages={37–46} }
@article{robert_grones_stepanova_robles_lokerse_alonso_weijers_friml_2013, title={Local Auxin Sources Orient the Apical-Basal Axis in Arabidopsis Embryos}, volume={23}, ISSN={["1879-0445"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84890790080&partnerID=MN8TOARS}, DOI={10.1016/j.cub.2013.09.039}, abstractNote={Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin to generate an asymmetric auxin response that specifies the embryonic apical-basal axis. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life.}, number={24}, journal={CURRENT BIOLOGY}, author={Robert, Helene S. and Grones, Peter and Stepanova, Anna N. and Robles, Linda M. and Lokerse, Annemarie S. and Alonso, Jose M. and Weijers, Dolf and Friml, Jiri}, year={2013}, month={Dec}, pages={2506–2512} }
@article{robles_stepanova_alonso_2013, title={Molecular Mechanisms of EthyleneAuxin Interaction}, volume={6}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84891933044&partnerID=MN8TOARS}, DOI={10.1093/mp/sst113}, abstractNote={During the century-long history of plant hormone research, the focus in this area has shifted from the original physiological experiments to molecular, genetic, biochemical, and, more recently, genomic approaches. During this journey, we have learned about the many effects these natural compounds have on plant growth and development at the morphological and molecular levels. We have also uncovered how these molecules are sensed by the plant cell and how they trigger signaling cascades that relay information to the nucleus, ultimately culminating in a transcriptional cascade.}, number={6}, journal={MOLECULAR PLANT}, author={Robles, Linda and Stepanova, Anna and Alonso, Jose}, year={2013}, month={Nov}, pages={1734–1737} }
@article{robles_stepanova_alonso_2013, title={Molecular mechanisms of ethylene–auxin interactions}, journal={Molecular plant}, author={Robles, Linda and Stepanova, Anna and Alonso, Jose}, year={2013}, pages={sst113} }
@article{péret_swarup_ferguson_seth_yang_dhondt_james_casimiro_perry_syed_2012, title={AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development}, volume={24}, DOI={10.1105/tpc.112.097766}, abstractNote={This article describes the role of AUX/LAX auxin influx carriers in plant development, revealing that the auxin influx carrier LAX2 regulates vascular patterning in cotyledons. Although the AUX1/LAX family members share auxin transport characteristics, these transport activities seem to be dependent on their unique cell- or tissue-type expression patterns. Auxin transport, which is mediated by specialized influx and efflux carriers, plays a major role in many aspects of plant growth and development. AUXIN1 (AUX1) has been demonstrated to encode a high-affinity auxin influx carrier. In Arabidopsis thaliana, AUX1 belongs to a small multigene family comprising four highly conserved genes (i.e., AUX1 and LIKE AUX1 [LAX] genes LAX1, LAX2, and LAX3). We report that all four members of this AUX/LAX family display auxin uptake functions. Despite the conservation of their biochemical function, AUX1, LAX1, and LAX3 have been described to regulate distinct auxin-dependent developmental processes. Here, we report that LAX2 regulates vascular patterning in cotyledons. We also describe how regulatory and coding sequences of AUX/LAX genes have undergone subfunctionalization based on their distinct patterns of spatial expression and the inability of LAX sequences to rescue aux1 mutant phenotypes, respectively. Despite their high sequence similarity at the protein level, transgenic studies reveal that LAX proteins are not correctly targeted in the AUX1 expression domain. Domain swapping studies suggest that the N-terminal half of AUX1 is essential for correct LAX localization. We conclude that Arabidopsis AUX/LAX genes encode a family of auxin influx transporters that perform distinct developmental functions and have evolved distinct regulatory mechanisms.}, number={7}, journal={The Plant Cell Online}, author={Péret, Benjamin and Swarup, Kamal and Ferguson, Alison and Seth, Malvika and Yang, Yaodong and Dhondt, Stijn and James, Nicholas and Casimiro, Ilda and Perry, Paula and Syed, Adnan}, year={2012}, pages={2874–2885} }
@article{peret_swarup_ferguson_seth_yang_dhondt_james_casimiro_perry_syed_et al._2012, title={AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development}, volume={24}, number={7}, journal={Plant Cell}, author={Peret, B. and Swarup, K. and Ferguson, A. and Seth, M. and Yang, Y. D. and Dhondt, S. and James, N. and Casimiro, I. and Perry, P. and Syed, A. and et al.}, year={2012}, pages={2874–2885} }
@article{he_brumos_li_ji_ke_gong_zeng_li_zhang_an_et al._2011, title={A Small-Molecule Screen Identifies l-Kynurenine as a Competitive Inhibitor of TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth in Arabidopsis}, volume={23}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.111.089029}, DOI={10.1105/tpc.111.089029}, abstractNote={Abstract}, number={11}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={He, Wenrong and Brumos, Javier and Li, Hongjiang and Ji, Yusi and Ke, Meng and Gong, Xinqi and Zeng, Qinglong and Li, Wenyang and Zhang, Xinyan and An, Fengying and et al.}, year={2011}, month={Nov}, pages={3944–3960} }
@article{zhou_benavente_stepanova_alonso_2011, title={A recombineering-based gene tagging system for Arabidopsis}, volume={66}, ISSN={["0960-7412"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79955809131&partnerID=MN8TOARS}, DOI={10.1111/j.1365-313x.2011.04524.x}, abstractNote={Summary}, number={4}, journal={PLANT JOURNAL}, author={Zhou, Rongrong and Benavente, Larissa M. and Stepanova, Anna N. and Alonso, Jose M.}, year={2011}, month={May}, pages={712–723} }
@article{stepanova_alonso_2011, title={Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions}, volume={21}, ISSN={["1534-5807"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80054765937&partnerID=MN8TOARS}, DOI={10.1016/j.devcel.2011.09.016}, abstractNote={In this issue of Developmental Cell, Marhavý et al. (2011) uncover a transcription-independent molecular mechanism of interaction between auxin and cytokinin in the regulation of plant meristem function. By modulating endocytic trafficking of PIN1, cytokinin controls auxin flux and, therefore, auxin gradients.}, number={4}, journal={DEVELOPMENTAL CELL}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2011}, month={Oct}, pages={608–610} }
@article{stepanova_yun_robles_novak_he_guo_ljung_alonso_2011, title={The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis}, volume={23}, ISSN={["1532-298X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84855168181&partnerID=MN8TOARS}, DOI={10.1105/tpc.111.088047}, abstractNote={Abstract}, number={11}, journal={PLANT CELL}, author={Stepanova, Anna N. and Yun, Jeonga and Robles, Linda M. and Novak, Ondrej and He, Wenrong and Guo, Hongwei and Ljung, Karin and Alonso, Jose M.}, year={2011}, month={Nov}, pages={3961–3973} }
@article{tsuchisaka_yu_jin_alonso_ecker_zhang_gao_theologis_2009, title={A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana}, volume={183}, DOI={10.1534/genetics.109.107102}, abstractNote={Abstract}, number={3}, journal={Genetics}, author={Tsuchisaka, Atsunari and Yu, Guixia and Jin, Hailing and Alonso, Jose M. and Ecker, Joseph R. and Zhang, Xiaoming and Gao, Shang and Theologis, Athanasios}, year={2009}, pages={979–1003} }
@misc{stepanova_alonso_2009, title={Ethylene signaling and response: where different regulatory modules meet}, volume={12}, ISSN={["1879-0356"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70349554136&partnerID=MN8TOARS}, DOI={10.1016/j.pbi.2009.07.009}, abstractNote={The structural simplicity of the gaseous hormone ethylene stands in contrast with the complexity of the physiological processes ethylene regulates. Initial studies suggested a simple linear arrangement of signaling molecules leading from the ethylene receptors to the EIN3 family of transcription factors. Recent discoveries have substantially changed this view. Current models suggest existence of a complex signaling pathway composed of several phosphorylation cascades, feedback-regulated transcriptional networks, and protein and mRNA turnover regulatory modules. Interactions between ethylene and other signals determine which of the ethylene-mediated responses get activated in a particular cell at a particular time. Tissue-specific regulation of auxin biosynthesis, transport, and response by ethylene is emerging as a key element in this signal integration process.}, number={5}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2009}, month={Oct}, pages={548–555} }
@article{ikeda_men_fischer_stepanova_alonso_ljung_grebe_2009, title={Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis}, volume={11}, ISSN={["1476-4679"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-67349090679&partnerID=MN8TOARS}, DOI={10.1038/ncb1879}, abstractNote={Arabidopsis root-hair position and orientation in epithelial cells is directed by an auxin gradient maximum at the root tip. The Raf-like kinase CTR1 negatively regulates local auxin biosynthesis in the root to determine root hair position. The coordination of cell polarity within the plane of a single tissue layer (planar polarity) is a crucial task during development of multicellular organisms. Mechanisms underlying establishment of planar polarity, however, differ substantially between plants and animals1,2,3. In Arabidopsis thaliana, planar polarity of root-hair positioning along epidermal cells is coordinated towards maximum concentration of an auxin gradient in the root tip3,4,5. This gradient has been hypothesized to be sink-driven6 and computational modelling suggests that auxin efflux carrier activity may be sufficient to generate the gradient in the absence of auxin biosynthesis in the root7. Here, we demonstrate that the Raf-like kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1; Refs 8, 9) acts as a concentration-dependent repressor of a biosynthesis-dependent auxin gradient that modulates planar polarity in the root tip. We analysed auxin biosynthesis and concentration gradients in a variety of root-hair-position mutants affected in CTR1 activity, auxin biosynthesis and transport. Our results reveal that planar polarity relies on influx- and efflux-carrier-mediated auxin redistribution from a local biosynthesis maximum. Thus, a local source of auxin biosynthesis contributes to gradient homeostasis during long-range coordination of cellular morphogenesis.}, number={6}, journal={NATURE CELL BIOLOGY}, author={Ikeda, Yoshihisa and Men, Shuzhen and Fischer, Urs and Stepanova, Anna N. and Alonso, Jose M. and Ljung, Karin and Grebe, Markus}, year={2009}, month={Jun}, pages={731–U70} }
@article{hu_mitchum_barnaby_ayele_ogawa_nam_lai_hanada_alonso_ecker_2008, title={Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis}, volume={20}, DOI={10.1105/tpc.107.057752}, abstractNote={Abstract}, number={2}, journal={The Plant Cell Online}, author={Hu, Jianhong and Mitchum, Melissa G. and Barnaby, Neel and Ayele, Belay T. and Ogawa, Mikihiro and Nam, Edward and Lai, Wei-Chu and Hanada, Atsushi and Alonso, Jose M. and Ecker, Joseph R.}, year={2008}, pages={320–336} }
@article{stepanova_robertson-hoyt_yun_benavente_xie_doležal_schlereth_jürgens_alonso_2008, title={TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development}, volume={133}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/j.cell.2008.01.047}, DOI={10.1016/j.cell.2008.01.047}, abstractNote={Plants have evolved a tremendous ability to respond to environmental changes by adapting their growth and development. The interaction between hormonal and developmental signals is a critical mechanism in the generation of this enormous plasticity. A good example is the response to the hormone ethylene that depends on tissue type, developmental stage, and environmental conditions. By characterizing the Arabidopsis wei8 mutant, we have found that a small family of genes mediates tissue-specific responses to ethylene. Biochemical studies revealed that WEI8 encodes a long-anticipated tryptophan aminotransferase, TAA1, in the essential, yet genetically uncharacterized, indole-3-pyruvic acid (IPA) branch of the auxin biosynthetic pathway. Analysis of TAA1 and its paralogues revealed a link between local auxin production, tissue-specific ethylene effects, and organ development. Thus, the IPA route of auxin production is key to generating robust auxin gradients in response to environmental and developmental cues.}, number={1}, journal={Cell}, publisher={Elsevier BV}, author={Stepanova, Anna N. and Robertson-Hoyt, Joyce and Yun, Jeonga and Benavente, Larissa M. and Xie, De-Yu and Doležal, Karel and Schlereth, Alexandra and Jürgens, Gerd and Alonso, Jose M.}, year={2008}, month={Apr}, pages={177–191} }
@article{leivar_monte_al-sady_carle_storer_alonso_ecker_quail_2008, title={The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels}, volume={20}, DOI={10.1105/tpc.107.052142}, abstractNote={Abstract}, number={2}, journal={The Plant Cell Online}, author={Leivar, Pablo and Monte, Elena and Al-Sady, Bassem and Carle, Christine and Storer, Alyssa and Alonso, Jose M. and Ecker, Joseph R. and Quail, Peter H.}, year={2008}, pages={337–352} }
@article{li_he_lu_lee_alonso_ecker_luan_2007, title={A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis}, volume={19}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.107.053579}, abstractNote={Abstract}, number={8}, journal={PLANT CELL}, author={Li, Hong and He, Zengyong and Lu, Guihua and Lee, Sung Chul and Alonso, Jose and Ecker, Joseph R. and Luan, Sheng}, year={2007}, month={Aug}, pages={2403–2416} }
@article{ronan c. o'malley_alonso_kim_leisse_ecker_2007, title={An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome}, volume={2}, ISSN={["1754-2189"]}, DOI={10.1038/nprot.2007.425}, abstractNote={Agrobacterium transfer DNA (T-DNA) is an effective plant mutagen that has been used to create sequence-indexed T-DNA insertion lines in Arabidopsis thaliana as a tool to study gene function. Creating T-DNA insertion lines requires a dependable method for locating the site of insertion in the genome. In this protocol, we describe an adapter ligation-mediated PCR method that we have used to screen a mutant library and identify over 150,000 T-DNA insertional mutants; the method can also be applied to map individual mutants. The procedure consists of three steps: a restriction enzyme-mediated ligation of an adapter to the genomic DNA; a PCR amplification of the T-DNA/genomic DNA junction with primers specific to the adapter and T-DNA; and sequencing of the T-DNA/genomic junction to enable mapping to the reference genome. In most cases, the sequenced genomic region extends to the T-DNA border, enabling the exact location of the insert to be identified. The entire process takes 2 weeks to complete.}, number={11}, journal={NATURE PROTOCOLS}, author={Ronan C. O'Malley and Alonso, Jose M. and Kim, Christopher J. and Leisse, Thomas J. and Ecker, Joseph R.}, year={2007}, pages={2910–2917} }
@article{chekanova_gregory_reverdatto_chen_kumar_hooker_yazaki_li_skiba_peng_2007, title={Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis Transcriptome}, volume={131}, DOI={10.1016/j.cell.2007.10.056}, abstractNote={The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.}, number={7}, journal={Cell}, author={Chekanova, Julia A. and Gregory, Brian D. and Reverdatto, Sergei V. and Chen, Huaming and Kumar, Ravi and Hooker, Tanya and Yazaki, Junshi and Li, Pinghua and Skiba, Nikolai and Peng, Qian}, year={2007}, pages={1340–1353} }
@article{stepanova_yun_likhacheva_alonso_2007, title={Multilevel interactions between ethylene and auxin in Arabidopsis roots}, volume={19}, ISSN={["1532-298X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548310412&partnerID=MN8TOARS}, DOI={10.1105/tpc.107.052068}, abstractNote={Abstract}, number={7}, journal={PLANT CELL}, author={Stepanova, Anna N. and Yun, Jeonga and Likhacheva, Alla V. and Alonso, Jose M.}, year={2007}, month={Jul}, pages={2169–2185} }
@article{mori_murata_yang_munemasa_wang_andreoli_tiriac_alonso_harper_ecker_2006, title={CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion-and Ca2+-permeable channels and stomatal closure}, volume={4}, number={10}, journal={PLoS biology}, author={Mori, Izumi C. and Murata, Yoshiyuki and Yang, Yingzhen and Munemasa, Shintaro and Wang, Yong-Fei and Andreoli, Shannon and Tiriac, Hervé and Alonso, Jose M. and Harper, Jeffery F. and Ecker, Joseph R.}, year={2006}, pages={e327} }
@article{rudella_friso_alonso_ecker_wijk_2006, title={Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis}, volume={18}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.106.042861}, abstractNote={Abstract}, number={7}, journal={PLANT CELL}, author={Rudella, Andrea and Friso, Giulia and Alonso, Jose M. and Ecker, Joseph R. and Wijk, Klaas J.}, year={2006}, month={Jul}, pages={1704–1721} }
@article{kim_punshon_lanzirotti_li_alonso_ecker_kaplan_guerinot_2006, title={Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1}, volume={314}, ISSN={["1095-9203"]}, DOI={10.1126/science.1132563}, abstractNote={
Iron deficiency is a major human nutritional problem wherever plant-based diets are common. Using synchrotron x-ray fluorescence microtomography to directly visualize iron in
Arabidopsis
seeds, we show that iron is localized primarily to the provascular strands of the embryo. This localization is completely abolished when the vacuolar iron uptake transporter VIT1 is disrupted. Vacuolar iron storage is also critical for seedling development because
vit1-1
seedlings grow poorly when iron is limiting. We have uncovered a fundamental aspect of seed biology that will ultimately aid the development of nutrient-rich seed, benefiting both human health and agricultural productivity.
}, number={5803}, journal={SCIENCE}, author={Kim, Sun A. and Punshon, Tracy and Lanzirotti, Antonio and Li, Liangtao and Alonso, Jose M. and Ecker, Joseph R. and Kaplan, Jerry and Guerinot, Mary Lou}, year={2006}, month={Nov}, pages={1295–1298} }
@article{benavente_alonso_2006, title={Molecular mechanisms of ethylene signaling in Arabidopsis}, volume={2}, ISSN={1742-206X 1742-2051}, url={http://dx.doi.org/10.1039/b513874d}, DOI={10.1039/b513874d}, abstractNote={Ethylene is a gaseous plant hormone involved in several important physiological processes throughout a plant's life cycle. Decades of scientific research devoted to deciphering how plants are able to sense and respond to this key molecule have culminated in the establishment of one of the best characterized signal transduction pathways in plants. The ethylene signaling pathway starts with the perception of this gaseous hormone by a family of membrane-anchored receptors followed by a Raf-like kinase CTR1 that is physically associated with the receptors and actively inhibits downstream components of the pathway. A major gap is represented by the mysterious plant protein EIN2 that genetically works downstream of CTR1 and upstream of the key transcription factor EIN3. Transcriptional regulation by EIN3 and EIN3-family members has emerged as a key aspect of ethylene responses. The major components of this transcriptional cascade have been characterized and the involvement of post-transcriptional control by ubiquitination has been determined. Nevertheless, many aspects of this pathway still remain unknown. Recent genomic studies aiming to provide a more comprehensive view of modulation of gene expression have further emphasized the ample role of ethylene in a myriad of cellular processes and particularly in its crosstalk with other important plant hormones. This review aims to serve as a guide to the main scientific discoveries that have shaped the field of ethylene biology in the recent years.}, number={3-4}, journal={Molecular BioSystems}, publisher={Royal Society of Chemistry (RSC)}, author={Benavente, Larissa M. and Alonso, Jose M.}, year={2006}, pages={165} }
@article{alonso_ecker_2006, title={Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis}, volume={7}, DOI={10.1038/nrg1893}, abstractNote={Genome sequencing, in combination with various computational and empirical approaches to sequence annotation, has made possible the identification of more than 30,000 genes in Arabidopsis thaliana. Increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of these genes gives rise to a complex organism. The combination of classical forward genetics with recently developed genome-wide, gene-indexed mutant collections is beginning to revolutionize the way in which gene functions are studied in plants. High-throughput screens using these mutant populations should provide a means to analyse plant gene functions--the phenome--on a genomic scale.}, number={7}, journal={Nature Reviews Genetics}, author={Alonso, Jose and Ecker, Joseph R.}, year={2006}, pages={524–536} }
@inbook{stepanova_alonso_2006, title={PCR-based screening for insertional mutants}, booktitle={Arabidopsis Protocols}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2006}, pages={163–172} }
@article{lariguet_schepens_hodgson_pedmale_trevisan_kami_carbonnel_alonso_ecker_liscum_2006, title={PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism}, volume={103}, DOI={10.1073/pnas.0603799103}, abstractNote={
Phototropism, or plant growth in response to unidirectional light, is an adaptive response of crucial importance. Lateral differences in low fluence rates of blue light are detected by phototropin 1 (phot1) in
Arabidopsis
. Only NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and root phototropism 2, both belonging to the same family of proteins, have been previously identified as phototropin-interacting signal transducers involved in phototropism. PHYTOCHROME KINASE SUBSTRATE (PKS) 1 and PKS2 are two phytochrome signaling components belonging to a small gene family in
Arabidopsis
(
PKS1
–
PKS4
). The strong enhancement of
PKS1
expression by blue light and its light induction in the elongation zone of the hypocotyl prompted us to study the function of this gene family during phototropism. Photobiological experiments show that the PKS proteins are critical for hypocotyl phototropism. Furthermore, PKS1 interacts with phot1 and NPH3
in vivo
at the plasma membrane and
in vitro
, indicating that the PKS proteins may function directly with phot1 and NPH3 to mediate phototropism. The phytochromes are known to influence phototropism but the mechanism involved is still unclear. We show that PKS1 induction by a pulse of blue light is phytochrome A-dependent, suggesting that the PKS proteins may provide a molecular link between these two photoreceptor families.
}, number={26}, journal={Proceedings of the National Academy of Sciences}, author={Lariguet, Patricia and Schepens, Isabelle and Hodgson, Daniel and Pedmale, Ullas V. and Trevisan, Martine and Kami, Chitose and Carbonnel, Matthieu and Alonso, José M. and Ecker, Joseph R. and Liscum, Emmanuel}, year={2006}, pages={10134–10139} }
@article{chen_ullah_temple_liang_guo_alonso_ecker_jones_2006, title={RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis}, volume={57}, DOI={10.1093/jxb/erl035}, abstractNote={The scaffold protein RACK1 (Receptor for Activated C Kinase 1) serves as an integrative point for diverse signal transduction pathways. The Arabidopsis genome contains three RACK1 orthologues, however, little is known about their functions. It is reported here that one member of this gene family, RACK1A, previously identified as the Arabidopsis homologue of the tobacco arcA gene, mediates hormone responses and plays a regulatory role in multiple developmental processes. RACK1A expresses ubiquitously in Arabidopsis. Loss-of-function mutations in RACK1A confer defects in multiple developmental processes including seed germination, leaf production, and flowering. rack1a mutants displayed reduced sensitivity to gibberellin and brassinosteroid in seed germination, hypersensitivity to abscisic acid in seed germination and early seedling development, and hyposensitivity to auxin in adventitious and lateral root formation. These results provide the first genetic evidence that RACK1A is involved in multiple signal transduction pathways.}, number={11}, journal={Journal of experimental botany}, author={Chen, Jin-Gui and Ullah, Hemayet and Temple, Brenda and Liang, Jiansheng and Guo, Jianjun and Alonso, José M. and Ecker, Joseph R. and Jones, Alan M.}, year={2006}, pages={2697–2708} }
@article{hutchison_li_argueso_gonzalez_lee_lewis_maxwell_perdue_schaller_alonso_2006, title={The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling}, volume={18}, DOI={10.1105/tpc.106.045674}, abstractNote={Abstract}, number={11}, journal={The Plant Cell Online}, author={Hutchison, Claire E. and Li, Jie and Argueso, Cristiana and Gonzalez, Monica and Lee, Eurie and Lewis, Michael W. and Maxwell, Bridey B. and Perdue, Tony D. and Schaller, G. Eric and Alonso, Jose M.}, year={2006}, pages={3073–3087} }
@article{pfund_tans-kersten_dunning_alonso_ecker_allen_bent_2005, title={" Flagellin is not a major defense elicitor in Ralstonia solanacearum cells (vol 17, pg 696, 2005)}, volume={18}, number={9}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Pfund, C. and Tans-Kersten, J. and Dunning, F. M. and Alonso, J. M. and Ecker, J. R. and Allen, C. and Bent, A. F.}, year={2005}, pages={1024} }
@article{stepanova_hoyt_hamilton_alonso_2005, title={A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis}, volume={17}, ISSN={["1532-298X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-27744445823&partnerID=MN8TOARS}, DOI={10.1105/tpc.105.033365}, abstractNote={The plant hormone ethylene participates in the regulation of a variety of developmental processes and serves as a key mediator of plant responses to biotic and abiotic stress factors. The diversity of ethylene functions is achieved, at least in part, by combinatorial interactions with other hormonal signals. Here, we show that ethylene-triggered inhibition of root growth, one of the classical effects of ethylene in Arabidopsis thaliana seedlings, is mediated by the action of the WEAK ETHYLENE INSENSITIVE2/ANTHRANILATE SYNTHASE α1 (WEI2/ASA1) and WEI7/ANTHRANILATE SYNTHASE β1 (ASB1) genes that encode α- and β-subunits of a rate-limiting enzyme of Trp biosynthesis, anthranilate synthase. Upregulation of WEI2/ASA1 and WEI7/ASB1 by ethylene results in the accumulation of auxin in the tip of primary root, whereas loss-of-function mutations in these genes prevent the ethylene-mediated auxin increase. Furthermore, wei2 and wei7 suppress the high-auxin phenotypes of superroot1 (sur1) and sur2, two auxin-overproducing mutants, suggesting that the roles of WEI2 and WEI7 in the regulation of auxin biosynthesis are not restricted to the ethylene response. Together, these findings reveal that ASA1 and ASB1 are key elements in the regulation of auxin production and an unexpected node of interaction between ethylene responses and auxin biosynthesis in Arabidopsis. This study provides a mechanistic explanation for the root-specific ethylene insensitivity of wei2 and wei7, illustrating how interactions between hormones can be used to achieve response specificity.}, number={8}, journal={PLANT CELL}, author={Stepanova, AN and Hoyt, JM and Hamilton, AA and Alonso, JM}, year={2005}, month={Aug}, pages={2230–2242} }
@article{liu_holub_alonso_ecker_fobert_2005, title={An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance}, volume={41}, ISSN={["1365-313X"]}, DOI={10.1111/j.1365-313x.2004.02296.x}, abstractNote={Summary}, number={2}, journal={PLANT JOURNAL}, author={Liu, GS and Holub, EB and Alonso, JM and Ecker, JR and Fobert, PR}, year={2005}, month={Jan}, pages={304–318} }
@article{stepanova_alonso_2005, title={Arabidopsis ethylene signaling pathway}, volume={2005}, number={276}, journal={Science Signaling}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2005}, pages={cm4} }
@article{nagpal_ellis_weber_ploense_barkawi_guilfoyle_hagen_alonso_cohen_farmer_2005, title={Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation}, volume={132}, number={18}, journal={Development}, author={Nagpal, Punita and Ellis, Christine M. and Weber, Hans and Ploense, Sara E. and Barkawi, Lana S. and Guilfoyle, Thomas J. and Hagen, Gretchen and Alonso, José M. and Cohen, Jerry D. and Farmer, Edward E.}, year={2005}, pages={4107–4118} }
@article{prigge_otsuga_alonso_ecker_drews_clark_2005, title={Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development}, volume={17}, number={1}, journal={The Plant Cell Online}, author={Prigge, Michael J. and Otsuga, Denichiro and Alonso, Jose M. and Ecker, Joseph R. and Drews, Gary N. and Clark, Steven E.}, year={2005}, pages={61–76} }
@article{stepanova_alonso_2005, title={Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs}, volume={123}, DOI={10.1111/j/1399-3054.2004.00447}, number={2}, journal={Physiologia Plantarum}, author={STEPANOVA, ANNA and Alonso, Jose}, year={2005}, pages={195–206} }
@article{okushima_overvoorde_arima_alonso_chan_chang_ecker_hughes_lui_nguyen_2005, title={Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19}, volume={17}, number={2}, journal={The Plant Cell Online}, author={Okushima, Yoko and Overvoorde, Paul J. and Arima, Kazunari and Alonso, Jose M. and Chan, April and Chang, Charlie and Ecker, Joseph R. and Hughes, Beth and Lui, Amy and Nguyen, Diana}, year={2005}, pages={444–463} }
@article{overvoorde_okushima_alonso_chan_chang_ecker_hughes_liu_onodera_quach_2005, title={Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana}, volume={17}, number={12}, journal={The Plant Cell Online}, author={Overvoorde, Paul J. and Okushima, Yoko and Alonso, José M. and Chan, April and Chang, Charlie and Ecker, Joseph R. and Hughes, Beth and Liu, Amy and Onodera, Courtney and Quach, Hong}, year={2005}, pages={3282–3300} }
@article{mason_mathews_argyros_maxwell_kieber_alonso_ecker_schaller_2005, title={Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis}, volume={17}, number={11}, journal={The Plant Cell Online}, author={Mason, Michael G. and Mathews, Dennis E. and Argyros, D. Aaron and Maxwell, Bridey B. and Kieber, Joseph J. and Alonso, Jose M. and Ecker, Joseph R. and Schaller, G. Eric}, year={2005}, pages={3007–3018} }
@article{wilmoth_wang_tiwari_joshi_hagen_guilfoyle_alonso_ecker_reed_2005, title={NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation}, volume={43}, number={1}, journal={The Plant Journal}, author={Wilmoth, Jill C. and Wang, Shucai and Tiwari, Shiv B. and Joshi, Atul D. and Hagen, Gretchen and Guilfoyle, Thomas J. and Alonso, Jose M. and Ecker, Joseph R. and Reed, Jason W.}, year={2005}, pages={118–130} }
@article{ryu_kim_kunkel_kim_cho_hong_kim_fernández_kim_alonso_et al._2005, title={Phytochrome-Specific Type 5 Phosphatase Controls Light Signal Flux by Enhancing Phytochrome Stability and Affinity for a Signal Transducer}, volume={120}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/j.cell.2004.12.019}, DOI={10.1016/j.cell.2004.12.019}, abstractNote={Environmental light information such as quality, intensity, and duration in red (approximately 660 nm) and far-red (approximately 730 nm) wavelengths is perceived by phytochrome photoreceptors in plants, critically influencing almost all developmental strategies from germination to flowering. Phytochromes interconvert between red light-absorbing Pr and biologically functional far-red light-absorbing Pfr forms. To ensure optimal photoresponses in plants, the flux of light signal from Pfr-phytochromes should be tightly controlled. Phytochromes are phosphorylated at specific serine residues. We found that a type 5 protein phosphatase (PAPP5) specifically dephosphorylates biologically active Pfr-phytochromes and enhances phytochrome-mediated photoresponses. Depending on the specific serine residues dephosphorylated by PAPP5, phytochrome stability and affinity for a downstream signal transducer, NDPK2, were enhanced. Thus, phytochrome photoreceptors have developed an elaborate biochemical tuning mechanism for modulating the flux of light signal, employing variable phosphorylation states controlled by phosphorylation and PAPP5-mediated dephosphorylation as a mean to control phytochrome stability and affinity for downstream transducers.}, number={3}, journal={Cell}, publisher={Elsevier BV}, author={Ryu, Jong Sang and Kim, Jeong-Il and Kunkel, Tim and Kim, Byung Chul and Cho, Dae Shik and Hong, Sung Hyun and Kim, Seong-Hee and Fernández, Aurora Piñas and Kim, Yumi and Alonso, Jose M. and et al.}, year={2005}, month={Feb}, pages={395–406} }
@article{ryu_kim_kunkel_kim_cho_hong_kim_fernández_kim_alonso_2005, title={Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer}, volume={120}, number={3}, journal={Cell}, author={Ryu, Jong Sang and Kim, Jeong-Il and Kunkel, Tim and Kim, Byung Chul and Cho, Dae Shik and Hong, Sung Hyun and Kim, Seong-Hee and Fernández, Aurora Piñas and Kim, Yumi and Alonso, Jose M.}, year={2005}, pages={395–406} }
@article{page_hamel_gabilly_zegzouti_perea_alonso_ecker_theg_christensen_merchant_2004, title={A Homolog of Prokaryotic Thiol Disulfide Transporter CcdA Is Required for the Assembly of the Cytochrome b6f Complex in Arabidopsis Chloroplasts}, volume={279}, ISSN={0021-9258 1083-351X}, url={http://dx.doi.org/10.1074/JBC.M404285200}, DOI={10.1074/JBC.M404285200}, abstractNote={The c-type cytochromes are defined by the occurrence of heme covalently linked to the polypeptide via thioether bonds between heme and the cysteine sulfhydryls in the CXXCH motif of apocytochrome. Maintenance of apocytochrome sulfhydryls in a reduced state is a prerequisite for covalent ligation of heme to the CXXCH motif. In bacteria, a thiol disulfide transporter and a thioredoxin are two components in a thio-reduction pathway involved in c-type cytochrome assembly. We have identified in photosynthetic eukaryotes nucleus-encoded homologs of a prokaryotic thiol disulfide transporter, CcdA, which all display an N-terminal extension with respect to their bacterial counterparts. The extension of Arabidopsis CCDA functions as a targeting sequence, suggesting a plastid site of action for CCDA in eukaryotes. Using PhoA and LacZ as topological reporters, we established that Arabidopsis CCDA is a polytopic protein with within-membrane strictly conserved cysteine residues. Insertional mutants in the Arabidopsis CCDA gene were identified, and loss-of-function alleles were shown to impair photosynthesis because of a defect in cytochrome b6f accumulation, which we attribute to a block in the maturation of holocytochrome f, whose heme binding domain resides in the thylakoid lumen. We postulate that plastid cytochrome c maturation requires CCDA, thioredoxin HCF164, and other molecules in a membrane-associated trans-thylakoid thiol-reducing pathway.}, number={31}, journal={Journal of Biological Chemistry}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Page, M. L. Dudley and Hamel, Patrice P. and Gabilly, Stéphane T. and Zegzouti, Hicham and Perea, John V. and Alonso, José M. and Ecker, Joseph R. and Theg, Steven M. and Christensen, Sioux K. and Merchant, Sabeeha}, year={2004}, month={May}, pages={32474–32482} }
@article{novillo_alonso_ecker_salinas_2004, title={CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.0303029101}, DOI={10.1073/PNAS.0303029101}, abstractNote={CBF/DREB1(C-repeat-binding factor/dehydration responsive element-binding factor 1) genes encode a small family of transcriptional activators that have been described as playing an important role in freezing tolerance and cold acclimation inArabidopsis. To specify this role, we used a reverse genetic approach and identified a mutant,cbf2, in which theCBF2/DREB1Cgene was disrupted. Here, we show thatcbf2plants have higher capacity to tolerate freezing than WT ones before and after cold acclimation and are more tolerant to dehydration and salt stress. All these phenotypes correlate with a stronger and more sustained expression of CBF/DREB1-regulated genes, which results from an increased expression ofCBF1/DREB1BandCBF3/DREB1Ain the mutant. In addition, we show that the expression ofCBF1/DREB1BandCBF3/DREB1Ain response to low temperature precedes that ofCBF2/DREB1C. These results indicate that CBF2/DREB1C negatively regulatesCBF1/DREB1BandCBF3/DREB1A, ensuring that their expression is transient and tightly controlled, which, in turn, guarantees the proper induction of downstream genes and the accurate development ofArabidopsistolerance to freezing and related stresses.}, number={11}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Novillo, F. and Alonso, J. M. and Ecker, J. R. and Salinas, J.}, year={2004}, month={Mar}, pages={3985–3990} }
@article{li_johnson_stepanova_alonso_ecker_2004, title={Convergence of signaling of differential cell growth pathways in the control in Arabidopsis}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-4344648019&partnerID=MN8TOARS}, DOI={10.1016/j.devcel.2004.07.002}, abstractNote={Abstract
Seedling apical hook development involves a complex interplay of hormones and light in the regulation of differential cell growth. However, the underlying molecular mechanisms that integrate these diverse signals to control bending of the embryonic stem are poorly understood. The Arabidopsis ethylene-regulated HOOKLESS1 (HLS1) gene is essential for apical hook formation. Herein, we identify two auxin response regulators that act downstream of HLS1 to control cell elongation in the hypocotyl. Extragenic suppressors of hls1 were identified as mutations in AUXIN RESPONSE FACTOR 2 (ARF2). The level of ARF2 protein was decreased by ethylene, and this response required HLS1. Exposure to light decreased HLS1 protein levels and evoked a concomitant increase in ARF2 accumulation. These studies demonstrate that both ethylene and light signals affect differential cell growth by acting through HLS1 to modulate the auxin response factors, pinpointing HLS1 as a key integrator of the signaling pathways that control hypocotyl bending.}, number={2}, journal={Developmental Cell}, author={Li, H. and Johnson, P. and Stepanova, A. and Alonso, J. M. and Ecker, J. R.}, year={2004}, pages={193–204} }
@article{tyler_thomas_hu_dill_alonso_ecker_sun_2004, title={DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis}, volume={135}, number={2}, journal={Plant Physiology}, author={Tyler, Ludmila and Thomas, Stephen G. and Hu, Jianhong and Dill, Alyssa and Alonso, Jose M. and Ecker, Joseph R. and Sun, Tai-ping}, year={2004}, pages={1008–1019} }
@article{pfund_tans-kersten_dunning_alonso_ecker_allen_bent_2004, title={Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana}, volume={17}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI.2004.17.6.696}, abstractNote={ The phytopathogenic bacterium Ralstonia solanacearum requires motility for full virulence, and its flagellin is a candidate pathogen-associated molecular pattern that may elicit plant defenses. Boiled extracts from R. solanacearum contained a strong elicitor of defense-associated responses. However, R. solanacearum flagellin is not this elicitor, because extracts from wild-type bacteria and fliC or flhDC mutants defective in flagellin production all elicited similar plant responses. Equally important, live R. solanacearum caused similar disease on Arabidopsis ecotype Col-0, regardless of the presence of flagellin in the bacterium or the FLS2-mediated flagellin recognition system in the plant. Unlike the previously studied flg22 flagellin peptide, a peptide based on the corresponding conserved N-terminal segment of R. solanacearum, flagellin did not elicit any response from Arabidopsis seedlings. Thus recognition of flagellin plays no readily apparent role in this pathosystem. Flagellin also was not the primary elicitor of responses in tobacco. The primary eliciting activity in boiled R. solanacearum extracts applied to Arabidopsis was attributable to one or more proteins other than flagellin, including species purifying at approximately 5 to 10 kDa and also at larger molecular masses, possibly due to aggregation. Production of this eliciting activity did not require hrpB (positive regulator of type III secretion), pehR (positive regulator of polygalacturonase production and motility), gspM (general secretion pathway), or phcA (LysR-type global virulence regulator). Wild-type R. solanacearum was virulent on Arabidopsis despite the presence of this elicitor in pathogen extracts. }, number={6}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Pfund, C and Tans-Kersten, J and Dunning, FM and Alonso, JM and Ecker, JR and Allen, C and Bent, AF}, year={2004}, month={Jun}, pages={696–706} }
@article{chen_pandey_huang_alonso_ecker_assmann_jones_2004, title={GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination}, volume={135}, number={2}, journal={Plant Physiology}, author={Chen, Jin-Gui and Pandey, Sona and Huang, Jirong and Alonso, José M. and Ecker, Joseph R. and Assmann, Sarah M. and Jones, Alan M.}, year={2004}, pages={907–915} }
@article{mockler_yu_shalitin_parikh_michael_liou_huang_smith_alonso_ecker_et al._2004, title={Regulation of flowering time in Arabidopsis by K homology domain proteins}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.0404552101}, DOI={10.1073/PNAS.0404552101}, abstractNote={
The transition from vegetative growth to reproductive development in
Arabidopsis
is regulated by multiple floral induction pathways, including the photoperiodic, the autonomous, the vernalization, and the hormonal pathways. These pathways converge to regulate the expression of a small set of genes critical for floral initiation and different signal transduction pathways can interact to govern the time to flower. One important regulator of floral initiation is the MADS-box transcription factor FLC, which acts as a negative regulator of flowering in response to both endogenous and environmental signals. In this report, we describe a study of the flowering-time gene,
FLK
[flowering locus K homology (KH) domain] that encodes a putative RNA-binding protein with three KH domains. The
flk
mutations cause delayed flowering without a significant effect on the photoperiodic or vernalization responses. FLK functions primarily as a repressor of
FLC
expression, although it also modestly affects expression of genes associated with the photoperiodic pathway. In addition to
FLK
, the expression of two other KH domain genes are modestly affected by the
flk
mutation, suggesting a possible involvement of more than one KH domain protein in the regulation of flowering time in
Arabidopsis
.
}, number={34}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Mockler, T. C. and Yu, X. and Shalitin, D. and Parikh, D. and Michael, T. P. and Liou, J. and Huang, J. and Smith, Z. and Alonso, J. M. and Ecker, J. R. and et al.}, year={2004}, month={Aug}, pages={12759–12764} }
@article{stepanova_alonso_2004, title={The canonical ethylene signaling pathway}, volume={2004}, number={221}, journal={Science Signaling}, author={Stepanova, Anna N. and Alonso, Jose M.}, year={2004}, pages={cm1} }
@article{alonso_stepanova_2004, title={The ethylene signaling pathway}, volume={306}, ISSN={["0036-8075"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-9444243287&partnerID=MN8TOARS}, DOI={10.1126/science.1104812}, abstractNote={
Plants use a structurally very simple gas molecule, the hydrocarbon ethylene, to modulate various developmental programs and coordinate responses to a multitude of external stress factors. How this simple molecule generates such a diverse array of effects has been the subject of intense research for the past two decades. A fascinating signaling pathway, with classical as well as novel plant-specific signaling elements, is emerging from these studies. We describe the four main modules that constitute this signaling pathway: a phosphotransfer relay, an EIN2-based unit, a ubiquitin-mediated protein degradation component, and a transcriptional cascade. The canonical and
Arabidopsis
ethylene signaling pathways in the Signal Transduction Knowledge Environment Connections Maps provide a complete panoramic view of these signaling events in plants.
}, number={5701}, journal={SCIENCE}, author={Alonso, JM and Stepanova, AN}, year={2004}, month={Nov}, pages={1513–1515} }
@article{monte_tepperman_al-sady_kaczorowski_alonso_ecker_li_zhang_quail_2004, title={The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0407107101}, DOI={10.1073/pnas.0407107101}, abstractNote={
The phytochrome (phy) family of sensory photoreceptors transduce informational light signals to selected nuclear genes, inducing plant growth and developmental responses appropriate to the environment. Existing data suggest that one signaling pathway by which this occurs involves direct, intranuclear interaction of the photoactivated phy molecule with PIF3, a basic helix-loop-helix transcription factor. Here, we provide evidence from recently identified
pif3
mutant alleles that PIF3 is necessary for early chloroplast greening and rapid phy-induced expression of nuclear genes encoding chloroplast components upon first exposure of seedlings to light. Therefore, these data indicate that PIF3 functions to transduce phy signals to genes involved in a critical facet of the early seedling deetiolation process, the generation of a functional photosynthetic apparatus. When transgenically expressed GUS:PIF3 fusion protein constructs were used, we found that PIF3 protein levels are rapidly and reversibly modulated by the photoreceptor over diurnal cycles in
Arabidopsis
seedlings. The PIF3 protein declines rapidly to a basal steady-state level upon initial light exposure, but reaccumulates to preirradiation levels in darkness during the subsequent night period. These data suggest that PIF3 may function in early phy signaling at the dark-to-light transition, not only during initial seedling deetiolation, but daily at dawn under diurnal light-dark cycles.
}, number={46}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Monte, E. and Tepperman, J. M. and Al-Sady, B. and Kaczorowski, K. A. and Alonso, J. M. and Ecker, J. R. and Li, X. and Zhang, Y. and Quail, P. H.}, year={2004}, month={Oct}, pages={16091–16098} }
@article{to_haberer_ferreira_deruère_mason_schaller_alonso_ecker_kieber_2004, title={Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling}, volume={16}, number={3}, journal={The Plant Cell Online}, author={To, Jennifer P. C. and Haberer, Georg and Ferreira, Fernando J. and Deruère, Jean and Mason, Michael G. and Schaller, G. Eric and Alonso, Jose M. and Ecker, Joseph R. and Kieber, Joseph J.}, year={2004}, pages={658–671} }
@article{mackey_belkhadir_alonso_ecker_dangl_2003, title={< i> Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance}, volume={112}, number={3}, journal={Cell}, author={Mackey, David and Belkhadir, Youssef and Alonso, Jose M. and Ecker, Joseph R. and Dangl, Jeffery L.}, year={2003}, pages={379–389} }
@article{lariguet_boccalandro_alonso_ecker_chory_casal_fankhauser_2003, title={A growth regulatory loop that provides homeostasis to phytochrome A signaling}, volume={15}, number={12}, journal={The Plant Cell Online}, author={Lariguet, Patricia and Boccalandro, Hernan E. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne and Casal, Jorge J. and Fankhauser, Christian}, year={2003}, pages={2966–2978} }
@article{strand_asami_alonso_ecker_chory_2003, title={Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX}, volume={421}, number={6918}, journal={Nature}, author={Strand, Åsa and Asami, Tadao and Alonso, Jose and Ecker, Joseph R. and Chory, Joanne}, year={2003}, pages={79–83} }
@article{michael_salome_hannah_spencer_sharp_mcpeek_alonso_ecker_mcclung_2003, title={Enhanced fitness conferred by naturally occurring variation in the circadian clock}, volume={302}, number={5647}, journal={Science}, author={Michael, Todd P. and Salome, Patrice A. and Hannah, J. Yu and Spencer, Taylor R. and Sharp, Emily L. and McPeek, Mark A. and Alonso, Jose M. and Ecker, Joseph R. and McClung, C. Robertson}, year={2003}, pages={1049–1053} }
@article{alonso_stepanova_solano_wisman_ferrari_ausubel_ecker_2003, title={Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis}, volume={100}, number={5}, journal={Proceedings of the National Academy of Sciences}, author={Alonso, Jose M. and Stepanova, Anna N. and Solano, Roberto and Wisman, Ellen and Ferrari, Simone and Ausubel, Frederick M. and Ecker, Joseph R.}, year={2003}, pages={2992–2997} }
@article{larkin_alonso_ecker_chory_2003, title={GUN4, a regulator of chlorophyll synthesis and intracellular signaling}, volume={299}, number={5608}, journal={Science}, author={Larkin, Robert M. and Alonso, Jose M. and Ecker, Joseph R. and Chory, Joanne}, year={2003}, pages={902–906} }
@article{alonso_stepanova_leisse_kim_chen_shinn_stevenson_zimmerman_barajas_cheuk_2003, title={Genome-wide insertional mutagenesis of Arabidopsis thaliana}, volume={301}, number={5633}, journal={Science}, author={Alonso, Jose M. and Stepanova, Anna N. and Leisse, Thomas J. and Kim, Christopher J. and Chen, Huaming and Shinn, Paul and Stevenson, Denise K. and Zimmerman, Justin and Barajas, Pascual and Cheuk, Rosa}, year={2003}, pages={653–657} }
@article{alonso_2003, title={Genome-wide insertional mutagenesis of Arabidopsis thaliana (vol 301, pg 653, 2003)}, volume={301}, number={5641}, journal={Science}, author={Alonso, J. M.}, year={2003}, pages={1849} }
@article{monte_alonso_ecker_zhang_li_young_austin-phillips_quail_2003, title={Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways}, volume={15}, number={9}, journal={The Plant Cell Online}, author={Monte, Elena and Alonso, José M. and Ecker, Joseph R. and Zhang, Yuelin and Li, Xin and Young, Jeff and Austin-Phillips, Sandra and Quail, Peter H.}, year={2003}, pages={1962–1980} }
@article{catalá_santos_alonso_ecker_martínez-zapater_salinas_2003, title={Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis}, volume={15}, number={12}, journal={The Plant Cell Online}, author={Catalá, Rafael and Santos, Elisa and Alonso, José M. and Ecker, Joseph R. and Martínez-Zapater, José M. and Salinas, Julio}, year={2003}, pages={2940–2951} }
@inbook{alonso_stepanova_2003, title={T-DNA mutagenesis in Arabidopsis}, ISBN={1588291456}, DOI={10.1385/1-59259-413-1:177}, abstractNote={Insertional mutagenesis is a basic genetic tool that allows for a rapid identification of the tagged genes responsible for a particular phenotype. Transposon and Agrobacterium-mediated DNA integration are the most commonly used biological mutagens in plants. The main drawback of these technologies is the relatively low frequency of mutations, as compared to those induced by conventional chemical or physical agents, thus limiting the use of insertional mutagens to the generation of large mutant populations in few genetic backgrounds. Recent improvements in Agrobacterium-mediated transformation efficiency and an increasing repertoire of transformation vectors available to the research community is making this type of mutagen very attractive for individual laboratories interested in the studies of mutations in particular genetic backgrounds. Herein, we describe a simple yet robust Arabidopsis transformation procedure that can be used to generate large numbers of insertional mutants in Arabidopsis thaliana. Using this protocol, transformation efficiencies of up to 5% can be achieved.}, booktitle={Plant Functional Genomics}, author={Alonso, Jose M. and Stepanova, Anna N.}, year={2003}, pages={177–187} }
@article{lariguet_boccalandro_alonso_ecker_chory_casal_fankhausera_2003, title={The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis}, journal={The Plant Cell Online}, author={Lariguet, Patricia and Boccalandro, Hernan E. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne and Casal, Jorge J. and Fankhausera, Christian}, year={2003} }
@article{ullah_chen_temple_boyes_alonso_davis_ecker_jones_2003, title={The β-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes}, volume={15}, number={2}, journal={The Plant Cell Online}, author={Ullah, Hemayet and Chen, Jin-Gui and Temple, Brenda and Boyes, Douglas C. and Alonso, José M. and Davis, Keith R. and Ecker, Joseph R. and Jones, Alan M.}, year={2003}, pages={393–409} }
@article{hu_aguirre_peto_alonso_ecker_chory_2002, title={A role for peroxisomes in photomorphogenesis and development of Arabidopsis}, volume={297}, number={5580}, journal={Science}, author={Hu, Jianping and Aguirre, Maria and Peto, Charles and Alonso, José and Ecker, Joseph and Chory, Joanne}, year={2002}, pages={405–409} }
@article{schroeder_gahrtz_maxwell_cook_kan_alonso_ecker_chory_2002, title={De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis Photomorphogenesis}, volume={12}, number={17}, journal={Current Biology}, author={Schroeder, Dana F. and Gahrtz, Manfred and Maxwell, Bridey B. and Cook, R. Kimberley and Kan, Jack M. and Alonso, José M. and Ecker, Joseph R. and Chory, Joanne}, year={2002}, pages={1462–1472} }
@article{zheng_bednarek_sanderfoot_alonso_ecker_raikhel_2002, title={NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE}, volume={129}, number={2}, journal={Plant physiology}, author={Zheng, Haiyan and Bednarek, Sebastian Y. and Sanderfoot, Anton A. and Alonso, Jose and Ecker, Joseph R. and Raikhel, Natasha V.}, year={2002}, pages={530–539} }
@article{friedrichsen_nemhauser_muramitsu_maloof_alonso_ecker_furuya_chory_2002, title={Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth}, volume={162}, number={3}, journal={Genetics}, author={Friedrichsen, Danielle M. and Nemhauser, Jennifer and Muramitsu, Takamichi and Maloof, Julin N. and Alonso, José and Ecker, Joseph R. and Furuya, Masaki and Chory, Joanne}, year={2002}, pages={1445–1456} }
@article{zhao_hull_gupta_goss_alonso_ecker_normanly_chory_celenza_2002, title={Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3}, volume={16}, number={23}, journal={Genes & Development}, author={Zhao, Yunde and Hull, Anna K. and Gupta, Neeru R. and Goss, Kendrick A. and Alonso, José and Ecker, Joseph R. and Normanly, Jennifer and Chory, Joanne and Celenza, John L.}, year={2002}, pages={3100–3112} }
@article{jarillo_capel_tang_yang_alonso_ecker_cashmore_2001, title={An Arabidopsis circadian clock component interacts with both CRY1 and phyB}, volume={410}, number={6827}, journal={Nature}, author={Jarillo, Jose A. and Capel, Juan and Tang, Ru-Hang and Yang, Hong-Quan and Alonso, Jose M. and Ecker, Joseph R. and Cashmore, Anthony R.}, year={2001}, pages={487–490} }
@article{jarillo_gabrys_capel_alonso_ecker_cashmore_2001, title={Phototropin-related NPL1 controls chloroplast relocation induced by blue light}, volume={410}, number={6831}, journal={Nature}, author={Jarillo, Jose A. and Gabrys, Halina and Capel, Juan and Alonso, Jose M. and Ecker, Joseph R. and Cashmore, Anthony R.}, year={2001}, pages={952–954} }
@article{alonso_ecker_2001, title={The ethylene pathway: a paradigm for plant hormone signaling and interaction}, volume={2001}, number={70}, journal={Science Signaling}, author={Alonso, Jose M. and Ecker, Joseph R.}, year={2001}, pages={re1} }
@article{hirayama_alonso_2000, title={Ethylene captures a metal! Metal ions are involved in ethylene perception and signal transduction}, volume={41}, number={5}, journal={Plant and Cell Physiology}, author={Hirayama, Takashi and Alonso, Jose M.}, year={2000}, pages={548–555} }
@article{curie_alonso_le jean_ecker_briat_2000, title={Involvement of NRAMP1 from Arabidopsis thaliana in iron transport}, volume={347}, DOI={10.1042/0264-6021:3470749}, abstractNote={Nramp genes code for a widely distributed class of proteins involved in a variety of processes, ranging from the control of susceptibility to bacterial infection in mammalian cells and taste behaviour in Drosophila to manganese uptake in yeast. Some of the NRAMP proteins in mammals and in yeast are capable of transporting metal ions, including iron. In plants, iron transport was shown to require a reduction/Fe(II) transport system. In Arabidopsis thaliana this process involves the IRT1 and Fro2 genes. Here we report the sequence of five NRAMP proteins from A. thaliana. Sequence comparison suggests that there are two classes of NRAMP proteins in plants: A. thaliana (At) NRAMP1 and Oriza sativa (Os) NRAMP1 and 3 (two rice isologues) represent one class, and AtNRAMP2-5 and OsNRAMP2 the other. AtNramp1 and OsNramp1 are able to complement the fet3fet4 yeast mutant defective both in low- and high-affinity iron transports, whereas AtNramp2 and OsNramp2 fail to do so. In addition, AtNramp1 transcript, but not AtNramp2 transcript, accumulates in response to iron deficiency in roots but not in leaves. Finally, overexpression of AtNramp1 in transgenic A. thaliana plants leads to an increase in plant resistance to toxic iron concentration. Taken together, these results demonstrate that AtNramp1 participates in the control of iron homoeostasis in plants.}, journal={Biochem. J}, author={Curie, Catherine and Alonso, J. and Le Jean, Marie and Ecker, J. and Briat, J.}, year={2000}, pages={749–755} }
@article{theologis_ecker_palm_federspiel_kaul_white_alonso_altafi_araujo_bowman_2000, title={Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana}, volume={408}, number={6814}, journal={Nature}, author={Theologis, Athanasios and Ecker, Joseph R. and Palm, Curtis J. and Federspiel, Nancy A. and Kaul, Samir and White, Owen and Alonso, Jose and Altafi, Hootan and Araujo, Rina and Bowman, Cheryl L.}, year={2000}, pages={816–820} }
@article{alonso_hirayama_roman_nourizadeh_ecker_1999, title={EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis}, volume={284}, number={5423}, journal={Science}, author={Alonso, Jose M. and Hirayama, Takashi and Roman, Gregg and Nourizadeh, Saeid and Ecker, Joseph R.}, year={1999}, pages={2148–2152} }
@inbook{cubells-martinez_alonso_sanchez-ballesta_granell_1999, title={Ethylene Perception and Response in Citrus Fruit}, booktitle={Biology and Biotechnology of the Plant Hormone Ethylene II}, author={Cubells-Martinez, X. and Alonso, J. M. and Sanchez-Ballesta, M. T. and Granell, A.}, year={1999}, pages={137–143} }
@article{hirayama_kieber_hirayama_kogan_guzman_nourizadeh_alonso_dailey_dancis_ecker_1999, title={RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease–Related Copper Transporter, Is Required for Ethylene Signaling in< i> Arabidopsis}, volume={97}, number={3}, journal={Cell}, author={Hirayama, Takashi and Kieber, Joseph J. and Hirayama, Noriko and Kogan, Mikhail and Guzman, Plinio and Nourizadeh, Saeid and Alonso, Jose M. and Dailey, William P. and Dancis, Andrew and Ecker, Joseph R.}, year={1999}, pages={383–393} }
@article{alonso_chamarro_granell_1995, title={A non-photosynthetic ferredoxin gene is induced by ethylene in Citrus organs}, volume={29}, number={6}, journal={Plant molecular biology}, author={Alonso, José Miguel and Chamarro, Jesús and Granell, Antonio}, year={1995}, pages={1211–1221} }
@article{alonso_granell_1995, title={A putative vacuolar processing protease is regulated by ethylene and also during fruit ripening in Citrus fruit}, volume={109}, number={2}, journal={Plant Physiology}, author={Alonso, Jose Miguel and Granell, Antonio}, year={1995}, pages={541–547} }
@article{alonso_chamarro_granell_1995, title={Evidence for the involvement of ethylene in the expression of specific RNAs during maturation of the orange, a non-climacteric fruit}, volume={29}, number={2}, journal={Plant molecular biology}, author={Alonso, Jose Miguel and Chamarro, Jesús and Granell, Antonio}, year={1995}, pages={385–390} }
@article{alonso_garcía‐martínez_chamarro_1992, title={Two dimensional gel electrophoresis patterns of total, in vivo labelled and in vitro translated polypeptides from orange flavedo during maturation and following ethylene treatment}, volume={85}, number={2}, journal={Physiologia Plantarum}, author={Alonso, José Miguel and García‐Martínez, José Luis and Chamarro, Jesús}, year={1992}, pages={147–156} }
@inproceedings{merchante_hu_stepanova_alonso_heber, title={Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants}, author={Merchante, Karen and Hu, Qiwen and Stepanova, Anna N. and Alonso, Jose M. and Heber, Steffen} }