@article{peng_dallas_ascencio-ibanez_hoyer_legg_hanley-bowdoin_grieve_yin_2022, title={Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-06372-8}, abstractNote={Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers' access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Peng, Yao and Dallas, Mary M. and Ascencio-Ibanez, Jose T. and Hoyer, J. Steen and Legg, James and Hanley-Bowdoin, Linda and Grieve, Bruce and Yin, Hujun}, year={2022}, month={Feb} }
 @article{hoyer_wilkins_munshi_wiese_dubey_renard_mortensen_dye_carbone_duffy_et al._2022, title={Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana}, volume={6}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-12-21-0077-R}, abstractNote={Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the replication-associated ( Rep) gene were readily compensated for by direct reversion or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B), indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Columbia-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .}, number={3}, journal={PHYTOBIOMES JOURNAL}, author={Hoyer, J. Steen and Wilkins, Olivia W. and Munshi, Aanandi and Wiese, Emma and Dubey, Divya and Renard, Savannah and Mortensen, Karoline Rosendal Harto and Dye, Anna E. and Carbone, Ignazio and Duffy, Siobain and et al.}, year={2022}, pages={227–235} }
 @article{aimone_de leon_dallas_ndunguru_ascencio-ibanez_hanley-bowdoin_2021, title={A New Type of Satellite Associated with Cassava Mosaic Begomoviruses}, volume={95}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00432-21}, abstractNote={Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.}, number={21}, journal={JOURNAL OF VIROLOGY}, author={Aimone, Catherine D. and De Leon, Leandro and Dallas, Mary M. and Ndunguru, Joseph and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2021}, month={Nov} }
 @article{ascencio-ibanez_bobay_2021, title={Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep}, volume={60}, ISSN={["0006-2960"]}, DOI={10.1021/acs.biochem.1c00408}, abstractNote={The geminivirus replication protein, Rep, has long been recognized as a high-value target for control of geminivirus infections as this protein is highly conserved and essential for viral replication and proliferation. In addition, inhibition of viral replication has been pursued through various antiviral strategies with varying degrees of success, including inhibitory peptides that target Rep. While much effort has centered around sequence characterization of the Rep protein and inhibitory peptides, detailed structural analysis has been missing. This study computationally investigated the presence of common structural features within these inhibitory peptides and if these features could inform if a particular peptide will bind Rep and/or interfere with viral replication. Molecular dynamics simulations of the inhibitory peptide library showed that simply possessing stable structural features does not inform interference of viral replication regardless of the binding of Rep. Additionally, nearly all known Rep inhibitory peptides sample a conserved β-sheet structural motif, possibly informing structure-function relationships in binding Rep. In particular, two peptides (A22 and A64) characterized by this structural motif were computationally docked against a wide variety of geminivirus Rep proteins to determine a mechanism of action. Computational docking revealed these peptides utilize a common Rep protein sequence motif for binding, HHN-x1/2-Q. The results identified residues in both Rep and the inhibitory peptides that play a significant role in the interaction, establishing the foundation for a rational structure-based design approach for the construction of both broadly reactive and geminivirus species-specific inhibitors.}, number={37}, journal={BIOCHEMISTRY}, author={Ascencio-Ibanez, J. Trinidad and Bobay, Benjamin G.}, year={2021}, month={Sep}, pages={2795–2809} }
 @misc{beam_ascencio-ibanez_2020, title={Geminivirus Resistance: A Minireview}, volume={11}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2020.01131}, abstractNote={A continuing challenge to crop production worldwide is the spectrum of diseases caused by geminiviruses, a large family of small circular single-stranded DNA viruses. These viruses are quite diverse, some containing mono- or bi-partite genomes, and infecting a multitude of monocot and dicot plants. There are currently many efforts directed at controlling these diseases. While some of the methods include controlling the insect vector using pesticides or genetic insect resistance (Rodríguez-López et al., 2011), this review will focus on the generation of plants that are resistant to geminiviruses themselves. Genetic resistance was traditionally found by surveying the wild relatives of modern crops for resistance loci; this method is still widely used and successful. However, the quick rate of virus evolution demands a rapid turnover of resistance genes. With better information about virus-host interactions, scientists are now able to target early stages of geminivirus infection in the host, preventing symptom development and viral DNA accumulation.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Beam, Kayla and Ascencio-Ibanez, Jose Trinidad}, year={2020}, month={Jul} }
 @article{saggaf_ndunguru_tairo_sseruwagi_ascencio-ibanez_kilalo_miano_2019, title={Immunohistochemical localization of Cassava brown streak virus and its morphological effect on cassava leaves}, volume={105}, ISSN={["0885-5765"]}, DOI={10.1016/j.pmpp.2018.06.001}, abstractNote={The localization of Cassava brown streak virus (CBSV) in cassava (Manihot esculenta) leaf tissues was determined and cellular morphological changes in CBSV-infected tissues were evaluated. CBSV-symptomatic leaves were screened with CBSV-specific primers using reverse-transcriptase polymerase chain reaction. Immunohistochemical reactions showed precipitation in CBSV-infected but not CBSV-free tissues, demonstrating successful localization of CBSV. Microscopic inspection showed significantly larger (P < 0.001) midribs in CBSV-infected compared with control (uninfected) leaves. Viral accumulation occurred in middle and lower but rarely in young upper leaves. This immunohistochemical method for virus localization will be invaluable for efficient screening of CBSV and for breeding resistant cassava.}, journal={PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY}, author={Saggaf, Maliha H. and Ndunguru, Joseph and Tairo, Fred and Sseruwagi, Peter and Ascencio-Ibanez, Jose Trino and Kilalo, Dora and Miano, Douglas W.}, year={2019}, month={Jan}, pages={67–76} }
 @article{rajabu_kennedy_ndunguru_ateka_tairo_hanley-bowdoin_ascencio-ibanez_2018, title={Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses}, volume={256}, ISSN={["1879-0984"]}, DOI={10.1016/j.jviromet.2018.03.002}, abstractNote={Geminiviruses are devastating single-stranded DNA viruses that infect a wide variety of crops in tropical and subtropical areas of the world. Tomato, which is a host for more than 100 geminiviruses, is one of the most affected crops. Developing plant models to study geminivirus-host interaction is important for the design of virus management strategies. In this study, “Florida Lanai” tomato was broadly characterized using three begomoviruses (Tomato yellow leaf curl virus, TYLCV; Tomato mottle virus, ToMoV; Tomato golden mosaic virus, TGMV) and a curtovirus (Beet curly top virus, BCTV). Infection rates of 100% were achieved by agroinoculation of TYLCV, ToMoV or BCTV. Mechanical inoculation of ToMoV or TGMV using a microsprayer as well as whitefly transmission of TYLCV or ToMoV also resulted in 100% infection frequencies. Symptoms appeared as early as four days post inoculation when agroinoculation or bombardment was used. Symptoms were distinct for each virus and a range of features, including plant height, flower number, fruit number, fruit weight and ploidy, was characterized. Due to its small size, rapid growth, ease of characterization and maintenance, and distinct responses to different geminiviruses, “Florida Lanai” is an excellent choice for comparing geminivirus infection in a common host.}, journal={JOURNAL OF VIROLOGICAL METHODS}, author={Rajabu, C. A. and Kennedy, G. G. and Ndunguru, J. and Ateka, E. M. and Tairo, F. and Hanley-Bowdoin, L. and Ascencio-Ibanez, J. T.}, year={2018}, month={Jun}, pages={89–99} }
 @article{shen_bobay_greeley_reyes_rajabu_blackburn_dallas_goshe_ascencio-ibanez_hanley-bowdoin_2018, title={Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection}, volume={178}, ISSN={["1532-2548"]}, DOI={10.1104/pp.18.00268}, abstractNote={Geminiviruses are single-stranded DNA viruses that infect a wide variety of plants and cause severe crop losses worldwide. The geminivirus replication initiator protein (Rep) binds to the viral replication origin and catalyzes DNA cleavage and ligation to initiate rolling circle replication. In this study, we found that the Tomato golden mosaic virus (TGMV) Rep is phosphorylated at serine-97 by sucrose nonfermenting 1-related protein kinase 1 (SnRK1), a master regulator of plant energy homeostasis and metabolism. Phosphorylation of Rep or the phosphomimic S97D mutation impaired Rep binding to viral DNA. A TGMV DNA-A replicon containing the Rep S97D mutation replicated less efficiently in tobacco (Nicotiana tabacum) protoplasts than in wild-type or Rep phosphorylation-deficient replicons. The TGMV Rep-S97D mutant also was less infectious than the wild-type virus in Nicotiana benthamiana and was unable to infect tomato (Solanum lycopersicum). Nearly all geminivirus Rep proteins have a serine residue at the position equivalent to TGMV Rep serine-97. SnRK1 phosphorylated the equivalent serines in the Rep proteins of Tomato mottle virus and Tomato yellow leaf curl virus and reduced DNA binding, suggesting that SnRK1 plays a key role in combating geminivirus infection. These results established that SnRK1 phosphorylates Rep and interferes with geminivirus replication and infection, underscoring the emerging role for SnRK1 in the host defense response against plant pathogens.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Shen, Wei and Bobay, Benjamin G. and Greeley, Laura A. and Reyes, Maria I. and Rajabu, Cyprian A. and Blackburn, R. Kevin and Dallas, Mary Beth and Goshe, Michael B. and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2018}, month={Sep}, pages={372–389} }
 @article{kyallo_ateka_sseruwagi_ascencio-ibanez_ssemakula_skilton_ndunguru_2017, title={Infectivity of Deinbollia mosaic virus, a novel weed-infecting begomovirus in East Africa}, volume={162}, ISSN={["1432-8798"]}, DOI={10.1007/s00705-017-3495-x}, abstractNote={Weed-infecting begomoviruses play an important role in the epidemiology of crop diseases because they can potentially infect crops and contribute to the genetic diversity of crop-infecting begomoviruses. Despite the important epidemiological role that weed-infecting begomoviruses play, they remain insufficiently studied in Africa. Recently, we identified Deinbollia mosaic virus (DMV), a distinct begomovirus found naturally infecting the weed host Deinbollia borbonica (Sapindaceae) in Kenya and Tanzania. In this study, we investigated the capacity of DMV to infect a restricted host range of Solanaceae and Euphorbiaceae species. Biolistic inoculation of Nicotiana benthamiana with concatemeric DNAs resulted in systemic infection associated with yellow mosaic symptoms, while DNA partial dimers caused asymptomatic systemic infection. DMV was not infectious to cassava (Manihot esculenta Crantz), suggesting host resistance to the virus. Here, we demonstrate the first experimental infectivity analysis of DMV in N. benthamiana and cassava.}, number={11}, journal={ARCHIVES OF VIROLOGY}, author={Kyallo, Martina and Ateka, Elijah Miinda and Sseruwagi, Peter and Ascencio-Ibanez, Jose Trinidad and Ssemakula, Mildred-Ochwo and Skilton, Robert and Ndunguru, Joseph}, year={2017}, month={Nov}, pages={3439–3445} }
 @article{ndunguru_de leon_doyle_sseruwagi_plata_legg_thompson_tohme_aveling_ascencio-ibanez_et al._2016, title={Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease}, volume={90}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02834-15}, abstractNote={Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies.Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.}, number={8}, journal={JOURNAL OF VIROLOGY}, author={Ndunguru, Joseph and De Leon, Leandro and Doyle, Catherine D. and Sseruwagi, Peter and Plata, German and Legg, James P. and Thompson, Graham and Tohme, Joe and Aveling, Theresa and Ascencio-Ibanez, Jose T. and et al.}, year={2016}, month={Apr}, pages={4160–4173} }
 @book{hardin_ascencio-ibaanez_knopp_2013, title={Experimental biochemistry: Theory, experiment, analysis and reporting}, publisher={Dubuque, Iowa: Kendall Hunt}, author={Hardin, C. and Ascencio-Ibaanez, T. and Knopp, J.}, year={2013} }
 @article{reyes_nash_dallas_ascencio-ibanez_hanley-bowdoin_2013, title={Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato}, volume={87}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.01095-13}, abstractNote={ABSTRACT Geminiviruses constitute a large family of single-stranded DNA viruses that cause serious losses in important crops worldwide. They often exist in disease complexes and have high recombination and mutation rates, allowing them to adapt rapidly to new hosts and environments. Thus, an effective resistance strategy must be general in character and able to target multiple viruses. The geminivirus replication protein (Rep) is a good target for broad-based disease control because it is highly conserved and required for viral replication. In an earlier study, we identified a set of peptide aptamers that bind to Rep and reduce viral replication in cultured plant cells. In this study, we selected 16 of the peptide aptamers for further analysis in yeast two-hybrid assays. The results of these experiments showed that all 16 peptide aptamers interact with all or most of the Rep proteins from nine viruses representing the three major Geminiviridae genera and identified two peptide aptamers (A22 and A64) that interact strongly with different regions in the Rep N terminus. Transgenic tomato lines expressing A22 or A64 and inoculated with Tomato yellow leaf curl virus or Tomato mottle virus exhibited delayed viral DNA accumulation and often contained lower levels of viral DNA. Strikingly, the effect on symptoms was stronger, with many of the plants showing no symptoms or strongly attenuated symptoms. Together, these results established the efficacy of using Rep-binding peptide aptamers to develop crops that are resistant to diverse geminiviruses.}, number={17}, journal={JOURNAL OF VIROLOGY}, author={Reyes, Maria Ines and Nash, Tara E. and Dallas, Mary M. and Ascencio-Ibanez, J. Trinidad and Hanley-Bowdoin, Linda}, year={2013}, month={Sep}, pages={9691–9706} }
 @article{nash_dallas_reyes_buhrman_ascencio-ibanez_hanley-bowdoin_2011, title={Functional Analysis of a Novel Motif Conserved across Geminivirus Rep Proteins}, volume={85}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02143-10}, abstractNote={ABSTRACT Members of the Geminiviridae have single-stranded DNA genomes that replicate in nuclei of infected plant cells. All geminiviruses encode a conserved protein (Rep) that catalyzes initiation of rolling-circle replication. Earlier studies showed that three conserved motifs—motifs I, II, and III—in the N termini of geminivirus Rep proteins are essential for function. In this study, we identified a fourth sequence, designated GRS ( g eminivirus R ep s equence), in the Rep N terminus that displays high amino acid sequence conservation across all geminivirus genera. Using the Rep protein of Tomato golden mosaic virus (TGMV AL1), we show that GRS mutants are not infectious in plants and do not support viral genome replication in tobacco protoplasts. GRS mutants are competent for protein-protein interactions and for both double- and single-stranded DNA binding, indicating that the mutations did not impair its global conformation. In contrast, GRS mutants are unable to specifically cleave single-stranded DNA, which is required to initiate rolling-circle replication. Interestingly, the Rep proteins of phytoplasmal and algal plasmids also contain GRS-related sequences. Modeling of the TGMV AL1 N terminus suggested that GRS mutations alter the relative positioning of motif II, which coordinates metal ions, and motif III, which contains the tyrosine involved in DNA cleavage. Together, these results established that the GRS is a conserved, essential motif characteristic of an ancient lineage of rolling-circle initiators and support the idea that geminiviruses may have evolved from plasmids associated with phytoplasma or algae.}, number={3}, journal={JOURNAL OF VIROLOGY}, author={Nash, Tara E. and Dallas, Mary B. and Reyes, Maria Ines and Buhrman, Gregory K. and Ascencio-Ibanez, J. Trinidad and Hanley-Bowdoin, Linda}, year={2011}, month={Feb}, pages={1182–1192} }
 @article{sanchez-duran_dallas_ascencio-ibanez_reyes_arroyo-mateos_ruiz-albert_hanley-bowdoin_bejarano_2011, title={Interaction between Geminivirus Replication Protein and the SUMO-Conjugating Enzyme Is Required for Viral Infection}, volume={85}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02566-10}, abstractNote={ABSTRACT Geminiviruses are small DNA viruses that replicate in nuclei of infected plant cells by using plant DNA polymerases. These viruses encode a protein designated AL1, Rep, or AC1 that is essential for viral replication. AL1 is an oligomeric protein that binds to double-stranded DNA, catalyzes the cleavage and ligation of single-stranded DNA, and induces the accumulation of host replication machinery. It also interacts with several host proteins, including the cell cycle regulator retinoblastoma-related protein (RBR), the DNA replication protein PCNA (proliferating cellular nuclear antigen), and the sumoylation enzyme that conjugates SUMO to target proteins (SUMO-conjugating enzyme [SCE1]). The SCE1-binding motif was mapped by deletion to a region encompassing AL1 amino acids 85 to 114. Alanine mutagenesis of lysine residues in the binding region either reduced or eliminated the interaction with SCE1, but no defects were observed for other AL1 functions, such as oligomerization, DNA binding, DNA cleavage, and interaction with AL3 or RBR. The lysine mutations reduced or abolished virus infectivity in plants and viral DNA accumulation in transient-replication assays, suggesting that the AL1-SCE1 interaction is required for viral DNA replication. Ectopic AL1 expression did not result in broad changes in the sumoylation pattern of plant cells, but specific changes were detected, indicating that AL1 modifies the sumoylation state of selected host proteins. These results established the importance of AL1-SCE1 interactions during geminivirus infection of plants and suggested that AL1 alters the sumoylation of selected host factors to create an environment suitable for viral infection.}, number={19}, journal={JOURNAL OF VIROLOGY}, author={Sanchez-Duran, Miguel A. and Dallas, Mary B. and Ascencio-Ibanez, Jose T. and Reyes, Maria Ines and Arroyo-Mateos, Manuel and Ruiz-Albert, Javier and Hanley-Bowdoin, Linda and Bejarano, Eduardo R.}, year={2011}, month={Oct}, pages={9789–9800} }
 @article{sozzani_maggio_giordo_umana_ascencio-ibañez_hanley-bowdoin_bergounioux_cella_albani_2010, title={The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis}, volume={72}, ISSN={1573-5028}, DOI={10.1007/s11103-009-9577-8}, number={4-5}, journal={Plant Molecular Biology}, author={Sozzani, Rosangela and Maggio, Caterina and Giordo, Roberta and Umana, Elisabetta and Ascencio-Ibañez, Jose Trinidad and Hanley-Bowdoin, Linda and Bergounioux, Catherine and Cella, Rino and Albani, Diego}, year={2010}, month={Mar}, pages={381–395} }
 @misc{ascencio-ibanez_sozzani_lee_chu_wolfinger_cella_hanley-bowdoin_2008, title={Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection}, volume={148}, number={1}, journal={Plant Physiology}, author={Ascencio-Ibanez, J. T. and Sozzani, R. and Lee, T. J. and Chu, T. M. and Wolfinger, R. D. and Cella, R. and Hanley-Bowdoin, L.}, year={2008}, pages={436–454} }
 @article{ascencio-ibanez_settlage_2007, title={DNA abrasion onto plants is an effective method for geminivirus infection and virus-induced gene silencing}, volume={142}, ISSN={["1879-0984"]}, DOI={10.1016/j.jviromet.2007.01.031}, abstractNote={Geminiviruses belong to a rapidly growing group of plant pathogens that contribute to crop losses in tropical and subtropical areas of the world. Geminivirus infection is a model for plant DNA replication and virus/host interactions. Geminiviruses are also used as vectors to induce silencing of endogenous genes in several plant species. A method was analyzed for inoculating geminiviruses using plasmid DNA rubbed onto leaves in the presence of an abrasive (DNA abrasion). Although the use of DNA abrasion to inoculate geminiviruses has been described previously, the technique has fallen out of favor and has not been systematically optimized. However, consistent efficiencies of 100% infection rates can be achieved by DNA abrasion. The symptoms of Tomato Golden Mosaic Virus or Cabbage Leaf Curl Virus infection on Nicotiana benthamiana were similar in timing and appearance to the symptoms observed in plants inoculated using Agrobacterium as the delivery method. More importantly, silencing of an endogenous gene was highly efficient when a geminivirus silencing vector was inoculated by the DNA abrasion method. Other plant species successfully inoculated with geminiviruses by DNA abrasion were Nicotiana tabacum, Capsicum annuum and Nicandra physalodes. Unfortunately, Arabidopsis thaliana could not be infected with Cabbage Leaf Curl Virus using leaf abrasion, demonstrating limitation of the method. However, leaf abrasion to inoculate geminiviruses is an easy and inexpensive method that should be considered as an accessible technique to the growing number of researchers using geminiviruses.}, number={1-2}, journal={JOURNAL OF VIROLOGICAL METHODS}, author={Ascencio-Ibanez, Jose Trinidad and Settlage, Sharon B.}, year={2007}, month={Jun}, pages={198–203} }
 @article{arguello-astorga_ascencio-ibanez_dallas_orozco_hanley-bowdoin_2007, title={High-frequency reversion of geminivirus replication protein mutants during infection}, volume={81}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00925-07}, abstractNote={ABSTRACT The geminivirus replication protein AL1 interacts with retinoblastoma-related protein (RBR), a key regulator of the plant division cell cycle, to induce conditions permissive for viral DNA replication. Previous studies of tomato golden mosaic virus (TGMV) AL1 showed that amino acid L148 in the conserved helix 4 motif is critical for RBR binding. In this work, we examined the effect of an L148V mutation on TGMV replication in tobacco cells and during infection of Nicotiana benthamiana plants. The L148V mutant replicated 100 times less efficiently than wild-type TGMV in protoplasts but produced severe symptoms that were delayed compared to those of wild-type infection in plants. Analysis of progeny viruses revealed that the L148V mutation reverted at 100% frequency in planta to methionine, leucine, isoleucine, or a second-site mutation depending on the valine codon in the initial DNA sequence. Similar results were seen with another geminivirus, cabbage leaf curl virus (CaLCuV), carrying an L145A mutation in the equivalent residue. Valine was the predominant amino acid recovered from N. benthamiana plants inoculated with the CaLCuV L145A mutant, while threonine was the major residue in Arabidopsis thaliana plants. Together, these data demonstrated that there is strong selection for reversion of the TGMV L148V and CaLCuV L145A mutations but that the nature of the selected revertants is influenced by both the viral background and host components. These data also suggested that high mutation rates contribute to the rapid evolution of geminivirus genomes in plants.}, number={20}, journal={JOURNAL OF VIROLOGY}, author={Arguello-Astorga, Gerardo and Ascencio-Ibanez, J. Trinidad and Dallas, Mary Beth and Orozco, Beverly M. and Hanley-Bowdoin, Linda}, year={2007}, month={Oct}, pages={11005–11015} }