@article{sheriff_salvato_andersen_chatterjee_kleiner_duerkop_2024, title={Enterococcal quorum-controlled protease alters phage infection}, volume={5}, ISSN={["2633-6685"]}, DOI={10.1093/femsmc/xtae022}, abstractNote={Increased prevalence of multidrug-resistant bacterial infections has sparked interest in alternative antimicrobials, including bacteriophages (phages). Limited understanding of the phage infection process hampers our ability to utilize phages to their full therapeutic potential. To understand phage infection dynamics, we performed proteomics on}, journal={FEMS MICROBES}, author={Sheriff, Emma K. and Salvato, Fernanda and Andersen, Shelby E. and Chatterjee, Anushila and Kleiner, Manuel and Duerkop, Breck A.}, year={2024}, month={Aug} }
 @article{salvato_vintila_finkel_dangl_kleiner_2022, title={Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes}, volume={35}, ISSN={["1943-7706"]}, url={https://doi.org/10.1094/MPMI-05-22-0116-TA}, DOI={10.1094/MPMI-05-22-0116-TA}, abstractNote={ Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species ( Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants.  [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . }, number={11}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Salvato, Fernanda and Vintila, Simina and Finkel, Omri M. and Dangl, Jeffery L. and Kleiner, Manuel}, year={2022}, month={Nov}, pages={977–988} }
 @article{smith_salvato_garikipati_kleiner_septer_2021, title={Activation of the Type VI Secretion System in the Squid Symbiont Vibrio fischeri Requires the Transcriptional Regulator TasR and the Structural Proteins TssM and TssA}, volume={203}, ISSN={["1098-5530"]}, DOI={10.1128/JB.00399-21}, abstractNote={
            Interbacterial weapons like the T6SS are often located on mobile genetic elements, and their expression is highly regulated. We found that two conserved structural proteins are required for T6SS expression in
            Vibrio fischeri
            .
          }, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Smith, Stephanie and Salvato, Fernanda and Garikipati, Aditi and Kleiner, Manuel and Septer, Alecia N.}, year={2021}, month={Nov} }
 @misc{salvato_hettich_kleiner_2021, title={Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes}, volume={17}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1009245}, DOI={10.1371/journal.ppat.1009245}, abstractNote={Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional [1] and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile [2]. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential [3]. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone [4]. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins [5,6]. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes [7]. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time” [8], and since then, a large array of metaproteomics approaches have been developed [7]. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.}, number={2}, journal={PLOS PATHOGENS}, publisher={Public Library of Science (PLoS)}, author={Salvato, Fernanda and Hettich, Robert L. and Kleiner, Manuel}, editor={Hogan, Deborah A.Editor}, year={2021}, month={Feb} }
 @misc{ahsan_rao_wilson_punyamurtula_salvato_petersen_ahmed_abid_verburgt_kihara_et al._2021, title={Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches}, volume={21}, ISSN={["1615-9861"]}, DOI={10.1002/pmic.202000279}, abstractNote={AbstractWhile protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)‐based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS‐CoV‐2‐mediated infections in humans. Comparative analysis of cell‐lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS‐CoV‐2 infection is still incomplete and the tissue‐specific response to SARS‐CoV‐2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross‐comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K‐Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS‐CoV‐2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS‐CoV‐2 responsive age‐, gender‐dependent, tissue‐specific protein targets.}, number={10}, journal={PROTEOMICS}, author={Ahsan, Nagib and Rao, R. Shyama Prasad and Wilson, Rashaun S. and Punyamurtula, Ujwal and Salvato, Fernanda and Petersen, Max and Ahmed, Mohammad Kabir and Abid, M. Ruhul and Verburgt, Jacob C. and Kihara, Daisuke and et al.}, year={2021}, month={May} }
 @article{wagner_tang_salvato_clouse_bartlett_vintila_phillips_sermons_hoffmann_balint-kurti_et al._2021, title={Microbe-dependent heterosis in maize}, volume={118}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2021965118}, DOI={10.1073/pnas.2021965118}, abstractNote={Significance
          Almost all grain crops grown on commercial farms are hybrid cultivars because these hybrid plants are reliably healthier, larger, and more productive than their inbred parent lines. The widespread and valuable phenomenon of hybrid superiority is called heterosis. Despite over a century of intensive research into heterosis, it is unclear how or why hybrid genomes give rise to superior phenotypes. Most hypotheses and research thus far have focused on genetic and physiological mechanisms of heterosis. In contrast, this article presents evidence for a microbe-driven mechanism of heterosis, whereby the activity of live soil microbes affects the expression of heterosis. This finding will open lines of research that could advance our understanding of heterosis.}, number={30}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Vintila, Simina and Phillips, Laura and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and et al.}, year={2021}, month={Jul} }
 @article{speare_smith_salvato_kleiner_septer_2020, title={Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition}, volume={11}, ISSN={["2150-7511"]}, DOI={10.1128/mBio.03060-19}, abstractNote={
            Bacteria often engage in interference competition to gain access to an ecological niche, such as a host. However, little is known about how the physical environment experienced by free-living or host-associated bacteria influences such competition. We used the bioluminescent squid symbiont
            Vibrio fischeri
            to study how environmental viscosity impacts bacterial competition. Our results suggest that upon transition from a planktonic environment to a host-like environment,
            V. fischeri
            cells activate their type VI secretion system, a contact-dependent interbacterial nanoweapon, to eliminate natural competitors. This work shows that competitor cells form aggregates under host-like conditions, thereby facilitating the contact required for killing, and reveals how
            V. fischeri
            regulates a key competitive mechanism in response to the physical environment.
          }, number={1}, journal={MBIO}, author={Speare, Lauren and Smith, Stephanie and Salvato, Fernanda and Kleiner, Manuel and Septer, Alecia N.}, year={2020} }
 @article{ahsan_wilson_rao_salvato_sabila_ullah_miernyk_2020, title={Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics}, volume={19}, url={https://doi.org/10.1021/acs.jproteome.9b00550}, DOI={10.1021/acs.jproteome.9b00550}, abstractNote={O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.}, number={2}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Ahsan, Nagib and Wilson, Rashaun S. and Rao, R. Shyama Prasad and Salvato, Fernanda and Sabila, Mercy and Ullah, Hemayet and Miernyk, Ján A.}, year={2020}, month={Feb}, pages={561–571} }
 @article{wagner_tang_salvato_clouse_bartlett_sermons_hoffmann_balint-kurti_kleiner_2020, title={Microbe-dependent heterosis in maize}, volume={5}, url={https://doi.org/10.1101/2020.05.05.078766}, DOI={10.1101/2020.05.05.078766}, abstractNote={ABSTRACTHybrids account for nearly all commercially planted varieties of maize and many other crop plants, because crosses between inbred lines of these species produce F1 offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, calledheterosisor hybrid vigor, are not well understood despite over a century of intensive research (1). The leading hypotheses—which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)—have been able to explain some but not all of the observed patterns of heterosis (2, 3). However, possible ecological drivers of heterosis have largely been ignored. Here we show that heterosis of root biomass and germination in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions, but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclavedvs.live soil slurries in a growth chamber, and for plants grown in fumigatedvs.untreated soil in the field. Together, our results demonstrate a novel, ecological mechanism for heterosis whereby soil microbes generally impair the germination and early growth of inbred but not hybrid maize.}, publisher={Cold Spring Harbor Laboratory}, author={Wagner, Maggie R. and Tang, Clara and Salvato, Fernanda and Clouse, Kayla M. and Bartlett, Alexandria and Sermons, Shannon and Hoffmann, Mark and Balint-Kurti, Peter J. and Kleiner, Manuel}, year={2020}, month={May} }
 @article{wang_peng_salvato_wang_yan_zhou_lin_2019, title={Salt-adaptive strategies in oil seed crop Ricinus communis early seedlings (cotyledon vs. true leaf) revealed from proteomics analysis}, volume={171}, ISSN={["1090-2414"]}, DOI={10.1016/j.ecoenv.2018.12.046}, abstractNote={Soil salinity is a major abiotic stress affecting crop growth and productivity. Ricinus communis has good salt tolerance and is also an important oilseed crop throughout the world. Early seedling stage (such as cotyledon expansion stage) is the most vulnerable period for plant under stresses. However, little information exist concerning the physiological and molecular mechanisms of Ricinus communis seedlings and the role play by cotyledons and true leaf under salt stress. In the present study, biomass, photosynthesis, chlorophyll fluorescence, inorganic ions and organic solutes contents were measured, and two dimensional gel electrophoresis-based proteomic technology was employed to identify the differentially abundant proteins in the salt-treated Ricinus communis cotyledons and true leaves. The results showed that salt stress reduced growth and photosynthesis in the seedlings. With increasing salinity, the Na+ content increased and K+ content decreased in both cotyledons and leaves, but the true leaves had lower Na+ and higher K+ contents. Soluble sugars and proline are the primary organic solutes to cope with osmotic stress. In addition, proteomic analysis revealed 30 and 42 differentially accumulated protein spots in castor cotyledon and true leaf under salt stress, respectively. Most of the identified proteins were involved in carbohydrate and energy metabolism, photosynthesis, genetic information process, reactive oxygen species metabolism, amino acid metabolism and cell structure. The physiological and proteomic results highlighted that cotyledons accumulated a large number of Na+ and provided more energy to help true leaves cope with salt stress. The true leaves saved carbon structures to synthesize osmotic substances, and the enhancement of chlorophyll synthesis and electron transfer in true leaves could also maintain photosynthesis under salt stress. These findings provide new insights into different physiological mechanisms in cotyledon and true leaf of Ricinus communis response to salt stress during early seedling stage.}, journal={ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY}, author={Wang, Yingnan and Peng, Xiaoyuan and Salvato, Fernanda and Wang, Yongcui and Yan, Xiufeng and Zhou, Zhiqiang and Lin, Jixiang}, year={2019}, month={Apr}, pages={12–25} }
 @article{borges_salvato_alcântara_nalin_piotto_azevedo_2018, title={Temporal dynamic responses of roots in contrasting tomato genotypes to cadmium tolerance}, volume={1}, url={https://doi.org/10.1007/s10646-017-1889-x}, DOI={10.1007/s10646-017-1889-x}, abstractNote={Despite numerous studies on cadmium (Cd) uptake and accumulation in crops, relatively little is available considering the temporal dynamic of Cd uptake and responses to stress focused on the root system. Here we highlighted the responses to Cd-induced stress in roots of two tomato genotypes contrasting in Cd-tolerance: the tolerant Pusa Ruby and the sensitive Calabash Rouge. Tomato genotypes growing in the presence of 35 μM CdCl 2  exhibited a similar trend of Cd accumulation in tissues, mainly in the root system and overall plants exhibited reduction in the dry matter weight. Both genotypes showed similar trends for malondialdehyde and hydrogen peroxide accumulation with increases when exposed to Cd, being this response more pronounced in the sensitive genotype. When the antioxidant machinery is concerned, in the presence of Cd the reduced glutathione content was decreased in roots while ascorbate peroxidase (APX), glutathione reductase (GR) and glutathione S-transferase (GST) activities were increased in the presence of Cd in the tolerant genotype. Altogether these results suggest APX, GR and GST as the main players of the antioxidant machinery against Cd-induced oxidative stress.}, journal={Ecotoxicology}, publisher={Springer Nature}, author={Borges, Karina Lima Reis and Salvato, Fernanda and Alcântara, Berenice Kussumoto and Nalin, Rafael Storto and Piotto, Fernando Ângelo and Azevedo, Ricardo Antunes}, year={2018}, month={Apr} }
 @article{ahsan_chen_salvato_wilson_rao_thelen_2017, title={Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from  Arabidopsis}, volume={165}, DOI={10.1016/j.jprot.2017.06.006}, abstractNote={{"Label"=>"UNLABELLED"} Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes. Decreased abundance of several ribosomal proteins, a DEAD box RNA helicase family protein (AtRH3), Clp protease (ClpP3) and proteins associated with cell division suggests a bottleneck in chloroplast ribosomal biogenesis and cell cycle regulation in AtPPI-2 mutant plants. In contrast, eight out of nine Arabidopsis TOPP isoforms were increased at the transcript level in AtPPI-2 leaves compared to WT. A protein-protein interaction network revealed that >75% of the differentially accumulated proteins have at least secondary and/or tertiary connections with AtPPI-2. Collectively, these data reveal a potential basis for the growth defects of AtPPI-2 and support the presumed role of AtPPI-2 as a master regulator for TOPPs, which regulate diverse growth and developmental processes. {"Label"=>"BIOLOGICAL SIGNIFICANCE"} Comparative label-free proteomics was used to characterize an AtPPI-2T-DNA knockdown mutant. The complex, reduced growth phenotype supports the notion that AtPPI-2 is a global regulator of TOPPs, and possibly other proteins. Comparative proteomics revealed a range of differences in protein abundance from various cellular processes such as chloroplast development, ribosome biogenesis, and transporter activity in the AtPPI-2 mutant relative to WT Arabidopsis. Collectively the results of proteomic analysis and the protein-protein network suggest that AtPPI-2 is involved in a wide range of biological processes either directly or indirectly including plastid biogenesis, translational mechanisms, and cell cycle regulation. The proposed protein interaction network comprises a testable model underlying changes in protein abundance in the AtPPI-2 mutant, and provides a better framework for future studies.}, journal={Journal of Proteomics}, publisher={Elsevier BV}, author={Ahsan, Nagib and Chen, Mingjie and Salvato, Fernanda and Wilson, Rashaun S. and Rao, R. Shyama Prasad and Thelen, Jay J.}, year={2017}, month={Aug}, pages={51–60} }
 @article{salvato_wilson_llerena_kiyota_reis_boaretto_balbuena_azevedo_thelen_mazzafera_2017, title={Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content}, volume={16}, url={https://doi.org/10.1021/acs.jproteome.7b00397}, DOI={10.1021/acs.jproteome.7b00397}, abstractNote={Sugar cane is an important crop for sugar and biofuel production. Its lignocellulosic biomass represents a promising option as feedstock for second-generation ethanol production. Nitrogen fertilization can affect differently tissues and its biopolymers, including the cell-wall polysaccharides and lignin. Lignin content and composition are the most important factors associated with biomass recalcitrance to convert cell-wall polysaccharides into fermentable sugars. Thus it is important to understand the metabolic relationship between nitrogen fertilization and lignin in this feedstock. In this study, a large-scale proteomics approach based on GeLC-MS/MS was employed to identify and relatively quantify proteins differently accumulated in two contrasting genotypes for lignin composition after excessive nitrogen fertilization. From the ∼1000 nonredundant proteins identified, 28 and 177 were differentially accumulated in response to nitrogen from IACSP04-065 and IACSP04-627 lines, respectively. These proteins were associated with several functional categories, including carbon metabolism, amino acid metabolism, protein turnover, and oxidative stress. Although nitrogen fertilization has not changed lignin content, phenolic acids and lignin composition were changed in both species but not in the same way. Sucrose and reducing sugars increased in plants of the genotype IACSP04-065 receiving nitrogen.}, number={10}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Salvato, Fernanda and Wilson, Rashaun and Llerena, Juan Pablo Portilla and Kiyota, Eduardo and Reis, Karina Lima and Boaretto, Luis Felipe and Balbuena, Tiago S. and Azevedo, Ricardo A. and Thelen, Jay J. and Mazzafera, Paulo}, year={2017}, month={Oct}, pages={3688–3703} }
 @article{salvato_santos_santana costa_rodriguez_2017, title={Proteomics for Bioenergy Production}, DOI={10.2174/9781681084619117010008}, journal={Plant-Based Genetic Tools for Biofuels Production}, publisher={BENTHAM SCIENCE PUBLISHERS}, year={2017}, month={Jun}, pages={103–121} }
 @article{rao_salvato_thal_eubel_thelen_m?ller_2017, title={The proteome of higher plant mitochondria}, volume={33}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84996551851&partnerID=MN8TOARS}, DOI={10.1016/j.mito.2016.07.002}, abstractNote={Plant mitochondria perform a wide range of functions in the plant cell ranging from providing energy and metabolic intermediates, via coenzyme biosynthesis and their own biogenesis to retrograde signaling and programmed cell death. To perform these functions, they contain a proteome of > 2000 different proteins expressed in some cells under some conditions. The vast majority of these proteins are imported, in many cases by a dedicated protein import machinery. Recent proteomic studies have identified about 1000 different proteins in both Arabidopsis and potato mitochondria, but even for energy-related proteins, the most well-studied functional protein group in mitochondria, < 75% of the proteins are recognized as mitochondrial by even one of six of the most widely used prediction algorithms. The mitochondrial proteomes contain proteins representing a wide range of different functions. Some protein groups, like energy-related proteins, membrane transporters, and de novo fatty acid synthesis, appear to be well covered by the proteome, while others like RNA metabolism appear to be poorly covered possibly because of low abundance. The proteomic studies have improved our understanding of basic mitochondrial functions, have led to the discovery of new mitochondrial metabolic pathways and are helping us towards appreciating the dynamic role of the mitochondria in the responses of the plant cell to biotic and abiotic stress.}, journal={Mitochondrion}, author={Rao, R.S.P. and Salvato, F. and Thal, B. and Eubel, H. and Thelen, J.J. and M?ller, I.M.}, year={2017}, pages={22–37} }
 @article{salvato_balbuena_nelson_rao_he_soderlund_gang_thelen_2015, title={Comparative Proteomic Analysis of Developing Rhizomes of the Ancient Vascular PlantEquisetum hyemaleand Different Monocot Species}, volume={14}, DOI={10.1021/pr501157w}, abstractNote={The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development, and function in plants. In this work, we characterized the proteome of rhizome apical tips and elongation zones from different species using a GeLC-MS/MS (one-dimensional electrophoresis in combination with liquid chromatography coupled online with tandem mass spectrometry) spectral-counting proteomics strategy. Five rhizomatous grasses and an ancient species were compared to study the protein regulation in rhizomes. An average of 2200 rhizome proteins per species were confidently identified and quantified. Rhizome-characteristic proteins showed similar functional distributions across all species analyzed. The over-representation of proteins associated with central roles in cellular, metabolic, and developmental processes indicated accelerated metabolism in growing rhizomes. Moreover, 61 rhizome-characteristic proteins appeared to be regulated similarly among analyzed plants. In addition, 36 showed conserved regulation between rhizome apical tips and elongation zones across species. These proteins were preferentially expressed in rhizome tissues regardless of the species analyzed, making them interesting candidates for more detailed investigative studies about their roles in rhizome development.}, number={4}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Salvato, Fernanda and Balbuena, Tiago S. and Nelson, William and Rao, R. Shyama Prasad and He, Ruifeng and Soderlund, Carol A. and Gang, David R. and Thelen, Jay J.}, year={2015}, month={Apr}, pages={1779–1791} }
 @article{fialho_andrade_bonatto_salvato_labate_pascholati_2016, title={Proteomic response of the phytopathogen Phyllosticta citricarpa to antimicrobial volatile organic compounds from Saccharomyces cerevisiae}, url={https://doi.org/10.1016/j.micres.2015.11.002}, DOI={10.1016/j.micres.2015.11.002}, abstractNote={Volatile organic compounds (VOCs) released by Saccharomyces cerevisiae inhibit plant pathogens, including the filamentous fungus Phyllosticta citricarpa, causal agent of citrus black spot. VOCs mediate relevant interactions between organisms in nature, and antimicrobial VOCs are promising, environmentally safer fumigants to control phytopathogens. As the mechanisms by which VOCs inhibit microorganisms are not well characterized, we evaluated the proteomic response in P. citricarpa after exposure for 12 h to a reconstituted mixture of VOCs (alcohols and esters) originally identified in S. cerevisiae. Total protein was extracted and separated by 2D-PAGE, and differentially expressed proteins were identified by LC–MS/MS. About 600 proteins were detected, of which 29 were downregulated and 11 were upregulated. These proteins are involved in metabolism, genetic information processing, cellular processes, and transport. Enzymes related to energy-generating pathways, particularly glycolysis and the tricarboxylic acid cycle, were the most strongly affected. Thus, the data indicate that antimicrobial VOCs interfere with essential metabolic pathways in P. citricarpa to prevent fungal growth.}, journal={Microbiological Research}, author={Fialho, Mauricio Batista and Andrade, Alexander and Bonatto, José Matheus Camargo and Salvato, Fernanda and Labate, Carlos Alberto and Pascholati, Sérgio Florentino}, year={2016}, month={Feb} }
 @article{santos_elbl_navarro_oliveira_salvato_balbuena_floh_2016, title={Quantitative proteomic analysis of Araucaria angustifolia (Bertol.) Kuntze cell lines with contrasting embryogenic potential}, volume={130}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84946433861&partnerID=MN8TOARS}, DOI={10.1016/j.jprot.2015.09.027}, abstractNote={GeLC–MS/MS based label free proteomic profiling was used in the large scale identification and quantification of proteins from Brazilian pine (Araucaria angustifolia) embryogenic cell (EC) lines that showed different propensities to form somatic embryos. Using a predicted protein sequence database that was derived from A. angustifolia RNA-Seq data, 2398 non-redundant proteins were identified. The log2 of the spectral count values of 858 proteins of these proteins showed a normal distribution, and were used for statistical analysis. Statistical tests indicated that 106 proteins were significantly differentially abundant between the two EC lines, and that 35 were more abundant in the responsive genotype (EC line SE1) and 71 were more abundant in the blocked genotype (EC line SE6). An increase in the abundance of proteins related to cell defense, anti-oxidative stress responses, and storage reserve deposition was observed in SE1. Moreover, in SE6 we observed an increased abundance of two proteins associated with seed development during the embryogenic cell proliferation stage, which we suggest is associated with genotypes showing a low responsiveness to embryo formation. Differences in protein abundance between the EC lines are discussed in terms of carbohydrate metabolism, cell division, defense response, gene expression, and response to reactive oxygen species.}, journal={Journal of Proteomics}, author={Santos, A.L.W. and Elbl, P. and Navarro, B.V. and Oliveira, L.F. and Salvato, F. and Balbuena, T.S. and Floh, E.I.S.}, year={2016}, pages={180–189} }
 @article{he_salvato_park_kim_nelson_balbuena_willer_crow_may_soderlund_et al._2014, title={A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84893701507&partnerID=MN8TOARS}, DOI={10.1186/1471-2229-14-46}, abstractNote={Abstract
          
            Background
            The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.
          
          
            Results
            We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.
          
          
            Conclusions
            A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.
          }, number={1}, journal={BMC Plant Biology}, author={He, R. and Salvato, F. and Park, J.-J. and Kim, M.-J. and Nelson, W. and Balbuena, T.S. and Willer, M. and Crow, J.A. and May, G.D. and Soderlund, C.A. and et al.}, year={2014} }
 @article{havelund_salvato_chen_rao_rogowska-wrzesinska_jensen_gang_thelen_ian_2014, title={Isolation of Mitochondria from Potato Tubers}, volume={4}, DOI={10.21769/bioprotoc.1226}, abstractNote={1Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark; 2Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-Columbia, Columbia, USA; 3Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-Colum, Columbia, USA; 4Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; 5Institute of Biological Chemistry, Washington State University, WA, USA *For correspondence: ian.max.moller@agrsci.dk}, number={17}, journal={BIO-PROTOCOL}, publisher={Bio-Protocol, LLC}, author={Havelund, Jesper and Salvato, Fernanda and Chen, Mingjie and Rao, R.S.P. and Rogowska-Wrzesinska, Adelina and Jensen, Ole and Gang, David and Thelen, Jay and Ian, M�ller}, year={2014} }
 @article{carvalho_lima leite_peres-buzalaf_salvato_labate_everett_whitford_buzalaf_2013, title={Renal Proteome in Mice with Different Susceptibilities to Fluorosis}, volume={8}, DOI={10.1371/journal.pone.0053261}, abstractNote={A/J and 129P3/J mouse strains have different susceptibilities to dental fluorosis due to their genetic backgrounds. They also differ with respect to several features of fluoride (F) metabolism and metabolic handling of water. This study was done to determine whether differences in F metabolism could be explained by diversities in the profile of protein expression in kidneys. Weanling, male A/J mice (susceptible to dental fluorosis, n = 18) and 129P3/J mice (resistant, n = 18) were housed in pairs and assigned to three groups given low-F food and drinking water containing 0, 10 or 50 ppm [F] for 7 weeks. Renal proteome profiles were examined using 2D-PAGE and LC-MS/MS. Quantitative intensity analysis detected between A/J and 129P3/J strains 122, 126 and 134 spots differentially expressed in the groups receiving 0, 10 and 50 ppmF, respectively. From these, 25, 30 and 32, respectively, were successfully identified. Most of the proteins were related to metabolic and cellular processes, followed by response to stimuli, development and regulation of cellular processes. In F-treated groups, PDZK-1, a protein involved in the regulation of renal tubular reabsorption capacity was down-modulated in the kidney of 129P3/J mice. A/J and 129P3/J mice exhibited 11 and 3 exclusive proteins, respectively, regardless of F exposure. In conclusion, proteomic analysis was able to identify proteins potentially involved in metabolic handling of F and water that are differentially expressed or even not expressed in the strains evaluated. This can contribute to understanding the molecular mechanisms underlying genetic susceptibility to dental fluorosis, by indicating key-proteins that should be better addressed in future studies.}, number={1}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Carvalho, Juliane Guimarães and Lima Leite, Aline and Peres-Buzalaf, Camila and Salvato, Fernanda and Labate, Carlos Alberto and Everett, Eric T. and Whitford, Gary Milton and Buzalaf, Marília Afonso Rabelo}, editor={Martens, LennartEditor}, year={2013}, month={Jan}, pages={e53261} }
 @article{salvato_havelund_chen_shyama prasad rao_rogowska-wrzesinska_jensen_gang_thelen_m?ller_2014, title={The potato tuber mitochondrial proteome}, volume={164}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84893484597&partnerID=MN8TOARS}, DOI={10.1104/pp.113.229054}, abstractNote={Abstract
               Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum ‘Folva’) and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more “extreme” proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.}, number={2}, journal={Plant Physiology}, author={Salvato, F. and Havelund, J.F. and Chen, M. and Shyama Prasad Rao, R. and Rogowska-Wrzesinska, A. and Jensen, O.N. and Gang, D.R. and Thelen, J.J. and M?ller, I.M.}, year={2014}, pages={637–653} }
 @article{balbuena_he_salvato_gang_thelen_2012, title={Large-Scale Proteome Comparative Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum Hyemale}, volume={3}, DOI={10.3389/fpls.2012.00131}, abstractNote={Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E. hyemale rhizomes using a GeLC-MS spectral-counting proteomics strategy. A total of 1,911 and 1,860 non-redundant proteins were identified in the rhizomes apical tip and elongation zone, respectively. Rhizome-characteristic proteins were determined by comparisons of the developing rhizome tissues to developing roots. A total of 87 proteins were found to be up-regulated in both horsetail rhizome tissues in relation to developing roots. Hierarchical clustering indicated a vast dynamic range in the regulation of the 87 characteristic proteins and revealed, based on the regulation profile, the existence of nine major protein groups. Gene ontology analyses suggested an over-representation of the terms involved in macromolecular and protein biosynthetic processes, gene expression, and nucleotide and protein binding functions. Spatial difference analysis between the rhizome apical tip and the elongation zone revealed that only eight proteins were up-regulated in the apical tip including RNA-binding proteins and an acyl carrier protein, as well as a KH domain protein and a T-complex subunit; while only seven proteins were up-regulated in the elongation zone including phosphomannomutase, galactomannan galactosyltransferase, endoglucanase 10 and 25, and mannose-1-phosphate guanyltransferase subunits alpha and beta. This is the first large-scale characterization of the proteome of a plant rhizome. Implications of the findings were discussed in relation to other underground organs and related species.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Balbuena, Tiago Santana and He, Ruifeng and Salvato, Fernanda and Gang, David R. and Thelen, Jay J.}, year={2012} }
 @article{salvato_carvalho_lima leite_2012, title={Strategies for Protein Separation}, DOI={10.5772/29363}, abstractNote={The proteome of a cell or tissue depends on cellular and environmental conditions, showing a dynamic system subject to large variations. To study these large changes of variability and quantity, proteomics has emerged, providing techniques dedicated to global characterization of all proteins simultaneously. The expectation is that this information will produce new insights into the biological function of proteins in different physiological states of a cell or tissue. The proteome has a dynamic and complex nature that is the result of many posttranslational modifications, molecular interactions, and a variety of proteins arising from alternative mRNA splicing. With this in mind, the number of modified and unmodified proteins found in any biological system is much bigger than the number of genes (Anderson et al., 2004), which is why mRNA expression may not correlate with protein content (Rogers et. al, 2008). In addition, not all proteins are expressed in the same or similar level in the proteome. For example, the enzyme Rubisco comprises 3050% of leaf proteome (Feller et al., 2008), which is a big issue in the proteomic assessment of low-abundance proteins. In fact, the majority of proteins are in the low-abundance level. To overcome these challenges, the proteome must be fractionated for effective detection and quantification by mass spectrometry (MS). Consequently, the analysis of proteins on the large or small scale is dependent on separation methods. As the ultimate goal in proteomics is to resolve all individual proteins in the cell, although it is quite difficult to find a separation method that could accommodate the diversity of proteins equally, protein separation methods directly affect the achievement of reliable results. Such methods are based on the physical or chemical properties of different proteins, such as their mass or net charge. The combination of sequential methods exploiting different properties can provide highresolution analysis of very complex protein mixtures. Then, current analytical strategies can reach different levels of resolution depending on the platform used. Two-dimensional gel electrophoresis (2DGE) and multidimensional liquid chromatography (MDLC) are the two methods that dominate the separation steps in proteomics. The differences of each strategy are basically related to sensitivity, automation, and high-throughput possibilities. In this chapter, the limitations and principles of these techniques will be discussed.}, journal={Integrative Proteomics}, publisher={InTech}, author={Salvato, Fernanda and Carvalho, Mayra Costa and Lima Leite, Aline}, year={2012}, month={Feb} }
 @article{giraldo_silva_salvato_terenzi_jorge_guimarães_2012, title={Thermostable invertases from Paecylomyces variotii produced under submerged and solid-state fermentation using agroindustrial residues}, volume={28}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84856480074&partnerID=MN8TOARS}, DOI={10.1007/s11274-011-0837-9}, abstractNote={The filamentous fungus Paecylomices variotii was able to produce high levels of cell extract and extracellular invertases when grown under submerged fermentation (SbmF) and solid-state fermentation, using agroindustrial products or residues as substrates, mainly soy bran and wheat bran, at 40°C for 72 h and 96 h, respectively. Addition of glucose or fructose (≥1%; w/v) in SbmF inhibited enzyme production, while the addition of 1% (w/v) peptone as organic nitrogen source enhanced the production by 3.7-fold. However, 1% (w/v) (NH(4))(2)HPO(4) inhibited enzyme production around 80%. The extracellular form was purified until electrophoretic homogeneity (10.5-fold with 33% recovery) by DEAE-Fractogel and Sephacryl S-200 chromatography. The enzyme is a monomer with molecular mass of 102 kDa estimated by SDS-PAGE with carbohydrate content of 53.6%. Optima of temperature and pH for both, extracellular and cell extract invertases, were 60°C and 4.0-4.5, respectively. Both invertases were stable for 1 h at 60°C with half-lives of 10 min at 70°C. Mg(2+), Ba(2+) and Mn(2+) activated both extracellular and cell extract invertases from P. variotii. The kinetic parameters K(m) and V(max) for the purified extracellular enzyme corresponded to 2.5 mM and 481 U/mg prot(-1), respectively.}, number={2}, journal={World Journal of Microbiology and Biotechnology}, author={Giraldo, M.A. and Silva, T.M. and Salvato, F. and Terenzi, H.F. and Jorge, J.A. and Guimarães, L.H.S.}, year={2012}, pages={463–472} }
 @article{salvato_carvalho_2010, title={Methods and strategies in proteomics and their applications in plants | Métodos e estratégias em proteômica e suas aplicações na área vegetal}, volume={40}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77953018551&partnerID=MN8TOARS}, number={3}, journal={Ciencia Rural}, author={Salvato, F. and Carvalho, M.C.C.G.}, year={2010}, pages={727–734} }
 @article{salvato_carvalho_2010, title={Métodos e estratégias em proteômica e suas aplicações na área vegetal}, volume={40}, DOI={10.1590/s0103-84782010005000018}, abstractNote={A implementação da espectrometria de massa (MS) para as análises de peptídeos (MS) e de aminoácidos (MS em tandem ou MS/MS) tornou possível a identificação de centenas de proteínas em experimentos únicos. Uma grande variedade de estratégias está disponível atualmente para o fracionamento e a purificação de amostras, a identificação de proteínas, a quantificação, a análise de modificações pós-traducionais (MPT's) e os estudos de interação. Dessa forma, a proteômica abre novas perspectivas na biologia de plantas com ênfase nos estudos de variabilidade genética, estresses fisiológicos e desenvolvimento de plantas.}, number={3}, journal={Ciência Rural}, publisher={FapUNIFESP (SciELO)}, author={Salvato, Fernanda and Carvalho, Mayra Costa}, year={2010}, month={Mar}, pages={727–734} }