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Kolkas H, Balliau T, Chourré J, Zivy M, Canut H, Jamet E. The Cell Wall Proteome of Marchantia polymorpha Reveals Specificities Compared to Those of Flowering Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:765846. [PMID: 35095945 PMCID: PMC8792609 DOI: 10.3389/fpls.2021.765846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/16/2021] [Indexed: 05/30/2023]
Abstract
Primary plant cell walls are composite extracellular structures composed of three major classes of polysaccharides (pectins, hemicelluloses, and cellulose) and of proteins. The cell wall proteins (CWPs) play multiple roles during plant development and in response to environmental stresses by remodeling the polysaccharide and protein networks and acting in signaling processes. To date, the cell wall proteome has been mostly described in flowering plants and has revealed the diversity of the CWP families. In this article, we describe the cell wall proteome of an early divergent plant, Marchantia polymorpha, a Bryophyte which belong to one of the first plant species colonizing lands. It has been possible to identify 410 different CWPs from three development stages of the haploid gametophyte and they could be classified in the same functional classes as the CWPs of flowering plants. This result underlied the ability of M. polymorpha to sustain cell wall dynamics. However, some specificities of the M. polymorpha cell wall proteome could be highlighted, in particular the importance of oxido-reductases such as class III peroxidases and polyphenol oxidases, D-mannose binding lectins, and dirigent-like proteins. These proteins families could be related to the presence of specific compounds in the M. polymorpha cell walls, like mannans or phenolics. This work paves the way for functional studies to unravel the role of CWPs during M. polymorpha development and in response to environmental cues.
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Affiliation(s)
- Hasan Kolkas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Thierry Balliau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, PAPPSO, Gif-sur-Yvette, France
| | - Josiane Chourré
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Michel Zivy
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, PAPPSO, Gif-sur-Yvette, France
| | - Hervé Canut
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
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Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes 2022; 10:proteomes10010002. [PMID: 35076627 PMCID: PMC8788469 DOI: 10.3390/proteomes10010002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.
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Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems 2021; 6:6/3/e01237-20. [PMID: 33975972 PMCID: PMC8125078 DOI: 10.1128/msystems.01237-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions varies from nonfixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont, but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy, and increased membrane permeability, leading to a loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics, and transcriptomics along with cytological analyses were used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establishes a poorly efficient symbiosis with A. afraspera despite the full activation of the bacterial symbiotic program. We found molecular signatures of high levels of stress in A. afraspera bacteroids, whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not coevolve with such a host. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Some, but not all, legume plants optimize their return on investment in the symbiosis by imposing on their microsymbionts a terminal differentiation program that increases their symbiotic efficiency but imposes a high level of stress and drastically reduces their viability. We combined multi-omics with physiological analyses to show that the symbiotic couple formed by Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera, in which the host and symbiont did not evolve together, is functional but displays a low symbiotic efficiency associated with a disconnection of terminal bacteroid differentiation features.
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Henriet C, Balliau T, Aimé D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2611-2626. [PMID: 33558872 DOI: 10.1093/jxb/eraa571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/19/2021] [Indexed: 05/17/2023]
Abstract
Pea is a legume crop producing protein-rich seeds and is increasingly in demand for human consumption and animal feed. The aim of this study was to explore the proteome of developing pea seeds at three key stages covering embryogenesis, the transition to seed-filling, and the beginning of storage-protein synthesis, and to investigate how the proteome was influenced by S deficiency and water stress, applied either separately or combined. Of the 3184 proteins quantified by shotgun proteomics, 2473 accumulated at particular stages, thus providing insights into the proteome dynamics at these stages. Differential analyses in response to the stresses and inference of a protein network using the whole proteomics dataset identified a cluster of antioxidant proteins (including a glutathione S-transferase, a methionine sulfoxide reductase, and a thioredoxin) possibly involved in maintaining redox homeostasis during early seed development and preventing cellular damage under stress conditions. Integration of the proteomics data with previously obtained transcriptomics data at the transition to seed-filling revealed the transcriptional events associated with the accumulation of the stress-regulated antioxidant proteins. This transcriptional defense response involves genes of sulfate homeostasis and assimilation, thus providing candidates for targeted studies aimed at dissecting the signaling cascade linking S metabolism to antioxidant processes in developing seeds.
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Affiliation(s)
- Charlotte Henriet
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Thierry Balliau
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Michel Zivy
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
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A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res 2020; 30:1593-1604. [PMID: 33060172 PMCID: PMC7605251 DOI: 10.1101/gr.255224.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic, and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified 15 loci with potential pleiotropic effects on the proteome. We showed that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein coexpression network, and a reprogramming of the genetic control of the abundance of many proteins, including those involved in stress response. Colocalizations between pQTLs and QTLs for ecophysiological traits, found mostly in the water deficit condition, indicated that this reprogramming may also affect the phenotypic level. Finally, we identified several candidate genes that are potentially responsible for both the coexpression of stress response proteins and the variations of ecophysiological traits under water deficit. Taken together, our findings provide novel insights into the molecular mechanisms of drought tolerance and suggest some pathways for further research and breeding.
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Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Sci Rep 2020; 10:8492. [PMID: 32444655 PMCID: PMC7244524 DOI: 10.1038/s41598-020-65087-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Most currently used antibiotics originate from Streptomycetes and phosphate limitation is an important trigger of their biosynthesis. Understanding the molecular processes underpinning such regulation is of crucial importance to exploit the great metabolic diversity of these bacteria and get a better understanding of the role of these molecules in the physiology of the producing bacteria. To contribute to this field, a comparative proteomic analysis of two closely related model strains, Streptomyces lividans and Streptomyces coelicolor was carried out. These strains possess identical biosynthetic pathways directing the synthesis of three well-characterized antibiotics (CDA, RED and ACT) but only S. coelicolor expresses them at a high level. Previous studies established that the antibiotic producer, S. coelicolor, is characterized by an oxidative metabolism and a reduced triacylglycerol content compared to the none producer, S. lividans, characterized by a glycolytic metabolism. Our proteomic data support these findings and reveal that these drastically different metabolic features could, at least in part, due to the weaker abundance of proteins of the two component system PhoR/PhoP in S. coelicolor compared to S. lividans. In condition of phosphate limitation, PhoR/PhoP is known to control positively and negatively, respectively, phosphate and nitrogen assimilation and our study revealed that it might also control the expression of some genes of central carbon metabolism. The tuning down of the regulatory role of PhoR/PhoP in S. coelicolor is thus expected to be correlated with low and high phosphate and nitrogen availability, respectively and with changes in central carbon metabolic features. These changes are likely to be responsible for the observed differences between S. coelicolor and S. lividans concerning energetic metabolism, triacylglycerol biosynthesis and antibiotic production. Furthermore, a novel view of the contribution of the bio-active molecules produced in this context, to the regulation of the energetic metabolism of the producing bacteria, is proposed and discussed.
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Affiliation(s)
- Aaron Millan-Oropeza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Lejeune
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michelle David
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Belouah I, Bénard C, Denton A, Blein-Nicolas M, Balliau T, Teyssier E, Gallusci P, Bouchez O, Usadel B, Zivy M, Gibon Y, Colombié S. Transcriptomic and proteomic data in developing tomato fruit. Data Brief 2020; 28:105015. [PMID: 31909114 PMCID: PMC6938935 DOI: 10.1016/j.dib.2019.105015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 01/06/2023] Open
Abstract
Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure. From 34,725 possible transcripts identified in the tomato, 22,877 were quantified in at least one of the nine developmental stages. For the proteome analysis, label-free liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used. Peptide ions, and subsequently the proteins from which they were derived, were quantified by integrating the signal intensities obtained from extracted ion currents (XIC) with the MassChroQ software. Absolute concentrations of individual proteins were estimated for 2375 proteins by using a mixed effects model from log10-transformed intensities and normalized to the total protein content. Transcriptomics data are available via GEO repository with accession number GSE128739. The raw MS output files and identification data were deposited on-line using the PROTICdb database (http://moulon.inra.fr/protic/tomato_fruit_development) and MS proteomics data have also been deposited to the ProteomeXchange with the dataset identifier PXD012877. The main added value of these quantitative datasets is their use in a mathematical model to estimate protein turnover in developing tomato fruit.
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Affiliation(s)
- Isma Belouah
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Camille Bénard
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Alisandra Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Mélisande Blein-Nicolas
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Thierry Balliau
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Emeline Teyssier
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, CS 50008, 33882 Villenave-d’Ornon, France
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, CS 50008, 33882 Villenave-d’Ornon, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg 3, RWTH Aachen University, Aachen, 52074, Germany
| | - Michel Zivy
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Yves Gibon
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
| | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ Bordeaux, F33883, Villenave d’Ornon, France
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Kilani J, Davanture M, Simon A, Zivy M, Fillinger S. Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca 2+ signalling pathways. J Proteomics 2019; 212:103580. [PMID: 31733416 DOI: 10.1016/j.jprot.2019.103580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/21/2019] [Accepted: 11/09/2019] [Indexed: 12/18/2022]
Abstract
Signal transduction (ST) is essential for rapid adaptive responses to changing environmental conditions. It acts through rapid post-translational modifications of signalling proteins and downstream effectors that regulate the activity and/or subcellular localisation of target proteins, or the expression of downstream genes. We have performed a quantitative, comparative proteomics study of ST mutants in the phytopathogenic fungus Botrytis cinerea during axenic growth under non-stressed conditions to decipher the roles of two kinases of the hyper-osmolarity pathway in B. cinerea physiology. We studied the mutants of the sensor histidine kinase Bos1 and of the MAP kinase Sak1. Label-free shotgun proteomics detected 2425 proteins, 628 differentially abundant between mutants and wild-type, 270 common to both mutants, indicating independent and shared regulatory functions for both kinases. Gene ontology analysis showed significant changes in functional categories that may explain in vitro growth and virulence defects of both mutants (secondary metabolism enzymes, lytic enzymes, proteins linked to osmotic, oxidative and cell wall stress). The proteome data also highlight a new link between Sak1 MAPK, cAMP and Ca2+ signalling. This study reveals the potential of proteomic analyses of signal transduction mutants to decipher their biological functions. TEXT-VULGARISATION: The fungus Botrytis cinerea is responsible for grey mold disease of hundreds of plant species. During infection, the fungus has to face important changes of its environment. Adaptation to these changing environmental conditions involves proteins of such called signal transduction pathways that regulate the production, activity or localisation of cellular components, mainly proteins. While the components of such signal transduction pathways are well known, their role globally understood, the precise impact on protein production remains unknown. In this study we have analysed and compared the global protein content of two Botrytis cinerea signal transduction mutants - both avirulent - to the pathogenic parental strain. The data of 628 differential proteins between mutants and wild-type, showed significant changes in proteins related to plant infection (secondary metabolism enzymes, lytic enzymes, proteins linked to osmotic, oxidative and cell wall stress) that may explain the virulence defects of both mutants. Moreover, we observed intracellular accumulation of secreted proteins in one of the mutants suggesting a potential secretion defect.
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Affiliation(s)
- Jaafar Kilani
- UMR BIOGER, INRA, AgroParisTech, Université Paris Saclay, Thiverval-Grignon, France; Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Marlène Davanture
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Adeline Simon
- UMR BIOGER, INRA, AgroParisTech, Université Paris Saclay, Thiverval-Grignon, France
| | - Michel Zivy
- PAPPSO, GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Sabine Fillinger
- UMR BIOGER, INRA, AgroParisTech, Université Paris Saclay, Thiverval-Grignon, France.
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Pocsfalvi G, Turiák L, Ambrosone A, del Gaudio P, Puska G, Fiume I, Silvestre T, Vékey K. Physiochemical and protein datasets related to citrus juice sac cells-derived nanovesicles and microvesicles. Data Brief 2019; 22:251-254. [PMID: 30591944 PMCID: PMC6305887 DOI: 10.1016/j.dib.2018.12.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/04/2022] Open
Abstract
Qualitative and quantitative data obtained on micro and nanovesicle enriched fractions isolated from four citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium are presented. It includes physiochemical characterization by transmission electron microscopy (TEM) and dynamic laser scattering (DLS); and molecular characterization of the biocargo of citrus vesicles by quantitative label-free proteomics. Vesicular transport related proteins of C. sinensis were predicted by (i) finding orthologues based on previously described vesicular transport proteins and (ii) GO term enrichment analysis. Based on the protein content different types of intra and intercellular vesicles were dissected and the distribution of different Enzyme classes (ECs) were determined. This data article is related to "Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicle populations" (Pocsfalvi et al., 2018).
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Affiliation(s)
- Gabriella Pocsfalvi
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Hungary
| | | | | | - Gina Puska
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Immacolata Fiume
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy
| | - Teresa Silvestre
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Hungary
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Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics 2018; 193:131-141. [PMID: 30312678 DOI: 10.1016/j.jprot.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 10/02/2018] [Accepted: 10/08/2018] [Indexed: 11/20/2022]
Abstract
In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the estimation of protein abundance depends on how peptide data are filtered and on which quantification method is used to express peptide intensity as protein abundance. So far, these two questions have been addressed independently. Here, we studied to what extent the relative performances of the quantification methods depend on the filters applied to peptide intensity data. To this end, we performed a spike-in experiment using Universal Protein Standard to evaluate the performances of five quantification methods in five datasets obtained after application of four peptide filters. Estimated protein abundances were not equally affected by filters depending on the computation mode and the type of data for quantification. Furthermore, we found that filters could have contrasting effects depending on the quantification objective. Intensity modeling proved to be the most robust method, providing the best results in the absence of any filter. However, the different quantification methods can achieve similar performances when appropriate peptide filters are used. Altogether, our findings provide insights into how best to handle intensity data according to the quantification objective and the experimental design. SIGNIFICANCE: We believe that our results are of major importance because they address, as far as we know for the first time, the crossed-effects of peptide intensity data filtering and XIC-based quantification methods on protein quantification. While previous papers have dealt with peptide filtering independently of the quantification method, here we combined four peptide filters (based on peptide sharing between proteins, retention time variability, peptides occurrence and peptide intensity profiles) with five XIC-based quantification methods representing different modes of calculating protein abundances from peptide intensities. For these different combinations, we analyzed the quality of protein quantification in terms of precision, accuracy and linearity of response to increasing protein concentration using a spike-in experiment. We showed that not only filters effect on the estimation of protein abundances depend on the quantification methods but also that quantification methods can reach similar performances when appropriate peptide filters are used. Also, depending on the quantification objective, i.e. absolute or relative, filters can have contrasting effects and we demonstrated that protein quantification by the peptide intensity modeling was the most robust method.
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Pocsfalvi G, Turiák L, Ambrosone A, Del Gaudio P, Puska G, Fiume I, Silvestre T, Vékey K. Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicle populations. JOURNAL OF PLANT PHYSIOLOGY 2018; 229:111-121. [PMID: 30056374 DOI: 10.1016/j.jplph.2018.07.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Cell-derived vesicles are membrane-enclosed organelles that transport material inside and outside the cell. Plant-derived vesicles are receiving more and more attention due to their potential as nanovectors for the delivery of biologically active substances. Here, we studied the heterogeneity and protein biocargo in citrus fruit juice sac cell-derived vesicles populations. Micro- and nano-sized vesicle fractions were isolated from four citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium, characterized using physicochemical methods and protein cargos were compared using label-free quantitative shotgun proteomics. In each sample approximately 600-800 proteins were identified. Orthologues of most of the top-ranking proteins have previously been reported in extracellular vesicles of mammalian origin. High expression levels of patellin-3-like, clathrin heavy chain, heat shock proteins, 14-3-3 protein, glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase 6 were measured in all samples while aquaporin was highly expressed only in the nanovesicle fractions. Bioinformatics revealed more than hundred protein orthologues potentially implicated in vesicular trafficking. In particular, the presence of CCV, COPI and COPII coat proteins indicates the presence of heterogeneous populations of intracellular transport vesicles. Moreover, a high number of different enzymes including hydrolases and oxidoreductases are ubiquities in citrus fruit sac cell-derived vesicles.
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Affiliation(s)
- Gabriella Pocsfalvi
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy.
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Hungary
| | | | | | - Gina Puska
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Immacolata Fiume
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy
| | - Teresa Silvestre
- Institute of Biosciences and BioResources, National Research Council of Italy, Italy
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Hungary
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12
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Nawaz K, Shahid AA, Bengyella L, Subhani MN, Ali M, Anwar W, Iftikhar S, Ali SW. Evidence of genetically diverse virulent mating types of Phytophthora capsici from Capsicum annum L. World J Microbiol Biotechnol 2018; 34:130. [PMID: 30101403 DOI: 10.1007/s11274-018-2511-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/28/2018] [Indexed: 11/25/2022]
Abstract
Chili pepper (Capsicum annum L.) is an important economic crop that is severely destroyed by the filamentous oomycete Phytophthora capsici. Little is known about this pathogen in key chili pepper farms in Punjab province, Pakistan. We investigated the genetic diversity of P. capsici strains using standard taxonomic and molecular tools, and characterized their colony growth patterns as well as their disease severity on chili pepper plants under the greenhouse conditions. Phylogenetic analysis based on ribosomal DNA (rDNA), β-tubulin and translation elongation factor 1α loci revealed divergent evolution in the population structure of P. capsici isolates. The mean oospore diameter of mating type A1 isolates was greater than that of mating type A2 isolates. We provide first evidence of an uneven distribution of highly virulent mating type A1 and A2 of P. capsici that are insensitive to mefenoxam, pyrimorph, dimethomorph, and azoxystrobin fungicides, and represent a risk factor that could ease outpacing the current P. capsici management strategies.
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Affiliation(s)
- Kiran Nawaz
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan.
| | - Ahmad Ali Shahid
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Louis Bengyella
- Tree Fruit Research and Extension Center (TFREC), College of Agricultural, Human and Natural Resource Sciences (CAHNRS), Washington State University, Wenatchee, USA.
- Department of Biological Control, Advanced Biotech Cooperative, Bali-Nyonga, Cameroon.
| | | | - Muhammad Ali
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Waheed Anwar
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Sehrish Iftikhar
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Shinawar Waseem Ali
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
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13
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Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J Proteome Res 2017; 16:2597-2613. [DOI: 10.1021/acs.jproteome.7b00163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aaron Millan-Oropeza
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Céline Henry
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mélisande Blein-Nicolas
- Génétique
Quantitative et Évolution (GQE) - Le Moulon, INRA, Univ Paris-Sud,
CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Anne Aubert-Frambourg
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fathi Moussa
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Jean Bleton
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Marie-Jöelle Virolle
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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14
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Duruflé H, Clemente HS, Balliau T, Zivy M, Dunand C, Jamet E. Cell wall proteome analysis of Arabidopsis thaliana
mature stems. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600449] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Harold Duruflé
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Thierry Balliau
- PAPPSO; GQE - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay; Gif-sur-Yvette France
| | - Michel Zivy
- PAPPSO; GQE - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay; Gif-sur-Yvette France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
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15
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Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J Proteome Res 2016; 16:494-503. [DOI: 10.1021/acs.jproteome.6b00632] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Olivier Langella
- PAPPSO,
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Benoît Valot
- UMR
6249 Chrono-Environnement, CNRS, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Thierry Balliau
- PAPPSO,
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Mélisande Blein-Nicolas
- PAPPSO,
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Ludovic Bonhomme
- INRA/UBP, UMR 1095, Genetics, Diversity
and Ecophysiology of Cereals, F63100 Clermont-Ferrand, France
| | - Michel Zivy
- PAPPSO,
GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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16
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Hervé V, Duruflé H, San Clemente H, Albenne C, Balliau T, Zivy M, Dunand C, Jamet E. An enlarged cell wall proteome ofArabidopsis thalianarosettes. Proteomics 2016; 16:3183-3187. [DOI: 10.1002/pmic.201600290] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/28/2016] [Accepted: 10/21/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Vincent Hervé
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
- INRS-Institut Armand Frappier; Laval Canada
| | - Harold Duruflé
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
| | - Thierry Balliau
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Gif sur Yvette France
| | - Michel Zivy
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Gif sur Yvette France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales; Université de Toulouse; CNRS, UPS Castanet Tolosan France
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17
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Bellati J, Champeyroux C, Hem S, Rofidal V, Krouk G, Maurel C, Santoni V. Novel Aquaporin Regulatory Mechanisms Revealed by Interactomics. Mol Cell Proteomics 2016; 15:3473-3487. [PMID: 27609422 PMCID: PMC5098044 DOI: 10.1074/mcp.m116.060087] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/31/2016] [Indexed: 12/22/2022] Open
Abstract
PIP1;2 and PIP2;1 are aquaporins that are highly expressed in roots and bring a major contribution to root water transport and its regulation by hormonal and abiotic factors. Interactions between cellular proteins or with other macromolecules contribute to forming molecular machines. Proteins that molecularly interact with PIP1;2 and PIP2;1 were searched to get new insights into regulatory mechanisms of root water transport. For that, a immuno-purification strategy coupled to protein identification and quantification by mass spectrometry (IP-MS) of PIPs was combined with data from the literature, to build thorough PIP1;2 and PIP2;1 interactomes, sharing about 400 interacting proteins. Such interactome revealed PIPs to behave as a platform for recruitment of a wide range of transport activities and provided novel insights into regulation of PIP cellular trafficking by osmotic and oxidative treatments. This work also pointed a role of lipid signaling in PIP function and enhanced our knowledge of protein kinases involved in PIP regulation. In particular we show that 2 members of the receptor-like kinase (RLK) family (RKL1 (At1g48480) and Feronia (At3g51550)) differentially modulate PIP activity through distinct molecular mechanisms. The overall work opens novel perspectives in understanding PIP regulatory mechanisms and their role in adjustment of plant water status.
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Affiliation(s)
- Jorge Bellati
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Chloé Champeyroux
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Sonia Hem
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Valérie Rofidal
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Gabriel Krouk
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Christophe Maurel
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Véronique Santoni
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
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18
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Blein-Nicolas M, Albertin W, da Silva T, Valot B, Balliau T, Masneuf-Pomarède I, Bely M, Marullo P, Sicard D, Dillmann C, de Vienne D, Zivy M. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol Cell Proteomics 2015; 14:2056-71. [PMID: 25971257 DOI: 10.1074/mcp.m115.048058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/06/2022] Open
Abstract
Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis.
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Affiliation(s)
- Mélisande Blein-Nicolas
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Warren Albertin
- CNRS, UMR 0320/UMR 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France; Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Telma da Silva
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France; Ariana Pharmaceuticals, 28 rue du Docteur Finlay, 75015 Paris, France
| | - Benoît Valot
- CNRS, Université de Franche-Comté, UMR 6249 Chrono-Environnement, F-25000, Besançon, France
| | - Thierry Balliau
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Isabelle Masneuf-Pomarède
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, Gradignan, France
| | - Marina Bely
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Philippe Marullo
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France; BIOLAFFORT, F-33034 Bordeaux, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France; INRA, UMR1083, 2 Place Viala, F-34060 Montpellier, France
| | - Christine Dillmann
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Dominique de Vienne
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
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19
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Davanture M, Dumur J, Bataillé-Simoneau N, Campion C, Valot B, Zivy M, Simoneau P, Fillinger S. Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola
and Botrytis cinerea
during exponential growth in axenic cultures. Proteomics 2014; 14:1639-45. [DOI: 10.1002/pmic.201300541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/21/2014] [Accepted: 05/08/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Marlène Davanture
- CNRS, Plateforme d’Analyse Protéomique de Paris Sud Ouest; PAPPSO; Gif-sur-Yvette France
- INRA/University Paris-Sud/CNRS/AgroParisTech; UMR 0320/UMR 8120 Génétique Végétale; Gif-sur-Yvette France
| | - Jérôme Dumur
- INRA/Université d’Angers/; /Agrocampus-Ouest; UMR 1345 IRHS; Angers France
| | | | - Claire Campion
- INRA/Université d’Angers/; /Agrocampus-Ouest; UMR 1345 IRHS; Angers France
| | - Benoît Valot
- CNRS, Plateforme d’Analyse Protéomique de Paris Sud Ouest; PAPPSO; Gif-sur-Yvette France
- INRA/University Paris-Sud/CNRS/AgroParisTech; UMR 0320/UMR 8120 Génétique Végétale; Gif-sur-Yvette France
| | - Michel Zivy
- CNRS, Plateforme d’Analyse Protéomique de Paris Sud Ouest; PAPPSO; Gif-sur-Yvette France
- INRA/University Paris-Sud/CNRS/AgroParisTech; UMR 0320/UMR 8120 Génétique Végétale; Gif-sur-Yvette France
| | - Philippe Simoneau
- INRA/Université d’Angers/; /Agrocampus-Ouest; UMR 1345 IRHS; Angers France
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20
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Meyrand M, Guillot A, Goin M, Furlan S, Armalyte J, Kulakauskas S, Cortes-Perez NG, Thomas G, Chat S, Péchoux C, Dupres V, Hols P, Dufrêne YF, Trugnan G, Chapot-Chartier MP. Surface proteome analysis of a natural isolate of Lactococcus lactis reveals the presence of pili able to bind human intestinal epithelial cells. Mol Cell Proteomics 2013; 12:3935-47. [PMID: 24002364 DOI: 10.1074/mcp.m113.029066] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Surface proteins of Gram-positive bacteria play crucial roles in bacterial adhesion to host tissues. Regarding commensal or probiotic bacteria, adhesion to intestinal mucosa may promote their persistence in the gastro-intestinal tract and their beneficial effects to the host. In this study, seven Lactococcus lactis strains exhibiting variable surface physico-chemical properties were compared for their adhesion to Caco-2 intestinal epithelial cells. In this test, only one vegetal isolate TIL448 expressed a high-adhesion phenotype. A nonadhesive derivative was obtained by plasmid curing from TIL448, indicating that the adhesion determinants were plasmid-encoded. Surface-exposed proteins in TIL448 were analyzed by a proteomic approach consisting in shaving of the bacterial surface with trypsin and analysis of the released peptides by LC-MS/MS. As the TIL448 complete genome sequence was not available, the tryptic peptides were identified by a mass matching approach against a database including all Lactococcus protein sequences and the sequences deduced from partial DNA sequences of the TIL448 plasmids. Two surface proteins, encoded by plasmids in TIL448, were identified as candidate adhesins, the first one displaying pilin characteristics and the second one containing two mucus-binding domains. Inactivation of the pilin gene abolished adhesion to Caco-2 cells whereas inactivation of the mucus-binding protein gene had no effect on adhesion. The pilin gene is located inside a cluster of four genes encoding two other pilin-like proteins and one class-C sortase. Synthesis of pili was confirmed by immunoblotting detection of high molecular weight forms of pilins associated to the cell wall as well as by electron and atomic force microscopy observations. As a conclusion, surface proteome analysis allowed us to detect pilins at the surface of L. lactis TIL448. Moreover we showed that pili appendages are formed and involved in adhesion to Caco-2 intestinal epithelial cells.
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