Delphine Vincent - Academia.edu (original) (raw)

Papers by Delphine Vincent

Frontiers in Genetics, 2016

Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such ... more Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones, and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows' milk. Method A (urea) involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone) involved a trichloroacetic acid (TCA)/acetone precipitation, and method C (methanol/chloroform) involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection) to assess reproducibility. Mass spectrometry (MS) data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform) yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea) yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone) was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows.

Frontiers in Plant Science, 2015

Antimicrobial peptides (AMPs) are natural products found across diverse taxa as part of the innat... more Antimicrobial peptides (AMPs) are natural products found across diverse taxa as part of the innate immune system against pathogen attacks. Some AMPs are synthesized through the canonical gene expression machinery and are called ribosomal AMPs. Other AMPs are assembled by modular enzymes generating nonribosomal AMPs and harbor unusual structural diversity. Plants synthesize an array of AMPs, yet are still subject to many pathogen invasions. Crop breeding programs struggle to release new cultivars in which complete disease resistance is achieved, and usually such resistance becomes quickly overcome by the targeted pathogens which have a shorter generation time. AMPs could offer a solution by exploring not only plant-derived AMPs, related or unrelated to the crop of interest, but also non-plant AMPs produced by bacteria, fungi, oomycetes or animals. This review highlights some promising candidates within the plant kingdom and elsewhere, and offers some perspectives on how to identify and validate their bioactivities. Technological advances, particularly in mass spectrometry (MS) and nuclear magnetic resonance (NMR), have been instrumental in identifying and elucidating the structure of novel AMPs, especially nonribosomal peptides which cannot be identified through genomics approaches. The majority of non-plant AMPs showing potential for plant disease immunity are often tested using in vitro assays. The greatest challenge remains the functional validation of candidate AMPs in plants through transgenic experiments, particularly introducing nonribosomal AMPs into crops.

Journal of Plant Biochemistry & Physiology, 2013

Figure 1: Number of publications listed in PubMed per year using "(((secretome[Title/Abstract]) O... more Figure 1: Number of publications listed in PubMed per year using "(((secretome[Title/Abstract]) OR secretomic[Title/Abstract]) OR secretomics[Title/Abstract])" keyword for all secretomics studies in grey, and "((((secretome[Title/Abstract]) OR secretomic[Title/Abstract]) OR secretomics[Title/Abstract]) AND fung*[Title/Abstract]) AND plant[Title/Abstract]" keyword for plant/fungi secretomics in black. Searches performed on 30 October 2013.

Plant Proteomics, 2007

Page 374. Chapter 21 Plant Proteome Responses to Abiotic Stress Delphine Vincent and Michel Zivy ... more Page 374. Chapter 21 Plant Proteome Responses to Abiotic Stress Delphine Vincent and Michel Zivy Abstract Proteomic studies of plant response to abiotic stress include analyses of the effects of water deficit, salt excess, low ...

Plant Physiology and Biochemistry, 2004

The proteome of the basal part of growing Zea mays leaves was analyzed from 4 to 14 d after stopp... more The proteome of the basal part of growing Zea mays leaves was analyzed from 4 to 14 d after stopping watering and in well watered controls. The relative quantity of 46 proteins was found to increase in leaves of plants submitted to water deficit. Different types of responses were observed, some proteins showing a constant increase during water deficit, while others showed stabilization after a first increase or a transient increase. Isoforms encoded by the same gene showed different responses. The response to water deficit showed genetic variation. Some increased proteins were induced specifically in one of the two studied genotypes (e.g. ASR1) while others were significantly induced in both genotypes but to a different level or with different kinetics. Analyses of relations between protein quantities, relative water content (RWC) and abscisic acid (ABA) concentration allowed us to show that the quantitative variation of some proteins (e.g. ABA45 and OSR40 proteins) was linked to differences in ABA accumulation between the genotypes. Other proteins showed genetic variations that were not related to differences in water status or ABA concentration (e.g. a cystatin). Data obtained from these experiments, together with data from other experiments, contribute to the characterization of maize proteome response to drought in different conditions and in different genotypes. This characterization allows the search for candidate proteins, i.e. for protein whose genetic variation of expression could be partly responsible for the variability of plant responses to drought.

Comp Biochem Physiol Pt a, 2008

The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symb... more The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, b-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.

Phytochemistry, Jul 1, 2009

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides  Popul... more Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides  Populus nigra, cv. 'Agathe_F' and 'Cima', were analysed over a short-term period of 18 days in glasshouse using 4month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra.

Electrophoresis, 2006

Protein extraction from grape berries has been challenging, particularly in mature berries, which... more Protein extraction from grape berries has been challenging, particularly in mature berries, which can have sugar concentrations as high as 26%. Grape skins and seeds contain large amounts of polyphenols, which can also interfere with efficient protein extraction. In plants, two extraction protocols, TCA/acetone-based and phenol-based methods, have been mainly used to extract proteins from different organs or tissues on many species. However, few results have been reported for grape berry clusters. We wanted to determine which of these protocols was optimal for berry clusters in order to achieve both efficient protein extraction and high spot resolution on 2-D gels. Four protocols, derived from either TCA/acetone or phenol procedures, were tested on mature Cabernet Sauvignon whole berry clusters. The phenol-based protocols were superior to the TCA/acetone methods, showing larger protein yields and greater spot resolution on 2-D gels. One method was clearly superior to the rest, a phe...

Drought is a major abiotic stress affecting all levels of plant organization and, in particular, ... more Drought is a major abiotic stress affecting all levels of plant organization and, in particular, leaf elongation. Several experiments were designed to study the effect of water deficits on maize (Zea mays) leaves at the protein level by taking into account the reduction of leaf elongation. Proteomic analyses of growing maize leaves allowed us to show that two isoforms of

ABSTRACT Water deficit progressively reduced growth of Cabernet Sauvignon shoots with time over a... more ABSTRACT Water deficit progressively reduced growth of Cabernet Sauvignon shoots with time over a 16-day period. Water deficit decreased shoot elongation, stomatal conductance and photosynthesis after day 4; 2277 proteins in shoot tips were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins clustered into four groups: increased and decreased abundance of early- and late-responding protein profiles. Vines sensed the water deficit early, prior to any physiological responses, because the abundance of some proteins changed before decreases in shoot elongation, stomatal conductance and photosynthesis. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, and growth-related categories (steroid metabolism and water transport), whereas those for late-responding proteins were involved with transport, antioxidants, amino acid and carbohydrate metabolism. Many of these early-responding proteins are likely to be regulated by post-transcriptional modifications.

Genetics, Genomics and Breeding of Poplar, 2011

Phytochemistry, 2009

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides x Popul... more Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides x Populus nigra, cv. 'Agathe_F' and 'Cima', were analysed over a short-term period of 18 days in glasshouse using 4-month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra. A reliable genotype effect was observed in the leaf proteome over experiment locations, water regimes and sampling dates. Quantitative differences between genotypes were found. Most of them corresponded to proteins matching isoforms or post-translational modification variants. However, 'Cima' displayed the highest abundance of antioxidant enzymes. In response to water deficit, about 10% of the reproducible spots significantly varied regardless of the experiment location, among which about 25% al...

Methods in Molecular Biology, 2011

Proteomics is a key technique that is helping elucidate many complex biological processes. The an... more Proteomics is a key technique that is helping elucidate many complex biological processes. The analysis of plant-pathogen interactions using proteomics is complicated by the presence of the proteomes of two species, but is benefiting from the developing maturity and power of these techniques. More and more pathogen genomes are being sequenced, so fungal proteomics is reaching its full potential and remains the chosen technology to unravel the molecular pathways of pathogenicity and resistance. In this chapter, we suggest proteomic strategies that have proved successful on various plant-interacting fungal species. Several protein extraction methods are described. For adequate quantitative analyses of protein abundances, we recommend either separation using two-dimensional gel electrophoresis or labelling with isobaric tags followed by two-dimensional HPLC separation. Proteins of interest are then identified using mass spectrometry. Identified proteins can assist in refining genome annotations, otherwise known as proteogenomics.

Journal of Integrated OMICS, 2011

PROTEOMICS, 2005

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obt... more PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.

PROTEOMICS, 2009

Genetic variation of leaf proteome in drought response was investigated among eight Populus Âeura... more Genetic variation of leaf proteome in drought response was investigated among eight Populus Âeuramericana genotypes contrasting for their leaf carbon isotope discrimination (D), an estimate of intrinsic water-use efficiency. Plants were grown in open field on two similar plots. Drought was induced by an 86-day irrigation cessation on one plot, whereas a second plot remained regularly irrigated. Using 2-DE, 863 reproducible spots were detected; about 60% presented at least one significant effect i.e. treatment, genotype and/or genotype by treatment interaction effect. A significant genotype by treatment interaction was detected for 62 reliably identified proteins among which, about 65% consisted in chloroplast-associated proteins either involved in the Calvin cycle or in the electron-transport chains. The other proteins were involved in oxidative stress, amino acid or protein metabolisms. Correlations between protein abundance and D variations were found for 45 reliably identified proteins. The abundance of ribulose-1,5-bisphosphate carboxylase/ oxygenase activase isoforms scaled negatively with D regardless of the treatment, suggesting that a large intrinsic water-use efficiency could be due to higher abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase activase. Under control condition, abundance of enzymes involved in carbon fixation was also negatively correlated with D, whereas abundance of enzymes involved in photorespiration or respiration was positively correlated with D.

Plant, Cell & Environment, 2012

Water deficit affects tree growth and limits wood production. In an attempt to identify the molec... more Water deficit affects tree growth and limits wood production. In an attempt to identify the molecular triggers of adaptation mechanisms to water deficit in Eucalyptus, we investigated protein expression patterns of two ecophysiologically contrasted Eucalyptus genotypes. They were grown in the field in either natural conditions or irrigated for 7 weeks during the dry season in the Republic of Congo. At the phenotypic level, genotype (G), treatment (T) and/or G ¥ T interaction effects were observed for aboveand below-ground biomass-related traits. At the molecular level, changes in protein abundance were recorded in leaves (acidic pH 4-7, and basic pH 7-11, proteomes) and stems (acidic proteome) using two-dimensional gel electrophoresis (2-DE). One third of the detected protein spots displayed significant G, T and/or G ¥ T effects, and 158 of them were identified by tandem mass spectrometry (LC-MS/MS) analysis. Thus, several proteins whose molecular plasticity was genetically controlled (i.e. G ¥ T effect) were revealed, highlighting adaptive mechanisms to water deficit specific to each genotype, namely cell wall modification, cell detoxification and osmoregulation. Transcript abundances corresponding to G ¥ T proteins were also investigated by quantitative RT-PCR. These proteins represent relevant targets to improve drought resistance in this ecologically and economically important forest tree genus.

Frontiers in Genetics, 2016

Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such ... more Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones, and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows' milk. Method A (urea) involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone) involved a trichloroacetic acid (TCA)/acetone precipitation, and method C (methanol/chloroform) involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS) analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection) to assess reproducibility. Mass spectrometry (MS) data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform) yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea) yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone) was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows.

Frontiers in Plant Science, 2015

Antimicrobial peptides (AMPs) are natural products found across diverse taxa as part of the innat... more Antimicrobial peptides (AMPs) are natural products found across diverse taxa as part of the innate immune system against pathogen attacks. Some AMPs are synthesized through the canonical gene expression machinery and are called ribosomal AMPs. Other AMPs are assembled by modular enzymes generating nonribosomal AMPs and harbor unusual structural diversity. Plants synthesize an array of AMPs, yet are still subject to many pathogen invasions. Crop breeding programs struggle to release new cultivars in which complete disease resistance is achieved, and usually such resistance becomes quickly overcome by the targeted pathogens which have a shorter generation time. AMPs could offer a solution by exploring not only plant-derived AMPs, related or unrelated to the crop of interest, but also non-plant AMPs produced by bacteria, fungi, oomycetes or animals. This review highlights some promising candidates within the plant kingdom and elsewhere, and offers some perspectives on how to identify and validate their bioactivities. Technological advances, particularly in mass spectrometry (MS) and nuclear magnetic resonance (NMR), have been instrumental in identifying and elucidating the structure of novel AMPs, especially nonribosomal peptides which cannot be identified through genomics approaches. The majority of non-plant AMPs showing potential for plant disease immunity are often tested using in vitro assays. The greatest challenge remains the functional validation of candidate AMPs in plants through transgenic experiments, particularly introducing nonribosomal AMPs into crops.

Journal of Plant Biochemistry & Physiology, 2013

Figure 1: Number of publications listed in PubMed per year using "(((secretome[Title/Abstract]) O... more Figure 1: Number of publications listed in PubMed per year using "(((secretome[Title/Abstract]) OR secretomic[Title/Abstract]) OR secretomics[Title/Abstract])" keyword for all secretomics studies in grey, and "((((secretome[Title/Abstract]) OR secretomic[Title/Abstract]) OR secretomics[Title/Abstract]) AND fung*[Title/Abstract]) AND plant[Title/Abstract]" keyword for plant/fungi secretomics in black. Searches performed on 30 October 2013.

Plant Proteomics, 2007

Page 374. Chapter 21 Plant Proteome Responses to Abiotic Stress Delphine Vincent and Michel Zivy ... more Page 374. Chapter 21 Plant Proteome Responses to Abiotic Stress Delphine Vincent and Michel Zivy Abstract Proteomic studies of plant response to abiotic stress include analyses of the effects of water deficit, salt excess, low ...

Plant Physiology and Biochemistry, 2004

The proteome of the basal part of growing Zea mays leaves was analyzed from 4 to 14 d after stopp... more The proteome of the basal part of growing Zea mays leaves was analyzed from 4 to 14 d after stopping watering and in well watered controls. The relative quantity of 46 proteins was found to increase in leaves of plants submitted to water deficit. Different types of responses were observed, some proteins showing a constant increase during water deficit, while others showed stabilization after a first increase or a transient increase. Isoforms encoded by the same gene showed different responses. The response to water deficit showed genetic variation. Some increased proteins were induced specifically in one of the two studied genotypes (e.g. ASR1) while others were significantly induced in both genotypes but to a different level or with different kinetics. Analyses of relations between protein quantities, relative water content (RWC) and abscisic acid (ABA) concentration allowed us to show that the quantitative variation of some proteins (e.g. ABA45 and OSR40 proteins) was linked to differences in ABA accumulation between the genotypes. Other proteins showed genetic variations that were not related to differences in water status or ABA concentration (e.g. a cystatin). Data obtained from these experiments, together with data from other experiments, contribute to the characterization of maize proteome response to drought in different conditions and in different genotypes. This characterization allows the search for candidate proteins, i.e. for protein whose genetic variation of expression could be partly responsible for the variability of plant responses to drought.

Comp Biochem Physiol Pt a, 2008

The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symb... more The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, b-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.

Phytochemistry, Jul 1, 2009

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides  Popul... more Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides  Populus nigra, cv. 'Agathe_F' and 'Cima', were analysed over a short-term period of 18 days in glasshouse using 4month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra.

Electrophoresis, 2006

Protein extraction from grape berries has been challenging, particularly in mature berries, which... more Protein extraction from grape berries has been challenging, particularly in mature berries, which can have sugar concentrations as high as 26%. Grape skins and seeds contain large amounts of polyphenols, which can also interfere with efficient protein extraction. In plants, two extraction protocols, TCA/acetone-based and phenol-based methods, have been mainly used to extract proteins from different organs or tissues on many species. However, few results have been reported for grape berry clusters. We wanted to determine which of these protocols was optimal for berry clusters in order to achieve both efficient protein extraction and high spot resolution on 2-D gels. Four protocols, derived from either TCA/acetone or phenol procedures, were tested on mature Cabernet Sauvignon whole berry clusters. The phenol-based protocols were superior to the TCA/acetone methods, showing larger protein yields and greater spot resolution on 2-D gels. One method was clearly superior to the rest, a phe...

Drought is a major abiotic stress affecting all levels of plant organization and, in particular, ... more Drought is a major abiotic stress affecting all levels of plant organization and, in particular, leaf elongation. Several experiments were designed to study the effect of water deficits on maize (Zea mays) leaves at the protein level by taking into account the reduction of leaf elongation. Proteomic analyses of growing maize leaves allowed us to show that two isoforms of

ABSTRACT Water deficit progressively reduced growth of Cabernet Sauvignon shoots with time over a... more ABSTRACT Water deficit progressively reduced growth of Cabernet Sauvignon shoots with time over a 16-day period. Water deficit decreased shoot elongation, stomatal conductance and photosynthesis after day 4; 2277 proteins in shoot tips were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins clustered into four groups: increased and decreased abundance of early- and late-responding protein profiles. Vines sensed the water deficit early, prior to any physiological responses, because the abundance of some proteins changed before decreases in shoot elongation, stomatal conductance and photosynthesis. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, and growth-related categories (steroid metabolism and water transport), whereas those for late-responding proteins were involved with transport, antioxidants, amino acid and carbohydrate metabolism. Many of these early-responding proteins are likely to be regulated by post-transcriptional modifications.

Genetics, Genomics and Breeding of Poplar, 2011

Phytochemistry, 2009

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides x Popul... more Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides x Populus nigra, cv. 'Agathe_F' and 'Cima', were analysed over a short-term period of 18 days in glasshouse using 4-month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra. A reliable genotype effect was observed in the leaf proteome over experiment locations, water regimes and sampling dates. Quantitative differences between genotypes were found. Most of them corresponded to proteins matching isoforms or post-translational modification variants. However, 'Cima' displayed the highest abundance of antioxidant enzymes. In response to water deficit, about 10% of the reproducible spots significantly varied regardless of the experiment location, among which about 25% al...

Methods in Molecular Biology, 2011

Proteomics is a key technique that is helping elucidate many complex biological processes. The an... more Proteomics is a key technique that is helping elucidate many complex biological processes. The analysis of plant-pathogen interactions using proteomics is complicated by the presence of the proteomes of two species, but is benefiting from the developing maturity and power of these techniques. More and more pathogen genomes are being sequenced, so fungal proteomics is reaching its full potential and remains the chosen technology to unravel the molecular pathways of pathogenicity and resistance. In this chapter, we suggest proteomic strategies that have proved successful on various plant-interacting fungal species. Several protein extraction methods are described. For adequate quantitative analyses of protein abundances, we recommend either separation using two-dimensional gel electrophoresis or labelling with isobaric tags followed by two-dimensional HPLC separation. Proteins of interest are then identified using mass spectrometry. Identified proteins can assist in refining genome annotations, otherwise known as proteogenomics.

Journal of Integrated OMICS, 2011

PROTEOMICS, 2005

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obt... more PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.

PROTEOMICS, 2009

Genetic variation of leaf proteome in drought response was investigated among eight Populus Âeura... more Genetic variation of leaf proteome in drought response was investigated among eight Populus Âeuramericana genotypes contrasting for their leaf carbon isotope discrimination (D), an estimate of intrinsic water-use efficiency. Plants were grown in open field on two similar plots. Drought was induced by an 86-day irrigation cessation on one plot, whereas a second plot remained regularly irrigated. Using 2-DE, 863 reproducible spots were detected; about 60% presented at least one significant effect i.e. treatment, genotype and/or genotype by treatment interaction effect. A significant genotype by treatment interaction was detected for 62 reliably identified proteins among which, about 65% consisted in chloroplast-associated proteins either involved in the Calvin cycle or in the electron-transport chains. The other proteins were involved in oxidative stress, amino acid or protein metabolisms. Correlations between protein abundance and D variations were found for 45 reliably identified proteins. The abundance of ribulose-1,5-bisphosphate carboxylase/ oxygenase activase isoforms scaled negatively with D regardless of the treatment, suggesting that a large intrinsic water-use efficiency could be due to higher abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase activase. Under control condition, abundance of enzymes involved in carbon fixation was also negatively correlated with D, whereas abundance of enzymes involved in photorespiration or respiration was positively correlated with D.

Plant, Cell & Environment, 2012

Water deficit affects tree growth and limits wood production. In an attempt to identify the molec... more Water deficit affects tree growth and limits wood production. In an attempt to identify the molecular triggers of adaptation mechanisms to water deficit in Eucalyptus, we investigated protein expression patterns of two ecophysiologically contrasted Eucalyptus genotypes. They were grown in the field in either natural conditions or irrigated for 7 weeks during the dry season in the Republic of Congo. At the phenotypic level, genotype (G), treatment (T) and/or G ¥ T interaction effects were observed for aboveand below-ground biomass-related traits. At the molecular level, changes in protein abundance were recorded in leaves (acidic pH 4-7, and basic pH 7-11, proteomes) and stems (acidic proteome) using two-dimensional gel electrophoresis (2-DE). One third of the detected protein spots displayed significant G, T and/or G ¥ T effects, and 158 of them were identified by tandem mass spectrometry (LC-MS/MS) analysis. Thus, several proteins whose molecular plasticity was genetically controlled (i.e. G ¥ T effect) were revealed, highlighting adaptive mechanisms to water deficit specific to each genotype, namely cell wall modification, cell detoxification and osmoregulation. Transcript abundances corresponding to G ¥ T proteins were also investigated by quantitative RT-PCR. These proteins represent relevant targets to improve drought resistance in this ecologically and economically important forest tree genus.