A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions.
Identifieur interne : 000227 ( Main/Corpus ); précédent : 000226; suivant : 000228A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions.
Auteurs : Manuel I. Villalobos Solis ; Suresh Poudel ; Clemence Bonnot ; Him K. Shrestha ; Robert L. Hettich ; Claire Veneault-Fourrey ; Francis Martin ; Paul E. AbrahamSource :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2020.
English descriptors
- KwdEn :
- Gene Expression Regulation, Plant (MeSH), Host Microbial Interactions (MeSH), Laccaria (physiology), Mycorrhizae (physiology), Peptides (chemistry), Plant Roots (chemistry), Plant Roots (microbiology), Populus (chemistry), Populus (microbiology), Proteolysis (MeSH), Sequence Analysis, Protein (MeSH).
- MESH :
- chemical , chemistry : Peptides.
- chemistry : Plant Roots, Populus.
- microbiology : Plant Roots, Populus.
- physiology : Laccaria, Mycorrhizae.
- Gene Expression Regulation, Plant, Host Microbial Interactions, Proteolysis, Sequence Analysis, Protein.
Abstract
Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor. In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor. These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.
DOI: 10.1094/MPMI-04-20-0082-TA
PubMed: 32597696
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pubmed:32597696Le document en format XML
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Villalobos Solis</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Poudel, Suresh" sort="Poudel, Suresh" uniqKey="Poudel S" first="Suresh" last="Poudel">Suresh Poudel</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Bonnot, Clemence" sort="Bonnot, Clemence" uniqKey="Bonnot C" first="Clemence" last="Bonnot">Clemence Bonnot</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Shrestha, Him K" sort="Shrestha, Him K" uniqKey="Shrestha H" first="Him K" last="Shrestha">Him K. Shrestha</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Hettich, Robert L" sort="Hettich, Robert L" uniqKey="Hettich R" first="Robert L" last="Hettich">Robert L. Hettich</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Veneault Fourrey, Claire" sort="Veneault Fourrey, Claire" uniqKey="Veneault Fourrey C" first="Claire" last="Veneault-Fourrey">Claire Veneault-Fourrey</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Martin, Francis" sort="Martin, Francis" uniqKey="Martin F" first="Francis" last="Martin">Francis Martin</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Abraham, Paul E" sort="Abraham, Paul E" uniqKey="Abraham P" first="Paul E" last="Abraham">Paul E. Abraham</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32597696</idno><idno type="pmid">32597696</idno><idno type="doi">10.1094/MPMI-04-20-0082-TA</idno><idno type="wicri:Area/Main/Corpus">000227</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000227</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions.</title><author><name sortKey="Villalobos Solis, Manuel I" sort="Villalobos Solis, Manuel I" uniqKey="Villalobos Solis M" first="Manuel I" last="Villalobos Solis">Manuel I. Villalobos Solis</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Poudel, Suresh" sort="Poudel, Suresh" uniqKey="Poudel S" first="Suresh" last="Poudel">Suresh Poudel</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Bonnot, Clemence" sort="Bonnot, Clemence" uniqKey="Bonnot C" first="Clemence" last="Bonnot">Clemence Bonnot</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Shrestha, Him K" sort="Shrestha, Him K" uniqKey="Shrestha H" first="Him K" last="Shrestha">Him K. Shrestha</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Hettich, Robert L" sort="Hettich, Robert L" uniqKey="Hettich R" first="Robert L" last="Hettich">Robert L. Hettich</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author><author><name sortKey="Veneault Fourrey, Claire" sort="Veneault Fourrey, Claire" uniqKey="Veneault Fourrey C" first="Claire" last="Veneault-Fourrey">Claire Veneault-Fourrey</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Martin, Francis" sort="Martin, Francis" uniqKey="Martin F" first="Francis" last="Martin">Francis Martin</name><affiliation><nlm:affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</nlm:affiliation></affiliation></author><author><name sortKey="Abraham, Paul E" sort="Abraham, Paul E" uniqKey="Abraham P" first="Paul E" last="Abraham">Paul E. Abraham</name><affiliation><nlm:affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation, Plant (MeSH)</term><term>Host Microbial Interactions (MeSH)</term><term>Laccaria (physiology)</term><term>Mycorrhizae (physiology)</term><term>Peptides (chemistry)</term><term>Plant Roots (chemistry)</term><term>Plant Roots (microbiology)</term><term>Populus (chemistry)</term><term>Populus (microbiology)</term><term>Proteolysis (MeSH)</term><term>Sequence Analysis, Protein (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptides</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Laccaria</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Host Microbial Interactions</term><term>Proteolysis</term><term>Sequence Analysis, Protein</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar <i>Populus</i> × <i>canescens</i> 717-1B4 in interaction with the ectomycorrhizal basidiomycete <i>Laccaria bicolor</i>. In total, we identified 1,660 and 2,870 <i>Populus</i> and <i>L. bicolor</i> unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of <i>L. bicolor</i>. These PCPs mapped to 64 <i>Populus</i> proteins and 69 <i>L. bicolor</i> proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">32597696</PMID><DateCompleted><Year>2020</Year><Month>11</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>33</Volume><Issue>10</Issue><PubDate><Year>2020</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions.</ArticleTitle><Pagination><MedlinePgn>1177-1188</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-04-20-0082-TA</ELocationID><Abstract><AbstractText>Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar <i>Populus</i> × <i>canescens</i> 717-1B4 in interaction with the ectomycorrhizal basidiomycete <i>Laccaria bicolor</i>. In total, we identified 1,660 and 2,870 <i>Populus</i> and <i>L. bicolor</i> unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of <i>L. bicolor</i>. These PCPs mapped to 64 <i>Populus</i> proteins and 69 <i>L. bicolor</i> proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Villalobos Solis</LastName><ForeName>Manuel I</ForeName><Initials>MI</Initials><AffiliationInfo><Affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Poudel</LastName><ForeName>Suresh</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bonnot</LastName><ForeName>Clemence</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shrestha</LastName><ForeName>Him K</ForeName><Initials>HK</Initials><AffiliationInfo><Affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hettich</LastName><ForeName>Robert L</ForeName><Initials>RL</Initials><AffiliationInfo><Affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Veneault-Fourrey</LastName><ForeName>Claire</ForeName><Initials>C</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9778-2659</Identifier><AffiliationInfo><Affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Francis</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abraham</LastName><ForeName>Paul E</ForeName><Initials>PE</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-2685-9123</Identifier><AffiliationInfo><Affiliation>Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Plant Microbe Interact</MedlineTA><NlmUniqueID>9107902</NlmUniqueID><ISSNLinking>0894-0282</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010455">Peptides</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000076662" MajorTopicYN="N">Host Microbial Interactions</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055399" MajorTopicYN="N">Laccaria</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010455" MajorTopicYN="N">Peptides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059748" MajorTopicYN="Y">Proteolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020539" MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">de novo peptide sequencing</Keyword><Keyword MajorTopicYN="N">liquid chromatography</Keyword><Keyword MajorTopicYN="N">small peptides</Keyword><Keyword MajorTopicYN="N">tandem mass spectrometry</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32597696</ArticleId><ArticleId IdType="doi">10.1094/MPMI-04-20-0082-TA</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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