Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain.
Identifieur interne : 001F89 ( Main/Exploration ); précédent : 001F88; suivant : 001F90Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain.
Auteurs : Jessica L. Linville ; Miguel Rodriguez ; Steven D. Brown ; Jonathan R. Mielenz ; Chris D. Cox [États-Unis]Source :
- BMC microbiology [ 1471-2180 ] ; 2014.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Antibactériens (isolement et purification), Antibactériens (pharmacologie), Cellulose (composition chimique), Clostridium thermocellum (croissance et développement), Clostridium thermocellum (effets des médicaments et des substances chimiques), Clostridium thermocellum (génétique), Extraits de plantes (isolement et purification), Extraits de plantes (pharmacologie), Hydrolyse (MeSH), Milieux de culture (composition chimique), Populus (composition chimique), Tolérance aux médicaments (MeSH), Voies et réseaux métaboliques (génétique).
- MESH :
- composition chimique : Cellulose, Milieux de culture, Populus.
- croissance et développement : Clostridium thermocellum.
- effets des médicaments et des substances chimiques : Clostridium thermocellum.
- génétique : Clostridium thermocellum, Voies et réseaux métaboliques.
- isolement et purification : Antibactériens, Extraits de plantes.
- pharmacologie : Antibactériens, Extraits de plantes.
- Analyse de profil d'expression de gènes, Hydrolyse, Tolérance aux médicaments.
English descriptors
- KwdEn :
- Anti-Bacterial Agents (isolation & purification), Anti-Bacterial Agents (pharmacology), Cellulose (chemistry), Clostridium thermocellum (drug effects), Clostridium thermocellum (genetics), Clostridium thermocellum (growth & development), Culture Media (chemistry), Drug Tolerance (MeSH), Gene Expression Profiling (MeSH), Hydrolysis (MeSH), Metabolic Networks and Pathways (genetics), Plant Extracts (isolation & purification), Plant Extracts (pharmacology), Populus (chemistry).
- MESH :
- chemical , chemistry : Cellulose, Culture Media.
- chemical , isolation & purification : Anti-Bacterial Agents, Plant Extracts.
- chemical , pharmacology : Anti-Bacterial Agents, Plant Extracts.
- chemistry : Populus.
- drug effects : Clostridium thermocellum.
- genetics : Clostridium thermocellum, Metabolic Networks and Pathways.
- growth & development : Clostridium thermocellum.
- Drug Tolerance, Gene Expression Profiling, Hydrolysis.
Abstract
BACKGROUND
The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum.
RESULTS
In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell defense mechanisms.
CONCLUSION
These results suggest the mechanisms of tolerance for the Populus hydrolysate-tolerant mutant strain of C. thermocellum are based on increased cellular efficiency caused apparently by downregulation of non-critical genes and increasing the expression of genes in energy production and conversion rather than tolerance to specific hydrolysate components. The wild type, conversely, responds to hydrolysate media by down-regulating growth genes and up-regulating stress response genes.
DOI: 10.1186/s12866-014-0215-5
PubMed: 25128475
PubMed Central: PMC4236516
Affiliations:
Links toward previous steps (curation, corpus...)
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Linville</name></author><author><name sortKey="Rodriguez, Miguel" sort="Rodriguez, Miguel" uniqKey="Rodriguez M" first="Miguel" last="Rodriguez">Miguel Rodriguez</name></author><author><name sortKey="Brown, Steven D" sort="Brown, Steven D" uniqKey="Brown S" first="Steven D" last="Brown">Steven D. Brown</name></author><author><name sortKey="Mielenz, Jonathan R" sort="Mielenz, Jonathan R" uniqKey="Mielenz J" first="Jonathan R" last="Mielenz">Jonathan R. Mielenz</name></author><author><name sortKey="Cox, Chris D" sort="Cox, Chris D" uniqKey="Cox C" first="Chris D" last="Cox">Chris D. Cox</name><affiliation wicri:level="2"><nlm:affiliation>Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA. ccox9@utk.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></analytic><series><title level="j">BMC microbiology</title><idno type="eISSN">1471-2180</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anti-Bacterial Agents (isolation & purification)</term><term>Anti-Bacterial Agents (pharmacology)</term><term>Cellulose (chemistry)</term><term>Clostridium thermocellum (drug effects)</term><term>Clostridium thermocellum (genetics)</term><term>Clostridium thermocellum (growth & development)</term><term>Culture Media (chemistry)</term><term>Drug Tolerance (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Hydrolysis (MeSH)</term><term>Metabolic Networks and Pathways (genetics)</term><term>Plant Extracts (isolation & purification)</term><term>Plant Extracts (pharmacology)</term><term>Populus (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Antibactériens (isolement et purification)</term><term>Antibactériens (pharmacologie)</term><term>Cellulose (composition chimique)</term><term>Clostridium thermocellum (croissance et développement)</term><term>Clostridium thermocellum (effets des médicaments et des substances chimiques)</term><term>Clostridium thermocellum (génétique)</term><term>Extraits de plantes (isolement et purification)</term><term>Extraits de plantes (pharmacologie)</term><term>Hydrolyse (MeSH)</term><term>Milieux de culture (composition chimique)</term><term>Populus (composition chimique)</term><term>Tolérance aux médicaments (MeSH)</term><term>Voies et réseaux métaboliques (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cellulose</term><term>Culture Media</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>Anti-Bacterial Agents</term><term>Plant Extracts</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Anti-Bacterial Agents</term><term>Plant Extracts</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Cellulose</term><term>Milieux de culture</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Clostridium thermocellum</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Clostridium thermocellum</term></keywords><keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Clostridium thermocellum</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Clostridium thermocellum</term><term>Metabolic Networks and Pathways</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Clostridium thermocellum</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Clostridium thermocellum</term><term>Voies et réseaux métaboliques</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Antibactériens</term><term>Extraits de plantes</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antibactériens</term><term>Extraits de plantes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Drug Tolerance</term><term>Gene Expression Profiling</term><term>Hydrolysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Hydrolyse</term><term>Tolérance aux médicaments</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell defense mechanisms.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>These results suggest the mechanisms of tolerance for the Populus hydrolysate-tolerant mutant strain of C. thermocellum are based on increased cellular efficiency caused apparently by downregulation of non-critical genes and increasing the expression of genes in energy production and conversion rather than tolerance to specific hydrolysate components. The wild type, conversely, responds to hydrolysate media by down-regulating growth genes and up-regulating stress response genes.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25128475</PMID><DateCompleted><Year>2015</Year><Month>03</Month><Day>03</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2180</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><PubDate><Year>2014</Year><Month>Aug</Month><Day>16</Day></PubDate></JournalIssue><Title>BMC microbiology</Title><ISOAbbreviation>BMC Microbiol</ISOAbbreviation></Journal><ArticleTitle>Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain.</ArticleTitle><Pagination><MedlinePgn>215</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12866-014-0215-5</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell defense mechanisms.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">These results suggest the mechanisms of tolerance for the Populus hydrolysate-tolerant mutant strain of C. thermocellum are based on increased cellular efficiency caused apparently by downregulation of non-critical genes and increasing the expression of genes in energy production and conversion rather than tolerance to specific hydrolysate components. The wild type, conversely, responds to hydrolysate media by down-regulating growth genes and up-regulating stress response genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Linville</LastName><ForeName>Jessica L</ForeName><Initials>JL</Initials></Author><Author ValidYN="Y"><LastName>Rodriguez</LastName><ForeName>Miguel</ForeName><Initials>M</Initials><Suffix>Jr</Suffix></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>Steven D</ForeName><Initials>SD</Initials></Author><Author ValidYN="Y"><LastName>Mielenz</LastName><ForeName>Jonathan R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Cox</LastName><ForeName>Chris D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA. ccox9@utk.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>08</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Microbiol</MedlineTA><NlmUniqueID>100966981</NlmUniqueID><ISSNLinking>1471-2180</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000900">Anti-Bacterial Agents</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003470">Culture Media</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010936">Plant Extracts</NameOfSubstance></Chemical><Chemical><RegistryNumber>9004-34-6</RegistryNumber><NameOfSubstance UI="D002482">Cellulose</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000900" MajorTopicYN="N">Anti-Bacterial Agents</DescriptorName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D048013" MajorTopicYN="N">Clostridium thermocellum</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="Y">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003470" MajorTopicYN="N">Culture Media</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004361" MajorTopicYN="Y">Drug Tolerance</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006868" MajorTopicYN="N">Hydrolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053858" MajorTopicYN="N">Metabolic Networks and Pathways</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010936" MajorTopicYN="N">Plant Extracts</DescriptorName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" 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IdType="pubmed">11179418</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><noCountry><name sortKey="Brown, Steven D" sort="Brown, Steven D" uniqKey="Brown S" first="Steven D" last="Brown">Steven D. Brown</name><name sortKey="Linville, Jessica L" sort="Linville, Jessica L" uniqKey="Linville J" first="Jessica L" last="Linville">Jessica L. Linville</name><name sortKey="Mielenz, Jonathan R" sort="Mielenz, Jonathan R" uniqKey="Mielenz J" first="Jonathan R" last="Mielenz">Jonathan R. Mielenz</name><name sortKey="Rodriguez, Miguel" sort="Rodriguez, Miguel" uniqKey="Rodriguez M" first="Miguel" last="Rodriguez">Miguel Rodriguez</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="Cox, Chris D" sort="Cox, Chris D" uniqKey="Cox C" first="Chris D" last="Cox">Chris D. Cox</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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