Rebuilding microbial genomes
Identifieur interne : 001E17 ( Istex/Corpus ); précédent : 001E16; suivant : 001E18Rebuilding microbial genomes
Auteurs : Robert A. Holt ; Rene Warren ; Stephane Flibotte ; Perseus I. Missirlis ; Duane E. SmailusSource :
- BioEssays [ 0265-9247 ] ; 2007-06.
English descriptors
- Teeft :
- Acad, Bioessays, Biol chem, Bipartite genome, British columbia, Cell hydrolase, Chromosome, Clone, Coli, Coli host, Donor, Donor chromosome, Donor genome, Escherichia, Escherichia coli, Essential genes, Gene, Genetic material, Genome, Genome assembly, Genome resolution, Genomic, Haemophilus, Haemophilus influenzae, Host cell, Host chromosome, Host genome, Host organism, Hydrolase, Influenzae, Influenzae chromosome, Influenzae genes, Influenzae genome, Large segments, Lethal genes, Microbial, Microbial genome, Minimal tiling, Model system, Natl, Plasmid, Proc, Proc natl acad, Recombination, Replication, Ribosomal, Ribosomal protein, Ribosomal proteins, Rnase, Synthetase, Synthetic genome, Toxic, Toxic genes, Toxicity, Transporter.
Abstract
Engineered microbes are of great potential utility in biotechnology and basic research. In principle, a cell can be built from scratch by assembling small molecule sets with auto‐catalytic properties. Alternatively, DNA can be isolated or directly synthesized and molded into a synthetic genome using existing genomic blueprints and molecular biology tools. Activating such a synthetic genome will yield a synthetic cell. Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from H. influenzae is fragmented, and the pieces are then modified and reassembled stepwise in an E. coli host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of H. influenzae genes in E. coli, and analysis of gap locations in H. influenzae and other microbial genome assemblies reveals few genes routinely incompatible with E. coli. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. BioEssays 29:580–590, 2007. © 2007 Wiley Periodicals, Inc.
Url:
DOI: 10.1002/bies.20585
Links to Exploration step
ISTEX:6FDFE0B8826F066DE4B55591C2C196674968813BLe document en format XML
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In principle, a cell can be built from scratch by assembling small molecule sets with auto‐catalytic properties. Alternatively, DNA can be isolated or directly synthesized and molded into a synthetic genome using existing genomic blueprints and molecular biology tools. Activating such a synthetic genome will yield a synthetic cell. Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from H. influenzae is fragmented, and the pieces are then modified and reassembled stepwise in an E. coli host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of H. influenzae genes in E. coli, and analysis of gap locations in H. influenzae and other microbial genome assemblies reveals few genes routinely incompatible with E. coli. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. 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Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from H. influenzae is fragmented, and the pieces are then modified and reassembled stepwise in an E. coli host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of H. influenzae genes in E. coli, and analysis of gap locations in H. influenzae and other microbial genome assemblies reveals few genes routinely incompatible with E. coli. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. 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<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract xml:lang="en" style="main"><head>Abstract</head><p>Engineered microbes are of great potential utility in biotechnology and basic research. In principle, a cell can be built from scratch by assembling small molecule sets with auto‐catalytic properties. Alternatively, DNA can be isolated or directly synthesized and molded into a synthetic genome using existing genomic blueprints and molecular biology tools. Activating such a synthetic genome will yield a synthetic cell. Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from <hi rend="italic">H. influenzae</hi> is fragmented, and the pieces are then modified and reassembled stepwise in an <hi rend="italic">E. coli</hi> host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of <hi rend="italic">H. influenzae</hi> genes in <hi rend="italic">E. coli</hi>, and analysis of gap locations in <hi rend="italic">H. influenzae</hi> and other microbial genome assemblies reveals few genes routinely incompatible with <hi rend="italic">E. coli</hi>. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. BioEssays 29:580–590, 2007. © 2007 Wiley Periodicals, Inc.</p></abstract><textClass><keywords rend="articleCategory"><term>Genes and Genomes</term></keywords><keywords rend="tocHeading1"><term>Genes and Genomes</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-C2V7CZB2-6/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Wiley Subscription Services, Inc., A Wiley Company</publisherName><publisherLoc>Hoboken</publisherLoc></publisherInfo><doi registered="yes">10.1002/(ISSN)1521-1878</doi><issn type="print">0265-9247</issn><issn type="electronic">1521-1878</issn><idGroup><id type="product" value="BIES"></id></idGroup><titleGroup><title type="main" xml:lang="en" sort="BIOESSAYS">BioEssays</title><title type="short">Bioessays</title></titleGroup></publicationMeta><publicationMeta level="part" position="60"><doi origin="wiley" registered="yes">10.1002/bies.v29:6</doi><numberingGroup><numbering type="journalVolume" number="29">29</numbering><numbering type="journalIssue">6</numbering></numberingGroup><coverDate startDate="2007-06">June 2007</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="100" status="forIssue"><doi origin="wiley" registered="yes">10.1002/bies.20585</doi><idGroup><id type="unit" value="BIES20585"></id></idGroup><countGroup><count type="pageTotal" number="11"></count></countGroup><titleGroup><title type="articleCategory">Genes and Genomes</title><title type="tocHeading1">Genes and Genomes</title></titleGroup><copyright ownership="publisher">Copyright © 2007 Wiley Periodicals, Inc.</copyright><eventGroup><event type="firstOnline" date="2007-05-16"></event><event type="publishedOnlineFinalForm" date="2007-05-16"></event><event type="xmlConverted" agent="Converter:JWSART34_TO_WML3G version:2.3.2 mode:FullText source:HeaderRef result:HeaderRef" date="2010-03-09"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-02-22"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-15"></event></eventGroup><numberingGroup><numbering type="pageFirst">580</numbering><numbering type="pageLast">590</numbering></numberingGroup><correspondenceTo>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:BIES.BIES20585.pdf"></link></linkGroup></publicationMeta><contentMeta><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="2"></count><count type="referenceTotal" number="31"></count><count type="wordTotal" number="853"></count></countGroup><titleGroup><title type="main" xml:lang="en">Rebuilding microbial genomes</title><title type="short" xml:lang="en">Genes and genomes</title></titleGroup><creators><creator xml:id="au1" creatorRole="author" affiliationRef="#af1" corresponding="yes"><personName><givenNames>Robert A.</givenNames><familyName>Holt</familyName></personName><contactDetails><email>rholt@bcgsc.ca</email></contactDetails></creator><creator xml:id="au2" creatorRole="author" affiliationRef="#af1"><personName><givenNames>Rene</givenNames><familyName>Warren</familyName></personName></creator><creator xml:id="au3" creatorRole="author" affiliationRef="#af1"><personName><givenNames>Stephane</givenNames><familyName>Flibotte</familyName></personName></creator><creator xml:id="au4" creatorRole="author" affiliationRef="#af1"><personName><givenNames>Perseus I.</givenNames><familyName>Missirlis</familyName></personName></creator><creator xml:id="au5" creatorRole="author" affiliationRef="#af1"><personName><givenNames>Duane E.</givenNames><familyName>Smailus</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="af1" countryCode="CA" type="organization"><unparsedAffiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</unparsedAffiliation></affiliation></affiliationGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>Engineered microbes are of great potential utility in biotechnology and basic research. In principle, a cell can be built from scratch by assembling small molecule sets with auto‐catalytic properties. Alternatively, DNA can be isolated or directly synthesized and molded into a synthetic genome using existing genomic blueprints and molecular biology tools. Activating such a synthetic genome will yield a synthetic cell. Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from <i>H. influenzae</i> is fragmented, and the pieces are then modified and reassembled stepwise in an <i>E. coli</i> host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of <i>H. influenzae</i> genes in <i>E. coli</i>, and analysis of gap locations in <i>H. influenzae</i> and other microbial genome assemblies reveals few genes routinely incompatible with <i>E. coli</i>. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. BioEssays 29:580–590, 2007. © 2007 Wiley Periodicals, Inc.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Rebuilding microbial genomes</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Genes and genomes</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Rebuilding microbial genomes</title></titleInfo><name type="personal"><namePart type="given">Robert A.</namePart><namePart type="family">Holt</namePart><affiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</affiliation><affiliation>E-mail: rholt@bcgsc.ca</affiliation><affiliation>Correspondence address: Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rene</namePart><namePart type="family">Warren</namePart><affiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Stephane</namePart><namePart type="family">Flibotte</namePart><affiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Perseus I.</namePart><namePart type="family">Missirlis</namePart><affiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Duane E.</namePart><namePart type="family">Smailus</namePart><affiliation>Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><place><placeTerm type="text">Hoboken</placeTerm></place><dateIssued encoding="w3cdtf">2007-06</dateIssued><copyrightDate encoding="w3cdtf">2007</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">4</extent><extent unit="tables">2</extent><extent unit="references">31</extent><extent unit="words">853</extent></physicalDescription><abstract lang="en">Engineered microbes are of great potential utility in biotechnology and basic research. In principle, a cell can be built from scratch by assembling small molecule sets with auto‐catalytic properties. Alternatively, DNA can be isolated or directly synthesized and molded into a synthetic genome using existing genomic blueprints and molecular biology tools. Activating such a synthetic genome will yield a synthetic cell. Here we examine obstacles associated with this latter approach using a model system whereby a donor genome from H. influenzae is fragmented, and the pieces are then modified and reassembled stepwise in an E. coli host cell. There are obstacles associated with this strategy related to DNA transfer, DNA replication, cross‐talk in gene regulation and compatibility of gene products between donor and host. Encouragingly, analysis of gene expression indicates widespread transcription of H. influenzae genes in E. coli, and analysis of gap locations in H. influenzae and other microbial genome assemblies reveals few genes routinely incompatible with E. coli. In conclusion, rebuilding and booting a genome remains a feasible and pragmatic approach to creating a synthetic microbial cell. 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Mol Microbiol 56: 1129–1138.</note><part><date>2005</date><detail type="volume"><caption>vol.</caption><number>56</number></detail><extent unit="pages"><start>1129</start><end>1138</end></extent></part><relatedItem type="host"><titleInfo><title>Mol Microbiol</title></titleInfo><part><date>2005</date><detail type="volume"><caption>vol.</caption><number>56</number></detail><extent unit="pages"><start>1129</start><end>1138</end></extent></part></relatedItem></relatedItem><identifier type="istex">6FDFE0B8826F066DE4B55591C2C196674968813B</identifier><identifier type="ark">ark:/67375/WNG-C2V7CZB2-6</identifier><identifier type="DOI">10.1002/bies.20585</identifier><identifier type="ArticleID">BIES20585</identifier><accessCondition type="use and reproduction" contentType="copyright">Copyright © 2007 Wiley Periodicals, Inc.</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-L0C46X92-X">wiley</recordContentSource><recordOrigin>Converted from (version ) to MODS version 3.6.</recordOrigin><recordCreationDate encoding="w3cdtf">2019-11-13</recordCreationDate></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-C2V7CZB2-6/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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