Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton▿
Identifieur interne : 000668 ( Pmc/Checkpoint ); précédent : 000667; suivant : 000669Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton▿
Auteurs : Erin J. Biers ; Kui Wang ; Catherine Pennington ; Robert Belas ; Feng Chen ; Mary Ann MoranSource :
- Applied and Environmental Microbiology [ 0099-2240 ] ; 2008.
Abstract
Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine
Url:
DOI: 10.1128/AEM.02129-07
PubMed: 18359833
PubMed Central: 2394915
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:2394915Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton<xref ref-type="fn" rid="fn2">▿</xref> </title><author><name sortKey="Biers, Erin J" sort="Biers, Erin J" uniqKey="Biers E" first="Erin J." last="Biers">Erin J. Biers</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wang, Kui" sort="Wang, Kui" uniqKey="Wang K" first="Kui" last="Wang">Kui Wang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Pennington, Catherine" sort="Pennington, Catherine" uniqKey="Pennington C" first="Catherine" last="Pennington">Catherine Pennington</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Belas, Robert" sort="Belas, Robert" uniqKey="Belas R" first="Robert" last="Belas">Robert Belas</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18359833</idno><idno type="pmc">2394915</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394915</idno><idno type="RBID">PMC:2394915</idno><idno type="doi">10.1128/AEM.02129-07</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000201</idno><idno type="wicri:Area/Pmc/Curation">000201</idno><idno type="wicri:Area/Pmc/Checkpoint">000668</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton<xref ref-type="fn" rid="fn2">▿</xref> </title><author><name sortKey="Biers, Erin J" sort="Biers, Erin J" uniqKey="Biers E" first="Erin J." last="Biers">Erin J. Biers</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wang, Kui" sort="Wang, Kui" uniqKey="Wang K" first="Kui" last="Wang">Kui Wang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Pennington, Catherine" sort="Pennington, Catherine" uniqKey="Pennington C" first="Catherine" last="Pennington">Catherine Pennington</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Belas, Robert" sort="Belas, Robert" uniqKey="Belas R" first="Robert" last="Belas">Robert Belas</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Applied and Environmental Microbiology</title><idno type="ISSN">0099-2240</idno><idno type="eISSN">1098-5336</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine <italic>Roseobacter</italic> clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured <italic>Alphaproteobacteria</italic>, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the <italic>Roseobacter</italic> clade member <italic>Silicibacter pomeroyi</italic> DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Appl Environ Microbiol</journal-id><journal-id journal-id-type="publisher-id">aem</journal-id><journal-title>Applied and Environmental Microbiology</journal-title><issn pub-type="ppub">0099-2240</issn><issn pub-type="epub">1098-5336</issn><publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18359833</article-id><article-id pub-id-type="pmc">2394915</article-id><article-id pub-id-type="publisher-id">2129-07</article-id><article-id pub-id-type="doi">10.1128/AEM.02129-07</article-id><article-categories><subj-group subj-group-type="heading"><subject>Microbial Ecology</subject></subj-group></article-categories><title-group><article-title>Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton<xref ref-type="fn" rid="fn2">▿</xref> </article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Biers</surname><given-names>Erin J.</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="fn1">†</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Kui</given-names></name><xref ref-type="aff" rid="aff1">2</xref></contrib><contrib contrib-type="author"><name><surname>Pennington</surname><given-names>Catherine</given-names></name><xref ref-type="aff" rid="aff1">3</xref></contrib><contrib contrib-type="author"><name><surname>Belas</surname><given-names>Robert</given-names></name><xref ref-type="aff" rid="aff1">2</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Feng</given-names></name><xref ref-type="aff" rid="aff1">2</xref></contrib><contrib contrib-type="author"><name><surname>Moran</surname><given-names>Mary Ann</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="aff1">Department of Marine Sciences, University of Georgia, Athens, Georgia 30602,<label>1</label> Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202,<label>2</label> Department of Microbiology, University of Georgia, Athens, Georgia 30602<label>3</label></aff><author-notes><fn id="cor1"><label>*</label><p>Corresponding author. Mailing address: Department of Marine Sciences, University of Georgia, Athens, GA 30602. Phone: (706) 542-6481. Fax: (706) 542-5888. E-mail: <email>mmoran@uga.edu</email></p></fn><fn id="fn1"><label>†</label><p>Present address: Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208.</p></fn></author-notes><pub-date pub-type="ppub"><month>5</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>21</day><month>3</month><year>2008</year></pub-date><volume>74</volume><issue>10</issue><fpage>2933</fpage><lpage>2939</lpage><history><date date-type="received"><day>17</day><month>9</month><year>2007</year></date><date date-type="accepted"><day>5</day><month>3</month><year>2008</year></date></history><permissions><copyright-statement>Copyright © 2008, American Society for Microbiology</copyright-statement></permissions><self-uri xlink:title="pdf" xlink:href="zam01008002933.pdf"></self-uri><abstract><p>Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine <italic>Roseobacter</italic> clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured <italic>Alphaproteobacteria</italic>, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the <italic>Roseobacter</italic> clade member <italic>Silicibacter pomeroyi</italic> DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.</p></abstract></article-meta></front><floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label><caption><p>Phylogenetic tree of concatenated amino acid sequences of orfg3 (portal protein), orfg5 (capsid protein), and orfg12 (unknown protein) homologs constructed with the neighbor-joining algorithm and percent accepted mutation correction for genomic data available as of 1 December 2007. Accession numbers for each concatenated gene are listed in parentheses; the numbers within squares indicate the numbers of <italic>R. capsulatus</italic>-like GTA genes contained within the genome (15 possible); the filled circles indicate marine bacteria, open stars indicate that gene neighborhoods are shown in Fig. <xref rid="f2" ref-type="fig">2</xref>, checkmarks indicate organisms for which GTA activity has been experimentally verified, and boldface text indicates members of the <italic>Roseobacter</italic> clade. Bootstrap values of >50% are indicated on the nodes. Two nonmarine <italic>Rhizobiales</italic>, <italic>Brucella melitensis</italic> 16 M and <italic>Brucella suis</italic> 1330, contain GTA-like genes but are omitted from this tree because they lack one of the three concatenated homologs (orfg5 and orfg3, respectively).</p></caption><graphic xlink:href="zam0100888370001"></graphic></fig><fig position="float" id="f2"><label>FIG. 2.</label><caption><p>Gene neighborhoods of <italic>R. capsulatus</italic>-like GTA genes in <italic>R. capsulatus</italic> and one representative bacterium from each clade shown in Fig. <xref rid="f1" ref-type="fig">1</xref>. The checkmarks indicate organisms for which GTA activity has been experimentally verified. The numbers within the arrows indicate <italic>R. capsulatus</italic>-like GTA gene homologs as defined by BLASTp matches having E values of 10<sup>−4</sup> or lower. The <italic>R. capsulatus</italic> gene orientation and order were taken from Lang et al. (<xref ref-type="bibr" rid="r20">20</xref>). Complete genome sequences are available at NCBI (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov">http://www.ncbi.nlm.nih.gov</ext-link>).</p></caption><graphic xlink:href="zam0100888370002"></graphic></fig><fig position="float" id="f3"><label>FIG. 3.</label><caption><p>Transmission electron micrograph of GTA-like particles filtered from <italic>S. pomeroyi</italic> DSS-3 cultures. The long filamentous structures are most likely flagellar filaments (<xref ref-type="bibr" rid="r8">8</xref>). Bars = 50 nm.</p></caption><graphic xlink:href="zam0100888370003"></graphic></fig><fig position="float" id="f4"><label>FIG. 4.</label><caption><p>Production of GTA particles in <italic>S. pomeroyi</italic> DSS-3 cultures. (A) Detection of GTA production by epifluorescence microscopy. (B) Expression of an <italic>S. pomeroyi</italic> DSS-3 GTA gene (orfg3; portal) (<italic>n</italic> = 4 ± standard deviation [SD]) as a function of the cell number (<italic>n</italic> = 2 ± SD). The dotted line indicates the transition between log growth phase and stationary phase.</p></caption><graphic xlink:href="zam0100888370004"></graphic></fig><fig position="float" id="f5"><label>FIG. 5.</label><caption><p>Transfer of genetic markers between mutant strains of <italic>S. pomeroyi</italic> DSS-3. (A) Cultures of DSS-3 spontaneous mutants (Rif<sup>r</sup> or Strep<sup>r</sup>) were grown together or individually and plated on double-antibiotic plates. CFU of double mutants when grown together (Rif<sup>r</sup> + Strep<sup>r</sup>; replicates 1 and 2) provide an estimate of GTA-mediated gene transfer, since spontaneous double mutants in individually grown cultures (Rif<sup>r</sup> or Strep<sup>r</sup>) occur at very low numbers. (B) CFU from Kan<sup>r</sup><sub>150</sub> <italic>S. pomeroyi</italic> DSS-3 filtrate incubated with WT cells provide evidence for GTA activity. The values are averages (<italic>n</italic> = 2 plus standard deviation).</p></caption><graphic xlink:href="zam0100888370005"></graphic></fig><fig position="float" id="f6"><label>FIG. 6.</label><caption><p>Presence of GTA genes in the GOS metagenomic library (<xref ref-type="bibr" rid="r29">29</xref>) calculated as percentages of cells carrying homologs for each of the 15 GTAs. The dark-gray bars represent “diagnostic genes” (i.e., genes present in >90% of GTA-containing organisms as listed in Fig. <xref rid="f1" ref-type="fig">1</xref>). The light-gray bars represent “nondiagnostic genes” (i.e., those less common in GTA-containing organisms). The mean abundances across all 15 homologs are given in parentheses.</p></caption><graphic xlink:href="zam0100888370006"></graphic></fig></floats-wrap></pmc><affiliations><list></list><tree><noCountry><name sortKey="Belas, Robert" sort="Belas, Robert" uniqKey="Belas R" first="Robert" last="Belas">Robert Belas</name><name sortKey="Biers, Erin J" sort="Biers, Erin J" uniqKey="Biers E" first="Erin J." last="Biers">Erin J. Biers</name><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><name sortKey="Pennington, Catherine" sort="Pennington, Catherine" uniqKey="Pennington C" first="Catherine" last="Pennington">Catherine Pennington</name><name sortKey="Wang, Kui" sort="Wang, Kui" uniqKey="Wang K" first="Kui" last="Wang">Kui Wang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000668 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000668 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Pmc
|étape= Checkpoint
|type= RBID
|clé= PMC:2394915
|texte= Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton▿
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:18359833" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |