The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.
Identifieur interne : 000841 ( Ncbi/Merge ); précédent : 000840; suivant : 000842The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.
Auteurs : D C Teixeira [Brésil] ; S. Eveillard ; P. Sirand-Pugnet ; A. Wulff ; C. Saillard ; A J Ayres ; J M BovéSource :
- International journal of systematic and evolutionary microbiology [ 1466-5026 ] ; 2008.
English descriptors
- KwdEn :
- Bacterial Proteins (genetics), Chromosome Walking, Citrus sinensis (microbiology), DNA, Bacterial (analysis), Molecular Sequence Data, Multigene Family, Phylogeny, Plant Diseases (microbiology), Plant Leaves (microbiology), RNA, Ribosomal, 16S (genetics), Rhizobiaceae (classification), Rhizobiaceae (genetics), Rhizobiaceae (isolation & purification), Ribosomal Proteins (genetics), Sequence Analysis, DNA, Species Specificity, Vinca (microbiology).
- MESH :
- chemical , analysis : DNA, Bacterial.
- chemical , genetics : Bacterial Proteins, RNA, Ribosomal, 16S, Ribosomal Proteins.
- classification : Rhizobiaceae.
- genetics : Rhizobiaceae.
- isolation & purification : Rhizobiaceae.
- microbiology : Citrus sinensis, Plant Diseases, Plant Leaves, Vinca.
- Chromosome Walking, Molecular Sequence Data, Multigene Family, Phylogeny, Sequence Analysis, DNA, Species Specificity.
Abstract
The rplKAJL-rpoBC operon or beta operon is a classic bacterial gene cluster, which codes for proteins K, A, J and L of the large ribosomal subunit, as well as proteins B (beta subunit) and C (beta' subunit) of RNA polymerase. In the early 1990s, the operon was obtained as a 2.6 kbp DNA fragment (In-2.6) by random cloning of DNA from periwinkle plants infected with the Poona (India) strain of the huanglongbing agent, later named 'Candidatus (Ca.) Liberibacter asiaticus'. DNA from periwinkle plants infected with the Nelspruit strain (South Africa) of 'Ca. L. africanus' was amplified with a primer pair designed from In-2.6 and yielded, after cloning and sequencing, a 1.7 kbp DNA fragment (AS-1.7) of the beta operon of 'Ca. L. africanus'. The beta operon of the American liberibacter, as well as the three upstream genes (tufB, secE, nusG), have now also been obtained by the technique of chromosome walking and extend over 4673 bp, comprising the following genes: tufB, secE, nusG, rplK, rplA, rplJ, rplL and rpoB. The sequence of the beta operon was also determined for a Brazilian strain of 'Ca. L. asiaticus', from nusG to rpoB (3025 bp), and was found to share 99 % identity with the corresponding beta operon sequences of an Indian and a Japanese strain. Finally, the beta operon sequence of 'Ca. L. africanus' was extended from 1673 bp (rplA to rpoB) to 3013 bp (nusG to rpoB), making it possible to compare the beta operon sequences of the African, Asian and American liberibacters over a length of approximately 3000 bp, from nusG to rpoB. While 'Ca. L. africanus' and 'Ca. L. asiaticus' shared 81.2 % sequence identity, the percentage for 'Ca. L. americanus' and 'Ca. L. africanus' was only 72.2 %, and identity for 'Ca. L. americanus' and 'Ca. L. asiaticus' was only 71.4 %. The approximately 3000 bp nusG-rpoB sequence was also used to construct a phylogenetic tree, and this tree was found to be identical to the known 16S rRNA gene sequence-based tree. These results confirm earlier findings that 'Ca. L. americanus' is a distinct liberibacter, more distantly related to 'Ca. L. africanus' and 'Ca. L. asiaticus' than 'Ca. L. africanus' is to 'Ca. L. asiaticus'. The dates of speciation have also been estimated.
DOI: 10.1099/ijs.0.65641-0
PubMed: 18523188
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.</title><author><name sortKey="Teixeira, D C" sort="Teixeira, D C" uniqKey="Teixeira D" first="D C" last="Teixeira">D C Teixeira</name><affiliation wicri:level="1"><nlm:affiliation>Fundecitrus, Araraquara, SP, CEP 14807-040, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Fundecitrus, Araraquara, SP, CEP 14807-040</wicri:regionArea><wicri:noRegion>CEP 14807-040</wicri:noRegion></affiliation></author><author><name sortKey="Eveillard, S" sort="Eveillard, S" uniqKey="Eveillard S" first="S" last="Eveillard">S. Eveillard</name></author><author><name sortKey="Sirand Pugnet, P" sort="Sirand Pugnet, P" uniqKey="Sirand Pugnet P" first="P" last="Sirand-Pugnet">P. Sirand-Pugnet</name></author><author><name sortKey="Wulff, A" sort="Wulff, A" uniqKey="Wulff A" first="A" last="Wulff">A. Wulff</name></author><author><name sortKey="Saillard, C" sort="Saillard, C" uniqKey="Saillard C" first="C" last="Saillard">C. Saillard</name></author><author><name sortKey="Ayres, A J" sort="Ayres, A J" uniqKey="Ayres A" first="A J" last="Ayres">A J Ayres</name></author><author><name sortKey="Bove, J M" sort="Bove, J M" uniqKey="Bove J" first="J M" last="Bové">J M Bové</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18523188</idno><idno type="pmid">18523188</idno><idno type="doi">10.1099/ijs.0.65641-0</idno><idno type="wicri:Area/PubMed/Corpus">000A50</idno><idno type="wicri:Area/PubMed/Curation">000A50</idno><idno type="wicri:Area/PubMed/Checkpoint">000A50</idno><idno type="wicri:Area/Ncbi/Merge">000841</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.</title><author><name sortKey="Teixeira, D C" sort="Teixeira, D C" uniqKey="Teixeira D" first="D C" last="Teixeira">D C Teixeira</name><affiliation wicri:level="1"><nlm:affiliation>Fundecitrus, Araraquara, SP, CEP 14807-040, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Fundecitrus, Araraquara, SP, CEP 14807-040</wicri:regionArea><wicri:noRegion>CEP 14807-040</wicri:noRegion></affiliation></author><author><name sortKey="Eveillard, S" sort="Eveillard, S" uniqKey="Eveillard S" first="S" last="Eveillard">S. Eveillard</name></author><author><name sortKey="Sirand Pugnet, P" sort="Sirand Pugnet, P" uniqKey="Sirand Pugnet P" first="P" last="Sirand-Pugnet">P. Sirand-Pugnet</name></author><author><name sortKey="Wulff, A" sort="Wulff, A" uniqKey="Wulff A" first="A" last="Wulff">A. Wulff</name></author><author><name sortKey="Saillard, C" sort="Saillard, C" uniqKey="Saillard C" first="C" last="Saillard">C. Saillard</name></author><author><name sortKey="Ayres, A J" sort="Ayres, A J" uniqKey="Ayres A" first="A J" last="Ayres">A J Ayres</name></author><author><name sortKey="Bove, J M" sort="Bove, J M" uniqKey="Bove J" first="J M" last="Bové">J M Bové</name></author></analytic><series><title level="j">International journal of systematic and evolutionary microbiology</title><idno type="ISSN">1466-5026</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacterial Proteins (genetics)</term><term>Chromosome Walking</term><term>Citrus sinensis (microbiology)</term><term>DNA, Bacterial (analysis)</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>Phylogeny</term><term>Plant Diseases (microbiology)</term><term>Plant Leaves (microbiology)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Rhizobiaceae (classification)</term><term>Rhizobiaceae (genetics)</term><term>Rhizobiaceae (isolation & purification)</term><term>Ribosomal Proteins (genetics)</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term><term>Vinca (microbiology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term><term>RNA, Ribosomal, 16S</term><term>Ribosomal Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Rhizobiaceae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Citrus sinensis</term><term>Plant Diseases</term><term>Plant Leaves</term><term>Vinca</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Walking</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The rplKAJL-rpoBC operon or beta operon is a classic bacterial gene cluster, which codes for proteins K, A, J and L of the large ribosomal subunit, as well as proteins B (beta subunit) and C (beta' subunit) of RNA polymerase. In the early 1990s, the operon was obtained as a 2.6 kbp DNA fragment (In-2.6) by random cloning of DNA from periwinkle plants infected with the Poona (India) strain of the huanglongbing agent, later named 'Candidatus (Ca.) Liberibacter asiaticus'. DNA from periwinkle plants infected with the Nelspruit strain (South Africa) of 'Ca. L. africanus' was amplified with a primer pair designed from In-2.6 and yielded, after cloning and sequencing, a 1.7 kbp DNA fragment (AS-1.7) of the beta operon of 'Ca. L. africanus'. The beta operon of the American liberibacter, as well as the three upstream genes (tufB, secE, nusG), have now also been obtained by the technique of chromosome walking and extend over 4673 bp, comprising the following genes: tufB, secE, nusG, rplK, rplA, rplJ, rplL and rpoB. The sequence of the beta operon was also determined for a Brazilian strain of 'Ca. L. asiaticus', from nusG to rpoB (3025 bp), and was found to share 99 % identity with the corresponding beta operon sequences of an Indian and a Japanese strain. Finally, the beta operon sequence of 'Ca. L. africanus' was extended from 1673 bp (rplA to rpoB) to 3013 bp (nusG to rpoB), making it possible to compare the beta operon sequences of the African, Asian and American liberibacters over a length of approximately 3000 bp, from nusG to rpoB. While 'Ca. L. africanus' and 'Ca. L. asiaticus' shared 81.2 % sequence identity, the percentage for 'Ca. L. americanus' and 'Ca. L. africanus' was only 72.2 %, and identity for 'Ca. L. americanus' and 'Ca. L. asiaticus' was only 71.4 %. The approximately 3000 bp nusG-rpoB sequence was also used to construct a phylogenetic tree, and this tree was found to be identical to the known 16S rRNA gene sequence-based tree. These results confirm earlier findings that 'Ca. L. americanus' is a distinct liberibacter, more distantly related to 'Ca. L. africanus' and 'Ca. L. asiaticus' than 'Ca. L. africanus' is to 'Ca. L. asiaticus'. The dates of speciation have also been estimated.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18523188</PMID><DateCreated><Year>2008</Year><Month>6</Month><Day>4</Day></DateCreated><DateCompleted><Year>2008</Year><Month>08</Month><Day>05</Day></DateCompleted><DateRevised><Year>2008</Year><Month>6</Month><Day>4</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1466-5026</ISSN><JournalIssue CitedMedium="Print"><Volume>58</Volume><Issue>Pt 6</Issue><PubDate><Year>2008</Year><Month>Jun</Month></PubDate></JournalIssue><Title>International journal of systematic and evolutionary microbiology</Title><ISOAbbreviation>Int. J. Syst. Evol. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation.</ArticleTitle><Pagination><MedlinePgn>1414-21</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1099/ijs.0.65641-0</ELocationID><Abstract><AbstractText>The rplKAJL-rpoBC operon or beta operon is a classic bacterial gene cluster, which codes for proteins K, A, J and L of the large ribosomal subunit, as well as proteins B (beta subunit) and C (beta' subunit) of RNA polymerase. In the early 1990s, the operon was obtained as a 2.6 kbp DNA fragment (In-2.6) by random cloning of DNA from periwinkle plants infected with the Poona (India) strain of the huanglongbing agent, later named 'Candidatus (Ca.) Liberibacter asiaticus'. DNA from periwinkle plants infected with the Nelspruit strain (South Africa) of 'Ca. L. africanus' was amplified with a primer pair designed from In-2.6 and yielded, after cloning and sequencing, a 1.7 kbp DNA fragment (AS-1.7) of the beta operon of 'Ca. L. africanus'. The beta operon of the American liberibacter, as well as the three upstream genes (tufB, secE, nusG), have now also been obtained by the technique of chromosome walking and extend over 4673 bp, comprising the following genes: tufB, secE, nusG, rplK, rplA, rplJ, rplL and rpoB. The sequence of the beta operon was also determined for a Brazilian strain of 'Ca. L. asiaticus', from nusG to rpoB (3025 bp), and was found to share 99 % identity with the corresponding beta operon sequences of an Indian and a Japanese strain. Finally, the beta operon sequence of 'Ca. L. africanus' was extended from 1673 bp (rplA to rpoB) to 3013 bp (nusG to rpoB), making it possible to compare the beta operon sequences of the African, Asian and American liberibacters over a length of approximately 3000 bp, from nusG to rpoB. While 'Ca. L. africanus' and 'Ca. L. asiaticus' shared 81.2 % sequence identity, the percentage for 'Ca. L. americanus' and 'Ca. L. africanus' was only 72.2 %, and identity for 'Ca. L. americanus' and 'Ca. L. asiaticus' was only 71.4 %. The approximately 3000 bp nusG-rpoB sequence was also used to construct a phylogenetic tree, and this tree was found to be identical to the known 16S rRNA gene sequence-based tree. These results confirm earlier findings that 'Ca. L. americanus' is a distinct liberibacter, more distantly related to 'Ca. L. africanus' and 'Ca. L. asiaticus' than 'Ca. L. africanus' is to 'Ca. L. asiaticus'. The dates of speciation have also been estimated.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Teixeira</LastName><ForeName>D C</ForeName><Initials>DC</Initials><AffiliationInfo><Affiliation>Fundecitrus, Araraquara, SP, CEP 14807-040, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eveillard</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Sirand-Pugnet</LastName><ForeName>P</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Wulff</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Saillard</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Ayres</LastName><ForeName>A J</ForeName><Initials>AJ</Initials></Author><Author ValidYN="Y"><LastName>Bové</LastName><ForeName>J M</ForeName><Initials>JM</Initials></Author></AuthorList><Language>ENG</Language><DataBankList 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UI="D005810" MajorTopicYN="Y">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012230" MajorTopicYN="N">Rhizobiaceae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012269" MajorTopicYN="N">Ribosomal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="Y">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031053" MajorTopicYN="N">Vinca</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>6</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>8</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>6</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18523188</ArticleId><ArticleId IdType="pii">58/6/1414</ArticleId><ArticleId IdType="doi">10.1099/ijs.0.65641-0</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Brésil</li></country></list><tree><noCountry><name sortKey="Ayres, A J" sort="Ayres, A J" uniqKey="Ayres A" first="A J" last="Ayres">A J Ayres</name><name sortKey="Bove, J M" sort="Bove, J M" uniqKey="Bove J" first="J M" last="Bové">J M Bové</name><name sortKey="Eveillard, S" sort="Eveillard, S" uniqKey="Eveillard S" first="S" last="Eveillard">S. Eveillard</name><name sortKey="Saillard, C" sort="Saillard, C" uniqKey="Saillard C" first="C" last="Saillard">C. Saillard</name><name sortKey="Sirand Pugnet, P" sort="Sirand Pugnet, P" uniqKey="Sirand Pugnet P" first="P" last="Sirand-Pugnet">P. Sirand-Pugnet</name><name sortKey="Wulff, A" sort="Wulff, A" uniqKey="Wulff A" first="A" last="Wulff">A. Wulff</name></noCountry><country name="Brésil"><noRegion><name sortKey="Teixeira, D C" sort="Teixeira, D C" uniqKey="Teixeira D" first="D C" last="Teixeira">D C Teixeira</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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