Size-variable zone in V3 region of 16S rRNA.
Identifieur interne : 000B29 ( PubMed/Checkpoint ); précédent : 000B28; suivant : 000B30Size-variable zone in V3 region of 16S rRNA.
Auteurs : Francisco Vargas-Albores [Mexique] ; Luis Enrique Ortiz-Suárez [Mexique] ; Enrique Villalpando-Canchola [Mexique] ; Marcel Martínez-Porchas [Mexique]Source :
- RNA biology [ 1555-8584 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Ribosomal, 16S.
- classification : Bacteria.
- genetics : Bacteria.
- statistics & numerical data : Sequence Analysis, RNA.
- Base Pairing, Base Sequence, Consensus Sequence, Databases, Genetic, Genes, Bacterial, Genetic Variation, Metagenome, Nucleic Acid Conformation, Phylogeny.
Abstract
The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.
DOI: 10.1080/15476286.2017.1317912
PubMed: 28440695
Affiliations:
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Hermosillo , Sonora , México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora </wicri:regionArea><wicri:noRegion>Sonora </wicri:noRegion></affiliation></author><author><name sortKey="Martinez Porchas, Marcel" sort="Martinez Porchas, Marcel" uniqKey="Martinez Porchas M" first="Marcel" last="Martínez-Porchas">Marcel Martínez-Porchas</name><affiliation wicri:level="1"><nlm:affiliation>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora , México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora </wicri:regionArea><wicri:noRegion>Sonora </wicri:noRegion></affiliation></author></analytic><series><title level="j">RNA biology</title><idno type="eISSN">1555-8584</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Base Pairing</term><term>Base Sequence</term><term>Consensus Sequence</term><term>Databases, Genetic</term><term>Genes, Bacterial</term><term>Genetic Variation</term><term>Metagenome</term><term>Nucleic Acid Conformation</term><term>Phylogeny</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Sequence Analysis, RNA (statistics & numerical data)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ribosomique 16S (génétique)</term><term>Analyse de séquence d'ARN ()</term><term>Appariement de bases</term><term>Bactéries ()</term><term>Bactéries (génétique)</term><term>Bases de données génétiques</term><term>Conformation d'acide nucléique</term><term>Gènes bactériens</term><term>Métagénome</term><term>Phylogénie</term><term>Séquence consensus</term><term>Séquence nucléotidique</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN ribosomique 16S</term><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Consensus Sequence</term><term>Databases, Genetic</term><term>Genes, Bacterial</term><term>Genetic Variation</term><term>Metagenome</term><term>Nucleic Acid Conformation</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Appariement de bases</term><term>Bactéries</term><term>Bases de données génétiques</term><term>Conformation d'acide nucléique</term><term>Gènes bactériens</term><term>Métagénome</term><term>Phylogénie</term><term>Séquence consensus</term><term>Séquence nucléotidique</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28440695</PMID><DateCompleted><Year>2018</Year><Month>07</Month><Day>19</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1555-8584</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>11</Issue><PubDate><Year>2017</Year><Month>11</Month><Day>02</Day></PubDate></JournalIssue><Title>RNA biology</Title><ISOAbbreviation>RNA Biol</ISOAbbreviation></Journal><ArticleTitle>Size-variable zone in V3 region of 16S rRNA.</ArticleTitle><Pagination><MedlinePgn>1514-1521</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/15476286.2017.1317912</ELocationID><Abstract><AbstractText>The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vargas-Albores</LastName><ForeName>Francisco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora , México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ortiz-Suárez</LastName><ForeName>Luis Enrique</ForeName><Initials>LE</Initials><AffiliationInfo><Affiliation>b Instituto Tecnológico de Morelia , Morelia Michoacán , México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Villalpando-Canchola</LastName><ForeName>Enrique</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora , México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martínez-Porchas</LastName><ForeName>Marcel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>a Centro de Investigación en Alimentación y Desarrollo , Carretera a La Victoria . Hermosillo , Sonora , México.</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></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>05</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>RNA Biol</MedlineTA><NlmUniqueID>101235328</NlmUniqueID><ISSNLinking>1547-6286</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020029" MajorTopicYN="N">Base Pairing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016384" MajorTopicYN="N">Consensus Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005798" MajorTopicYN="Y">Genes, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054892" MajorTopicYN="Y">Metagenome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000706" MajorTopicYN="Y">statistics & numerical data</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">16S gene</Keyword><Keyword MajorTopicYN="Y">5-way junction</Keyword><Keyword MajorTopicYN="Y">V3 pattern</Keyword><Keyword MajorTopicYN="Y">V3 size different</Keyword><Keyword MajorTopicYN="Y">bacterial rRNA</Keyword><Keyword MajorTopicYN="Y">helix 17</Keyword><Keyword MajorTopicYN="Y">k-mers</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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Canchola E" first="Enrique" last="Villalpando-Canchola">Enrique Villalpando-Canchola</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:28440695
|texte= Size-variable zone in V3 region of 16S rRNA.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:28440695" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |