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High or low correlation between co-occuring gene clusters and 16S rRNA phylogeny.
MedLine Citation:
PMID:  23136894     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Ribosomal RNA (rRNA) genes are universal for all living organisms. Yet, the correspondence between genome composition and rRNA phylogeny remains poorly known. The aim of this work was to use the information from genome sequence databases to address the correlation between rRNA gene phylogeny and total gene composition in bacteria. This was done by analyzing 327 genomes with TIGRFAM functional gene annotations. Our approach consisted of two steps. First, we searched for discriminatory clusters of co-occurring genes. Using a multivariate statistical approach, we identified 11 such clusters which contain genes that were co-occurring only in a subset of genomes and contributed to explain the gene content differences between genome subsets. Second, we mapped the discovered clusters to 16S rRNA-based phylogeny and calculated the correlation between co-occuring genes and phylogeny. We found that 6 of the 11 clusters exhibited significant correlation with 16S rRNA gene phylogeny. The most distinct phylogenetic correlation was a high correlation between iron-sulfur oxidoreductases in combination with carbon nitrogen ligases and Chlorobium. The other correlations identified covered relatively large phylogroups: Actinobacteria were positively associated with kinases, while Gamma-proteobacteria were positively associated with methylases and acyltransferases. The suggested functional differences between higher phylogroups, however, need experimental verification. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
Authors:
Knut Rudi; Monika Sekelja
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Publication Detail:
Type:  LETTER     Date:  2012-11-9
Journal Detail:
Title:  FEMS microbiology letters     Volume:  -     ISSN:  1574-6968     ISO Abbreviation:  FEMS Microbiol. Lett.     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-9     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  7705721     Medline TA:  FEMS Microbiol Lett     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
Affiliation:
Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, Ås, Norway.
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