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PMID: 9045836 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2.

Journal of bacteriology ·Vol. 179 ·No. 5 ·1997-03-00 ·Pages 1734-47

Gruber TM, Bryant DA

Abstract

Sigma factors of the sigma70 family were used as a phylogenetic tool to compare evolutionary relationships among eubacteria. Several new sigma factor genes were cloned and sequenced to increase the variety of available sequences. Forty-two group 1 sigma factor sequences of various species were analyzed with the help of a distance matrix method to establish a phylogenetic tree. The tree derived by using sigma factors yielded subdivisions, including low-G+C and high-G+C gram-positive bacteria, cyanobacteria, and the alpha, beta, gamma, and delta subdivisions of proteobacteria, consistent with major bacterial groups found in trees derived from analyses with other molecules. However, some groupings (e.g., the chlamydiae, mycoplasmas, and green sulfur bacteria) are found in different positions than for trees obtained by using other molecular markers. A direct comparison to the most extensively used molecule in systematic studies, small-subunit rRNA, was made by deriving trees from essentially the same species set and using similar phylogenetic methods. Differences and similarities based on the two markers are discussed. Additionally, 31 group 2 sigma factors were analyzed in combination with the group 1 proteins in order to detect functional groupings of these alternative sigma factors. The data suggest that promoters recognized by the major vegetative sigma factors of eubacteria will contain sequence motifs and spacing very similar to those for the sigma70 sigma factors of Escherichia coli.

MeSH Terms
Amino Acid Sequence Bacteria/classification,genetics Blotting, Southern Cloning, Molecular Conserved Sequence DNA-Directed RNA Polymerases/chemistry,classification,genetics Evolution, Molecular Molecular Sequence Data Phylogeny Sequence Alignment Sigma Factor/chemistry,classification,genetics
Chemicals
Sigma Factor RNA polymerase sigma 70 DNA-Directed RNA Polymerases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Gruber T M
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA.
Bryant D A
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Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/jb.179.5.1734-1747.1997
Published
1997-03-00
Pages
1734-47
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC178889
Subset
IM
Grants
NIGMS NIH HHS · GM-31625 · United States
Databases
GENBANK
U67423, U67424, U67425
External Links
PubMed source DOI: 10.1128/jb.179.5.1734-1747.1997 PMC Full Text View journal details
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