This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Gruber, T. M.
Right arrow Articles by Bryant, D. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gruber, T. M.
Right arrow Articles by Bryant, D. A.
Right arrowPubmed/NCBI databases
*Gene*Protein

 Previous Article  |  Next Article 

J. Bacteriol., 03 1997, 1734-1747, Vol 179, No. 5
Copyright © 1997, American Society for Microbiology

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

TM Gruber and DA Bryant
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA.

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.


This article has been cited by other articles:

  • Ni, L., Jensen, S. O., Ky Tonthat, N., Berg, T., Kwong, S. M., Guan, F. H. X., Brown, M. H., Skurray, R. A., Firth, N., Schumacher, M. A. (2009). The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. Nucleic Acids Res 37: 6970-6983 [Abstract] [Full Text]  
  • Feklistov, A., Darst, S. A. (2009). Promoter recognition by bacterial alternative {sigma} factors: the price of high selectivity?. Genes Dev. 23: 2371-2375 [Abstract] [Full Text]  
  • Klein-Marcuschamer, D., Stephanopoulos, G. (2008). Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc. Natl. Acad. Sci. USA 105: 2319-2324 [Abstract] [Full Text]  
  • Vingadassalom, D., Kolb, A., Mayer, C., Collatz, E., Podglajen, I. (2007). Probing the Importance of Selected Phylum-specific Amino Acids in {sigma}A of Bacteroides fragilis, a Primary {sigma} Factor Naturally Devoid of an N-terminal Acidic Region 1.1. J. Biol. Chem. 282: 3442-3449 [Abstract] [Full Text]  
  • Sorenson, M. K., Darst, S. A. (2006). Disulfide cross-linking indicates that FlgM-bound and free {sigma}28 adopt similar conformations. Proc. Natl. Acad. Sci. USA 103: 16722-16727 [Abstract] [Full Text]  
  • Arvik, T., Conterno, L., Worobo, R., Fermin, G., Henick-Kling, T. (2005). Identification of the Macromolecular Synthesis Operon of Oenococcus oeni. Am. J. Enol. Vitic. 56: 60-67 [Abstract] [Full Text]  
  • Baymann, F., Lebrun, E., Nitschke, W. (2004). Mitochondrial cytochrome c1 is a collapsed di-heme cytochrome. Proc. Natl. Acad. Sci. USA 101: 17737-17740 [Abstract] [Full Text]  
  • Soler, L., Yanez, M. A., Chacon, M. R., Aguilera-Arreola, M. G., Catalan, V., Figueras, M. J., Martinez-Murcia, A. J. (2004). Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes. Int. J. Syst. Evol. Microbiol. 54: 1511-1519 [Abstract] [Full Text]  
  • Lavire, C., Blaha, D., Cournoyer, B. (2004). Selection of Unusual Actinomycetal Primary {sigma}70 Factors by Plant-Colonizing Frankia Strains. Appl. Environ. Microbiol. 70: 991-998 [Abstract] [Full Text]  
  • Gupta, R. S., Pereira, M., Chandrasekera, C., Johari, V. (2003). Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. Int. J. Syst. Evol. Microbiol. 53: 1833-1842 [Abstract] [Full Text]  
  • Ross, W., Schneider, D. A., Paul, B. J., Mertens, A., Gourse, R. L. (2003). An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev. 17: 1293-1307 [Abstract] [Full Text]  
  • Tuominen, I., Tyystjarvi, E., Tyystjarvi, T. (2003). Expression of Primary Sigma Factor (PSF) and PSF-Like Sigma Factors in the Cyanobacterium Synechocystis sp. Strain PCC 6803. J. Bacteriol. 185: 1116-1119 [Abstract] [Full Text]  
  • Camarero, J. A., Shekhtman, A., Campbell, E. A., Chlenov, M., Gruber, T. M., Bryant, D. A., Darst, S. A., Cowburn, D., Muir, T. W. (2002). Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc. Natl. Acad. Sci. USA 99: 8536-8541 [Abstract] [Full Text]  
  • Murakami, K. S., Masuda, S., Darst, S. A. (2002). Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 A Resolution. Science 296: 1280-1284 [Abstract] [Full Text]  
  • Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., Darst, S. A. (2002). Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex. Science 296: 1285-1290 [Abstract] [Full Text]  
  • Yamamoto, I., Ujiiye, T., Ohshima, Y., Satoh, T. (2001). Mutational Analysis of Regulatory cis-acting Elements for the Transcriptional Activation of the dmsCBA Operon in Rhodobacter sphaeroides f. sp. denitrificans. Plant Cell Physiol 42: 703-709 [Abstract] [Full Text]  
  • Muro-Pastor, A. M., Herrero, A., Flores, E. (2001). Nitrogen-Regulated Group 2 Sigma Factor from Synechocystis sp. Strain PCC 6803 Involved in Survival under Nitrogen Stress. J. Bacteriol. 183: 1090-1095 [Abstract] [Full Text]  
  • Huckauf, J., Nomura, C., Forchhammer, K., Hagemann, M. (2000). Stress responses of Synechocystis sp. strain PCC 6803 mutants impaired in genes encoding putative alternative sigma factors. Microbiology 146: 2877-2889 [Abstract] [Full Text]  
  • Hutchings, M. I., Spiro, S. (2000). The nitric oxide regulated nor promoter of Paracoccus denitrificans. Microbiology 146: 2635-2641 [Abstract] [Full Text]  
  • Hakimi, M.-A., Privat, I., Valay, J.-G., Lerbs-Mache, S. (2000). Evolutionary Conservation of C-terminal Domains of Primary Sigma70-type Transcription Factors between Plants and Bacteria. J. Biol. Chem. 275: 9215-9221 [Abstract] [Full Text]  
  • Tan, S., Troxler, R. F. (1999). Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: Photoregulation and differential expression. Proc. Natl. Acad. Sci. USA 96: 5316-5321 [Abstract] [Full Text]  
  • Marczynski, G. T. (1999). Chromosome Methylation and Measurement of Faithful, Once and Only Once per Cell Cycle Chromosome Replication in Caulobacter crescentus. J. Bacteriol. 181: 1984-1993 [Abstract] [Full Text]  
  • Baker, S. C., Ferguson, S. J., Ludwig, B., Page, M. D., Richter, O.-M. H., van Spanning, R. J. M. (1998). Molecular Genetics of the Genus Paracoccus: Metabolically Versatile Bacteria with Bioenergetic Flexibility. Microbiol. Mol. Biol. Rev. 62: 1046-1078 [Abstract] [Full Text]  
  • Gupta, R. S. (1998). Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol. Mol. Biol. Rev. 62: 1435-1491 [Abstract] [Full Text]  
  • Wösten, M. M. S. M., Boeve, M., Koot, M. G. A., van Nuenen, A. C., van der Zeijst, B. A. M. (1998). Identification of Campylobacter jejuni Promoter Sequences. J. Bacteriol. 180: 594-599 [Abstract] [Full Text]  
  • MacGregor, B. J., Karls, R. K., Donohue, T. J. (1998). Transcription of the Rhodobacter sphaeroides cycA P1 Promoter by Alternate RNA Polymerase Holoenzymes. J. Bacteriol. 180: 1-9 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»