This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Conlan, S. Articles by McCue, L. A. Search for Related Content PubMed PubMed Citation Articles by Conlan, S. Articles by McCue, L. A. Agricola Articles by Conlan, S. Articles by McCue, L. A.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, November 2005, p. 7442-7452, Vol. 71, No. 11
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.11.7442-7452.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Rhodopseudomonas palustris Regulons Detected by Cross-Species Analysis of Alphaproteobacterial Genomes

The Wadsworth Center, New York State Department of Health, Albany, New York 12201,¹ Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912²

Received 17 January 2005/ Accepted 14 June 2005

Rhodopseudomonas palustris, an -proteobacterium, carries out three of the chemical reactions that support life on this planet: the conversion of sunlight to chemical-potential energy; the absorption of carbon dioxide, which it converts to cellular material; and the fixation of atmospheric nitrogen into ammonia. Insight into the transcription-regulatory network that coordinates these processes is fundamental to understanding the biology of this versatile bacterium. With this goal in mind, we predicted regulatory signals genomewide, using a two-step phylogenetic-footprinting and clustering process that we had developed previously. In the first step, 4,963 putative transcription factor binding sites, upstream of 2,044 genes and operons, were identified using cross-species Gibbs sampling. Bayesian motif clustering was then employed to group the cross-species motifs into regulons. We have identified 101 putative regulons in R. palustris, including 8 that are of particular interest: a photosynthetic regulon, a flagellar regulon, an organic hydroperoxide resistance regulon, the LexA regulon, and four regulons related to nitrogen metabolism (FixK₂, NnrR, NtrC, and ⁵⁴). In some cases, clustering allowed us to assign functions to proteins that previously had been annotated with only putative functions; we have identified RPA0828 as the organic hydroperoxide resistance regulator and RPA1026 as a cell cycle methylase. In addition to predicting regulons, we identified a novel inverted repeat that likely forms a highly conserved stem-loop and that occurs downstream of over 100 genes.

This article has been cited by other articles:

• Liu, J., Xu, X., Stormo, G. D. (2008). The cis-regulatory map of Shewanella genomes. Nucleic Acids Res 36: 5376-5390 [Abstract] [Full Text]  
• Thompson, W. A., Newberg, L. A., Conlan, S., McCue, L. A., Lawrence, C. E. (2007). The Gibbs Centroid Sampler. Nucleic Acids Res 35: W232-W237 [Abstract] [Full Text]