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Bioinformatics Advance Access originally published online on June 17, 2008
Bioinformatics 2008 24(16):1793-1797; doi:10.1093/bioinformatics/btn314
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Sequence analysis of GerM and SpoVS, uncharacterized bacterial ‘sporulation’ proteins with widespread phylogenetic distribution

Daniel J. Rigden 1,* and Michael Y. Galperin 2

1School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK and 2NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA

*To whom correspondence should be addressed.


  Abstract

Sporulation in low-G+C gram-positive bacteria (Firmicutes) is an important survival mechanism that involves up to 150 genes, acting in a highly regulated manner. Many sporulation genes have close homologs in non-sporulating bacteria, including cyanobacteria, proteobacteria and spirochaetes, indicating that their products play a wider biological role. Most of them have been characterized as regulatory proteins or enzymes of peptidoglycan turnover; functions of others remain unknown but they are likely to have a general role in cell division and/or development. We have compiled a list of such widely conserved sporulation and germination proteins with poorly characterized functions, ranked them by the width of their phylogenetic distribution, and performed detailed sequence analysis and, where possible, structural modeling aimed at estimating their potential functions. Here we report the results of sequence analysis of Bacillus subtilis spore germination protein GerM, suggesting that it is a widespread cell development protein, whose function might involve binding to peptidoglycan. GerM consists of two tandem copies of a new domain (designated the GERMN domain) that forms phylum-specific fusions with two other newly described domains, GERMN-associated domains 1 and 2 (GMAD1 and GMAD2). Fold recognition reveals a β-propeller fold for GMAD1, while ab initio modeling suggests that GMAD2 adopts a fibronectin type III fold. SpoVS is predicted to adopt the AlbA archaeal chromatin protein fold, which suggests that it is a DNA-binding protein, most likely a novel transcriptional regulator.

Contact: drigden{at}liverpool.ac.uk

Supplementary information: Supplementary data are available at ftp://ftp.ncbi.nih.gov/pub/galperin/Sporulation.html

Associate Editor: Burkhard Rost

Received on May 16, 2008; revised on June 13, 2008; accepted on June 13, 2008

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