Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach

Abstract

Background: Bacillus subtilis is one of the best-characterized organisms in Gram-positive bacteria. It represents a paradigm of gene regulation in bacteria due its complex life style (which could involve a transition between stages as diverse as vegetative cell and spore formation). In order to gain insight into the organization and evolution of the B. subtilis regulatory network and to provide an alternative framework for further studies in bacteria, we identified and analyzed its repertoire of DNA-binding transcription factors in terms of their abundance, family distribution and regulated genes.

Results: A collection of 237 DNA-binding Transcription Factors (TFs) was identified in B. subtilis, half of them with experimental evidence. 59% of them were predicted to be repressors, 17% activators, 17% were putatively identified as dual regulatory proteins and the remaining 6.3% could not be associated with a regulatory role. From this collection 56 TFs were found to be autoregulated, most of them negatively, though a significant proportion of positive feedback circuits were also identified. TFs were clustered into 51 regulatory protein families and then traced on 58 genomes from Firmicutes to detect their presence. From this analysis three families were found conserved in all the Firmicutes; fifteen families were distributed in all Firmicutes except in the phyla Mollicutes; two were constrained to Bacillales and finally two families were found to be specific to B. subtilis, due to their specie specific distribution. Repression seems to be the most common regulatory mechanism in Firmicutes due to the high proportion of repressors in the detected collection in these genomes. In addition, six global regulators were defined in B. subtilis based on the number and function of their regulated genes.

Conclusion: In this work we identified and described the characteristics associated to the repertoire of DNA-binding TFs in B. subtilis. We also quantified their abundance, family distribution, and regulatory roles in the context of Firmicutes. This work should not only contribute to our understanding of the regulation of gene expression in bacteria from the perspective of B. subtilis but also provide us the basis for comprehensive modeling of transcriptional regulatory networks in Firmicutes.

Figure 1

Total number of TFs identified per genome for all the firmicutes analyzed in this study. The proportion of activators (yellow), repressors (black), dual (red) and proteins with unknown (gray) regulatory role is shown.

Figure 2

Distribution of DNA-binding sites in B. subtilis for repressors and activators. Data was retrieved from DBTBS [6]. 0 represents the start of transcription site (+1). The data was fitted using a Gaussian kernelwith a bandwidth of 13.92 for repressor sites and12.42 for activator sites using the density estimation function in the R statistics package.

Figure 3

Matrix of characterized interactions among TFs in B. subtilis. Each filled box shows the sign of the regulatory effect of the TF in the corresponding column on the expression of the TF in the corresponding row. Repression is denoted by -, activation is denoted by + and dual regulation is denoted by *.

Figure 4

Distribution of TF families and their abundance in Firmicutes. We present the abundance of TFs per genome at intervals of five proteins. Nomenclature is as follows: Bacillales: Ban, Bacillus anthracis Ames Ancestor; Bce, B. cereus 10987; Bcl, B. clausii KSM-K16; Bha, B. halodurans C-125; Bli, B. licheniformis ATCC14580 (DSM 13); Bsu, B. subtilis 168; Bth, B. thuringiensis konkukian; Gka, Geobacillus kaustophilus HTA426; Lin, Listeria innocua CLIP 11262; Lmo, L. monocytogenes 4b F2365; Oih, O. iheyensis HTE831; Sau, Staphylococcus aureus subsp. aureus COL; Sep, S. epidermidis ATCC 12228. Clostridia: Cac, Clostridium acetobutylicum ATCC824; Cpe, C. perfringens 13; Cte, C.tetani E88; Tte, Thermoanaerobacter tengcongensis MB4(T). Lactobacillales: Efa, Enterococcus faecalis V583; Lac, Lactobacillus acidophilus NCFM; Ljo, L. johnsonii NCC 533; Lla, Lactococcus lactis subsp. lactis IL1403; Lpl, L. plantarum WCFS1; Sag, Streptococcus agalactiae 2603V/R; Smu, S. mutans UA159; Spn, S.pneumoniae TIGR4; Spy, S.pyogenes MGAS315; Sth, S.thermophilus CNRZ1066. Mollicutes: Mfl, Mesoplasma florum L1; Mhy, Mycoplasma hyopneumoniae 232; Mmo, M. mobile 163K; Mmy, M.mycoides SC PG1; Mga, M.gallisepticum strain R; Mge, M.genitalium G-37; Mpe, M.penetrans HF-2; Mpn, M.pneumoniae M129; Mpu, M.pulmonis UAB CTIP; Uur, Ureaplasma urealyticum parvum biovar serovar 3.