Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation

Graduate School of Information Science, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 01/2011; 39(2):414-28. DOI: 10.1093/nar/gkq780
Source: PubMed

ABSTRACT AbrB is a global transcriptional regulator of Bacillus subtilis that represses the expression of many genes during exponential growth. Here, we demonstrate that AbrB and its homolog Abh bind to hundreds of sites throughout the entire B. subtilis genome during exponential growth. Comparison of regional binding of AbrB and Abh in wild-type, ΔabrB and Δabh backgrounds revealed that they bind as homomer and/or heteromer forms with different specificities and affinities. We found four AbrB and Abh binding patterns were major. Three of these contain pairs of TGGNA motifs connected by A/T-rich sequences, differing in arrangement and spacing. We also assessed the direct involvement of these complexes in the control of gene expression. Our data indicate that AbrB usually acts as a repressor, and that the ability of Abh to act as a transcriptional regulator was limited. We found that changes to AbrB/Abh levels affect their binding at several promoters and consequently transcriptional regulation. Surprisingly, most AbrB/Abh binding events had no impact on transcription, suggesting an interesting possibility that AbrB/Abh binding is analogous to nucleoid-associated protein binding in Escherichia coli.

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Available from: Shigehiko Kanaya, Aug 20, 2015
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    • "All 129 fully-sequenced cyanobacterial genomes [10] possess at least one AbrB-encoding gene, which define three paralogous clades, clades A and B, and a clade specific to marine cyanobacteria [11]. Like their bacterial counterparts, which regulate sporulation, biofilm formation, antibiotic resistance, etc [12], cyanobacterial AbrB regulators operate in many cellular processes. They were shown to bind to the upstream region of the Rubisco-encoding rbc operon in Synechococcus PCC7002 [13]; the Anabaena PCC7120 sodB (iron superoxide dismutase) and hypC (hydrogen production) genes [14] [15]; and the hepatotoxin synthesis gene aoaC in Aphanizomenon ovalisporum [16] [17]. "
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    ABSTRACT: We show that the Synechocystis AbrB2 repressor of hydrogen production, down regulates the defence against oxidative stress. The single widely conserved cysteine of AbrB2 is also shown to play a crucial role in AbrB2 oligomerisation, and in AbrB2-mediated repression of the hydrogenase encoding operon (hoxEFUYH) and a wealth of other genes. Very interestingly, our results indicate that this cysteine is the target of glutathionylation, which affects the binding of AbrB2 on the hox operon-promoter DNA, as well as the stability of AbrB2 at the non-standard temperature of 39°C. Similarly, we show that the cysteine of the other hoxEFUYH regulator AbrB1 can also be glutathionylated in vitro. These novel findings will certainly stimulate the in depth analysis of the influence of glutathionylation on the production of hydrogen, a field totally overlooked so far. They also emphasize on the evolutionary conservation of glutathionylation, a process mostly described in eukaryotes, so far.
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    • "cription were the major groups represented . The transcription of the majority of these genes increased during the LC phase and was maintained in the SC ( Fig . 3 ) . The most abundant transcript in cluster IV , encoding for the AbrB family transcriptional regulator , declined during the vegetative growth phases . Interestingly , in B . subtilis ( Chumsakul et al . , 2011 ) and C . acetobutylicum ( Alsaker and Papoutsakis , 2005 ; Scotcher et al . , 2005 ) , AbrB is a transi - tional stage gene regulator that prevents inappropriate gene expression during the vegetative phase , particularly by acting as antagonist of Spo0A and inhibiting the sporulation process . In contrast , the same repressor , AbrB , "
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    • "Recent investigations support this idea. In a genome wide search for AbrB and Abh binding sites more than 700 candidates (Chumsakul et al. 2010) could be determined in B. subtilis during the exponential growth. In addition, more than 50% of the recognized sites were located within coding regions without any effect on transcription indicating a possible role of AbrB and Abh in nucleoid organization according to the small basic H-NS proteins in E. coli (Dame et al. 2005). "
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