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


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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    • "AbrB binds a number of DNA target sequences with the common feature of being structurally flexible and undergoing a conformational change upon TR binding (Bobay et al., 2004). AbrB acts as a global TR (Chumsakul et al., 2011), regulating the expression of stationary-phase functions. Recently, AbrB was reported to be phosphorylated at residue Ser86 in a phosphoproteomics study (Soufi et al., 2010). "
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    ABSTRACT: Reversible phosphorylation of bacterial transcriptional regulators belonging to the family of two-component systems is a well-established mechanism for regulating gene expression. Recent evidence points to the fact that reversible phosphorylation of bacterial transcriptional regulators on other types of residues, namely serine, threonine, tyrosine and cysteine, is also quite common. The phosphorylation of the ester type (phospho-serine/threonine/tyrosine) is more stable than the aspartate phosphorylation of two-component systems. The kinases which catalyze these phosphorylation events (Hanks-type serine/threonine-protein kinases and bacterial protein-tyrosine kinases) are also much more promiscuous than the two-component system kinases, i.e. each of them can phosphorylate several substrate proteins. By consequence, the dynamics and the topology of the signal transduction networks depending on these kinases differ significantly from the two component systems. Here we present an overview of different classes of bacterial transcriptional regulators phosphorylated and regulated by serine/threonine- and tyrosine-kinases. Particular attention is given to examples when serine/threonine- and tyrosine-kinases interact with two component systems, phosphorylating either the histidine kinases or the response regulators. We argue that these promiscuous kinases connect several signal transduction pathways, and serve the role of signal integration.
    Microbiology 07/2015; 161(9). DOI:10.1099/mic.0.000148 · 2.56 Impact Factor
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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.
    International Journal of Hydrogen Energy 09/2013; 38:13547-13555. DOI:10.1016/j.ijhydene.2013.07.124 · 3.31 Impact Factor
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    • "Specifically, we clearly demonstrate here that the consensus sequence for the high-affinity AbrB binding is comprised of bipartite TGGNA motifs gapped by a 4- or 5-bp AT-rich sequence arranged in direct, reverse direct, inverted, and everted repeat orientations. This result is consistent with a previous in vitro SELEX study,17 and our informatics analysis showing that various bipartite motifs are enriched in AbrB-binding regions determined by ChIP-chip.14 Thus, the GeF-seq results reported here show, for the first time, the highly flexible proposed consensus sequences, which are actually recognized by AbrB molecules in in vivo. "
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    ABSTRACT: Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-throughput sequencing (GeF-seq), which combines in vivo DNase I digestion of genomic DNA with ChIP coupled with high-throughput sequencing. We have determined the in vivo binding sites of a Bacillus subtilis global regulator, AbrB, using GeF-seq. This method shows that exact DNA-binding sequences, which were protected from in vivo DNase I digestion, were resolved at a comparable resolution to that achieved by in vitro DNase I footprinting, and this was simply attained without the necessity of prediction by peak-calling programs. Moreover, DNase I digestion of the bacterial nucleoid resolved the closely positioned AbrB-binding sites, which had previously appeared as one peak in ChAP-chip and ChAP-seq experiments. The high-resolution determination of AbrB-binding sites using GeF-seq enabled us to identify bipartite TGGNA motifs in 96% of the AbrB-binding sites. Interestingly, in a thousand binding sites with very low-binding intensities, single TGGNA motifs were also identified. Thus, GeF-seq is a powerful method to elucidate the molecular mechanism of target protein binding to its cognate DNA sequences.
    DNA Research 04/2013; 20(4). DOI:10.1093/dnares/dst013 · 5.48 Impact Factor
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