Article

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.

Download full-text

Full-text

Available from: Shigehiko Kanaya, Aug 20, 2015
0 Followers
 · 
153 Views
  • Source
    • "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]. "
    [Show abstract] [Hide abstract]
    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 · 2.93 Impact Factor
  • Source
    • "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 , "
    [Show abstract] [Hide abstract]
    ABSTRACT: The members of the genus Clostridium, including the spore-forming anaerobic bacteria, have a complex and strictly regulated life cycle, but very little is known about the genetic pathways involved in the different stages of their life cycle. Clostridium sporogenes, a Gram-positive bacterium usually involved in food spoilage and frequently isolated from late blowing cheese, is genetically indistinguishable from the proteolytic Clostridium botulinum. As the non-neurotoxic counterpart, it is often used as an exemplar for the toxic subtypes. In this work, we performed a microscopic study combined with a custom array-based analysis of the C. sporogenes cycle, from dormant spores to the early stationary phase. We identified a total of 211 transcripts in spores, validating the hypothesis that mRNAs are abundant in spores and the pattern of mRNA expression is strikingly different from that present in growing cells. The spore transcripts included genes responsible for different life-sustaining functions, suggesting there was transcript entrapment or basic poly-functional gene activation for future steps. In addition, 3 h after the beginning of the germination process, 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appeared to be more active in terms of gene transcription and protein synthesis than the spore, and genes coding for germination and sporulation factors seemed to be expressed at this point. These results suggest that spores are not silent entities, and a broader knowledge of the genetic pathways involved in the Clostridium life cycle could provide a better understanding of pathogenic clostridia types.
    Food Microbiology 02/2013; 33(1):11-23. DOI:10.1016/j.fm.2012.08.004 · 3.37 Impact Factor
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    ABSTRACT: AbrB is a global regulator of transition state that is known to repress more than 100 genes in Bacillus species. Although AbrB is involved in the regulation of most cellular processes, a conserved binding motif seems to be elusive. Thus, the mechanism of AbrB-mediated transcriptional control is still unclear. In our previous work we identified two separate AbrB-binding sites within phytase gene region (phyC) of Bacillus amyloliquefaciens FZB45, whose integrity is essential for repression. Comparable architecture of AbrB-binding sites is also described for tycA that encodes an antibiotic synthesis enzyme. Considering the size of the AbrB tetramer (56 kDa) and other AbrB binding motifs (~20 to 98 bp) we hypothesized preferred binding positions within both AbrB sites of phyC that exhibit higher affinities to AbrB. Thus, we used surface plasmon resonance (SPR) to study the binding kinetics between AbrB and 40-bp ds-oligonucleotides that were derived from both binding sites. Surface plasmon resonance sensorgrams revealed strong binding kinetics that showed nearly no dissociation and positive cooperativity of the AbrB-DNA interaction to the whole AbrB-binding site 2 and to a small part of AbrB-binding site 1. Using chemically modified DNA we found bases contacting AbrB mainly at one face of the DNA-helix within a core region separated by one helical turn each. High content of modified guanines presented in the control reaction of the KMnO(4) interference assay indicated distortion of the DNA-structure of phyC. In vitro transcription assays and base substitutions within the core region support this idea and the cooperativity of AbrB binding.
    MGG Molecular & General Genetics 12/2011; 287(2):111-22. DOI:10.1007/s00438-011-0666-4 · 2.83 Impact Factor
Show more