Roles of hinge region, loops 3 and 4 in the activation of Escherichia coli cyclic AMP receptor protein

Gao, Zhengya; Li, Feng; Wu, Guangrong; Zhu, Yanrun; Yu, Ting; Yu, Shaoning

doi:10.1016/j.ijbiomac.2011.08.016

Cited by 5 publications

(2 citation statements)

References 26 publications

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“…This indicates that the OsdR regulon may be larger than anticipated, and some members of the regulon may be controlled by so-called class II binding sites, in other words, sites that do not conform to the predicted consensus sequence site. Similar duality has been shown for many other functionally diverse global regulatory networks in bacteria, including those controlled by LexA ( 62 ) and Crp ( 63 ) in E. coli , Spo0A in B. subtilis ( 64 ), CtrA in Caulobacter crescentus ( 65 ), and Crp ( 66 ), GlnR ( 67 ), PhoP ( 68 ), and DasR ( 69 ) in Streptomyces . For B. subtilis Spo0A, some 15% of the total binding sites were not bound in vitro ( 64 ).…”

Section: Discussionsupporting

confidence: 68%

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons

et al. 2016

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Dormancy is a state of growth cessation that allows bacteria to escape the host defense system and antibiotic challenge. Understanding the mechanisms that control dormancy is of key importance for the treatment of latent infections, such as those from Mycobacterium tuberculosis. In mycobacteria, dormancy is controlled by the response regulator DevR, which responds to conditions of hypoxia. Here, we show that OsdR of Streptomyces coelicolor recognizes the same regulatory element and controls a regulon that consists of genes involved in the control of stress and development. Only the core regulon in the direct vicinity of dosR and osdR is conserved between M. tuberculosis and S. coelicolor, respectively. Thus, we show how the system has diverged from allowing escape from the host defense system by mycobacteria to the control of sporulation by complex multicellular streptomycetes. This provides novel insights into how bacterial growth and development are coordinated with the environmental conditions.

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Section: Discussionsupporting

confidence: 68%

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons

et al. 2016

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“…Genome-wide analysis of the regulons of several other globally acting bacterial transcription factors show similar duality, with binding to both their cognate (consensus) target sequences and to non-canonical sites in vivo , even though the latter binding sites show no similarity to the consensus sequence and they are not bound in vitro . Other examples include LexA [ 60 ], Crp [ 61 ] and FNR [ 62 ] in E . coli , Spo0A in Bacillus subtilis [ 63 ], CtrA in Caulobacter crescentus [ 64 ] and notably also Crp [ 65 ], GlnR [ 66 ] and PhoP [ 67 ] in Streptomyces .…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets

et al. 2015

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Streptomycetes produce a wealth of natural products, including over half of all known antibiotics. It was previously demonstrated that N-acetylglucosamine and secondary metabolism are closely entwined in streptomycetes. Here we show that DNA recognition by the N-acetylglucosamine-responsive regulator DasR is growth-phase dependent, and that DasR can bind to sites in the S. coelicolor genome that have no obvious resemblance to previously identified DasR-responsive elements. Thus, the regulon of DasR extends well beyond what was previously predicted and includes a large number of genes with functions far removed from N-acetylglucosamine metabolism, such as genes for small RNAs and DNA transposases. Conversely, the DasR regulon during vegetative growth largely correlates to the presence of canonical DasR-responsive elements. The changes in DasR binding in vivo following N-acetylglucosamine induction were studied in detail and a possible molecular mechanism by which the influence of DasR is extended is discussed. Discussion of DasR binding was further informed by a parallel transcriptome analysis of the respective cultures. Evidence is provided that DasR binds directly to the promoters of all genes encoding pathway-specific regulators of antibiotic production in S. coelicolor, thereby providing an exquisitely simple link between nutritional control and secondary metabolism.

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Overestimated accuracy of circular dichroism in determining protein secondary structure

et al. 2013

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Circular dichroism (CD) is a spectroscopic technique widely used for estimating protein secondary structures in aqueous solution, but its accuracy has been doubted in recent work. In the present paper, the contents of nine globular proteins with known secondary structures were determined by CD spectroscopy and Fourier transform infrared spectroscopy (FTIR) in aqueous solution. A large deviation was found between the CD spectra and X-ray data, even when the experimental conditions were optimized. The content determined by FTIR was in good agreement with the X-ray crystallography data. Therefore, CD spectra are not recommended for directly calculating the content of a protein's secondary structure.

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Roles of hinge region, loops 3 and 4 in the activation of Escherichia coli cyclic AMP receptor protein

Cited by 5 publications

References 26 publications

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons

Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets

Overestimated accuracy of circular dichroism in determining protein secondary structure

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