Characterization of a protein–protein interaction within the SigO–RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO

Xue, Xiaowei; Davis, Maria C.; Steeves, Thomas; Bishop, A. R.; Breen, Jillian; MacEacheron, Allison; Kesthely, Christopher A.; Hsu, FoSheng; MacLellan, Shawn R.

doi:10.1099/mic.0.000358

Cited by 6 publications

(6 citation statements)

References 45 publications

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“…Crl stimulates S -dependent transcription at least in part by interacting with S and promoting its assembly into holoenzyme (Banta et al 2013(Banta et al , 2014. RsoA, which possesses some sequence similarity to , interacts with the amino terminus of the ECF-like factor SigO and displays weak interaction activity with the clamp helices region of the RNAP ␤= subunit (MacLellan et al 2009;Xue et al 2016). The mechanism of RsoA action is not currently known, but it is co-required along with SigO for transcription from target promoters in vivo (MacLellan et al 2008), and for open-complex formation in vitro (MacLellan et al 2009).…”

Section: (Ii) Factor Interaction With Transcription Factorsmentioning

confidence: 99%

The essential activities of the bacterial sigma factor

et al. 2017

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Abstract:Transcription is the first and most heavily regulated step in gene expression. Sigma () factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the 70 family of proteins and the essential roles they play in the transcription process.Key words: transcription, bacteria, RNA polymerase, sigma factor, gene expression.

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Section: (Ii) Factor Interaction With Transcription Factorsmentioning

confidence: 99%

The essential activities of the bacterial sigma factor

et al. 2017

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“…Therefore, to generate such a system, we exploited the B. subtilis two-subunit sigma factor system SigO-RsoA. Various studies have demonstrated that both SigO and RsoA, which constitute domains σ 4 and σ 2 of the sigma factor, respectively, must cooperate to initiate transcription from the promoter P oxdC . , This system thus effectively acts as a natural biological AND gate, which should be amenable for engineering such regulatory logic in synthetic circuits. To facilitate fast assembly of the AND gate, we generated a series of new plasmids termed SANDBOX ( Subtilis AND BOX) based on the Golden Gate assembly format using the type II restriction enzyme Bsa I.…”

Section: Results and Discussionmentioning

confidence: 99%

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis

2023

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Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.

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“…The strategy to follow could be similar to work made on ECF43, the group of VP0055 from Vibrio parahaemolyticus , which was expanded from the 69 non-redundant proteins identified in this work, to more than 900 members of ECF43 ( 20 ). Likewise, a similar approach could be used to identify and expand knowledge around bacterial ECF factors with split domains, such as B. subtilis SigO-RsoA, which contain the σ 2 and σ 4 domains in two separate polypeptides ( 58 , 59 ).…”

Section: Discussionmentioning

confidence: 99%

Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

Casas-Pastor

Müller

Jaenicke

et al. 2021

Nucleic Acids Research

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Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As a result, we identified an average of ∼10 ECFs per bacterial genome and 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands previous classification efforts ∼50-fold, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences and an openly accessible data repository called ‘ECF Hub’ (https://www.computational.bio.uni-giessen.de/ecfhub), will serve as a powerful hypothesis-generator to guide future research in the field.

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Characterization of a protein–protein interaction within the SigO–RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO

Cited by 6 publications

References 45 publications

The essential activities of the bacterial sigma factor

The essential activities of the bacterial sigma factor

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis

Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

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