Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor

Xu, Jingui; Cui, Kaijie; Shen, Liqiang; Shi, Jing; Li, Lingting; You, Linlin; Fang, Chengli; Zhao, Guoping; Feng, Yu; Yang, Bei; Zhang, Yu

doi:10.7554/elife.50928

Cited by 25 publications

(26 citation statements)

References 65 publications

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“…Considering that Mtsp17 is a lipid-binding protein and lack of DNA-binding domain, this transcriptional regulator may work in a DNA-contact independent way by protein-protein interactions. Such mechanism has been utilized by Crl in E. coli, which activates transcription by interacting with sigma factor [24]. More investigations are needed to explore the potential interacting protein of Mtsp17 to complete the transcriptional regulatory network of Mtsp17.…”

Section: Discussionmentioning

confidence: 99%

Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation

Zhou

Zhong

Wei³

et al. 2020

Preprint

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Background Tuberculosis caused by the pathogen Mycobacterium tuberculosis (MTB), remains a significant threat to global health. Elucidating the mechanism of essential MTB genes will provide a theoretical basis for drug exploitation. Gene mtsp17 is essential and conserved in the Mycobacterium genus. Although the structure of Mtsp17 exhibits as a typical steroidogenic acute regulatory protein-related lipid transfer (START) family protein, its biological function is different from other START proteins. This study characterized the transcriptomes of Mycobacterium smegmatis to address the problem how suppressing mtsp17 reduces bacterial growth rate. Results 3% down- and 1% up-regulated protein-coding genes were significantly differentiated expressed by suppressing mtsp17 gene. Among them, desA1, an essential gene involved in mycolic acid synthesis, was found to be significantly depressed (3.1-fold). Further analyses showed that mstp17 can activate desA1 to regulate the bacterial growth. In addition, the anti-anti-SigF gene was dramatically decreased (8.9-fold) and 70 of the 79 differentially expressed genes showed the same change trends in the SigF knockout strain. The data indicate that Mtsp17 regulates SigF regulon by modulating mRNA abundance of the anti-sigma factor antagonist. Conclusions Our findings discover the role of Mtsp17 in transcriptional regulation that was unknown before, which provides new insights into the molecular mechanisms of START family and introduces a new node to the regulatory network of mycobacteria.

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Section: Discussionmentioning

confidence: 99%

Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation

Zhou

Zhong

Wei³

et al. 2020

Preprint

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“…As observed for RbpA, Crl facilitates transcription initiation by stabilizing the σ S -RNAP holoenzyme and stimulating RPo formation (Banta et al, 2013;Xu et al, 2019). Two high resolution cryo-EM-based structures of Crl-σ S -RNAP RPo have been recently described (Cartagena et al, 2019;Xu et al, 2019). Cartagena et al, suggested that Crl stabilizes σ S -RNAP by tethering σ S directly to RNAP though contacts with the β -clamp-toe domain (β -CT, residues 144-179).…”

Section: Crlmentioning

confidence: 96%

“…Although Crl does not bind to σ 70 because of the steric clash with σ 70 -NCR (Cartagena et al, 2019) it can activate σ 70 -dependent transcription (Gaal et al, 2006). As observed for RbpA, Crl facilitates transcription initiation by stabilizing the σ S -RNAP holoenzyme and stimulating RPo formation (Banta et al, 2013;Xu et al, 2019). Two high resolution cryo-EM-based structures of Crl-σ S -RNAP RPo have been recently described (Cartagena et al, 2019;Xu et al, 2019).…”

Section: Crlmentioning

confidence: 98%

“…Cartagena et al, suggested that Crl stabilizes σ S -RNAP by tethering σ S directly to RNAP though contacts with the β -clamp-toe domain (β -CT, residues 144-179). Based on structure and hydrogen-deuterium exchange mass spectrometry analysis of σ S conformation, Xu et al (2019) suggested that Crl acts as a chaperone that facilitates the σ S -RNAP holoenzyme assembly mainly by modifying σ2 conformation, but not through its contacts with the β -clamp. In addition, interaction of Crl residue R51 with residues D135 and E137 in the "specificity loop" of region 2.3 of σ ( Figure 1C) stabilizes its optimal conformation for binding to the −10 element ssDNA.…”

Section: Crlmentioning

confidence: 99%

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The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation

Vishwakarma

Brodolin

2020

Front. Microbiol.

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Transcription initiation is a key checkpoint and highly regulated step of gene expression. The sigma (σ) subunit of RNA polymerase (RNAP) controls all transcription initiation steps, from recognition of the −10/−35 promoter elements, upon formation of the closed promoter complex (RPc), to stabilization of the open promoter complex (RPo) and stimulation of the primary steps in RNA synthesis. The canonical mechanism to regulate σ activity upon transcription initiation relies on activators that recognize specific DNA motifs and recruit RNAP to promoters. This mini-review describes an emerging group of transcriptional regulators that form a complex with σ or/and RNAP prior to promoter binding, remodel the σ subunit conformation, and thus modify RNAP activity. Such strategy is widely used by bacteriophages to appropriate the host RNAP. Recent findings on RNAP-binding protein A (RbpA) from Mycobacterium tuberculosis and Crl from Escherichia coli suggest that activator-driven changes in σ conformation can be a widespread regulatory mechanism in bacteria.

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“…25 Essentially, this observation was consistent with the structure and function of E. coli RpoD: the regions 1 and 2 were responsible for the binding of the RNAP holoenzyme to the typical promoter sequence-10 region, and for forming an open complex favoring initiation and elongation of transcription. 33,34 Designing artificial TFs Compared with the approach of finding the desired TFs from a mutant library generated by random mutagenesis, the advantages of designing TFs are obvious: evaluating the performance of the designed TFs does not depend on the availability of an HTS method. A satisfactory synthetic bacterial TF should be orthogonal to the endogenous promoters of the host's to ensure minimal off-target effects, and the TF should also be friendly to activity re-programming for a wide range of user-specified translation start sites.…”

Section: Employing Compatible Heterogeneous Tfsmentioning

confidence: 99%

Transcriptional factor engineering in microbes for industrial biotechnology

Wang

Liang

Xing

et al. 2020

J of Chemical Tech & Biotech

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Transcription can be regulated by controlling the provision of transcriptional factors (TFs), because TFs determine the transcription process by specifying the binding of RNA polymerase holoenzyme on promoters. Manipulations, such as replacing endogenous TFs with mutants obtained through directed evolution (or rational design), and introducing compatible heterogeneous TFs, are effective ways to regulate transcription. Designing artificial TFs with desired properties by following the principles of protein design and reconstructing ancestral TFs with the information gained from a perspective of evolution by multiple sequence alignments of the related TFs, are feasible alternative options. The engineered TFs can be used to create inducible protein expression systems that respond to a specific stimulus. Moreover, the engineered TFs could lead to a transcriptional profile different from that of the wild-type strains. Accordingly, these engineered TFs could be utilized to construct strains resistant to adverse conditions, since the emergence of resistance generally requires global transcriptional changes at the transcriptomic scale. Meanwhile, these engineered TFs can also be employed in the construction of sophisticatedly designed genetic circuits for diverse purposes. In this paper, we reviewed the advances in the above-mentioned aspects.

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Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor

Cited by 25 publications

References 65 publications

Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation

Discovery of a role for the single START-domain protein Mtsp17 in transcriptional regulation

The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation

Transcriptional factor engineering in microbes for industrial biotechnology

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