Modulation of extracytoplasmic function (ECF) sigma factor promoter selectivity by spacer region sequence

Gaballa, Ahmed; Guariglia-Oropeza, Veronica; Dürr, Franziska; Butcher, Bronwyn G.; Chen, Albert Y.; Chandrangsu, Pete; Helmann, John D.

doi:10.1093/nar/gkx953

Cited by 19 publications

(26 citation statements)

References 83 publications

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“…D). The linker regions of ECF sigma factors differ dramatically in both length and composition, and have been suggested to impact promoter recognition properties (Gaballa et al ). Thus, while the molecular details are not entirely clear, we hypothesized that these substitutions in RNAP core likely hinder binding of SigM to RNAP, and thereby reduce SigM activity.…”

Section: Resultsmentioning

confidence: 99%

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Zhao

Roistacher

Helmann

2019

Molecular Microbiology

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Bacteria use alternative sigma factors to adapt to different growth and stress conditions. The Bacillus subtilis extracytoplasmic function sigma factor SigM regulates genes for cell wall synthesis and is crucial for maintaining cell wall homeostasis under stress conditions. The activity of SigM is regulated by its anti-sigma factor, YhdL, and the accessory protein YhdK. Here, we show that dysregulation of SigM caused by the absence of either component of the anti-sigma factor complex leads to toxic levels of SigM and severe growth defects. High SigM activity results from a dysregulated positive feedback loop, and can be suppressed by overexpression of the housekeeping sigma, SigA. Using a sigM merodiploid strain, we selected for suppressor mutations that allow survival of yhdL depletion strain. The recovered suppressor mutations map to the beta and beta-prime subunits of RNA polymerase core enzyme and selectively reduce SigM activity, and in some cases increase the activity of other alternative sigma factors. This work highlights the ability of mutations in RNA polymerase that remodel the sigma-core interface to differentially affect sigma factor activity, and thereby alter the transcriptional landscape of the cell.

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Section: Resultsmentioning

confidence: 99%

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Zhao

Roistacher

Helmann

2019

Molecular Microbiology

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“…(2020) 10:5177 | https://doi.org/10.1038/s41598-020-62101-z www.nature.com/scientificreports www.nature.com/scientificreports/ when altered in one nucleotide, may affect the transcription 37 . Another example of this can be found in Bacillus subtilis, where transcription led by ECFs σ M , σ V , σ W and σ X is modulated by a T-stretch that affects the spatial conformation of the spacer region 38 . In a scenario in which these four ECFs regulate overlapping sets of genes, the properties conferred by the T-stretch aid in the promoter selectivity, although it is not the only feature that allows the promoter specificity in that case 39,40 .…”

Section: Scientific Reports |mentioning

confidence: 99%

Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA

Dios

Rivas-Marín

Santero

et al. 2020

Sci Rep

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two paralogous ecfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli tfA Rubén de Dios, elena Rivas-Marin, eduardo Santero & francisca Reyes-Ramírez *Under ever-changing environmental conditions, the General Stress Response (GSR) represents a lifesaver for bacteria in order to withstand hostile situations. in α-proteobacteria, the ecfG-type extracytoplasmic function (ecf) σ factors are the key activators of this response at the transcriptional level. in this work, we address the hierarchical function of the ecf σ factor paralogs EcfG1 and EcfG2 in triggering the GSR in Sphingopyxis granuli TFA and describe the role of EcfG2 as global switch of this response. In addition, we define a GSR regulon for TFA and use in vitro transcription analysis to study the relative contribution of each ecfG paralog to the expression of selected genes. We show that the features of each promoter ultimately dictate this contribution, though EcfG2 always produced more transcripts than EcfG1 regardless of the promoter. These first steps in the characterisation of the GSR in tfA suggest a tight regulation to orchestrate an adequate protective response in order to survive in conditions otherwise lethal.In an environment where conditions are constantly changing, bacteria need to adapt their physiology in order to increase their chances of survival. These adaptations are not only mediated by particular responses to certain stimuli, but also by global changes in the transcriptional profile. These changes allow bacteria to thrive in conditions that otherwise would be considered hostile habitats for them. Global transcriptional adaptations can be exerted by a number of mechanisms, all of them ending up in a regulator that allows or prevents the expression of certain genes 1 . One direct way to alter the transcription is the swapping of σ factors, small switchable subunits of the RNA polymerase (RNAP) whose main functions are the promoter recognition and the double strand unwinding to form the transcription bubble 2 . The general classification of σ factors comprises two main groups: the σ 70 and the σ 54 families.

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“…ECF30‐dependent promoters, which includes σ V , have a consensus sequence of ‐35 tgaAAC and ‐10 CGTC (Staroń et al , ). Recently, more detailed experimental analysis of the σ V regulon in B. subtilis identified σ V responsive and nonresponsive promoters (Gaballa et al , ). The key feature of the σ V responsive promoters was conservation of an extended run of tttt in the ‐35 region (tgaAACntttt) (Gaballa et al , ).…”

Section: σV Promoter Recognitionmentioning

confidence: 99%

Activation of the extracytoplasmic function σ factor σ^V by lysozyme

Ellermeier

2019

Molecular Microbiology

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σ V is an extracytoplasmic function (ECF) σ factor that is found exclusively in Firmicutes including Bacillus subtilis and the opportunistic pathogens Clostridioides difficile and Enterococcus faecalis. σ V is activated by lysozyme and is required for lysozyme resistance. The activity of σ V is normally inhibited by the anti-σ factor RsiV, a transmembrane protein. RsiV acts as a receptor for lysozyme. The binding of lysozyme to RsiV triggers a signal transduction cascade which results in degradation of RsiV and activation of σ V . Like the anti-σ factors for several other ECF σ factors, RsiV is degraded by a multistep proteolytic cascade that is regulated at the step of site-1 cleavage. Unlike other anti-σ factors, site-1 cleavage of RsiV is not dependent upon a site-1 protease whose activity is regulated. Instead constitutively active signal peptidase cleaves RsiV at site-1 in a lysozyme-dependent manner. The activation of σ V leads to the transcription of genes, which encode proteins required for lysozyme resistance. Extracytoplasmic function (ECF) σ factor backgroundECF σ factors belong to the σ 70 family of σ factors and contain only the σ 2 and σ 4.2 domains. These are homologous to the σ 70 σ 2 and σ 4.2 domains and are required for binding to the -35 and -10 regions of target promoters (Helmann, 2002;2016;Staroń et al., 2009). In addition, most ECF σ factors are required for their own expression. The activity of most ECF σ factors is inhibited by a cognate anti-σ factor which is often encoded within the σ factor operon. Many but not all anti-σ factors are membrane proteins (Staroń et al., 2009). The σ factor activity is induced by inhibiting the function of the anti-σ factor. Activation of the σ factor can occur by one of several mechanisms; a conformational change in the anti-σ factor releases the σ factor, an anti-anti-σ factor binds to the anti-σ factor inducing σ factor release, or destruction of the anti-σ factor via regulated intramembrane proteolysis (Ho and Ellermeier, 2012;Helmann, 2016). Here, we will focus on activation of ECF σ factors by degradation of the anti-σ factor. In the presence of an inducing signal, a site-1 protease cleaves the extracellular domain of an anti-σ factor. Following site-1 protease cleavage, the truncated anti-σ factor is cleaved by a site-2 protease within the transmembrane region of the anti-σ factor. The remainder of the anti-σ factor is then degraded by cytosolic proteases. This frees the σ factor to interact with RNA polymerase and transcribe target genes (Brown et al., 2000;Ho and Ellermeier, 2012;Helmann, 2016).The ECF σ factor σ V is found exclusively in Firmicutes or low GC Gram-positive bacteria and belongs to the ECF30 family of ECF σ factors (Staroń et al., 2009). The σ V system is encoded by the model organism Bacillus subtilis, as well as the opportunistic pathogens Enterococcus faecalis and Clostridioides difficile (Fig. 1). σ V is not present in all Firmicutes or even closely related species. While present in B. subtilis, σ V is not present in B. anthrac...

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Modulation of extracytoplasmic function (ECF) sigma factor promoter selectivity by spacer region sequence

Cited by 19 publications

References 83 publications

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA

Activation of the extracytoplasmic function σ factor σ^V by lysozyme

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Modulation of extracytoplasmic function (ECF) sigma factor promoter selectivity by spacer region sequence

Cited by 19 publications

References 83 publications

Deciphering the essentiality and function of the anti‐σM factors in Bacillus subtilis

Deciphering the essentiality and function of the anti‐σM factors in Bacillus subtilis

Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA

Activation of the extracytoplasmic function σ factor σV by lysozyme

Contact Info

Product

Resources

About

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Deciphering the essentiality and function of the anti‐σ^M factors in Bacillus subtilis

Activation of the extracytoplasmic function σ factor σ^V by lysozyme