1
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Mascher T. Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction. Annu Rev Microbiol 2023; 77:625-644. [PMID: 37437215 DOI: 10.1146/annurev-micro-032221-024032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Responding to environmental cues is a prerequisite for survival in the microbial world. Extracytoplasmic function σ factors (ECFs) represent the third most abundant and by far the most diverse type of bacterial signal transduction. While archetypal ECFs are controlled by cognate anti-σ factors, comprehensive comparative genomics efforts have revealed a much higher abundance and regulatory diversity of ECF regulation than previously appreciated. They have also uncovered a diverse range of anti-σ factor-independent modes of controlling ECF activity, including fused regulatory domains and phosphorylation-dependent mechanisms. While our understanding of ECF diversity is comprehensive for well-represented and heavily studied bacterial phyla-such as Proteobacteria, Firmicutes, and Actinobacteria (phylum Actinomycetota)-our current knowledge about ECF-dependent signaling in the vast majority of underrepresented phyla is still far from complete. In particular, the dramatic extension of bacterial diversity in the course of metagenomic studies represents both a new challenge and an opportunity in expanding the world of ECF-dependent signal transduction.
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Affiliation(s)
- Thorsten Mascher
- General Microbiology, Technische Universität Dresden, Dresden, Germany;
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2
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Marcos-Torres FJ, Moraleda-Muñoz A, Contreras-Moreno FJ, Muñoz-Dorado J, Pérez J. Mechanisms of Action of Non-Canonical ECF Sigma Factors. Int J Mol Sci 2022; 23:ijms23073601. [PMID: 35408957 PMCID: PMC8999054 DOI: 10.3390/ijms23073601] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are subunits of the RNA polymerase specialized in activating the transcription of a subset of genes responding to a specific environmental condition. The signal-transduction pathways where they participate can be activated by diverse mechanisms. The most common mechanism involves the action of a membrane-bound anti-sigma factor, which sequesters the ECF sigma factor, and releases it after the stimulus is sensed. However, despite most of these systems following this canonical regulation, there are many ECF sigma factors exhibiting a non-canonical regulatory mechanism. In this review, we aim to provide an updated and comprehensive view of the different activation mechanisms known for non-canonical ECF sigma factors, detailing their inclusion to the different phylogenetic groups and describing the mechanisms of regulation of some of their representative members such as EcfG from Rhodobacter sphaeroides, showing a partner-switch mechanism; EcfP from Vibrio parahaemolyticus, with a phosphorylation-dependent mechanism; or CorE from Myxococcus xanthus, regulated by a metal-sensing C-terminal extension.
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Affiliation(s)
| | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda, Fuentenueva s/n, 18071 Granada, Spain; (F.J.C.-M.); (J.M.-D.)
- Correspondence: (A.M.-M.); (J.P.); Tel.: +34-95-824-2858 (A.M.-M.); +34-95-824-9830 (J.P.)
| | - Francisco Javier Contreras-Moreno
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda, Fuentenueva s/n, 18071 Granada, Spain; (F.J.C.-M.); (J.M.-D.)
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda, Fuentenueva s/n, 18071 Granada, Spain; (F.J.C.-M.); (J.M.-D.)
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda, Fuentenueva s/n, 18071 Granada, Spain; (F.J.C.-M.); (J.M.-D.)
- Correspondence: (A.M.-M.); (J.P.); Tel.: +34-95-824-2858 (A.M.-M.); +34-95-824-9830 (J.P.)
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3
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Butt AT, Banyard CD, Haldipurkar SS, Agnoli K, Mohsin M, Vitovski S, Paleja A, Tang Y, Lomax R, Ye F, Green J, Thomas M. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3709-3726. [PMID: 35234897 PMCID: PMC9023288 DOI: 10.1093/nar/gkac137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board ‘anti-σ factor’ in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.
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Affiliation(s)
- Aaron T Butt
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Christopher D Banyard
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Sayali S Haldipurkar
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Kirsty Agnoli
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Muslim I Mohsin
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Srdjan Vitovski
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Ameya Paleja
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Yingzhi Tang
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Rebecca Lomax
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield S10 2RX, UK
| | - Fuzhou Ye
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Jeffrey Green
- Correspondence may also be addressed to Jeffrey Green. Tel: +44 114 222 4403; Fax: +44 114 222 2800;
| | - Mark S Thomas
- To whom correspondence should be addressed. Tel: +44 114 215 9557; Fax: +44 114 271 1863;
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4
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de Dios R, Santero E, Reyes-Ramírez F. Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. Int J Mol Sci 2021; 22:ijms22083900. [PMID: 33918849 PMCID: PMC8103513 DOI: 10.3390/ijms22083900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/03/2023] Open
Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
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5
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Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res 2021; 49:986-1005. [PMID: 33398323 PMCID: PMC7826278 DOI: 10.1093/nar/gkaa1229] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
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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Affiliation(s)
- Delia Casas-Pastor
- Center for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Germany
| | - Raphael R Müller
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Sebastian Jaenicke
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Karina Brinkrolf
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Germany
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Georg Fritz
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
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6
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Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA. Rewiring the specificity of extracytoplasmic function sigma factors. Proc Natl Acad Sci U S A 2020; 117:33496-33506. [PMID: 33318184 PMCID: PMC7776599 DOI: 10.1073/pnas.2020204117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Kevin S Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Hao Li
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Timothy J Donohue
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158
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7
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Oliveira R, Bush MJ, Pires S, Chandra G, Casas-Pastor D, Fritz G, Mendes MV. The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis. Sci Rep 2020; 10:21728. [PMID: 33303917 PMCID: PMC7730460 DOI: 10.1038/s41598-020-78520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2-σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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Affiliation(s)
- Rute Oliveira
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCBiology), ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sílvia Pires
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delia Casas-Pastor
- Center for Synthetic Microbiology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Georg Fritz
- School for Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Marta V Mendes
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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8
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Pinto D, da Fonseca RR. Evolution of the extracytoplasmic function σ factor protein family. NAR Genom Bioinform 2020; 2:lqz026. [PMID: 33575573 PMCID: PMC7671368 DOI: 10.1093/nargab/lqz026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/04/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022] Open
Abstract
Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF σ factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF σ factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF σ factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated σ factor. At last, we also demonstrate horizontal transfer of ECF σ factors between soil bacteria.
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Affiliation(s)
- Daniela Pinto
- Technische Universität Dresden, Institute of Microbiology, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
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9
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Otero-Asman JR, Wettstadt S, Bernal P, Llamas MA. Diversity of extracytoplasmic function sigma (σ ECF ) factor-dependent signaling in Pseudomonas. Mol Microbiol 2019; 112:356-373. [PMID: 31206859 DOI: 10.1111/mmi.14331] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/23/2022]
Abstract
Pseudomonas bacteria are widespread and are found in soil and water, as well as pathogens of both plants and animals. The ability of Pseudomonas to colonize many different environments is facilitated by the multiple signaling systems these bacteria contain that allow Pseudomonas to adapt to changing circumstances by generating specific responses. Among others, signaling through extracytoplasmic function σ (σECF ) factors is extensively present in Pseudomonas. σECF factors trigger expression of functions required under particular conditions in response to specific signals. This manuscript reviews the phylogeny and biological roles of σECF factors in Pseudomonas, and highlights the diversity of σECF -signaling pathways of this genus in terms of function and activation. We show that Pseudomonas σECF factors belong to 16 different phylogenetic groups. Most of them are included within the iron starvation group and are mainly involved in iron acquisition. The second most abundant group is formed by RpoE-like σECF factors, which regulate the responses to cell envelope stress. Other groups controlling solvent tolerance, biofilm formation and the response to oxidative stress, among other functions, are present in lower frequency. The role of σECF factors in the virulence of Pseudomonas pathogenic species is described.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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10
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Szurmant H. Evolutionary couplings of amino acid residues reveal structure and function of bacterial signaling proteins. Mol Microbiol 2019; 112:432-437. [PMID: 31102561 DOI: 10.1111/mmi.14282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
The genomic era along with major advances in high-throughput sequencing technology has led to a rapid expansion of the genomic and consequently the protein sequence space. Bacterial extracytoplasmic function sigma factors have emerged as an important group of signaling proteins in bacteria involved in many regulatory decisions, most notably the adaptation to cell envelope stress. Their wide prevalence and amplification among bacterial genomes has led to sub-group classification and the realization of diverse signaling mechanisms. Mathematical frameworks have been developed to utilize extensive protein sequence alignments to extract co-evolutionary signals of interaction. This has proven useful in a number of different biological fields, including de novo structure prediction, protein-protein partner identification and the elucidation of alternative protein conformations for signal proteins, to name a few. The mathematical tools, commonly referred to under the name 'Direct Coupling Analysis' have now been applied to deduce molecular mechanisms of activation for sub-groups of extracytoplasmic sigma factors adding to previous successes on bacterial two-component signaling proteins. The amplification of signal transduction protein genes in bacterial genomes made them the first to be amenable to this approach but the sequences are available now to aid the molecular microbiologist, no matter their protein pathway of interest.
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Affiliation(s)
- Hendrik Szurmant
- Basic Medical Science, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
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11
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Pinto D, Liu Q, Mascher T. ECF σ factors with regulatory extensions: the one-component systems of the σ universe. Mol Microbiol 2019; 112:399-409. [PMID: 31175685 DOI: 10.1111/mmi.14323] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2019] [Indexed: 12/18/2022]
Abstract
The σ subunit of the bacterial RNA polymerase determines promoter specificity. The extracytoplasmic function σ factors (ECFs) represent the most abundant and diverse group of alternative σ factors and are present in the vast majority of bacterial genomes. Typically, ECFs are regulated by anti-σ factors that sequester their cognate ECFs, thereby preventing their interaction with the RNA polymerase. Beyond these ECF paradigms, a number of distinct modes of regulation have been proposed and experimentally investigated. Regulatory extensions represent one such alternative mechanism of ECF regulation that can be found in 18 phylogenetically distinct ECF groups. Here, the σ factors contain additional domains that are fused to the ECF core domains and are involved in stimulus perception and modulation of σ factor activity. We will summarize the current state of knowledge on regulating ECF activity by C-terminal extensions. We will also discuss newly identified ECF groups containing either N- or C-terminal extensions and propose possible mechanisms by which these extensions have been generated and affect ECF σ factor activity. Based on their modular architecture and the resulting physical connection between stimulus perception and transcriptional output, these ECFs are analogous to one-component systems, the primary mechanism of bacterial signal transduction.
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Affiliation(s)
- Daniela Pinto
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217, Dresden, Germany
| | - Qiang Liu
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217, Dresden, Germany.,Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217, Dresden, Germany
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12
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Wu H, Liu Q, Casas-Pastor D, Dürr F, Mascher T, Fritz G. The role of C-terminal extensions in controlling ECF σ factor activity in the widely conserved groups ECF41 and ECF42. Mol Microbiol 2019; 112:498-514. [PMID: 30990934 DOI: 10.1111/mmi.14261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2019] [Indexed: 01/01/2023]
Abstract
The activity of extracytoplasmic function σ-factors (ECFs) is typically regulated by anti-σ factors. In a number of highly abundant ECF groups, including ECF41 and ECF42, σ-factors contain fused C-terminal protein domains, which provide the necessary regulatory function instead. Here, we identified the contact interface between the C-terminal extension and the core σ-factor regions required for controlling ECF activity. We applied direct coupling analysis (DCA) to infer evolutionary covariation between contacting amino acid residues for groups ECF41 and ECF42. Mapping the predicted interactions to a recently solved ECF41 structure demonstrated that DCA faithfully identified an important contact interface between the SnoaL-like extension and the linker between the σ2 and σ4 domains. Systematic alanine substitutions of contacting residues support this model and suggest that this interface stabilizes a compact conformation of ECF41 with low transcriptional activity. For group ECF42, DCA supports a structural homology model for their C-terminal tetratricopeptide repeat (TPR) domains and predicts an intimate contact between the first TPR-helix and the σ4 domain. Mutational analyses demonstrate the essentiality of the predicted interactions for ECF42 activity. These results indicate that C-terminal extensions indeed bind and regulate the core ECF regions, illustrating the potential of DCA for discovering regulatory motifs in the ECF subfamily.
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Affiliation(s)
- Hao Wu
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Qiang Liu
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany.,Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Delia Casas-Pastor
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Franziska Dürr
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062, Dresden, Germany
| | - Georg Fritz
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Marburg, Germany
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