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Leite JP, Lourenço F, Oliveira R, Sousa SF, Mendes MV, Gales L. Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG. J Struct Biol 2023; 215:108038. [PMID: 37858875 DOI: 10.1016/j.jsb.2023.108038] [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] [Received: 08/03/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Transcription of specific genes in bacteria under environmental stress is frequently initiated by extracytoplasmic function (ECF) σ factors. ECFs σ factors harbour two conserved domains, σ2 and σ4, for transcription initiation by recognition of the promoter region and recruitment of RNA polymerase (RNAP). The crystal structure of Streptomyces tsukubaensis SigG1, an ECF56-family σ factor, was determined revealing σ2, σ4 and the additional carboxi-terminal domain SnoaL_2 tightly packed in a compact conformation. The structure of anti-sigma RsfG was also determined by X-ray crystallography and shows a rare β-barrel fold. Analysis of the metal binding motifs inside the protein barrel are consistent with Fe(III) binding, which is in agreement with previous findings that the Streptomyces tsukubaensis ECF56 SigG1-RsfG system is involved in metal-ion homeostasis.
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Affiliation(s)
- José P Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, Porto, Porto 4050-313, Portugal
| | - Frederico Lourenço
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal
| | - Rute Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, Porto, Porto 4050-313, Portugal
| | - Sérgio F Sousa
- UCIBIO/REQUIMTE, BioSIM, Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto 4200-319, Portugal
| | - Marta V Mendes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal
| | - Luís Gales
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, Porto, Porto 4050-313, Portugal.
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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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Pleiotropic effects of ActVI-ORFA as an unusual regulatory factor identified in the biosynthetic pathway of actinorhodin in Streptomyces coelicolor. Microbiol Res 2021; 250:126792. [PMID: 34082307 DOI: 10.1016/j.micres.2021.126792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/22/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022]
Abstract
Regulatory networks play critical roles in controlling the the biosynthesis of natural products in Streptomyces. ActVI-ORFA, a regulatory factor encoded by the actinorhodin biosynthetic gene cluster (act cluster), positively controls the production of actinorhodin (ACT) in Streptomyces coelicolor, although its regulatory mechanism remains obscure. This study aimed to identify the regulatory targets of ActVI-ORFA. Deletion of ActVI-ORFA caused the differential expression of hundreds of proteins, as determined by two-dimensional electrophoresis and peptide mass fingerprinting analysis. qRT-PCR analysis of some genes encoding these differentially expressed proteins, including act genes and non-act genes, confirmed that ActVI-ORFA could control their transcriptional levels. In an electrophoretic mobility shift assay with a promoter region of a target gene located in the act cluster, no binding was detected, consistent with the lack of a recognizable DNA-binding domain in ActVI-ORFA. Overall, our findings suggest that ActVI-ORFA is a pleiotropic regulatory factor that controls multiple physiological pathways, including secondary metabolite production, probably via an indirect mode.
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