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Avramova MM, Stevenson CEM, Chandra G, Holmes NA, Bush MJ, Findlay KC, Buttner MJ. Global Effects of the Developmental Regulator BldB in Streptomyces venezuelae. J Bacteriol 2023; 205:e0013523. [PMID: 37249447 PMCID: PMC10294661 DOI: 10.1128/jb.00135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
In Streptomyces, the Bld (Bald) regulators control formation of the reproductive aerial hyphae. The functions of some of these regulators have been well characterized, but BldB has remained enigmatic. In addition to the bldB gene itself, Streptomyces venezuelae has 10 paralogs of bldB that sit next to paralogs of whiJ and abaA. Transcriptome sequencing (RNA-seq) revealed that loss of BldB function causes the dramatic transcriptional upregulation of the abaA paralogs and a novel inhibitor of sporulation, iosA, and that cooverexpression of just two of these genes, iosA and abaA6, was sufficient to recapitulate the bldB mutant phenotype. Further RNA-seq analysis showed that the transcription factor WhiJ9 is required for the activation of iosA seen in the bldB mutant, and biochemical studies showed that WhiJ9 mediates the activation of iosA expression by binding to direct repeats in the iosA-whiJ9 intergenic region. BldB and BldB9 hetero-oligomerize, providing a potential link between BldB and the iosA-whiJ9-bldB9 locus. This work greatly expands our overall understanding of the global effects of the BldB developmental regulator. IMPORTANCE To reproduce and disperse, the filamentous bacterium Streptomyces develops specialized reproductive structures called aerial hyphae. The formation of these structures is controlled by the bld (bald) genes, many of which encode transcription factors whose functions have been characterized. An exception is BldB, a protein whose biochemical function is unknown. In this study, we gain insight into the global effects of BldB function by examining the genome-wide transcriptional effects of deleting bldB. We identify a small set of genes that are dramatically upregulated in the absence of BldB. We show that their overexpression causes the bldB phenotype and characterize a transcription factor that mediates the upregulation of one of these target genes. Our results provide new insight into how BldB influences Streptomyces development.
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Affiliation(s)
- Marieta M. Avramova
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Clare E. M. Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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2
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Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Proc Natl Acad Sci U S A 2023; 120:e2220785120. [PMID: 36888660 PMCID: PMC10243135 DOI: 10.1073/pnas.2220785120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023] Open
Abstract
Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae (Sven), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of σA (σA4) of the σA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σA4 housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Finally, we compare the architecture of the WhiA/B σA-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.
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Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Alexandra K. Marti
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - David A. Widdick
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, UK
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Steven Koh
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
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3
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Gomez-Escribano JP, Holmes NA, Schlimpert S, Bibb MJ, Chandra G, Wilkinson B, Buttner MJ, Bibb MJ. Streptomyces venezuelae NRRL B-65442: genome sequence of a model strain used to study morphological differentiation in filamentous actinobacteria. J Ind Microbiol Biotechnol 2021; 48:6294913. [PMID: 34100946 PMCID: PMC8788739 DOI: 10.1093/jimb/kuab035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
For over a decade, Streptomyces venezuelae has been used to study the molecular mechanisms that control morphological development in streptomycetes and it is now a well-established model strain. Its rapid growth and ability to sporulate in a near-synchronised manner in liquid culture, unusual among streptomycetes, greatly facilitates the application of modern molecular techniques such as ChIP-seq and RNA-seq, as well as fluorescence time-lapse imaging of the complete Streptomyces life cycle. Here we describe a high-quality genome sequence of our isolate of the strain (NRRL B-65442) consisting of an 8.2 Mb chromosome and a 158 kb plasmid, pSVJI1, which had not been reported previously. Surprisingly, while NRRL B-65442 yields green spores on MYM agar, the ATCC type strain 10712 (from which NRRL B-65442 was derived) produces grey spores. While comparison of the genome sequences of the two isolates revealed almost total identity, it did reveal a single nucleotide substitution in a gene, vnz_33525, likely to be involved in spore pigment biosynthesis. Replacement of the vnz_33525 allele of ATCC 10712 with that of NRRL B-65442 resulted in green spores, explaining the discrepancy in spore pigmentation. We also applied CRISPR-Cas9 to delete the essential parB of pSVJI1 to cure the plasmid from the strain without obvious phenotypic consequences.
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Affiliation(s)
| | - Neil A Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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4
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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: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Stewart MYY, Bush MJ, Crack JC, Buttner MJ, Le Brun NE. Interaction of the Streptomyces Wbl protein WhiD with the principal sigma factor σ HrdB depends on the WhiD [4Fe-4S] cluster. J Biol Chem 2020; 295:9752-9765. [PMID: 32303639 PMCID: PMC7363131 DOI: 10.1074/jbc.ra120.012708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/15/2020] [Indexed: 12/29/2022] Open
Abstract
The bacterial protein WhiD belongs to the Wbl family of iron-sulfur [Fe-S] proteins present only in the actinomycetes. In Streptomyces coelicolor, it is required for the late stages of sporulation, but precisely how it functions is unknown. Here, we report results from in vitro and in vivo experiments with WhiD from Streptomyces venezuelae (SvWhiD), which differs from S. coelicolor WhiD (ScWhiD) only at the C terminus. We observed that, like ScWhiD and other Wbl proteins, SvWhiD binds a [4Fe-4S] cluster that is moderately sensitive to O2 and highly sensitive to nitric oxide (NO). However, although all previous studies have reported that Wbl proteins are monomers, we found that SvWhiD exists in a monomer-dimer equilibrium associated with its unusual C-terminal extension. Several Wbl proteins of Mycobacterium tuberculosis are known to interact with its principal sigma factor SigA. Using bacterial two-hybrid, gel filtration, and MS analyses, we demonstrate that SvWhiD interacts with domain 4 of the principal sigma factor of Streptomyces, σHrdB (σHrdB 4). Using MS, we determined the dissociation constant (Kd ) for the SvWhiD-σHrdB 4 complex as ∼0.7 μm, consistent with a relatively tight binding interaction. We found that complex formation was cluster dependent and that a reaction with NO, which was complete at 8-10 NO molecules per cluster, resulted in dissociation into the separate proteins. The SvWhiD [4Fe-4S] cluster was significantly less sensitive to reaction with O2 and NO when SvWhiD was bound to σHrdB 4, consistent with protection of the cluster in the complex.
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Affiliation(s)
- Melissa Y Y Stewart
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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6
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Becher PG, Verschut V, Bibb MJ, Bush MJ, Molnár BP, Barane E, Al-Bassam MM, Chandra G, Song L, Challis GL, Buttner MJ, Flärdh K. Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal. Nat Microbiol 2020; 5:821-829. [DOI: 10.1038/s41564-020-0697-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/21/2020] [Indexed: 12/28/2022]
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7
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Dorman CJ, Schumacher MA, Bush MJ, Brennan RG, Buttner MJ. When is a transcription factor a NAP? Curr Opin Microbiol 2020; 55:26-33. [PMID: 32120333 DOI: 10.1016/j.mib.2020.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 02/03/2023]
Abstract
Proteins that regulate transcription often also play an architectural role in the genome. Thus, it has been difficult to define with precision the distinctions between transcription factors and nucleoid-associated proteins (NAPs). Anachronistic descriptions of NAPs as 'histone-like' implied an organizational function in a bacterial chromatin-like complex. Definitions based on protein abundance, regulatory mechanisms, target gene number, or the features of their DNA-binding sites are insufficient as marks of distinction, and trying to distinguish transcription factors and NAPs based on their ranking within regulatory hierarchies or positions in gene-control networks is also unsatisfactory. The terms 'transcription factor' and 'NAP' are ad hoc operational definitions with each protein lying along a spectrum of structural and functional features extending from highly specific actors with few gene targets to those with a pervasive influence on the transcriptome. The Streptomyces BldC protein is used to illustrate these issues.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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8
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Gallagher KA, Schumacher MA, Bush MJ, Bibb MJ, Chandra G, Holmes NA, Zeng W, Henderson M, Zhang H, Findlay KC, Brennan RG, Buttner MJ. c-di-GMP Arms an Anti-σ to Control Progression of Multicellular Differentiation in Streptomyces. Mol Cell 2020; 77:586-599.e6. [PMID: 31810759 PMCID: PMC7005675 DOI: 10.1016/j.molcel.2019.11.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022]
Abstract
Streptomyces are our primary source of antibiotics, produced concomitantly with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σWhiG). We present the structure of the RsiG-(c-di-GMP)2-σWhiG complex, revealing an unusual, partially intercalated c-di-GMP dimer bound at the RsiG-σWhiG interface. RsiG binds c-di-GMP in the absence of σWhiG, employing a novel E(X)3S(X)2R(X)3Q(X)3D motif repeated on each helix of a coiled coil. Further studies demonstrate that c-di-GMP is essential for RsiG to inhibit σWhiG. These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.
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Affiliation(s)
- Kelley A. Gallagher
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria A. Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA,Corresponding author
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maureen J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Max Henderson
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hengshan Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G. Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK,Corresponding author
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9
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Schumacher MA, Bush MJ, Bibb MJ, Ramos-León F, Chandra G, Zeng W, Buttner MJ. The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor. Nucleic Acids Res 2019; 46:7405-7417. [PMID: 29905823 PMCID: PMC6101532 DOI: 10.1093/nar/gky493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Streptomyces are filamentous bacteria with a complex developmental life cycle characterized by the formation of spore-forming aerial hyphae. Transcription of the chaplin and rodlin genes, which are essential for aerial hyphae production, is directed by the extracytoplasmic function (ECF) σ factor BldN, which is in turn controlled by an anti-σ factor, RsbN. RsbN shows no sequence similarity to known anti-σ factors and binds and inhibits BldN in an unknown manner. Here we describe the 2.23 Å structure of the RsbN–BldN complex. The structure shows that BldN harbors σ2 and σ4 domains that are individually similar to other ECF σ domains, which bind −10 and −35 promoter regions, respectively. The anti-σ RsbN consists of three helices, with α3 forming a long helix embraced between BldN σ2 and σ4 while RsbN α1–α2 dock against σ4 in a manner that would block −35 DNA binding. RsbN binding also freezes BldN in a conformation inactive for simultaneous −10 and −35 promoter interaction and RNAP binding. Strikingly, RsbN is structurally distinct from previously solved anti-σ proteins. Thus, these data characterize the molecular determinants controlling a central Streptomyces developmental switch and reveal RsbN to be the founding member of a new structural class of anti-σ factor.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Félix Ramos-León
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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10
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Abstract
This special issue of Molecular Microbiology marks the 25th anniversary of the discovery of the extracytoplasmic function (ECF) σ factors, proteins that subsequently emerged as the largest group of alternative σ factors and one of the three major pillars of signal transduction in bacteria, alongside one- and two-component systems. A single bacterial genome can encode > 100 ECF σ factors, and combined with their cognate anti-σ factors, they represent a modular design that primarily functions in transmembrane signal transduction. Here, we first describe the immediate events that led to the 1994 publication in the Proceeding of the National Academy of Sciences USA, and then set them in the broader context of key events in the history of σ biology research.
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Affiliation(s)
- Michael A Lonetto
- Department of Informatics, Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Timothy J Donohue
- Department of Bacteriology, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Carol A Gross
- Department of Microbiology and Immunology and Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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11
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Tran NT, Huang X, Hong HJ, Bush MJ, Chandra G, Pinto D, Bibb MJ, Hutchings MI, Mascher T, Buttner MJ. Defining the regulon of genes controlled by σ E , a key regulator of the cell envelope stress response in Streptomyces coelicolor. Mol Microbiol 2019; 112:461-481. [PMID: 30907454 PMCID: PMC6767563 DOI: 10.1111/mmi.14250] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
The extracytoplasmic function (ECF) σ factor, σE , is a key regulator of the cell envelope stress response in Streptomyces coelicolor. Although its role in maintaining cell wall integrity has been known for over a decade, a comprehensive analysis of the genes under its control has not been undertaken. Here, using a combination of chromatin immunoprecipitation-sequencing (ChIP-seq), microarray transcriptional profiling and bioinformatic analysis, we attempt to define the σE regulon. Approximately half of the genes identified encode proteins implicated in cell envelope function. Seventeen novel targets were validated by S1 nuclease mapping or in vitro transcription, establishing a σE -binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the σE target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under σE control across the genus include the actin homolog MreB, three penicillin-binding proteins, two L,D-transpeptidases, a LytR-CpsA-Psr-family protein predicted to be involved in cell wall teichoic acid deposition and a predicted MprF protein, which adds lysyl groups to phosphatidylglycerol to neutralize membrane surface charge. Taken together, these analyses provide biological insight into the σE -mediated cell envelope stress response in the genus Streptomyces.
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Affiliation(s)
- Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xiaoluo Huang
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Hee-Jeon Hong
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniela Pinto
- Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thorsten Mascher
- Department Biology I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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12
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Schumacher MA, Bush MJ, Bibb MJ, Ramos-León F, Chandra G, Zeng W, Buttner MJ. The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor. Nucleic Acids Res 2018; 46:7467-7468. [PMID: 29986080 PMCID: PMC6101582 DOI: 10.1093/nar/gky616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Félix Ramos-León
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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13
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Buttner MJ, Schäfer M, Lawson DM, Maxwell A. Structural insights into simocyclinone as an antibiotic, effector ligand and substrate. FEMS Microbiol Rev 2018; 42:4604775. [PMID: 29126195 PMCID: PMC5812520 DOI: 10.1093/femsre/fux055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022] Open
Abstract
Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins.
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Affiliation(s)
- Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Schäfer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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14
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Schumacher MA, Zeng W, Findlay KC, Buttner MJ, Brennan RG, Tschowri N. The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex. Nucleic Acids Res 2017; 45:6923-6933. [PMID: 28449057 PMCID: PMC5499655 DOI: 10.1093/nar/gkx287] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/12/2017] [Indexed: 01/05/2023] Open
Abstract
Streptomyces are ubiquitous soil bacteria that undergo a complex developmental transition coinciding with their production of antibiotics. This transition is controlled by binding of a novel tetrameric form of the second messenger, 3΄-5΄ cyclic diguanylic acid (c-di-GMP) to the master repressor, BldD. In all domains of life, nucleotide-based second messengers allow a rapid integration of external and internal signals into regulatory pathways that control cellular responses to changing conditions. c-di-GMP can assume alternative oligomeric states to effect different functions, binding to effector proteins as monomers, intercalated dimers or, uniquely in the case of BldD, as a tetramer. However, at physiological concentrations c-di-GMP is a monomer and little is known about how higher oligomeric complexes assemble on effector proteins and if intermediates in assembly pathways have regulatory significance. Here, we show that c-di-GMP binds BldD using an ordered, sequential mechanism and that BldD function necessitates the assembly of the BldD2-(c-di-GMP)4 complex.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27701, USA
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27701, USA
| | - Kim C Findlay
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27701, USA
| | - Natalia Tschowri
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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15
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Bush MJ, Chandra G, Findlay KC, Buttner MJ. Multi-layered inhibition of Streptomyces development: BldO is a dedicated repressor of whiB. Mol Microbiol 2017; 104:700-711. [PMID: 28271577 PMCID: PMC5485038 DOI: 10.1111/mmi.13663] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2017] [Indexed: 02/07/2023]
Abstract
BldD‐(c‐di‐GMP) sits on top of the regulatory network that controls differentiation in Streptomyces, repressing a large regulon of developmental genes when the bacteria are growing vegetatively. In this way, BldD functions as an inhibitor that blocks the initiation of sporulation. Here, we report the identification and characterisation of BldO, an additional developmental repressor that acts to sustain vegetative growth and prevent entry into sporulation. However, unlike the pleiotropic regulator BldD, we show that BldO functions as the dedicated repressor of a single key target gene, whiB, and that deletion of bldO or constitutive expression of whiB is sufficient to induce precocious hypersporulation.
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Affiliation(s)
- Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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16
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Schäfer M, Stevenson CEM, Wilkinson B, Lawson DM, Buttner MJ. Substrate-Assisted Catalysis in Polyketide Reduction Proceeds via a Phenolate Intermediate. Cell Chem Biol 2016; 23:1091-1097. [PMID: 27617849 PMCID: PMC5039031 DOI: 10.1016/j.chembiol.2016.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/17/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022]
Abstract
SimC7 is a polyketide ketoreductase involved in biosynthesis of the angucyclinone moiety of the gyrase inhibitor simocyclinone D8 (SD8). SimC7, which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, catalyzes reduction of the C-7 carbonyl of the angucyclinone, and the resulting hydroxyl is essential for antibiotic activity. SimC7 shares little sequence similarity with characterized ketoreductases, suggesting it might have a distinct mechanism. To investigate this possibility, we determined the structures of SimC7 alone, with NADP+, and with NADP+ and the substrate 7-oxo-SD8. These structures show that SimC7 is distinct from previously characterized polyketide ketoreductases, lacking the conserved catalytic triad, including the active-site tyrosine that acts as central acid-base catalyst in canonical SDR proteins. Taken together with functional analyses of active-site mutants, our data suggest that SimC7 catalyzes a substrate-assisted, two-step reaction for reduction of the C-7 carbonyl group involving intramolecular transfer of a substrate-derived proton to generate a phenolate intermediate. SimC7 catalyzes reduction of the C-7 carbonyl of the angucyclinone of simocyclinone SimC7 lacks the conserved catalytic triad characteristic of canonical ketoreductases SimC7 reduces the C-7 carbonyl via a substrate-assisted, two-step reaction This involves intramolecular transfer of a substrate proton to generate a phenolate
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Affiliation(s)
- Martin Schäfer
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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17
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Schäfer M, Le TBK, Hearnshaw SJ, Maxwell A, Challis GL, Wilkinson B, Buttner MJ. SimC7 Is a Novel NAD(P)H-Dependent Ketoreductase Essential for the Antibiotic Activity of the DNA Gyrase Inhibitor Simocyclinone. J Mol Biol 2015; 427:2192-204. [PMID: 25861759 PMCID: PMC4451461 DOI: 10.1016/j.jmb.2015.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 01/02/2023]
Abstract
Simocyclinone D8 (SD8) is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü6040. The simocyclinone (sim) biosynthetic gene cluster has been sequenced and a hypothetical biosynthetic pathway has been proposed. The tetraene linker in SD8 was suggested to be the product of a modular type I polyketide synthase working in trans with two monofunctional enzymes. One of these monofunctional enzymes, SimC7, was proposed to supply a dehydratase activity missing from two modules of the polyketide synthase. In this study, we report the function of SimC7. We isolated the entire ~ 72-kb sim cluster on a single phage artificial chromosome clone and produced simocyclinone heterologously in a Streptomyces coelicolor strain engineered for improved antibiotic production. Deletion of simC7 resulted in the production of a novel simocyclinone, 7-oxo-SD8, which unexpectedly carried a normal tetraene linker but was altered in the angucyclinone moiety. We demonstrate that SimC7 is an NAD(P)H-dependent ketoreductase that catalyzes the conversion of 7-oxo-SD8 into SD8. 7-oxo-SD8 was essentially inactive as a DNA gyrase inhibitor, and the reduction of the keto group by SimC7 was shown to be crucial for high-affinity binding to the enzyme. Thus, SimC7 is an angucyclinone ketoreductase that is essential for the biological activity of simocyclinone. The ~ 75-kb simocyclinone biosynthetic cluster was expressed in a heterologous system. SimC7 is a novel NAD(P)H-dependent ketoreductase. SimC7 function is essential for the antibiotic activity of the DNA gyrase inhibitor simocyclinone.
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Affiliation(s)
- Martin Schäfer
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Stephen J Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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18
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Tschowri N, Schumacher MA, Schlimpert S, Chinnam NB, Findlay KC, Brennan RG, Buttner MJ. Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell 2015; 158:1136-1147. [PMID: 25171413 PMCID: PMC4151990 DOI: 10.1016/j.cell.2014.07.022] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/27/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]
Abstract
The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes during vegetative growth in a manner that depends on c-di-GMP-mediated dimerization. Structural and biochemical analyses show that tetrameric c-di-GMP links two subunits of BldD through their C-terminal domains, which are otherwise separated by ∼10 Å and thus cannot effect dimerization directly. Binding of the c-di-GMP tetramer by BldD is selective and requires a bipartite RXD-X8-RXXD signature. The findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions. c-di-GMP controls development in the multicellular bacteria Streptomyces c-di-GMP developmental signaling is directly mediated by the master regulator BldD A heretofore unseen tetrameric form of c-di-GMP binds BldD to effect its dimerization BldD-(c-di-GMP) represses transcription of sporulation genes during vegetative growth
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Affiliation(s)
- Natalia Tschowri
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Naga Babu Chinnam
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kim C Findlay
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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19
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Sidda JD, Song L, Poon V, Al-Bassam M, Lazos O, Buttner MJ, Challis GL, Corre C. Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chem Sci 2014. [DOI: 10.1039/c3sc52536h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Tzanis A, Dalton KA, Hesketh A, den Hengst CD, Buttner MJ, Thibessard A, Kelemen GH. A sporulation-specific, sigF-dependent protein, SspA, affects septum positioning in Streptomyces coelicolor. Mol Microbiol 2013; 91:363-80. [PMID: 24261854 PMCID: PMC4282423 DOI: 10.1111/mmi.12466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2013] [Indexed: 01/17/2023]
Abstract
The RNA polymerase sigma factor SigF controls late development during sporulation in the filamentous bacterium Streptomyces coelicolor. The only known SigF-dependent gene identified so far, SCO5321, is found in the biosynthetic cluster encoding spore pigment synthesis. Here we identify the first direct target for SigF, the gene sspA, encoding a sporulation-specific protein. Bioinformatic analysis suggests that SspA is a secreted lipoprotein with two PepSY signature domains. The sspA deletion mutant exhibits irregular sporulation septation and altered spore shape, suggesting that SspA plays a role in septum formation and spore maturation. The fluorescent translational fusion protein SspA–mCherry localized first to septum sites, then subsequently around the surface of the spores. Both SspA protein and sspA transcription are absent from the sigF null mutant. Moreover, in vitro transcription assay confirmed that RNA polymerase holoenzyme containing SigF is sufficient for initiation of transcription from a single sspA promoter. In addition, in vivo and in vitro experiments showed that sspA is a direct target of BldD, which functions to repress sporulation genes, including whiG, ftsZ and ssgB, during vegetative growth, co-ordinating their expression during sporulation septation.
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Affiliation(s)
- Angelos Tzanis
- University of East Anglia, Norwich Research Park, Norwich, UK
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21
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Smith MCM, Hendrix RW, Dedrick R, Mitchell K, Ko CC, Russell D, Bell E, Gregory M, Bibb MJ, Pethick F, Jacobs-Sera D, Herron P, Buttner MJ, Hatfull GF. Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J Bacteriol 2013; 195:4924-35. [PMID: 23995638 PMCID: PMC3807479 DOI: 10.1128/jb.00618-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/14/2013] [Indexed: 11/20/2022] Open
Abstract
The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, Hau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage Hau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species.
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Affiliation(s)
| | - Roger W. Hendrix
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebekah Dedrick
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kaitlin Mitchell
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ching-Chung Ko
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel Russell
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emma Bell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Maureen J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Florence Pethick
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paul Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Graham F. Hatfull
- Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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22
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Bush MJ, Bibb MJ, Chandra G, Findlay KC, Buttner MJ. Genes required for aerial growth, cell division, and chromosome segregation are targets of WhiA before sporulation in Streptomyces venezuelae. mBio 2013; 4:e00684-13. [PMID: 24065632 PMCID: PMC3781837 DOI: 10.1128/mbio.00684-13] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED WhiA is a highly unusual transcriptional regulator related to a family of eukaryotic homing endonucleases. WhiA is required for sporulation in the filamentous bacterium Streptomyces, but WhiA homologues of unknown function are also found throughout the Gram-positive bacteria. To better understand the role of WhiA in Streptomyces development and its function as a transcription factor, we identified the WhiA regulon through a combination of chromatin immunoprecipitation-sequencing (ChIP-seq) and microarray transcriptional profiling, exploiting a new model organism for the genus, Streptomyces venezuelae, which sporulates in liquid culture. The regulon encompasses ~240 transcription units, and WhiA appears to function almost equally as an activator and as a repressor. Bioinformatic analysis of the upstream regions of the complete regulon, combined with DNase I footprinting, identified a short but highly conserved asymmetric sequence, GACAC, associated with the majority of WhiA targets. Construction of a null mutant showed that whiA is required for the initiation of sporulation septation and chromosome segregation in S. venezuelae, and several genes encoding key proteins of the Streptomyces cell division machinery, such as ftsZ, ftsW, and ftsK, were found to be directly activated by WhiA during development. Several other genes encoding proteins with important roles in development were also identified as WhiA targets, including the sporulation-specific sigma factor σ(WhiG) and the diguanylate cyclase CdgB. Cell division is tightly coordinated with the orderly arrest of apical growth in the sporogenic cell, and filP, encoding a key component of the polarisome that directs apical growth, is a direct target for WhiA-mediated repression during sporulation. IMPORTANCE Since the initial identification of the genetic loci required for Streptomyces development, all of the bld and whi developmental master regulators have been cloned and characterized, and significant progress has been made toward understanding the cell biological processes that drive morphogenesis. A major challenge now is to connect the cell biological processes and the developmental master regulators by dissecting the regulatory networks that link the two. Studies of these regulatory networks have been greatly facilitated by the recent introduction of Streptomyces venezuelae as a new model system for the genus, a species that sporulates in liquid culture. Taking advantage of S. venezuelae, we have characterized the regulon of genes directly under the control of one of these master regulators, WhiA. Our results implicate WhiA in the direct regulation of key steps in sporulation, including the cessation of aerial growth, the initiation of cell division, and chromosome segregation.
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Affiliation(s)
- Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.
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23
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Saalbach G, Hempel AM, Vigouroux M, Flärdh K, Buttner MJ, Naldrett MJ. Determination of phosphorylation sites in the DivIVA cytoskeletal protein of Streptomyces coelicolor by targeted LC-MS/MS. J Proteome Res 2013; 12:4187-92. [PMID: 23905541 PMCID: PMC3787806 DOI: 10.1021/pr400524d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The
filamentous bacterium Streptomyces coelicolor modulates
polar growth and branching by phosphorylating the cytoskeletal
protein DivIVA. Previous MALDI-TOF analysis of DivIVA showed that
a large 7.2 kDa tryptic peptide was multiply phosphorylated. To aid
localization of the phosphorylation sites, we introduced additional
tryptic cleavage sites into DivIVA, and the resulting phosphopeptides
were analyzed by LC–MS/MS. Phosphopeptide isomers could be
separated chromatographically, but because of overlapping elution
and spectrum quality, site assignment by standard software tools was
ambiguous. Because fragment ions carrying the phosphate group are
essential for confident localization, large numbers of spectra were
collected using targeted LC–MS/MS, and a special script was
developed for plotting the elution of site-determining fragments from
those spectra under the XIC of the parent ions. Where multiple phosphopeptide
isomers were present, the elution of the site-determining y-ions perfectly
coincided with the elution of the corresponding phosphopeptide isomer.
This method represents a useful tool for user inspection of spectra
derived from phosphopeptide isomers and significantly increases confidence
when defining phosphorylation sites. In this way, we show that DivIVA
is phosphorylated in vivo on five sites in the C-terminal part of
the protein (T304, S309, S338, S344, and S355). The data have been
deposited to the ProteomeXchange Consortium with identifier PXD000095.
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Affiliation(s)
- Gerhard Saalbach
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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24
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Jones AC, Gust B, Kulik A, Heide L, Buttner MJ, Bibb MJ. Phage p1-derived artificial chromosomes facilitate heterologous expression of the FK506 gene cluster. PLoS One 2013; 8:e69319. [PMID: 23874942 PMCID: PMC3708917 DOI: 10.1371/journal.pone.0069319] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/12/2013] [Indexed: 01/19/2023] Open
Abstract
We describe a procedure for the conjugative transfer of phage P1-derived Artificial Chromosome (PAC) library clones containing large natural product gene clusters (≥70 kilobases) to Streptomyces coelicolor strains that have been engineered for improved heterologous production of natural products. This approach is demonstrated using the gene cluster for FK506 (tacrolimus), a clinically important immunosuppressant of high commercial value. The entire 83.5 kb FK506 gene cluster from Streptomyces tsukubaensis NRRL 18488 present in one 130 kb PAC clone was introduced into four different S. coelicolor derivatives and all produced FK506 and smaller amounts of the related compound FK520. FK506 yields were increased by approximately five-fold (from 1.2 mg L-1 to 5.5 mg L-1) in S. coelicolor M1146 containing the FK506 PAC upon over-expression of the FK506 LuxR regulatory gene fkbN. The PAC-based gene cluster conjugation methodology described here provides a tractable means to evaluate and manipulate FK506 biosynthesis and is readily applicable to other large gene clusters encoding natural products of interest to medicine, agriculture and biotechnology.
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Affiliation(s)
- Adam C. Jones
- Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Lutz Heide
- Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (M. Buttner); (M. Bibb)
| | - Mervyn J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (M. Buttner); (M. Bibb)
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Flärdh K, Richards DM, Hempel AM, Howard M, Buttner MJ. Regulation of apical growth and hyphal branching in Streptomyces. Curr Opin Microbiol 2012; 15:737-43. [PMID: 23153774 DOI: 10.1016/j.mib.2012.10.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 01/19/2023]
Abstract
The filamentous bacteria Streptomyces grow by tip extension and through the initiation of new branches, and this apical growth is directed by a polarisome-like complex involving the essential polarity protein DivIVA. New branch sites must be marked de novo and, until recently, there was no understanding of how these new sites are selected. Equally, hyphal branching patterns are affected by environmental conditions, but there was no insight into how polar growth and hyphal branching might be regulated in response to external or internal cues. This review focuses on recent discoveries that reveal the principal mechanism of branch site selection in Streptomyces, and the first mechanism to be identified that regulates polarisome behaviour to modulate polar growth and hyphal branching.
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Affiliation(s)
- Klas Flärdh
- Department of Biology, Lund University, 223 62 Lund, Sweden
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26
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Bibb MJ, Domonkos A, Chandra G, Buttner MJ. Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σ(BldN) and a cognate anti-sigma factor, RsbN. Mol Microbiol 2012; 84:1033-49. [PMID: 22582857 DOI: 10.1111/j.1365-2958.2012.08070.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chaplin and rodlin proteins together constitute the major components of the hydrophobic sheath that coats the aerial hyphae and spores in Streptomyces, and mutants lacking the chaplins are unable to erect aerial hyphae and differentiate on minimal media. We have gained insight into the developmental regulation of the chaplin (chp) and rodlin (rdl) genes by exploiting a new model species, Streptomyces venezuelae, which sporulates in liquid culture. Using microarrays, the chaplin and rodlin genes were found to be highly induced during submerged sporulation in a bldN-dependent manner. Using σ(BldN) ChIP-chip, we show that this dependence arises because the chaplin and rodlin genes are direct biochemical targets of σ(BldN) . sven3186 (here named rsbN for regulator of sigma BldN), the gene lying immediately downstream of bldN, was also identified as a target of σ(BldN) . Disruption of rsbN causes precocious sporulation and biochemical experiments demonstrate that RsbN functions as a σ(BldN) -specific anti-sigma factor.
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Affiliation(s)
- Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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27
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Richards DM, Hempel AM, Flärdh K, Buttner MJ, Howard M. Mechanistic basis of branch-site selection in filamentous bacteria. PLoS Comput Biol 2012; 8:e1002423. [PMID: 22423220 PMCID: PMC3297577 DOI: 10.1371/journal.pcbi.1002423] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/26/2012] [Indexed: 11/18/2022] Open
Abstract
Many filamentous organisms, such as fungi, grow by tip-extension and by forming new branches behind the tips. A similar growth mode occurs in filamentous bacteria, including the genus Streptomyces, although here our mechanistic understanding has been very limited. The Streptomyces protein DivIVA is a critical determinant of hyphal growth and localizes in foci at hyphal tips and sites of future branch development. However, how such foci form was previously unknown. Here, we show experimentally that DivIVA focus-formation involves a novel mechanism in which new DivIVA foci break off from existing tip-foci, bypassing the need for initial nucleation or de novo branch-site selection. We develop a mathematical model for DivIVA-dependent growth and branching, involving DivIVA focus-formation by tip-focus splitting, focus growth, and the initiation of new branches at a critical focus size. We quantitatively fit our model to the experimentally-measured tip-to-branch and branch-to-branch length distributions. The model predicts a particular bimodal tip-to-branch distribution results from tip-focus splitting, a prediction we confirm experimentally. Our work provides mechanistic understanding of a novel mode of hyphal growth regulation that may be widely employed.
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Affiliation(s)
| | - Antje M. Hempel
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- Department of Biology, Lund University, Lund, Sweden
| | - Klas Flärdh
- Department of Biology, Lund University, Lund, Sweden
- * E-mail: (KF); (MH)
| | - Mark J. Buttner
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (KF); (MH)
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28
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Le TBK, Schumacher MA, Lawson DM, Brennan RG, Buttner MJ. The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding. Nucleic Acids Res 2011; 39:9433-47. [PMID: 21835774 PMCID: PMC3241653 DOI: 10.1093/nar/gkr640] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
SimR, a TetR-family transcriptional regulator (TFR), controls the export of simocyclinone, a potent DNA gyrase inhibitor made by Streptomyces antibioticus. Simocyclinone is exported by a specific efflux pump, SimX and the transcription of simX is repressed by SimR, which binds to two operators in the simR-simX intergenic region. The DNA-binding domain of SimR has a classical helix-turn-helix motif, but it also carries an arginine-rich N-terminal extension. Previous structural studies showed that the N-terminal extension is disordered in the absence of DNA. Here, we show that the N-terminal extension is sensitive to protease cleavage, but becomes protease resistant upon binding DNA. We demonstrate by deletion analysis that the extension contributes to DNA binding, and describe the crystal structure of SimR bound to its operator sequence, revealing that the N-terminal extension binds in the minor groove. In addition, SimR makes a number of sequence-specific contacts to the major groove via its helix-turn-helix motif. Bioinformatic analysis shows that an N-terminal extension rich in positively charged residues is a feature of the majority of TFRs. Comparison of the SimR–DNA and SimR–simocyclinone complexes reveals that the conformational changes associated with ligand-mediated derepression result primarily from rigid-body rotation of the subunits about the dimer interface.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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29
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Le TBK, Stevenson CEM, Fiedler HP, Maxwell A, Lawson DM, Buttner MJ. Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression. J Mol Biol 2011; 408:40-56. [PMID: 21354180 DOI: 10.1016/j.jmb.2011.02.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/12/2011] [Accepted: 02/15/2011] [Indexed: 11/19/2022]
Abstract
Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to operators in the intergenic region between simR and simX. Previously, we have shown that the mature antibiotic SD8 or its biosynthetic intermediate, simocyclinone C4, can dissociate SimR from its operators, leading to derepression of simX and export of SD8 from the cell. This provides a mechanism that couples the biosynthesis of the antibiotic to its export. Here, we report the crystal structures of SimR alone and in complex with either SD8 or simocyclinone C4. The ligand-binding pocket is unusual compared to those of other characterized TetR-family transcriptional regulators: the structures show an extensive ligand-binding pocket spanning both monomers in the functional dimeric unit, with the aminocoumarin moiety of SD8 buried in the protein core, while the angucyclic polyketide moiety is partially exposed to bulk solvent. Through comparisons of the structures, we postulate a derepression mechanism for SimR that invokes rigid-body motions of the subunits relative to one another, coupled with a putative locking mechanism to restrict further conformational change.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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30
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Le TBK, Stevenson CEM, Buttner MJ, Lawson DM. Crystallization and preliminary X-ray analysis of the TetR-like efflux pump regulator SimR. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:307-9. [PMID: 21393832 DOI: 10.1107/s1744309110053078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/17/2010] [Indexed: 11/10/2022]
Abstract
Crystals of SimR were grown by vapour diffusion. The protein crystallized with trigonal symmetry and X-ray data were recorded to a resolution of 2.3 Å from a single crystal at the synchrotron. SimR belongs to the TetR family of bacterial transcriptional regulators. In the absence of the antibiotic simocyclinone, SimR represses the transcription of a divergently transcribed gene encoding the simocyclinone efflux pump SimX in Streptomyces antibioticus by binding to operators in the simR-simX intergenic region. Simocyclinone binding causes SimR to dissociate from its operators, leading to expression of the SimX efflux pump. Thus, SimR represents an intimate link between the biosynthesis of simocyclinone and its export, which may also provide the mechanism of self-resistance to the antibiotic in the producer strain.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, England
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31
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Crack JC, Smith LJ, Stapleton MR, Peck J, Watmough NJ, Buttner MJ, Buxton RS, Green J, Oganesyan VS, Thomson AJ, Le Brun NE. Mechanistic insight into the nitrosylation of the [4Fe-4S] cluster of WhiB-like proteins. J Am Chem Soc 2010; 133:1112-21. [PMID: 21182249 PMCID: PMC3117330 DOI: 10.1021/ja109581t] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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The reactivity of protein bound iron−sulfur clusters with nitric oxide (NO) is well documented, but little is known about the actual mechanism of cluster nitrosylation. Here, we report studies of members of the Wbl family of [4Fe−4S] containing proteins, which play key roles in regulating developmental processes in actinomycetes, including Streptomyces and Mycobacteria, and have been shown to be NO responsive. Streptomyces coelicolor WhiD and Mycobacterium tuberculosis WhiB1 react extremely rapidly with NO in a multiphasic reaction involving, remarkably, 8 NO molecules per [4Fe−4S] cluster. The reaction is 104-fold faster than that observed with O2 and is by far the most rapid iron−sulfur cluster nitrosylation reaction reported to date. An overall stoichiometry of [Fe4S4(Cys)4]2− + 8NO → 2[FeI2(NO)4(Cys)2]0 + S2− + 3S0 has been established by determination of the sulfur products and their oxidation states. Kinetic analysis leads to a four-step mechanism that accounts for the observed NO dependence. DFT calculations suggest the possibility that the nitrosylation product is a novel cluster [FeI4(NO)8(Cys)4]0 derived by dimerization of a pair of Roussin’s red ester (RRE) complexes.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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32
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Den Hengst CD, Tran NT, Bibb MJ, Chandra G, Leskiw BK, Buttner MJ. Genes essential for morphological development and antibiotic production in Streptomyces coelicolor are targets of BldD during vegetative growth. Mol Microbiol 2010; 78:361-79. [DOI: 10.1111/j.1365-2958.2010.07338.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Crack JC, den Hengst CD, Jakimowicz P, Subramanian S, Johnson MK, Buttner MJ, Thomson AJ, Le Brun NE. Characterization of [4Fe-4S]-containing and cluster-free forms of Streptomyces WhiD. Biochemistry 2010; 48:12252-64. [PMID: 19954209 DOI: 10.1021/bi901498v] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
WhiD, a member of the WhiB-like (Wbl) family of iron-sulfur proteins found exclusively within the actinomycetes, is required for the late stages of sporulation in Streptomyces coelicolor. Like all other Wbl proteins, WhiD has not so far been purified in a soluble form that contains a significant amount of cluster, and characterization has relied on cluster-reconstituted protein. Thus, a major goal in Wbl research is to obtain and characterize native protein containing iron-sulfur clusters. Here we report the analysis of S. coelicolor WhiD purified anaerobically from Escherichia coli as a soluble protein containing a single [4Fe-4S](2+) cluster ligated by four cysteines. Upon exposure to oxygen, spectral features associated with the [4Fe-4S] cluster were lost in a slow reaction that unusually yielded apo-WhiD directly without significant concentrations of cluster intermediates. This process was found to be highly pH dependent with an optimal stability observed between pH 7.0 and pH 8.0. Low molecular weight thiols, including a mycothiol analogue and thioredoxin, exerted a small but significant protective effect against WhiD cluster loss, an activity that could be of physiological importance. [4Fe-4S](2+) WhiD was found to react much more rapidly with superoxide than with either oxygen or hydrogen peroxide, which may also be of physiological significance. Loss of the [4Fe-4S] cluster to form apoprotein destabilized the protein fold significantly but did not lead to complete unfolding. Finally, apo-WhiD exhibited negligible activity in an insulin-based disulfide reductase assay, demonstrating that it does not function as a general protein disulfide reductase.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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34
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Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CEM, Le TBK, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A. A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science 2010; 326:1415-8. [PMID: 19965760 DOI: 10.1126/science.1179123] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.
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Affiliation(s)
- Marcus J Edwards
- Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK
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35
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Le TBK, Fiedler HP, den Hengst CD, Ahn SK, Maxwell A, Buttner MJ. Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus. Mol Microbiol 2009; 72:1462-74. [PMID: 19460097 DOI: 10.1111/j.1365-2958.2009.06735.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because most antibiotics are potentially lethal to the producing organism, there must be mechanisms to ensure that the machinery responsible for export of the mature antibiotic is in place at the time of biosynthesis. Simocyclinone D8 is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü 6040. Within the simocyclinone biosynthetic cluster are two divergently transcribed genes, simR and simX, encoding proteins that resemble the TetR/TetA repressor-efflux pump pair that cause widespread resistance to clinically important tetracyclines. Engineered expression of simX from a strong, heterologous promoter conferred high level simocyclinone D8 resistance on Streptomyces lividans, showing that simX encodes a simocyclinone efflux pump. Transcription of simX is controlled by SimR, which directly represses the simX and simR promoters by binding to two operator sites in the simX-simR intergenic region. Simocyclinone D8 abolishes DNA binding by SimR, providing a mechanism that couples the biosynthesis of simocyclinone to its export. In addition, an intermediate in the biosynthetic pathway, simocyclinone C4, which is essentially inactive as a DNA gyrase inhibitor, also induces simX expression in vivo and relieves simX repression by SimR in vitro.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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36
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Sello JK, Buttner MJ. The oligoribonuclease gene inStreptomyces coelicoloris not transcriptionally or translationally coupled toadpA, a keybldAtarget. FEMS Microbiol Lett 2008; 286:60-5. [DOI: 10.1111/j.1574-6968.2008.01260.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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37
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Hong HJ, Paget MSB, Buttner MJ. A signal transduction system in Streptomyces coelicolorthat activates expression of a putative cell wall glycan operon in response to vancomycin and other cell wall-specific antibiotics. Mol Microbiol 2008. [DOI: 10.1111/j.1365-2958.2008.06368.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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den Hengst CD, Buttner MJ. Redox control in actinobacteria. Biochim Biophys Acta Gen Subj 2008; 1780:1201-16. [PMID: 18252205 DOI: 10.1016/j.bbagen.2008.01.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/07/2008] [Accepted: 01/14/2008] [Indexed: 10/22/2022]
Abstract
As most actinobacteria are obligate aerobes, they have to cope with endogenously generated reactive oxygen species, and actinobacterial pathogens have to resist oxidative attack by phagocytes. Actinobacteria also have to survive long periods under low oxygen tension; for example, Mycobacterium tuberculosis can persist in the host for years under apparently hypoxic conditions in a latent, non-replicative state. Here we focus on the regulatory switches that control actinobacterial responses to peroxide stress, disulfide stress and low oxygen tension. Other unique aspects of their redox biology will be highlighted, including the use of the pseudodisaccharide mycothiol as their major low-molecular-weight thiol buffer, and the [4Fe-4S]-containing WhiB-like proteins, which play diverse, important roles in actinobacterial biology, but whose biochemical role is still controversial.
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Affiliation(s)
- Chris D den Hengst
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
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39
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Ausmees N, Wahlstedt H, Bagchi S, Elliot MA, Buttner MJ, Flärdh K. SmeA, a small membrane protein with multiple functions in Streptomyces sporulation including targeting of a SpoIIIE/FtsK-like protein to cell division septa. Mol Microbiol 2007; 65:1458-73. [PMID: 17824926 DOI: 10.1111/j.1365-2958.2007.05877.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sporulation in aerial hyphae of Streptomyces coelicolor involves profound changes in regulation of fundamental morphogenetic and cell cycle processes to convert the filamentous and multinucleoid cells to small unigenomic spores. Here, a novel sporulation locus consisting of smeA (encoding a small putative membrane protein) and sffA (encoding a SpoIIIE/FtsK-family protein) is characterized. Deletion of smeA-sffA gave rise to pleiotropic effects on spore maturation, and influenced the segregation of chromosomes and placement of septa during sporulation. Both smeA and sffA were expressed specifically in apical cells of sporogenic aerial hyphae simultaneously with or slightly after Z-ring assembly. The presence of smeA-like genes in streptomycete chromosomes, plasmids and transposons, often paired with a gene for a SpoIIIE/FtsK- or Tra-like protein, indicates that SmeA and SffA functions might be related to DNA transfer. During spore development SffA accumulated specifically at sporulation septa where it colocalized with FtsK. However, sffA did not show redundancy with ftsK, and SffA function appeared distinct from the DNA translocase activity displayed by FtsK during closure of sporulation septa. The septal localization of SffA was dependent on SmeA, suggesting that SmeA may act as an assembly factor for SffA and possibly other proteins required during spore maturation.
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Affiliation(s)
- Nora Ausmees
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, 75124, Uppsala, Sweden.
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40
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Abstract
Morphogenesis in the streptomycetes features the differentiation of substrate-associated vegetative hyphae into upwardly growing aerial filaments. This transition requires the activity of bld genes and the secretion of biosurfactants that reduce the surface tension at the colony-air interface enabling the emergence of nascent aerial hyphae. Streptomyces coelicolor produces two classes of surface-active molecules, SapB and the chaplins. While both molecules are important for aerial development, nothing is known about the functional redundancy or interaction of these surfactants apart from the observation that aerial hyphae formation can proceed via one of two pathways: a SapB-dependent pathway when cells are grown on rich medium and a SapB-independent pathway on poorly utilized carbon sources such as mannitol. We used mutant analysis to show that while the chaplins are important, but not required, for development on rich medium, they are essential for differentiation on MS (soy flour mannitol) medium, and the corresponding developmental defects could be suppressed by the presence of SapB. Furthermore, the chaplins are produced by conditional bld mutants during aerial hyphae formation when grown on the permissive medium, MS, suggesting that the previously uncharacterized SapB-independent pathway is chaplin dependent. In contrast, a bld mutant blocked in aerial morphogenesis on all media makes neither SapB nor chaplins. Finally, we show that a constructed null mutant that lacks all chaplin and SapB biosynthetic genes fails to differentiate in any growth condition. We propose that the biosurfactant activities of both SapB and the chaplins are essential for normal aerial hyphae formation on rich medium, while chaplin biosynthesis and secretion alone drives aerial morphogenesis on MS medium.
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Affiliation(s)
- David S Capstick
- Department of Biology, McMaster University, Hamilton, Ontario L8S4K1, Canada
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41
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Hutchings MI, Hong HJ, Leibovitz E, Sutcliffe IC, Buttner MJ. The sigma(E) cell envelope stress response of Streptomyces coelicolor is influenced by a novel lipoprotein, CseA. J Bacteriol 2006; 188:7222-9. [PMID: 17015661 PMCID: PMC1636229 DOI: 10.1128/jb.00818-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We have investigated the role of CseA in the sigma(E) cell envelope stress response of the gram-positive bacterium Streptomyces coelicolor. sigma(E) is an extracytoplasmic function RNA polymerase sigma factor required for normal cell envelope integrity in S. coelicolor. sigma(E) is encoded within a four-gene operon that also encodes CseA, a protein of unknown function, CseB, a response regulator and CseC, a transmembrane sensor histidine kinase (Cse represents control of sigma E). Previous work has shown that transcription of the sigE gene is completely dependent on the CseBC two-component system and that the CseBC-sigma(E) signal transduction system is induced by a wide variety of cell-wall-damaging agents. Here we address the role of CseA, a protein with no homologues outside the streptomycetes. We show that CseA is a novel lipoprotein localized to the extracytoplasmic face of the cell membrane and that loss of CseA results in upregulation of the sigE promoter.
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Affiliation(s)
- Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom.
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Hoskisson PA, Rigali S, Fowler K, Findlay KC, Buttner MJ. DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor. J Bacteriol 2006; 188:5014-23. [PMID: 16816174 PMCID: PMC1539961 DOI: 10.1128/jb.00307-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 04/20/2006] [Indexed: 11/20/2022] Open
Abstract
The gram-positive filamentous bacterium Streptomyces coelicolor has a complex developmental cycle with three distinct phases: growth of the substrate mycelium, development of reproductive structures called aerial hyphae, and differentiation of these aerial filaments into long chains of exospores. During a transposon mutagenesis screen, we identified a novel gene (devA) required for proper development. The devA mutant produced only rare aerial hyphae, and those that were produced developed aberrant spore chains that were much shorter than wild-type chains and had misplaced septa. devA encodes a member of the GntR superfamily, a class of transcriptional regulators that typically respond to metabolite effector molecules. devA forms an operon with the downstream gene devB, which encodes a putative hydrolase that is also required for aerial mycelium formation on R5 medium. S1 nuclease protection analysis showed that transcription from the single devA promoter was temporally associated with vegetative growth, and enhanced green fluorescent protein transcriptional fusions showed that transcription was spatially confined to the substrate hyphae in the wild type. In contrast, devAB transcript levels were dramatically upregulated in a devA mutant and the devA promoter was also active in aerial hyphae and spores in this background, suggesting that DevA might negatively regulate its own production. This suggestion was confirmed by gel mobility shift assays that showed that DevA binds its own promoter region in vitro.
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Affiliation(s)
- Paul A Hoskisson
- Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom.
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Zdanowski K, Doughty P, Jakimowicz P, O'Hara L, Buttner MJ, Paget MSB, Kleanthous C. Assignment of the Zinc Ligands in RsrA, a Redox-Sensing ZAS Protein from Streptomyces coelicolor. Biochemistry 2006; 45:8294-300. [PMID: 16819828 DOI: 10.1021/bi060711v] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ZAS proteins are widespread bacterial zinc-containing anti-sigma factors that regulate the activity of sigma factors in response to diverse cues. One of the best characterized ZAS proteins is RsrA from Streptomyces coelicolor, which responds to disulfide stress. Zn-RsrA binds and represses the transcriptional activity of sigmaR in the reducing environment of the cytoplasm but undergoes reversible, intramolecular disulfide bond formation during oxidative stress. This expels the single metal ion and causes dramatic structural changes in RsrA that result in its dissociation from sigmaR, leaving the sigma factor free to activate the transcription of antioxidant genes. We showed recently that Zn2+ serves a critical role in modulating the redox activity of RsrA thiols but uncertainty remains as to how the metal ion is coordinated in RsrA and related ZAS proteins. Using a combination of random and site-specific mutagenesis with zinc K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy, we have assigned unambiguously the metal ligands in RsrA, thereby distinguishing between the different ligation models that have been proposed. The data show that the zinc site in RsrA is comprised of Cys11, His37, Cys41, and Cys44. Three of these residues are part of a conserved ZAS-specific sequence motif (H37xxxC41xxC44), with the fourth ligand, Cys11, found in a subset of ZAS proteins. Cys11 and Cys44 form the trigger disulfide in RsrA, explaining why the metal ion is expelled during oxidation. We discuss these data in the context of redox sensing by RsrA and the sensory mechanisms of other ZAS proteins.
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Affiliation(s)
- Konrad Zdanowski
- Department of Biology (Area 10), University of York, P.O. Box 373, York YO10 5YW, UK
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Jakimowicz P, Tello M, Meyers CLF, Walsh CT, Buttner MJ, Field RA, Lawson DM. The 1.6-A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides. Proteins 2006; 63:261-5. [PMID: 16411240 DOI: 10.1002/prot.20818] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Piotr Jakimowicz
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Abstract
We took advantage of the vancomycin-dependent phenotype of Streptomyces coelicolor femX null mutants to isolate a collection of spontaneous, drug-independent femX suppressor mutants that expressed the vancomycin-resistance (van) genes constitutively. All of the suppressor mutations were in vanS but, unexpectedly, many were predicted to be loss-of-function mutations. Confirming this interpretation, a constructed vanS deletion mutation also resulted in constitutive expression of the van genes, suggesting that VanS negatively regulated VanR function in the absence of drug. In contrast, a vanS pta ackA triple mutant, which should not be able synthesize acetyl phosphate, failed to express the van genes, whereas a pta ackA double mutant showed wild-type, regulated induction of the van genes. These results suggest that in the absence of vancomycin, acetyl phosphate phosphorylates VanR, and VanS acts as a phosphatase to suppress the levels of VanR approximately P. On exposure to vancomycin, VanS activity switches from a phosphatase to a kinase and vancomycin resistance is induced. In S. coelicolor, the van genes are induced by both vancomycin and the glycopeptide A47934, whereas in Streptomyces toyocaensis (the A47934 producer) resistance is induced by A47934 but not by vancomycin. We exploited this distinction to replace the S. coelicolor vanRS genes with the vanRS genes from S. toyocaensis. The resulting strain acquired the inducer profile of S. toyocaensis, providing circumstantial evidence that the VanS effector ligand is the drug itself, and not an intermediate in cell wall biosynthesis that accumulates as result of drug action. Consistent with this suggestion, we found that non-glycopeptide inhibitors of the late steps in cell wall biosynthesis such as moenomycin A, bacitracin and ramoplanin were not inducers of the S. coelicolor VanRS system, in contrast to results obtained in enterococcal VanRS systems.
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Affiliation(s)
- Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.
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Tello M, Jakimowicz P, Errey JC, Freel Meyers CL, Walsh CT, Buttner MJ, Lawson DM, Field RA. Characterisation of Streptomyces spheroides NovW and revision of its functional assignment to a dTDP-6-deoxy-d-xylo-4-hexulose 3-epimerase. Chem Commun (Camb) 2006:1079-81. [PMID: 16514445 DOI: 10.1039/b515763c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterisation of recombinant Streptomyces spheroides NovW in vitro suggests that it is not a kinetically competent dual action dTDP-6-deoxy-d-xylo-4-hexulose 3,5-epimerase, but possesses only significant 3-epimerase activity.
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Affiliation(s)
- Mónica Tello
- Centre for Carbohydrate Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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Huang J, Shi J, Molle V, Sohlberg B, Weaver D, Bibb MJ, Karoonuthaisiri N, Lih CJ, Kao CM, Buttner MJ, Cohen SN. Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Mol Microbiol 2005; 58:1276-87. [PMID: 16313616 DOI: 10.1111/j.1365-2958.2005.04879.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted.
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Affiliation(s)
- Jianqiang Huang
- Department of Genetics, MC 5120, Stanford University, Stanford, CA 94305, USA
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Jakimowicz P, Cheesman MR, Bishai WR, Chater KF, Thomson AJ, Buttner MJ. Evidence That the Streptomyces Developmental Protein WhiD, a Member of the WhiB Family, Binds a [4Fe-4S] Cluster. J Biol Chem 2005; 280:8309-15. [PMID: 15615709 DOI: 10.1074/jbc.m412622200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WhiD is required for the late stages of sporulation in the Gram-positive bacterium Streptomyces coelicolor. WhiD is a member of the WhiB-like family of putative transcription factors that are present throughout the actinomycetes but absent from other organisms. This family of proteins has four near-invariant cysteines, suggesting that these residues might act as ligands for a metal cofactor. Overexpressed WhiD, purified from Escherichia coli, contained substoichiometric amounts of iron and had an absorption spectrum characteristic of a [2Fe-2S] cluster. After Fe-S cluster reconstitution under anaerobic conditions, WhiD contained approximately 4 iron atoms/monomer and similar amounts of sulfide ion and gave an absorption spectrum characteristic of a [4Fe-4S] cluster. Reconstituted WhiD gave no electron paramagnetic resonance signal as prepared but, after reduction with dithionite, gave an electron paramagnetic resonance signal (g approximately 2.06, 1.94) consistent with a one-electron reduction of a [4Fe-4S](2+) cluster to a [4Fe-4S](1+) state with electron spin of S = (1/2). The anaerobically reconstituted [4Fe-4S] cluster was oxygen sensitive. Upon exposure to air, absorption at 410 and 505 nm first increased and then showed a steady decrease with time until the protein was colorless in the near UV/visible region. These changes are consistent with an oxygen-induced change from a [4Fe-4S] to a [2Fe-2S] cluster, followed by complete loss of cluster from the protein. Each of the four conserved cysteine residues, Cys-23, -53, -56, and -62, was essential for WhiD function in vivo.
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Affiliation(s)
- Piotr Jakimowicz
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
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Hunt AC, Servín-González L, Kelemen GH, Buttner MJ. The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA-binding domains of the MerR family. J Bacteriol 2005; 187:716-28. [PMID: 15629942 PMCID: PMC543565 DOI: 10.1128/jb.187.2.716-728.2005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bldC locus, required for formation of aerial hyphae in Streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids D17 and D25 of a minimal ordered library. Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. BldC family members are found in a wide range of gram-positive and gram-negative bacteria. Constructed DeltabldC mutants were defective in differentiation and antibiotic production. They failed to form an aerial mycelium on minimal medium and showed severe delays in aerial mycelium formation on rich medium. In addition, they failed to produce the polyketide antibiotic actinorhodin, and bldC was shown to be required for normal and sustained transcription of the pathway-specific activator gene actII-orf4. Although DeltabldC mutants produced the tripyrrole antibiotic undecylprodigiosin, transcripts of the pathway-specific activator gene (redD) were reduced to almost undetectable levels after 48 h in the bldC mutant, in contrast to the bldC+ parent strain in which redD transcription continued during aerial mycelium formation and sporulation. This suggests that bldC may be required for maintenance of redD transcription during differentiation. bldC is expressed from a single promoter. S1 nuclease protection assays and immunoblotting showed that bldC is constitutively expressed and that transcription of bldC does not depend on any of the other known bld genes. The bldC18 mutation that originally defined the locus causes a Y49C substitution that results in instability of the protein.
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Affiliation(s)
- Alison C Hunt
- Department of Molecular Microbiology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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Abstract
The non-pathogenic, non-glycopeptide-producing actinomycete Streptomyces coelicolor carries a cluster of seven genes (vanSRJKHAX) that confers inducible, high level resistance to vancomycin. The vanK gene has no counterpart in previously characterized vancomycin resistance clusters, yet vanK is required for vancomycin resistance in S. coelicolor. VanK belongs to the Fem family of enzymes, which add the branch amino acid(s) to the stem pentapeptide of peptidoglycan precursors. Upon exposure to vancomycin, the VanRS two-component system switches on expression of all seven van genes, and the VanHAX enzymes reprogram the cell wall such that precursors terminate D-Ala-D-lactate (Lac) rather than D-Ala-D-Ala, thus conferring resistance to vancomycin, which only binds D-Ala-D-Ala-containing precursors. Here we provide biochemical and genetic evidence that VanK is required for vancomycin resistance because the constitutively expressed FemX enzyme, encoded elsewhere on the chromosome, cannot recognize D-Lac-containing precursors as a substrate, whereas VanK can. Consistent with this view, D-Lac-containing precursors carrying the Gly branch are present in the wild type transiently exposed to vancomycin but are undetectable in a vanK mutant treated in the same way. Further, femX null mutants are viable in the presence of vancomycin but die in its absence. Because only VanK can recognize D-Lac-containing precursors, vancomycin-induced expression of VanHAX in a vanK mutant is lethal, and so vanK is required for vancomycin resistance.
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Affiliation(s)
- Hee-Jeon Hong
- Department of Molecular Microbiology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom.
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