1
|
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.
Collapse
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
| |
Collapse
|
2
|
McDonald HP, Alford A, Devine R, Hems ES, Nepogodiev SA, Arnold CJ, Rejzek M, Stanley-Smith A, Holmes NA, Hutchings MI, Wilkinson B. Heterologous Expression of the Formicamycin Biosynthetic Gene Cluster Unveils Glycosylated Fasamycin Congeners. J Nat Prod 2023. [PMID: 37327570 PMCID: PMC10391614 DOI: 10.1021/acs.jnatprod.3c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Formicamycins and their biosynthetic intermediates the fasamycins are polyketide antibiotics produced by Streptomyces formicae KY5 from a pathway encoded by the for biosynthetic gene cluster. In this work the ability of Streptomyces coelicolor M1146 and the ability of Saccharopolyspora erythraea Δery to heterologously express the for biosynthetic gene cluster were assessed. This led to the identification of eight new glycosylated fasamycins modified at different phenolic groups with either a monosaccharide (glucose, galactose, or glucuronic acid) or a disaccharide comprised of a proximal hexose (either glucose or galactose), with a terminal pentose (arabinose) moiety. In contrast to the respective aglycones, minimal inhibitory screening assays showed these glycosylated congeners lacked antibacterial activity.
Collapse
Affiliation(s)
- Hannah P McDonald
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Abigail Alford
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Edward S Hems
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Sergey A Nepogodiev
- NMR Platform, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Corinne J Arnold
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | | | - Neil A Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K
| |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Darrington M, Leftwich PT, Holmes NA, Friend LA, Clarke NVE, Worsley SF, Margaritopolous JT, Hogenhout SA, Hutchings MI, Chapman T. Characterisation of the symbionts in the Mediterranean fruit fly gut. Microb Genom 2022; 8. [PMID: 35446250 PMCID: PMC9453069 DOI: 10.1099/mgen.0.000801] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Indexed: 12/25/2022] Open
Abstract
Symbioses between bacteria and their insect hosts can range from loose associations through to obligate interdependence. While fundamental evolutionary insights have been gained from the in-depth study of obligate mutualisms, there is increasing interest in the evolutionary potential of flexible symbiotic associations between hosts and their gut microbiomes. Understanding relationships between microbes and hosts also offers the potential for exploitation for insect control. Here, we investigate the gut microbiome of a global agricultural pest, the Mediterranean fruit fly (Ceratitis capitata). We used 16S rRNA profiling to compare the gut microbiomes of laboratory and wild strains raised on different diets and from flies collected from various natural plant hosts. The results showed that medfly guts harbour a simple microbiome that is primarily determined by the larval diet. However, regardless of the laboratory diet or natural plant host on which flies were raised, Klebsiella spp. dominated medfly microbiomes and were resistant to removal by antibiotic treatment. We sequenced the genome of the dominant putative Klebsiella spp. (‘Medkleb’) isolated from the gut of the Toliman wild-type strain. Genome-wide ANI analysis placed Medkleb within the K. oxytoca / michiganensis group. Species level taxonomy for Medkleb was resolved using a mutli-locus phylogenetic approach - and molecular, sequence and phenotypic analyses all supported its identity as K. michiganensis. Medkleb has a genome size (5825435 bp) which is 1.6 standard deviations smaller than the mean genome size of free-living Klebsiella spp. Medkleb also lacks some genes involved in environmental sensing. Moreover, the Medkleb genome contains at least two recently acquired unique genomic islands as well as genes that encode pectinolytic enzymes capable of degrading plant cell walls. This may be advantageous given that the medfly diet includes unripe fruits containing high proportions of pectin. The results suggest that the medfly harbours a commensal gut bacterium that may have developed a mutualistic association with its host and provide nutritional benefits.
Collapse
Affiliation(s)
- Mike Darrington
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lucy A Friend
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naomi V E Clarke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John T Margaritopolous
- Department of Plant Protection, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization-DEMETER, Volos, Greece
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
5
|
Worsley SF, Innocent TM, Holmes NA, Al-Bassam MM, Schiøtt M, Wilkinson B, Murrell JC, Boomsma JJ, Yu DW, Hutchings MI. Competition-based screening helps to secure the evolutionary stability of a defensive microbiome. BMC Biol 2021; 19:205. [PMID: 34526023 PMCID: PMC8444595 DOI: 10.1186/s12915-021-01142-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/07/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of other bacterial strains. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by providing abundant resources to foment interference competition between bacterial species and by using Pseudonocardia to bias the outcome of competition in favour of antibiotic producers. RESULTS Here, we use RNA-stable isotope probing (RNA-SIP) to confirm that Acromyrmex ants can maintain a range of microbial symbionts on their cuticle by supplying public resources. We then used RNA sequencing, bioassays, and competition experiments to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately biassing the bacterial competition to allow the selective establishment of secondary antibiotic-producing strains while excluding non-antibiotic-producing strains that would parasitise the symbiosis. CONCLUSIONS Our findings are consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition.
Collapse
Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Neil A Holmes
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Mahmoud M Al-Bassam
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Morten Schiøtt
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - J Colin Murrell
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Douglas W Yu
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Matthew I Hutchings
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Som NF, Heine D, Holmes NA, Munnoch JT, Knowles F, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The MtrAB-LpqB two component system links development with secondary metabolite production in Streptomyces species and can be manipulated to switch on silent secondary metabolite clusters. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | - John T. Munnoch
- 3Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, United Kingdom
| | | | | | - Ryan F. Seipke
- 6The Astbury Centre for Structural Molecular Biology, Leeds, United Kingdom
| | - Paul A. Hoskisson
- 7Strat Strathclyde Institute of Pharmacy and Biomedical Scienceshclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, United Kingdom
| | | | | |
Collapse
|
9
|
Heine D, Holmes NA, Worsley SF, Santos ACA, Innocent TM, Scherlach K, Patrick EH, Yu DW, Murrell JC, Vieria PC, Boomsma JJ, Hertweck C, Hutchings MI, Wilkinson B. Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen. Nat Commun 2018; 9:2208. [PMID: 29880868 PMCID: PMC5992151 DOI: 10.1038/s41467-018-04520-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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] [Received: 11/14/2017] [Accepted: 04/24/2018] [Indexed: 11/14/2022] Open
Abstract
Acromyrmex leafcutter ants form a mutually beneficial symbiosis with the fungus Leucoagaricus gongylophorus and with Pseudonocardia bacteria. Both are vertically transmitted and actively maintained by the ants. The fungus garden is manured with freshly cut leaves and provides the sole food for the ant larvae, while Pseudonocardia cultures are reared on the ant-cuticle and make antifungal metabolites to help protect the cultivar against disease. If left unchecked, specialized parasitic Escovopsis fungi can overrun the fungus garden and lead to colony collapse. We report that Escovopsis upregulates the production of two specialized metabolites when it infects the cultivar. These compounds inhibit Pseudonocardia and one, shearinine D, also reduces worker behavioral defenses and is ultimately lethal when it accumulates in ant tissues. Our results are consistent with an active evolutionary arms race between Pseudonocardia and Escovopsis, which modifies both bacterial and behavioral defenses such that colony collapse is unavoidable once Escovopsis infections escalate. Acromyrmex ants cultivate fungus gardens that can be parasitized by Escovopsis sp., leading to colony collapse. Here, Heine et al. identify two secondary metabolites produced by Escovopsis that accumulate in Acromyrmex tissue, reduce behavioural defenses and suppress symbiotic Pseudonocardia bacteria.
Collapse
Affiliation(s)
- Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Ana Carolina A Santos
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany.,Friedrich Schiller University, Jena, Germany.,Departmento de Química, Universidade Federal de São Carlos, UFSCar, Via Washington Luiz KM 235, CP 676, São Carlos, SP, Brazil
| | - Tabitha M Innocent
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Paulo C Vieria
- Departmento de Química, Universidade Federal de São Carlos, UFSCar, Via Washington Luiz KM 235, CP 676, São Carlos, SP, Brazil
| | - Jacobus J Boomsma
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstraße 11a, Jena, 07745, Germany.,Friedrich Schiller University, Jena, Germany
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK.
| |
Collapse
|
10
|
Holmes NA, Devine R, Qin Z, Seipke RF, Wilkinson B, Hutchings MI. Complete genome sequence of Streptomyces formicae KY5, the formicamycin producer. J Biotechnol 2018; 265:116-118. [PMID: 29191667 DOI: 10.1016/j.jbiotec.2017.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 10/31/2017] [Revised: 11/17/2017] [Accepted: 11/25/2017] [Indexed: 11/24/2022]
Abstract
Here we report the complete genome of the new species Streptomyces formicae KY5 isolated from Tetraponera fungus growing ants. S. formicae was sequenced using the PacBio and 454 platforms to generate a single linear chromosome with terminal inverted repeats. Illumina MiSeq sequencing was used to correct base changes resulting from the high error rate associated with PacBio. The genome is 9.6 Mbps, has a GC content of 71.38% and contains 8162 protein coding sequences. Predictive analysis shows this strain encodes at least 45 gene clusters for the biosynthesis of secondary metabolites, including a type 2 polyketide synthase encoding cluster for the antibacterial formicamycins. Streptomyces formicae KY5 is a new, taxonomically distinct Streptomyces species and this complete genome sequence provides an important marker in the genus of Streptomyces.
Collapse
Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ryan F Seipke
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| |
Collapse
|
11
|
Som NF, Heine D, Holmes NA, Munnoch JT, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The Conserved Actinobacterial Two-Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B-65442. Front Microbiol 2017; 8:1145. [PMID: 28702006 PMCID: PMC5487470 DOI: 10.3389/fmicb.2017.01145] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/06/2017] [Indexed: 12/30/2022] Open
Abstract
Streptomyces bacteria make numerous secondary metabolites, including half of all known antibiotics. Production of antibiotics is usually coordinated with the onset of sporulation but the cross regulation of these processes is not fully understood. This is important because most Streptomyces antibiotics are produced at low levels or not at all under laboratory conditions and this makes large scale production of these compounds very challenging. Here, we characterize the highly conserved actinobacterial two-component system MtrAB in the model organism Streptomyces venezuelae and provide evidence that it coordinates production of the antibiotic chloramphenicol with sporulation. MtrAB are known to coordinate DNA replication and cell division in Mycobacterium tuberculosis where TB-MtrA is essential for viability but MtrB is dispensable. We deleted mtrB in S. venezuelae and this resulted in a global shift in the metabolome, including constitutive, higher-level production of chloramphenicol. We found that chloramphenicol is detectable in the wild-type strain, but only at very low levels and only after it has sporulated. ChIP-seq showed that MtrA binds upstream of DNA replication and cell division genes and genes required for chloramphenicol production. dnaA, dnaN, oriC, and wblE (whiB1) are DNA binding targets for MtrA in both M. tuberculosis and S. venezuelae. Intriguingly, over-expression of TB-MtrA and gain of function TB- and Sv-MtrA proteins in S. venezuelae also switched on higher-level production of chloramphenicol. Given the conservation of MtrAB, these constructs might be useful tools for manipulating antibiotic production in other filamentous actinomycetes.
Collapse
Affiliation(s)
- Nicolle F. Som
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Neil A. Holmes
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - John T. Munnoch
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Ryan F. Seipke
- School of Biological Sciences, University of East AngliaNorwich, United Kingdom
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of StrathclydeGlasgow, United Kingdom
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | | |
Collapse
|
12
|
Qin Z, Munnoch JT, Devine R, Holmes NA, Seipke RF, Wilkinson KA, Wilkinson B, Hutchings MI. Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci 2017; 8:3218-3227. [PMID: 28507698 PMCID: PMC5414599 DOI: 10.1039/c6sc04265a] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/09/2017] [Indexed: 12/03/2022] Open
Abstract
We report a new Streptomyces species named S. formicae that was isolated from the African fungus-growing plant-ant Tetraponera penzigi and show that it produces novel pentacyclic polyketides that are active against MRSA and VRE. The chemical scaffold of these compounds, which we have called the formicamycins, is similar to the fasamycins identified from the heterologous expression of clones isolated from environmental DNA, but has significant differences that allow the scaffold to be decorated with up to four halogen atoms. We report the structures and bioactivities of 16 new molecules and show, using CRISPR/Cas9 genome editing, that biosynthesis of these compounds is encoded by a single type 2 polyketide synthase biosynthetic gene cluster in the S. formicae genome. Our work has identified the first antibiotic from the Tetraponera system and highlights the benefits of exploring unusual ecological niches for new actinomycete strains and novel natural products.
Collapse
Affiliation(s)
- Zhiwei Qin
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
| | - John T Munnoch
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Rebecca Devine
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Neil A Holmes
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Ryan F Seipke
- School of Molecular and Cellular Biology , Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Karl A Wilkinson
- Scientific Research Computing Unit , Department of Chemistry , University of Cape Town , Rondebosch 7701 , Cape Town , South Africa
| | - Barrie Wilkinson
- 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 .
| |
Collapse
|
13
|
Holmes NA, Innocent TM, Heine D, Bassam MA, Worsley SF, Trottmann F, Patrick EH, Yu DW, Murrell JC, Schiøtt M, Wilkinson B, Boomsma JJ, Hutchings MI. Genome Analysis of Two Pseudonocardia Phylotypes Associated with Acromyrmex Leafcutter Ants Reveals Their Biosynthetic Potential. Front Microbiol 2016; 7:2073. [PMID: 28082956 PMCID: PMC5183585 DOI: 10.3389/fmicb.2016.02073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 10/15/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are the Atta and Acromyrmex leafcutter ants, which harvest fresh leaves to feed their fungus. Acromyrmex and many other attines vertically transmit a mutualistic strain of Pseudonocardia and use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genus Escovopsis. Pseudonocardia mutualists associated with the attines Apterostigma dentigerum and Trachymyrmex cornetzi make novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derived Acromyrmex octospinosus makes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites of Pseudonocardia on a genome-wide scale. Here, we report a genomic analysis of the Pseudonocardia phylotypes Ps1 and Ps2 that are consistently associated with Acromyrmex ants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines the Pseudonocardia species associated with Acromyrmex ants and supports the hypothesis that Pseudonocardia species could provide a valuable source of new antimicrobials.
Collapse
Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Mahmoud Al Bassam
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Felix Trottmann
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia (UEA)Norwich, UK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyKunming, China
| | - J C Murrell
- School of Environmental Sciences, University of East Anglia (UEA) Norwich, UK
| | - Morten Schiøtt
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | | |
Collapse
|
14
|
Schwenzer KJ, Holmes NA. The incidence of ventricular dysrhythmias during pulmonary artery catheter removal. J Cardiothorac Vasc Anesth 1991; 5:306. [PMID: 1863756 DOI: 10.1016/1053-0770(91)90317-m] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|