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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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2
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Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG. Correction: Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. PLoS Biol 2024; 22:e3002531. [PMID: 38359383 PMCID: PMC10869162 DOI: 10.1371/journal.pbio.3002531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pbio.3001988.].
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3
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Gallego-Parrilla JJ, Severi E, Chandra G, Palmer T. Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase. Microbiology (Reading) 2024; 170:001431. [PMID: 38363712 PMCID: PMC10924467 DOI: 10.1099/mic.0.001431] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The twin-arginine protein transport (Tat) system exports folded proteins across the cytoplasmic membranes of prokaryotes and the energy transducing-membranes of plant thylakoids and mitochondria. Proteins are targeted to the Tat machinery by N-terminal signal peptides with a conserved twin-arginine motif, and some substrates are exported as heterodimers where the signal peptide is present on one of the partner proteins. A subset of Tat substrates is found in the membrane. Tat-dependent membrane proteins usually have large globular domains and a single transmembrane helix present at the N- or C-terminus. Five Tat substrates that have C-terminal transmembrane helices have previously been characterized in the model bacterium Escherichia coli. Each of these is an iron-sulfur cluster-containing protein involved in electron transfer from hydrogen or formate. Here we have undertaken a bioinformatic search to identify further tail-anchored Tat substrates encoded in bacterial genomes. Our analysis has revealed additional tail-anchored iron-sulfur proteins associated in modules with either a b-type cytochrome or a quinol oxidase. We also identified further candidate tail-anchored Tat substrates, particularly among members of the actinobacterial phylum, that are not predicted to contain cofactors. Using reporter assays, we show experimentally that six of these have both N-terminal Tat signal peptides and C-terminal transmembrane helices. The newly identified proteins include a carboxypeptidase and a predicted protease, and four sortase substrates for which membrane integration is a prerequisite for covalent attachment to the cell wall.
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Affiliation(s)
- José Jesús Gallego-Parrilla
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Emmanuele Severi
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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McLean TC, Beaton ADM, Martins C, Saalbach G, Chandra G, Wilkinson B, Hutchings MI. Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145. Microbiology (Reading) 2023; 169:001358. [PMID: 37418299 PMCID: PMC10433416 DOI: 10.1099/mic.0.001358] [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] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023]
Abstract
CutRS was the first two-component system to be identified in Streptomyces species and is highly conserved in this genus. It was reported >25 years ago that deletion of cutRS increases the production of the antibiotic actinorhodin in Streptomyces coelicolor. However, despite this early work, the function of CutRS has remained enigmatic until now. Here we show that deletion of cutRS upregulates the production of the actinorhodin biosynthetic enzymes up to 300-fold, explaining the increase in actinorhodin production. However, while ChIP-seq identified 85 CutR binding sites in S. coelicolor none of these are in the actinorhodin biosynthetic gene cluster, meaning the effect is indirect. The directly regulated CutR targets identified in this study are implicated in extracellular protein folding, including two of the four highly conserved HtrA-family foldases: HtrA3 and HtrB, and a putative VKOR enzyme, which is predicted to recycle DsbA following its catalysis of disulphide bond formation in secreted proteins. Thus, we tentatively propose a role for CutRS in sensing and responding to protein misfolding outside the cell. Since actinorhodin can oxidise cysteine residues and induce disulphide bond formation in proteins, its over production in the ∆cutRS mutant may be a response to protein misfolding on the extracellular face of the membrane.
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Affiliation(s)
- Thomas C. McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Ainsley D. M. Beaton
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Carlo Martins
- Department Biochemistry and Metabolism, Proteomics Facility, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Gerhard Saalbach
- Department Biochemistry and Metabolism, Proteomics Facility, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
| | - Matthew I. Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norwich Research Park, NR4 7UH, UK
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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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6
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Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG. Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. PLoS Biol 2023; 21:e3001988. [PMID: 36787297 PMCID: PMC9928087 DOI: 10.1371/journal.pbio.3001988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/04/2023] [Indexed: 02/15/2023] Open
Abstract
Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.
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Affiliation(s)
- Catriona M. A. Thompson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Crown Street, Liverpool, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Supakan Panturat
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Susannah M. Bird
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Samuel Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Richard H. Little
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ainelen Piazza
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Robert W. Jackson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Jacob G. Malone
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
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7
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Appia-Ayme C, Little R, Chandra G, de Oliveira Martins C, Bueno Batista M, Dixon R. Interactions between paralogous bacterial enhancer-binding proteins enable metal-dependent regulation of alternative nitrogenases in Azotobacter vinelandii. Mol Microbiol 2022; 118:105-124. [PMID: 35718936 PMCID: PMC9542535 DOI: 10.1111/mmi.14955] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
All diazotrophic bacteria and archaea isolated so far utilise a nitrogenase enzyme‐containing molybdenum in the active site co‐factor to fix atmospheric dinitrogen to ammonia. However, in addition to the Mo‐dependent nitrogenase, some nitrogen‐fixing prokaryotes also express genetically distinct alternative nitrogenase isoenzymes, namely the V‐dependent and Fe‐only nitrogenases, respectively. Nitrogenase isoenzymes are expressed hierarchically according to metal availability and catalytic efficiency. In proteobacteria, this hierarchy is maintained via stringent transcriptional regulation of gene clusters by dedicated bacterial enhancer‐binding proteins (bEBPs). The model diazotroph Azotobacter vinelandii contains two paralogs of the vanadium nitrogenase activator VnfA (henceforth, VnfA1), designated VnfA2 and VnfA3, with unknown functions. Here we demonstrate that the VnfA1 and VnfA3 bEBPs bind to the same target promoters in the Azotobacter vinelandii genome and co‐activate a subset of genes in the absence of V, including the structural genes for the Fe‐only nitrogenase. Co‐activation is inhibited by the presence of V and is dependent on an accessory protein VnfZ that is co‐expressed with VnfA3. Our studies uncover a plethora of interactions between bEBPs required for nitrogen fixation, revealing the unprecedented potential for fine‐tuning the expression of alternative nitrogenases in response to metal availability.
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Affiliation(s)
| | - Richard Little
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | | | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
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8
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Stratton K, Bush M, Chandra G, Findlay K, Schlimpert S. How do Streptomyces coordinate DNA repair and cell division following DNA damage? Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0308] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA damage often results in a pause of cell division until damage is repaired. In bacteria, a widely conserved response to DNA damage is the SOS response which relies on two proteins: the multifunctional recombinase RecA and the transcriptional repressor LexA. Under DNA-damaging conditions, this response activates proteins involved in DNA repair and the inhibition of cell division which in most unicellular bacteria results in temporarily filamentous growth. However, it is unknown how naturally filamentous growing bacteria like Streptomyces cope with DNA damage and how DNA damage repair is coordinated with cell division.
To identify novel regulators of cell division in Streptomyces that specifically function during DNA damaging growth conditions, we investigated the global response of Streptomyces venezuelae to several genotoxic agents, including mitomycin C, ciprofloxacin and methane methylsulfonate. To this end we have performed ChIP-seq experiments to identify the LexA regulon in Streptomycesandconducted RNA-seq experiments to determine the global response to DNA damaging agents in the wildtype and a recA mutant. The combined analysis of the available data sets has allowed us to obtain a comprehensive overview about the genes involved in the SOS response in Streptomycesand further analysis will enable us to understand how damage repair and cell division are coordinated in these bacteria.
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Affiliation(s)
- Kathryn Stratton
- Department of Molecular Microbiology, John Innes Centre, United Kingdom
| | - Matthew Bush
- Department of Molecular Microbiology, John Innes Centre, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, United Kingdom
| | - Kim Findlay
- Department of Cell and Developmental Biology, John Innes Centre, United Kingdom
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, United Kingdom
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9
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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10
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Huergo LF, Conzentino M, Gonçalves MV, Gernet MV, Reis RA, Pedrosa FO, Baura VA, Pires A, Gerhardt ECM, Tuleski TR, Balsanelli E, Guizelini D, Souza EM, Chandra G, Cruz LM. The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides. World J Microbiol Biotechnol 2021; 37:210. [PMID: 34719741 DOI: 10.1007/s11274-021-03174-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we obtained few Streptomyces isolates from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.
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Affiliation(s)
| | | | | | | | | | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Valter A Baura
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Araceli Pires
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | | | - Thalita R Tuleski
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Dieval Guizelini
- Programa de Pós-graduação em Bioinformática, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Leonardo M Cruz
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
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11
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Fopp-Bayat D, Nitkiewicz A, Chandra G. First report on embryonic and larval development of 2n/3n mosaic sterlet. Animal 2021; 15:100317. [PMID: 34340140 DOI: 10.1016/j.animal.2021.100317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Mosaicism is frequently observed in aquaculture practices, and it adversely affects the production as well as the restoration programme of the sturgeon. The purpose of the present study was the induction of 2n/3n mosaic in sterlet, Acipenser ruthenus L., and compare their embryonic and larval development with diploid control sterlet. Microsatellite DNA loci genotyping was conducted for the identification of the genotypes and parentage analysis. Embryonic development was monitored in experimental groups at every 24 h interval. Identification of individual stages of embryonic development was recorded based on a 36-degree scale of development. Additionally, the BW and body length (LT) of experimental fishes were taken during 110 days of the rearing period. The Fulton's condition coefficient (F), length-weight parameters, and specific growth rate (SGR) coefficient were calculated. The analysis of embryonic development of the 2n/3n mosaic and the diploid control group did not show differences. However, higher mortality (88%) was observed in 2n/3n mosaic groups in comparison to the diploid control groups (55%). BW and body length of 2n/3n mosaic sterlet were slightly lower than the diploid control sterlet, but the differences were not statistically significant. F analysis did not confirm a lower growth performance of the fishes in the 2n/3n mosaic group. Microsatellite DNA loci genotyping confirmed both the incidence of polyspermy and retention of the second polar body. This paper presents the first report on embryonic development and growth performance of 2n/3n mosaic sturgeons.
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Affiliation(s)
- D Fopp-Bayat
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland.
| | - A Nitkiewicz
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland
| | - G Chandra
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland
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12
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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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13
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Ramos-León F, Bush MJ, Sallmen JW, Chandra G, Richardson J, Findlay KC, McCormick JR, Schlimpert S. A conserved cell division protein directly regulates FtsZ dynamics in filamentous and unicellular actinobacteria. eLife 2021; 10:e63387. [PMID: 33729912 PMCID: PMC7968930 DOI: 10.7554/elife.63387] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/23/2020] [Accepted: 03/03/2021] [Indexed: 01/05/2023] Open
Abstract
Bacterial cell division is driven by the polymerization of the GTPase FtsZ into a contractile structure, the so-called Z-ring. This essential process involves proteins that modulate FtsZ dynamics and hence the overall Z-ring architecture. Actinobacteria like Streptomyces and Mycobacterium lack known key FtsZ-regulators. Here we report the identification of SepH, a conserved actinobacterial protein that directly regulates FtsZ dynamics. We show that SepH is crucially involved in cell division in Streptomyces venezuelae and that it binds FtsZ via a conserved helix-turn-helix motif, stimulating the assembly of FtsZ protofilaments. Comparative in vitro studies using the SepH homolog from Mycobacterium smegmatis further reveal that SepH can also bundle FtsZ protofilaments, indicating an additional Z-ring stabilizing function in vivo. We propose that SepH plays a crucial role at the onset of cytokinesis in actinobacteria by promoting the assembly of FtsZ filaments into division-competent Z-rings that can go on to mediate septum synthesis.
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Affiliation(s)
- Félix Ramos-León
- Department of Molecular Microbiology, John Innes CentreNorwichUnited Kingdom
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes CentreNorwichUnited Kingdom
| | - Joseph W Sallmen
- Department of Molecular Microbiology, John Innes CentreNorwichUnited Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes CentreNorwichUnited Kingdom
| | - Jake Richardson
- Department of Cell and Developmental Biology, John Innes CentreNorwichUnited Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes CentreNorwichUnited Kingdom
| | - Joseph R McCormick
- Department of Biological Sciences, Duquesne UniversityPittsburghUnited States
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes CentreNorwichUnited Kingdom
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14
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Devine R, McDonald HP, Qin Z, Arnold CJ, Noble K, Chandra G, Wilkinson B, Hutchings MI. Re-wiring the regulation of the formicamycin biosynthetic gene cluster to enable the development of promising antibacterial compounds. Cell Chem Biol 2021; 28:515-523.e5. [PMID: 33440167 PMCID: PMC8062789 DOI: 10.1016/j.chembiol.2020.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022]
Abstract
The formicamycins are promising antibiotics first identified in Streptomyces formicae KY5, which produces the compounds at low levels. Here, we show that by understanding the regulation of the for biosynthetic gene cluster (BGC), we can rewire the BGC to increase production levels. The for BGC consists of 24 genes expressed on nine transcripts. The MarR regulator ForJ represses expression of seven transcripts encoding the major biosynthetic genes as well as the ForGF two-component system that initiates biosynthesis. We show that overexpression of forGF in a ΔforJ background increases formicamycin production 10-fold compared with the wild-type. De-repression, by deleting forJ, also switches on biosynthesis in liquid culture and induces the production of additional, previously unreported formicamycin congeners. Furthermore, combining de-repression with mutations in biosynthetic genes leads to biosynthesis of additional bioactive precursors. Formicamycin biosynthesis requires 24 genes expressed on nine transcripts Deleting the MarR regulator ForJ increases formicamycin biosynthesis De-repressing formicamycin biosynthesis induces production in liquid culture Re-wiring regulation and biosynthesis results in the production of new congeners
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Affiliation(s)
- Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Hannah P McDonald
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Corinne J Arnold
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katie Noble
- 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.
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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15
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Moffat AD, Santos-Aberturas J, Chandra G, Truman AW. Correction to: A User Guide for the Identification of New RiPP Biosynthetic Gene Clusters Using a RiPPER-Based Workflow. Methods Mol Biol 2021; 2296:C1. [PMID: 34581995 DOI: 10.1007/978-1-0716-1358-0_26] [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: 06/13/2023]
Affiliation(s)
- Alaster D Moffat
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
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16
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Oliveira R, Bush MJ, Pires S, Chandra G, Casas-Pastor D, Fritz G, Mendes MV. The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis. Sci Rep 2020; 10:21728. [PMID: 33303917 PMCID: PMC7730460 DOI: 10.1038/s41598-020-78520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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: 07/24/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2-σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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Affiliation(s)
- Rute Oliveira
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCBiology), ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sílvia Pires
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delia Casas-Pastor
- Center for Synthetic Microbiology, Philipps-University Marburg, 35032, Marburg, Germany
| | - Georg Fritz
- School for Molecular Sciences, University of Western Australia, Perth, 6009, Australia
| | - Marta V Mendes
- Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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17
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Grenga L, Little RH, Chandra G, Woodcock SD, Saalbach G, Morris RJ, Malone JG. Control of mRNA translation by dynamic ribosome modification. PLoS Genet 2020; 16:e1008837. [PMID: 32584816 PMCID: PMC7343187 DOI: 10.1371/journal.pgen.1008837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/04/2020] [Revised: 07/08/2020] [Accepted: 05/07/2020] [Indexed: 01/28/2023] Open
Abstract
Control of mRNA translation is a crucial regulatory mechanism used by bacteria to respond to their environment. In the soil bacterium Pseudomonas fluorescens, RimK modifies the C-terminus of ribosomal protein RpsF to influence important aspects of rhizosphere colonisation through proteome remodelling. In this study, we show that RimK activity is itself under complex, multifactorial control by the co-transcribed phosphodiesterase trigger enzyme (RimA) and a polyglutamate-specific protease (RimB). Furthermore, biochemical experimentation and mathematical modelling reveal a role for the nucleotide second messenger cyclic-di-GMP in coordinating these activities. Active ribosome regulation by RimK occurs by two main routes: indirectly, through changes in the abundance of the global translational regulator Hfq and directly, with translation of surface attachment factors, amino acid transporters and key secreted molecules linked specifically to RpsF modification. Our findings show that post-translational ribosomal modification functions as a rapid-response mechanism that tunes global gene translation in response to environmental signals.
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Affiliation(s)
- Lucia Grenga
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | | | - Govind Chandra
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | | | - Gerhard Saalbach
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Richard James Morris
- Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Jacob George Malone
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
- * E-mail:
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18
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Chandra G, Pandey A. Preparation Strategies for Mg-alloys for Biodegradable Orthopaedic Implants and Other Biomedical Applications: A Review. Ing Rech Biomed 2020. [DOI: 10.1016/j.irbm.2020.06.003] [Citation(s) in RCA: 14] [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: 12/14/2022]
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19
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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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20
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Vior NM, Cea-Torrescassana E, Eyles TH, Chandra G, Truman AW. Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator. Front Microbiol 2020; 11:495. [PMID: 32273872 PMCID: PMC7113386 DOI: 10.3389/fmicb.2020.00495] [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: 08/07/2019] [Accepted: 03/06/2020] [Indexed: 01/18/2023] Open
Abstract
Bottromycin is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by several streptomycetes, including the plant pathogen Streptomyces scabies. There is significant interest in this molecule as it possesses strong antibacterial activity against clinically relevant multidrug resistant pathogens and is structurally distinct from all other antibiotics. However, studies into its efficacy are hampered by poor yields. An understanding of how bottromycin biosynthesis is regulated could aid the development of strategies to increase titres. Here, we use 5′-tag-RNA-seq to identify the transcriptional organization of the gene cluster, which includes an internal transcriptional start site that precedes btmD, the gene that encodes the bottromycin precursor peptide. We show that the gene cluster does not encode a master regulator that controls pathway expression and instead encodes a regulatory gene, btmL, which functions as a modulator that specifically affects the expression of btmD but not genes up- or downstream of btmD. In order to identify non-cluster associated proteins involved in regulation, proteins were identified that bind to the main promoter of the pathway, which precedes btmC. This study provides insights into how this deceptively complex pathway is regulated in the absence of a pathway specific master regulator, and how it might coordinate with the central metabolism of the cell.
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Affiliation(s)
- Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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21
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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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22
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Scott TA, Batey SFD, Wiencek P, Chandra G, Alt S, Francklyn CS, Wilkinson B. Immunity-Guided Identification of Threonyl-tRNA Synthetase as the Molecular Target of Obafluorin, a β-Lactone Antibiotic. ACS Chem Biol 2019; 14:2663-2671. [PMID: 31675206 DOI: 10.1021/acschembio.9b00590] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To meet the ever-growing demands of antibiotic discovery, new chemical matter and antibiotic targets are urgently needed. Many potent natural product antibiotics which were previously discarded can also provide lead molecules and drug targets. One such example is the structurally unique β-lactone obafluorin, produced by Pseudomonas fluorescens ATCC 39502. Obafluorin is active against both Gram-positive and -negative pathogens; however, the biological target was unknown. We now report that obafluorin targets threonyl-tRNA synthetase, and we identify a homologue, ObaO, which confers immunity to the obafluorin producer. Disruption of obaO in P. fluorescens ATCC 39502 results in obafluorin sensitivity, whereas expression in sensitive E. coli strains confers resistance. Enzyme assays demonstrate that E. coli threonyl-tRNA synthetase is fully inhibited by obafluorin, whereas ObaO is only partly susceptible, exhibiting a very unusual partial inhibition mechanism. Altogether, our data highlight the utility of an immunity-guided approach for the identification of an antibiotic target de novo and will ultimately enable the generation of improved obafluorin variants.
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Affiliation(s)
- Thomas A. Scott
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Sibyl F. D. Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Patrick Wiencek
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Silke Alt
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Christopher S. Francklyn
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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23
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Santos-Aberturas J, Chandra G, Frattaruolo L, Lacret R, Pham TH, Vior NM, Eyles TH, Truman AW. Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Res 2019; 47:4624-4637. [PMID: 30916321 PMCID: PMC6511847 DOI: 10.1093/nar/gkz192] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [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: 12/21/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 01/26/2023] Open
Abstract
The rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, which are proposed to be introduced by YcaO-TfuA proteins. Using RiPPER, we show that previously undescribed RiPP gene clusters encoding YcaO and TfuA proteins are widespread in Actinobacteria and encode a highly diverse landscape of precursor peptides that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new structural class of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.
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Affiliation(s)
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Luca Frattaruolo
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Thu H Pham
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
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24
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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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25
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Batista MB, Chandra G, Monteiro RA, de Souza EM, Dixon R. Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae. Nucleic Acids Res 2019. [PMID: 29529262 PMCID: PMC5934665 DOI: 10.1093/nar/gky142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/14/2022] Open
Abstract
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors. Comparison of DNA binding motifs between the three promoter groups suggests Group III promoters are potentially co-activated by Fnr3–Fnr1 heterodimers. Specific interaction between Fnr1 and Fnr3, detected in two-hybrid assays, was dependent on conserved residues in their dimerization interfaces, indicative of heterodimer formation in vivo. The requirements for co-activation of the fnr1 promoter, belonging to Group III, suggest either sequential activation by Fnr3 and Fnr1 homodimers or the involvement of Fnr3–Fnr1 heterodimers. Analysis of Fnr proteins with swapped activation domains provides evidence that co-activation by Fnr1 and Fnr3 at Group III promoters optimises interactions with RNA polymerase to fine-tune transcription in response to prevailing oxygen concentrations.
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Affiliation(s)
- Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, P.O. Box 19046, Curitiba, PR 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, P.O. Box 19046, Curitiba, PR 81531-990, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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26
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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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27
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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
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28
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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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29
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Gimenez MR, Chandra G, Van Overvelt P, Voulhoux R, Bleves S, Ize B. Genome wide identification and experimental validation of Pseudomonas aeruginosa Tat substrates. Sci Rep 2018; 8:11950. [PMID: 30093651 PMCID: PMC6085387 DOI: 10.1038/s41598-018-30393-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 05/11/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
In bacteria, the twin-arginine translocation (Tat) pathway allows the export of folded proteins through the inner membrane. Proteins targeted to this system are synthesized with N-terminal signal peptides bearing a conserved twin-arginine motif. The Tat pathway is critical for many bacterial processes including pathogenesis and virulence. However, the full set of Tat substrates is unknown in many bacteria, and the reliability of in silico prediction methods largely uncertain. In this work, we performed a combination of in silico analysis and experimental validation to identify a core set of Tat substrates in the opportunistic pathogen Pseudomonas aeruginosa. In silico analysis predicted 44 putative Tat signal peptides in the P. aeruginosa PA14 proteome. We developed an improved amidase-based Tat reporter assay to show that 33 of these are real Tat signal peptides. In addition, in silico analysis of the full translated genome revealed a Tat candidate with a missassigned start codon. We showed that it is a new periplasmic protein in P. aeruginosa. Altogether we discovered and validated 34 Tat substrates. These show little overlap with Escherichia coli Tat substrates, and functional analysis points to a general role for the P. aeruginosa Tat system in the colonization of environmental niches and pathogenicity.
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Affiliation(s)
- Maxime Rémi Gimenez
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Perrine Van Overvelt
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Romé Voulhoux
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Sophie Bleves
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Bérengère Ize
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France.
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30
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Chandra G, Shenoi RA, Anand R, Rajamma U, Mohanakumar KP. Reinforcing mitochondrial functions in aging brain: An insight into Parkinson's disease therapeutics. J Chem Neuroanat 2017; 95:29-42. [PMID: 29269015 DOI: 10.1016/j.jchemneu.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/16/2017] [Accepted: 12/17/2017] [Indexed: 12/19/2022]
Abstract
Mitochondria, the powerhouse of the neural cells in the brain, are also the seat of certain essential gene signaling pathways that control neuronal functions. Deterioration of mitochondrial functions has been widely reported in normal aging as well as in a spectrum of age-associated neurological diseases, including Parkinson's disease (PD). Evidences accumulated in the recent past provide not only advanced information on the causes of mitochondrial bioenergetics defects and redox imbalance in PD brains, but also much insight into mitochondrial biogenesis, quality control of mitochondrial proteins, and genes, which regulate intra- and extra-mitochondrial signaling that control the general health of neural cells. The mitochondrial quality control machinery is affected in aging and especially in PD, thus affecting intraneuronal protein transport and degradation, which are primarily responsible for accumulation of misfolded proteins and mitochondrial damage in sporadic as well as familial PD. Essentially we considered in the first half of this review, mitochondria-based targets such as mitochondrial oxidative stress and mitochondrial quality control pathways in PD, relevance of mitochondrial DNA mutations, mitophagy, mitochondrial proteases, mitochondrial flux, and finally mitochondria-based therapies possible for PD. Therapeutic aspects are considered in the later half and mitochondria-targeted antioxidant therapy, mitophagy enhancers, mitochondrial biogenesis boasters, mitochondrial dynamics modulators, and gene-based therapeutic approaches are discussed. The present review is a critical assessment of this information to distinguish some exemplary mitochondrial therapeutic targets, and provides a utilitarian perception of some avenues for therapeutic designs on identified mitochondrial targets for PD, a very incapacitating disorder of the geriatric population, world over.
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Affiliation(s)
- G Chandra
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board P.O., Kottayam, Kerala - 686009, India.
| | - R A Shenoi
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board P.O., Kottayam, Kerala - 686009, India
| | - R Anand
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board P.O., Kottayam, Kerala - 686009, India
| | - U Rajamma
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board P.O., Kottayam, Kerala - 686009, India
| | - K P Mohanakumar
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board P.O., Kottayam, Kerala - 686009, India
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31
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Som NF, Heine D, Holmes N, Knowles F, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI. The MtrAB two-component system controls antibiotic production in Streptomyces coelicolor A3(2). Microbiology (Reading) 2017; 163:1415-1419. [PMID: 28884676 PMCID: PMC5845573 DOI: 10.1099/mic.0.000524] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/15/2017] [Indexed: 12/24/2022]
Abstract
MtrAB is a highly conserved two-component system implicated in the regulation of cell division in the Actinobacteria. It coordinates DNA replication with cell division in the unicellular Mycobacterium tuberculosis and links antibiotic production to sporulation in the filamentous Streptomyces venezuelae. Chloramphenicol biosynthesis is directly regulated by MtrA in S. venezuelae and deletion of mtrB constitutively activates MtrA and results in constitutive over-production of chloramphenicol. Here we report that in Streptomyces coelicolor, MtrA binds to sites upstream of developmental genes and the genes encoding ActII-1, ActII-4 and RedZ, which are cluster-situated regulators of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red). Consistent with this, deletion of mtrB switches on the production of Act, Red and streptorubin B, a product of the Red pathway. Thus, we propose that MtrA is a key regulator that links antibiotic production to development and can be used to upregulate antibiotic production in distantly related streptomycetes.
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Affiliation(s)
- Nicolle F. Som
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Neil Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Felicity Knowles
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan F. Seipke
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161, Cathedral Street, Glasgow, G4 0RE, UK
| | - 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
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32
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Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG. Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach. Front Microbiol 2017; 8:1784. [PMID: 29033902 PMCID: PMC5627042 DOI: 10.3389/fmicb.2017.01784] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022] Open
Abstract
The ability of bacteria to respond to environmental change is based on the ability to coordinate, redirect and fine-tune their genetic repertoire as and when required. While we can learn a great deal from reductive analysis of individual pathways and global approaches to gene regulation, a deeper understanding of these complex signaling networks requires the simultaneous consideration of several regulatory layers at the genome scale. To highlight the power of this approach we analyzed the Hfq transcriptional/translational regulatory network in the model bacterium Pseudomonas fluorescens. We first used extensive ‘omics’ analyses to assess how hfq deletion affects mRNA abundance, mRNA translation and protein abundance. The subsequent, multi-level integration of these datasets allows us to highlight the discrete contributions by Hfq to gene regulation at different levels. The integrative approach to regulatory analysis we describe here has significant potential, for both dissecting individual signaling pathways and understanding the strategies bacteria use to cope with external challenges.
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Affiliation(s)
- Lucia Grenga
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom.,School of Biological Sciences, University of East AngliaNorwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom
| | - Carla V Galmozzi
- Center for Molecular Biology of the University of Heidelberg, DKFZ-ZMBH AllianceHeidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg, DKFZ-ZMBH AllianceHeidelberg, Germany.,German Cancer Research CenterHeidelberg, Germany
| | - Jacob G Malone
- Department of Molecular Microbiology, John Innes CentreNorwich, United Kingdom.,School of Biological Sciences, University of East AngliaNorwich, United Kingdom
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33
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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.
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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
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34
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Campilongo R, Fung RKY, Little RH, Grenga L, Trampari E, Pepe S, Chandra G, Stevenson CEM, Roncarati D, Malone JG. One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet 2017; 13:e1006839. [PMID: 28658302 PMCID: PMC5489143 DOI: 10.1371/journal.pgen.1006839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG, an Entner Doudoroff (ED) pathway intermediate. KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR. RccR inversely controls the glyoxylate shunt, gluconeogenesis and pyruvate metabolism, suppressing the first two pathways as pyruvate metabolism genes are expressed, and vice versa. This complex regulation is enabled by two distinct RccR-binding consensus sequences in the RccR regulon promoters. KDPG binding simultaneously increases RccR affinity for the glyoxylate shunt and gluconeogenesis promoters, and releases repression of pyruvate metabolism. This elegant two-regulator circuit allows Pseudomonas to rapidly respond to carbon source availability by sensing a single key intermediate, KDPG.
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Affiliation(s)
- Rosaria Campilongo
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- Istituto Pasteur- Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘C. Darwin”, Sapienza Universita`di Roma, Roma, Italy
| | - Rowena K. Y. Fung
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Richard H. Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Eleftheria Trampari
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Simona Pepe
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Davide Roncarati
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Tooke FJ, Babot M, Chandra G, Buchanan G, Palmer T. A unifying mechanism for the biogenesis of membrane proteins co-operatively integrated by the Sec and Tat pathways. eLife 2017; 6. [PMID: 28513434 PMCID: PMC5449189 DOI: 10.7554/elife.26577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 03/07/2017] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
The majority of multi-spanning membrane proteins are co-translationally inserted into the bilayer by the Sec pathway. An important subset of membrane proteins have globular, cofactor-containing extracytoplasmic domains requiring the dual action of the co-translational Sec and post-translational Tat pathways for integration. Here, we identify further unexplored families of membrane proteins that are dual Sec-Tat-targeted. We establish that a predicted heme-molybdenum cofactor-containing protein, and a complex polyferredoxin, each require the concerted action of two translocases for their assembly. We determine that the mechanism of handover from Sec to Tat pathway requires the relatively low hydrophobicity of the Tat-dependent transmembrane domain. This, coupled with the presence of C-terminal positive charges, results in abortive insertion of this transmembrane domain by the Sec pathway and its subsequent release at the cytoplasmic side of the membrane. Together, our data points to a simple unifying mechanism governing the assembly of dual targeted membrane proteins.
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Affiliation(s)
- Fiona J Tooke
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marion Babot
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Grant Buchanan
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Tracy Palmer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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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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Thanapipatsiri A, Gomez‐Escribano JP, Song L, Bibb MJ, Al‐Bassam M, Chandra G, Thamchaipenet A, Challis GL, Bibb MJ. Discovery of Unusual Biaryl Polyketides by Activation of a Silent Streptomyces venezuelae Biosynthetic Gene Cluster. Chembiochem 2016; 17:2189-2198. [PMID: 27605017 PMCID: PMC5132015 DOI: 10.1002/cbic.201600396] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 07/13/2016] [Indexed: 11/22/2022]
Abstract
Comparative transcriptional profiling of a ΔbldM mutant of Streptomyces venezuelae with its unmodified progenitor revealed that the expression of a cryptic biosynthetic gene cluster containing both type I and type III polyketide synthase genes is activated in the mutant. The 29.5 kb gene cluster, which was predicted to encode an unusual biaryl metabolite, which we named venemycin, and potentially halogenated derivatives, contains 16 genes including one-vemR-that encodes a transcriptional activator of the large ATP-binding LuxR-like (LAL) family. Constitutive expression of vemR in the ΔbldM mutant led to the production of sufficient venemycin for structural characterisation, confirming its unusual biaryl structure. Co-expression of the venemycin biosynthetic gene cluster and vemR in the heterologous host Streptomyces coelicolor also resulted in venemycin production. Although the gene cluster encodes two halogenases and a flavin reductase, constitutive expression of all three genes led to the accumulation only of a monohalogenated venemycin derivative, both in the native producer and the heterologous host. A competition experiment in which equimolar quantities of sodium chloride and sodium bromide were fed to the venemycin-producing strains resulted in the preferential incorporation of bromine, thus suggesting that bromide is the preferred substrate for one or both halogenases.
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Affiliation(s)
- Anyarat Thanapipatsiri
- Department of GeneticsFaculty of ScienceKasetsart University, 50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | | | - Lijiang Song
- Department of ChemistryUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Maureen J. Bibb
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Mahmoud Al‐Bassam
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of BioengineeringUniversity of California San Diego9500 Gilman Drive, MC 0412La JollaCA92093-0412USA
| | - Govind Chandra
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Arinthip Thamchaipenet
- Department of GeneticsFaculty of ScienceKasetsart University, 50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
- Center for Advanced Studies in Tropical Natural ResourcesNRU–KUKasetsart University50 Ngamwongwan Road, Ladyao, ChatuchakBangkok10900Thailand
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Mervyn J. Bibb
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
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38
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Koliwer-Brandl H, Syson K, van de Weerd R, Chandra G, Appelmelk B, Alber M, Ioerger TR, Jacobs WR, Geurtsen J, Bornemann S, Kalscheuer R. Metabolic Network for the Biosynthesis of Intra- and Extracellular α-Glucans Required for Virulence of Mycobacterium tuberculosis. PLoS Pathog 2016; 12:e1005768. [PMID: 27513637 PMCID: PMC4981310 DOI: 10.1371/journal.ppat.1005768] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 03/08/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis synthesizes intra- and extracellular α-glucans that were believed to originate from separate pathways. The extracellular glucose polymer is the main constituent of the mycobacterial capsule that is thought to be involved in immune evasion and virulence. However, the role of the α-glucan capsule in pathogenesis has remained enigmatic due to an incomplete understanding of α-glucan biosynthetic pathways preventing the generation of capsule-deficient mutants. Three separate and potentially redundant pathways had been implicated in α-glucan biosynthesis in mycobacteria: the GlgC-GlgA, the Rv3032 and the TreS-Pep2-GlgE pathways. We now show that α-glucan in mycobacteria is exclusively assembled intracellularly utilizing the building block α-maltose-1-phosphate as the substrate for the maltosyltransferase GlgE, with subsequent branching of the polymer by the branching enzyme GlgB. Some α-glucan is exported to form the α-glucan capsule. There is an unexpected convergence of the TreS-Pep2 and GlgC-GlgA pathways that both generate α-maltose-1-phosphate. While the TreS-Pep2 route from trehalose was already known, we have now established that GlgA forms this phosphosugar from ADP-glucose and glucose 1-phosphate 1000-fold more efficiently than its hitherto described glycogen synthase activity. The two routes are connected by the common precursor ADP-glucose, allowing compensatory flux from one route to the other. Having elucidated this unexpected configuration of the metabolic pathways underlying α-glucan biosynthesis in mycobacteria, an M. tuberculosis double mutant devoid of α-glucan could be constructed, showing a direct link between the GlgE pathway, α-glucan biosynthesis and virulence in a mouse infection model. Capsule formation is critical for the virulence of many bacterial and fungal pathogens. Mycobacterium tuberculosis cells are known to be surrounded by a capsule layer that is mainly composed of an α-glucan glucose polymer that resembles glycogen. Progress in understanding its role in the virulence of this important human pathogen has been held back by a lack of knowledge of its biosynthesis, preventing the generation of α-glucan-deficient mutants that could be tested in animal infection models. In this work, we unraveled an unexpected metabolic network configuration revealing the exclusive production of both intracellular and capsular α-glucans by the maltosyltransferase GlgE in mycobacteria. GlgE polymerizes an α-maltose 1-phosphate building block, which is generated by two alternative pathways that are connected by a common intermediate allowing rechanneling of flux from one route to the other. Elucidation of this unexpected configuration of the metabolic pathways underlying α-glucan biosynthesis allowed the rational construction of an M. tuberculosis mutant strain devoid of α-glucan, showing a direct link between the GlgE pathway, α-glucan biosynthesis and virulence in a mouse infection model.
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Affiliation(s)
- Hendrik Koliwer-Brandl
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karl Syson
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Robert van de Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ben Appelmelk
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - William R. Jacobs
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jeroen Geurtsen
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Stephen Bornemann
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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Tkacz A, Cheema J, Chandra G, Grant A, Poole PS. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J 2015; 9:2349-59. [PMID: 25909975 PMCID: PMC4611498 DOI: 10.1038/ismej.2015.41] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]
Abstract
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.
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Affiliation(s)
- Andrzej Tkacz
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
| | - Jitender Cheema
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alastair Grant
- Earth and Life Systems Alliance, The School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
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Mauchline TH, Chedom-Fotso D, Chandra G, Samuels T, Greenaway N, Backhaus A, McMillan V, Canning G, Powers SJ, Hammond-Kosack KE, Hirsch PR, Clark IM, Mehrabi Z, Roworth J, Burnell J, Malone JG. An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota. Environ Microbiol 2015; 17:4764-78. [PMID: 26337499 PMCID: PMC4832304 DOI: 10.1111/1462-2920.13038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 01/22/2023]
Abstract
Manipulation of the soil microbiota associated with crop plants has huge promise for the control of crop pathogens. However, to fully realize this potential we need a better understanding of the relationship between the soil environment and the genes and phenotypes that enable microbes to colonize plants and contribute to biocontrol. A recent 2 years of investigation into the effect of wheat variety on second year crop yield in the context of take‐all fungal infection presented the opportunity to examine soil microbiomes under closely defined field conditions. Amplicon sequencing of second year soil samples showed that Pseudomonas spp. were particularly affected by the wheat cultivar grown in year one. Consequently, 318 rhizosphere‐associated Pseudomonas fluorescens strains were isolated and characterized across a variety of genetic and phenotypic traits. Again, the wheat variety grown in the first year of the study was shown to exert considerable selective pressure on both the extent and nature of Pseudomonas genomic diversity. Furthermore, multiple significant correlations were identified within the phenotypic/genetic structure of the Pseudomonas population, and between individual genotypes and the external wheat field environment. The approach outlined here has considerable future potential for our understanding of plant–microbe interactions, and for the broader analysis of complex microbial communities.
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Affiliation(s)
- T H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, UK
| | | | - G Chandra
- Molecular Microbiology Department, John Innes Centre, Norwich, UK
| | - T Samuels
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - N Greenaway
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - A Backhaus
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - V McMillan
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
| | - G Canning
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
| | - S J Powers
- Department of Computational and Systems Biology, Rothamsted Research, Harpenden, UK
| | - K E Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
| | - P R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, UK
| | - I M Clark
- Department of AgroEcology, Rothamsted Research, Harpenden, UK
| | - Z Mehrabi
- Department of AgroEcology, Rothamsted Research, Harpenden, UK.,Oxford Long-term Ecology and Resource Stewardship Lab, University of Oxford, Oxford, UK
| | - J Roworth
- Department of AgroEcology, Rothamsted Research, Harpenden, UK.,Department of Computational and Systems Biology, Rothamsted Research, Harpenden, UK
| | - J Burnell
- Department of AgroEcology, Rothamsted Research, Harpenden, UK
| | - J G Malone
- Molecular Microbiology Department, John Innes Centre, Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, UK
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Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews B, Asenjo JA, Bibb MJ. The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genomics 2015; 16:485. [PMID: 26122045 PMCID: PMC4487206 DOI: 10.1186/s12864-015-1652-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [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] [Received: 02/25/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Background Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics. Results Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialised metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides. Conclusions The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1652-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo Gomez-Escribano
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Jean Franco Castro
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Valeria Razmilic
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Hamilton JJ, Marlow VL, Owen RA, Costa MDAA, Guo M, Buchanan G, Chandra G, Trost M, Coulthurst SJ, Palmer T, Stanley-Wall NR, Sargent F. A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens. ACTA ACUST UNITED AC 2015; 207:615-26. [PMID: 25488919 PMCID: PMC4259817 DOI: 10.1083/jcb.201404127] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 11/22/2022]
Abstract
Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
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Affiliation(s)
- Jaeger J Hamilton
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Victoria L Marlow
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Richard A Owen
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marília de Assis Alcoforado Costa
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Manman Guo
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Grant Buchanan
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7TJ, England, UK
| | - Matthias Trost
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tracy Palmer
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Frank Sargent
- Division of Molecular Microbiology and Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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Chandra G, Aggarwal A, Kumar M, Singh AK, Sharma VK, Upadhyay RC. Effect of additional vitamin E and zinc supplementation on immunological changes in peripartum Sahiwal cows. J Anim Physiol Anim Nutr (Berl) 2014; 98:1166-75. [DOI: 10.1111/jpn.12190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 03/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- G. Chandra
- Dairy Cattle Physiology Division; National Dairy Research Institute Karnal; Haryana India
| | - A. Aggarwal
- Dairy Cattle Physiology Division; National Dairy Research Institute Karnal; Haryana India
| | - M. Kumar
- Department of Animal Nutrition; DUVASU Mathura; Uttar Pradesh India
| | - A. K. Singh
- Dairy Cattle Physiology Division; National Dairy Research Institute Karnal; Haryana India
| | - V. K. Sharma
- Dairy Cattle Nutrition Division; National Dairy Research Institute Karnal; Haryana India
| | - R. C. Upadhyay
- Dairy Cattle Physiology Division; National Dairy Research Institute Karnal; Haryana India
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Chaudhary A, Bogra J, Singh PK, Saxena S, Chandra G, Verma R. Efficacy of spinal ropivacaine versus ropivacaine with fentanyl in transurethral resection operations. Saudi J Anaesth 2014; 8:88-91. [PMID: 24665247 PMCID: PMC3950461 DOI: 10.4103/1658-354x.125951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 11/29/2022] Open
Abstract
Background: The low-dose ropivacaine provides differential spinal block to reduce adverse hemodynamic effects in elderly patients. Addition of intrathecal fentanyl with ropivacaine may enhance analgesia and early postoperative mobility. The present study was performed to evaluate the efficacy of intrathecal ropivacaine alone and in combination with fentanyl in transurethral resection operation. Methods: Sixty male patients aged >50 years of ASA I-III scheduled for elective transurethral resection were included in a prospective, randomized, double-blinded study and they were divided in two groups of 30 each. Group A (n = 30) received intrathecal injection of ropivacaine 2 ml (0.75%) and Group B (n = 30) ropivacaine 1.8 ml (0.75%) with fentanyl 10 μg. The characteristics of onset and regression of sensory and motor blockade, hemodynamic stability, and side effects were observed. Student's t test (for parametric data) and Mann-Whitney U test (for non-parametric data) were used for statistical analyses. Results: There were no significant differences between the two groups for patient demographic data, intraoperative hemodynamic parameters, side effects, and satisfaction to patients and surgeon. The highest level of sensory block was at T10 in group A and T9 in group B (P = 0.001). Duration of motor block was longer in group B being 210.51 ± 61.25 min than in group A being 286.25 ± 55.65 min (P < 0.001). Conclusion: The addition of fentanyl to ropivacaine may offer the advantage of shorter duration of complete motor block, hemodynamic stability, and without any increase in the frequency of major side effects.
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Affiliation(s)
- A Chaudhary
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
| | - J Bogra
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
| | - P K Singh
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
| | - S Saxena
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
| | - G Chandra
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
| | - R Verma
- Department of Anesthesia, KG's Medical University, Lucknow, Uttar Pradesh, India
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Chandra G, Aggarwal A, Singh AK, Kumar M, Upadhyay RC. Effect of vitamin e and zinc supplementation on energy metabolites, lipid peroxidation, and milk production in peripartum sahiwal cows. Asian-Australas J Anim Sci 2013; 26:1569-76. [PMID: 25049743 PMCID: PMC4093816 DOI: 10.5713/ajas.2012.12682] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/12/2013] [Accepted: 02/22/2013] [Indexed: 11/27/2022]
Abstract
The study was conducted to evaluate the effect of vitamin E and zinc supplementation on energy metabolites, lipid peroxidation, and milk production in peripartum Sahiwal cows. For this, thirty-two pregnant dry Sahiwal cows were selected at sixty days prepartum and divided into four groups viz control, T1, T2, and T3 of eight each. Group T1 were supplemented with zinc at 60 ppm/d/cow, group T2 were supplemented with vitamin E at 1,000 IU/d/cow and group T3 were supplemented with combination of vitamin E at 1,000 IU/d/cow and zinc at 60 ppm/d/cow during d 60 prepartum to d 90 postpartum. Blood samples were collected on d -60, -45, -30, -15, -7, -3, 0, 3, 7, 15, 30, 45, 60, 90, and 120 with respect to day of parturition and analysed for glucose, non esterified fatty acid, and thiobarbituric acid reactive substance. Body condition score was maintained significantly better (p<0.05) in T3 than in the control, T1 and T2 groups. Overall glucose level was higher (p<0.05) in T3 than control, T1, and T2 groups. Levels of nonesterified fatty acid, and thiobarbituric acid reactive substance were lower (p<0.05) in T3 than control, T1, and T2 groups. Milk yield was higher (p<0.05) in T3 than control, T1, and T2 groups. In conclusion, the present study indicated that the supplementation of vitamin E and zinc in peripartum Sahiwal cows enhanced milk production by reducing negative energy balance.
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Affiliation(s)
- G. Chandra
- Dairy Cattle Physiology Division, National Dairy Research Institute, Karnal-132001 Haryana,
India
| | - A. Aggarwal
- Dairy Cattle Physiology Division, National Dairy Research Institute, Karnal-132001 Haryana,
India
| | - A. K. Singh
- Dairy Cattle Physiology Division, National Dairy Research Institute, Karnal-132001 Haryana,
India
| | - M. Kumar
- Dairy Cattle Physiology Division, National Dairy Research Institute, Karnal-132001 Haryana,
India
| | - R. C. Upadhyay
- Dairy Cattle Physiology Division, National Dairy Research Institute, Karnal-132001 Haryana,
India
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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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Stevenson CEM, Assaad A, Chandra G, Le TBK, Greive SJ, Bibb MJ, Lawson DM. Investigation of DNA sequence recognition by a streptomycete MarR family transcriptional regulator through surface plasmon resonance and X-ray crystallography. Nucleic Acids Res 2013; 41:7009-22. [PMID: 23748564 PMCID: PMC3737563 DOI: 10.1093/nar/gkt523] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [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: 12/31/2022] Open
Abstract
Consistent with their complex lifestyles and rich secondary metabolite profiles, the genomes of streptomycetes encode a plethora of transcription factors, the vast majority of which are uncharacterized. Herein, we use Surface Plasmon Resonance (SPR) to identify and delineate putative operator sites for SCO3205, a MarR family transcriptional regulator from Streptomyces coelicolor that is well represented in sequenced actinomycete genomes. In particular, we use a novel SPR footprinting approach that exploits indirect ligand capture to vastly extend the lifetime of a standard streptavidin SPR chip. We define two operator sites upstream of sco3205 and a pseudopalindromic consensus sequence derived from these enables further potential operator sites to be identified in the S. coelicolor genome. We evaluate each of these through SPR and test the importance of the conserved bases within the consensus sequence. Informed by these results, we determine the crystal structure of a SCO3205-DNA complex at 2.8 Å resolution, enabling molecular level rationalization of the SPR data. Taken together, our observations support a DNA recognition mechanism involving both direct and indirect sequence readout.
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Affiliation(s)
- Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Abstract
Streptomycetes are the most abundant source of antibiotics. Typically, each species produces several antibiotics, with the profile being species specific. Streptomyces coelicolor, the model species, produces at least five different antibiotics. We review the regulation of antibiotic biosynthesis in S. coelicolor and other, nonmodel streptomycetes in the light of recent studies. The biosynthesis of each antibiotic is specified by a large gene cluster, usually including regulatory genes (cluster-situated regulators [CSRs]). These are the main point of connection with a plethora of generally conserved regulatory systems that monitor the organism's physiology, developmental state, population density, and environment to determine the onset and level of production of each antibiotic. Some CSRs may also be sensitive to the levels of different kinds of ligands, including products of the pathway itself, products of other antibiotic pathways in the same organism, and specialized regulatory small molecules such as gamma-butyrolactones. These interactions can result in self-reinforcing feed-forward circuitry and complex cross talk between pathways. The physiological signals and regulatory mechanisms may be of practical importance for the activation of the many cryptic secondary metabolic gene cluster pathways revealed by recent sequencing of numerous Streptomyces genomes.
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Affiliation(s)
- Gang Liu
- State Key Laboratory of Microbial Resources
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F. Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Huergo LF, Chandra G, Merrick M. PIIsignal transduction proteins: nitrogen regulation and beyond. FEMS Microbiol Rev 2013; 37:251-83. [DOI: 10.1111/j.1574-6976.2012.00351.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/26/2012] [Accepted: 07/26/2012] [Indexed: 01/12/2023] Open
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