1
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Jeon BJ, Yoo N, Kim JD, Choi J. A peptide encoded by a highly conserved gene belonging to the genus Streptomyces shows antimicrobial activity against plant pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1250906. [PMID: 37868322 PMCID: PMC10585065 DOI: 10.3389/fpls.2023.1250906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023]
Abstract
The genus Streptomyces has been unceasingly highlighted for the versatility and diversity of the antimicrobial agents they produce. Moreover, it is a heavily sequenced taxon in the phylum Actinobacteria. In this study, 47 sequence profiles were identified as proteins highly conserved within the genus Streptomyces. Significant hits to the 38 profiles were found in more than 2000 Streptomyces genomes, 11 of which were further conserved in more than 90% of Actinobacterial genomes analyzed. Only a few genes corresponding to these sequence profiles were functionally characterized, which play regulatory roles in the morphology and biosynthesis of antibiotics. Here a highly conserved sequence, namely, SHC-AMP (Streptomyces highly conserved antimicrobial peptide), which exhibited antimicrobial activity against bacterial and fungal plant pathogens, was reported. In particular, Arabidopsis thaliana was effectively protected against infection with Pseudomonas syringae pv. tomato DC3000 by treatment with this peptide. Results indicated the potential application of this peptide as an antimicrobial agent for control of plant diseases. Our results suggest putative target genes for controlling Streptomyces spp., including the one exhibiting antimicrobial activity against a wide range of phytopathogens.
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Affiliation(s)
- Byeong Jun Jeon
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Nayeon Yoo
- Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jeong Do Kim
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Jaeyoung Choi
- Department of Oriental Medicine Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
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2
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Schulz S, Sletta H, Fløgstad Degnes K, Krysenko S, Williams A, Olsen SM, Vernstad K, Mitulski A, Wohlleben W. Optimization of FK-506 production in Streptomyces tsukubaensis by modulation of Crp-mediated regulation. Appl Microbiol Biotechnol 2023; 107:2871-2886. [PMID: 36949330 PMCID: PMC10033298 DOI: 10.1007/s00253-023-12473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/24/2023]
Abstract
FK-506 is a potent immunosuppressive macrocyclic polyketide with growing pharmaceutical interest, produced by Streptomyces tsukubaensis. However, due to low levels synthesized by the wild-type strain, biotechnological production of FK-506 is rather limited. Optimization strategies to enhance the productivity of S. tsukubaensis by means of genetic engineering have been established. In this work primarily global regulatory aspects with respect to the FK-506 biosynthesis have been investigated with the focus on the global Crp (cAMP receptor protein) regulator. In expression analyses and protein-DNA interaction studies, the role of Crp during FK-506 biosynthesis was elucidated. Overexpression of Crp resulted in two-fold enhancement of FK-506 production in S. tsukubaensis under laboratory conditions. Further optimizations using fermentors proved that the strategy described in this study can be transferred to industrial scale, presenting a new approach for biotechnological FK-506 production. KEY POINTS: • The role of the global Crp (cAMP receptor protein) regulator for FK-506 biosynthesis in S. tsukubaensis was demonstrated • Crp overexpression in S. tsukubaensis was applied as an optimization strategy to enhance FK-506 and FK-520 production resulting in two-fold yield increase.
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Affiliation(s)
- Susann Schulz
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Novartis AG, Stein, Switzerland
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway.
| | - Kristin Fløgstad Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway
| | - Sergii Krysenko
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Valent BioSciences, 1910 Innovation Wy Suite 100, Libertyville, IL, 60048, USA
| | - Alicia Williams
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Silje Malene Olsen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, Trondheim, Norway
| | - Kai Vernstad
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Sem Sælands veg 2a, Trondheim, Norway
| | - Agnieszka Mitulski
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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3
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Werten S, Waack P, Palm GJ, Virolle MJ, Hinrichs W. Crystal structures of free and ligand-bound forms of the TetR/AcrR-like regulator SCO3201 from Streptomyces coelicolor suggest a novel allosteric mechanism. FEBS J 2023; 290:521-532. [PMID: 36017630 PMCID: PMC10087246 DOI: 10.1111/febs.16606] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 02/05/2023]
Abstract
TetR/AcrR-like transcription regulators enable bacteria to sense a wide variety of chemical compounds and to dynamically adapt the expression levels of specific genes in response to changing growth conditions. Here, we describe the structural characterisation of SCO3201, an atypical TetR/AcrR family member from Streptomyces coelicolor that strongly represses antibiotic production and morphological development under conditions of overexpression. We present crystal structures of SCO3201 in its ligand-free state as well as in complex with an unknown inducer, potentially a polyamine. In the ligand-free state, the DNA-binding domains of the SCO3201 dimer are held together in an unusually compact conformation and, as a result, the regulator cannot span the distance between the two half-sites of its operator. Interaction with the ligand coincides with a major structural rearrangement and partial conversion of the so-called hinge helix (α4) to a 310 -conformation, markedly increasing the distance between the DNA-binding domains. In sharp contrast to what was observed for other TetR/AcrR-like regulators, the increased interdomain distance might facilitate rather than abrogate interaction of the dimer with the operator. Such a 'reverse' induction mechanism could expand the regulatory repertoire of the TetR/AcrR family and may explain the dramatic impact of SCO3201 overexpression on the ability of S. coelicolor to generate antibiotics and sporulate.
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Affiliation(s)
- Sebastiaan Werten
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Austria
| | - Paul Waack
- Institute of Biochemistry, University of Greifswald, Germany
| | | | - Marie-Joëlle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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4
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Vassallo A, Palazzotto E, Renzone G, Botta L, Faddetta T, Scaloni A, Puglia AM, Gallo G. The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production. Front Microbiol 2020; 11:224. [PMID: 32140146 PMCID: PMC7042404 DOI: 10.3389/fmicb.2020.00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open reading frames (smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) – whose product modulates L-tryptophan biosynthesis – impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact with PepA (SCO2179), a putative cytosol aminopeptidase playing a key role in antibiotic production and sporulation. In this work, a S. coelicolor trpM knock-in (Sco-trpMKI) mutant strain was generated by cloning trpM into overexpressing vector to further investigate the role of trpM in actinomycete growth and morpho-physiological differentiation. Results highlighted that trpM: (i) stimulates growth and actinorhodin (ACT) production; (ii) decreases calcium-dependent antibiotic (CDA) production; (iii) has no effect on undecylprodigiosin production. Metabolic pathways influenced by trpM knock-in were investigated by combining two-difference in gel electrophoresis/nanoliquid chromatography coupled to electrospray linear ion trap tandem mass spectrometry (2D-DIGE/nanoLC-ESI-LIT-MS/MS) and by LC-ESI-MS/MS procedures, respectively. These analyses demonstrated that over-expression of trpM causes an over-representation of factors involved in protein synthesis and nucleotide metabolism as well as a down-representation of proteins involved in central carbon and amino acid metabolism. At the metabolic level, this corresponded to a differential accumulation pattern of different amino acids – including aromatic ones but tryptophan – and central carbon intermediates. PepA was also down-represented in Sco-trpMKI. The latter was produced as recombinant His-tagged protein and was originally proven having the predicted aminopeptidase activity. Altogether, these results highlight the stimulatory effect of trpM in S. coelicolor growth and ACT biosynthesis, which are elicited through the modulation of various metabolic pathways and PepA representation, further confirming the complexity of regulatory networks that control antibiotic production in actinomycetes.
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Affiliation(s)
- Alberto Vassallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy.,Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Giovanni Renzone
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Luigi Botta
- Dipartimento di Ingegneria, Università di Palermo, Palermo, Italy
| | - Teresa Faddetta
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Andrea Scaloni
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
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5
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Lewis RA, Wahab A, Bucca G, Laing EE, Möller-Levet CS, Kierzek A, Smith CP. Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2). PLoS One 2019; 14:e0200673. [PMID: 30969967 PMCID: PMC6457490 DOI: 10.1371/journal.pone.0200673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/10/2019] [Indexed: 01/31/2023] Open
Abstract
The AbsA1-AbsA2 two component signalling system of Streptomyces coelicolor has long been known to exert a powerful negative influence on the production of the antibiotics actinorhodin, undecylprodiginine and the Calcium-Dependent Antibiotic (CDA). Here we report the analysis of a ΔabsA2 deletion strain, which exhibits the classic precocious antibiotic hyper-production phenotype, and its complementation by an N-terminal triple-FLAG-tagged version of AbsA2. The complemented and non-complemented ΔabsA2 mutant strains were used in large-scale microarray-based time-course experiments to investigate the effect of deleting absA2 on gene expression and to identify the in vivo AbsA2 DNA-binding target sites using ChIP-on chip. We show that in addition to binding to the promoter regions of redZ and actII-orfIV AbsA2 binds to several previously unidentified sites within the cda biosynthetic gene cluster within and/or upstream of SCO3215—SCO3216, SCO3217, SCO3229—SCO3230, and SCO3226, and we relate the pattern of AbsA2 binding to the results of the transcriptomic study and antibiotic phenotypic assays. Interestingly, dual ‘biphasic’ ChIP peaks were observed with AbsA2 binding across the regulatory genes actII-orfIV and redZ and the absA2 gene itself, while more conventional single promoter-proximal peaks were seen at the CDA biosynthetic genes suggesting a different mechanism of regulation of the former loci. Taken together the results shed light on the complex mechanism of regulation of antibiotic biosynthesis in Streptomyces coelicolor and the important role of AbsA2 in controlling the expression of three antibiotic biosynthetic gene clusters.
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Affiliation(s)
- Richard A. Lewis
- Demuris Ltd, William Leech Building, University of Newcastle Medical School, Framlington Place, Newcastle-upon-Tyne, United Kingdom
- * E-mail: (RAL); (CPS)
| | - Abdul Wahab
- Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Giselda Bucca
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Moulsecoomb, Brighton, United Kingdom
| | - Emma E. Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Carla S. Möller-Levet
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Andrzej Kierzek
- Certara, Blades Enterprise Centre, John Street, Sheffield, United Kingdom
| | - Colin P. Smith
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Moulsecoomb, Brighton, United Kingdom
- * E-mail: (RAL); (CPS)
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6
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Lurthy T, Alloisio N, Fournier P, Anchisi S, Ponsero A, Normand P, Pujic P, Boubakri H. Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli. Res Microbiol 2018; 169:90-100. [PMID: 29378337 DOI: 10.1016/j.resmic.2017.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/21/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022]
Abstract
The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p < 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) ≥ 2), as well as significant downregulation of 48 other genes (FC ≤ 0.5). Interestingly, there were 104 Frankia genes upregulated in vitro that were also significantly upregulated in symbiosis with Alnus glutinosa, while the other 148 genes were not, showing that the physiology of in vitro fixation is markedly different from that under symbiotic conditions. In particular,in vitro fixing cells were seen to upregulate genes identified as coding for a nitrite reductase, and amidases that were not upregulated in symbiosis. Confirmatory assays for nitrite reductase showed that Frankia indeed reduced nitrite and used it as a nitrogen source. An Escherichia coli fosmid clone carrying the nirB region was able to grow better in the presence of 5 mM nitrite than without it, confirming the function of the genome region. The physiological pattern that emerges shows that Frankia undergoes nitrogen starvation that induces a molecular response different from that seen in symbiosis.
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Affiliation(s)
- Tristan Lurthy
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Stéphanie Anchisi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Alise Ponsero
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France.
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7
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Li Z, Liu X, Wang J, Wang Y, Zheng G, Lu Y, Zhao G, Wang J. Insight into the Molecular Mechanism of the Transcriptional Regulation of amtB Operon in Streptomyces coelicolor. Front Microbiol 2018. [PMID: 29515546 PMCID: PMC5826061 DOI: 10.3389/fmicb.2018.00264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In Streptomyces coelicolor, amtB transcription is promptly regulated by the global nitrogen regulator GlnR. Although the GlnR binding cis-element has been characterized in amtB promoter, consisting of three GlnR boxes of a3-b3, a1-b1, and a2-b2, its role in GlnR-mediated transcriptional regulation remains unclear. Here, we showed that GlnR had different binding affinity against each pair of GlnR binding sites in amtB promoter (i.e., a3-b3, a1-b1, and a2-b2 sites), and GlnR was able to bind a3-b3 and a1-b1, respectively, but not a2-b2 alone. Consistently, a2 was not a typical GlnR binding site and further experiments showed that a2 was non-essential for GlnR-mediated binding in vitro and transcriptional regulation in vivo. To uncover the physiological role of the three GlnR boxes, we then mutated the wild-type amtB promoter to a typical GlnR-binding motif containing two GlnR boxes (a3-b3–a2-b2), and found although the transcription of the mutated promoter could still be activated by GlnR, its increasing rate was less than that of the wild-type. Based on these findings, one could conclude that the three GlnR boxes assisted GlnR in more promptly activating amtB transcription in response to nitrogen limitation, facilitating bacterial growth under nitrogen stresses.
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Affiliation(s)
- Zhendong Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinqiang Liu
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingzhi Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guosong Zheng
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinhua Lu
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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8
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Urem M, Świątek-Połatyńska MA, Rigali S, van Wezel GP. Intertwining nutrient-sensory networks and the control of antibiotic production inStreptomyces. Mol Microbiol 2016; 102:183-195. [DOI: 10.1111/mmi.13464] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Mia Urem
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
| | - Magdalena A. Świątek-Połatyńska
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 Marburg 35043 Germany
| | - Sébastien Rigali
- InBioS, Centre for Protein Engineering; University of Liège; Liège B-4000 Belgium
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Droevendaalsesteeg 10 Wageningen 6708 PB The Netherlands
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9
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Cen XF, Wang JZ, Zhao GP, Wang Y, Wang J. Molecular evidence for the coordination of nitrogen and carbon metabolisms, revealed by a study on the transcriptional regulation of the agl3EFG operon that encodes a putative carbohydrate transporter in Streptomyces coelicolor. Biochem Biophys Res Commun 2016; 471:510-4. [DOI: 10.1016/j.bbrc.2016.02.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/12/2016] [Indexed: 11/25/2022]
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10
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Tsypik O, Yushchuk O, Zaburannyi N, Flärdh K, Walker S, Fedorenko V, Ostash B. Transcriptional regulators of GntR family in Streptomyces coelicolor A3(2): analysis in silico and in vivo of YtrA subfamily. Folia Microbiol (Praha) 2015; 61:209-20. [PMID: 26433722 DOI: 10.1007/s12223-015-0426-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/27/2015] [Indexed: 01/27/2023]
Abstract
Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.
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Affiliation(s)
- O Tsypik
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - O Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - N Zaburannyi
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - K Flärdh
- Department of Biology, Lund University, Lund, 22362, Sweden
| | - S Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - V Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine
| | - B Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
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11
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Yu Z, Zhu H, Zheng G, Jiang W, Lu Y. A genome-wide transcriptomic analysis reveals diverse roles of the two-component system DraR-K in the physiological and morphological differentiation of Streptomyces coelicolor. Appl Microbiol Biotechnol 2014; 98:9351-63. [PMID: 25316091 DOI: 10.1007/s00253-014-6102-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/06/2023]
Abstract
A novel two-component system (TCS) of DraR-K was previously identified as playing differential roles in the biosynthesis of antibiotics (blue-pigmented type II polyketide actinorhodin (ACT), red-pigmented tripyrrole undecylprodigiosin (RED), and yellow-pigmented type I polyketide (yCPK)) in Streptomyces coelicolor M145 under the conditions of minimal medium (MM) supplemented with a high concentration of different nitrogen sources (e.g., 75 mM glutamine). To assess whether DraR-K has more globalized roles, a genome-wide transcriptomic analysis of the parental strain M145 and a ΔdraR-K mutant under the condition of MM supplemented with 75 mM glutamine was performed using DNA microarray analysis combined with real-time reverse transcriptase PCR (RT-qPCR). The analyses showed that deletion of the draR-K genes led to the differential expression not only of the biosynthetic gene clusters of ACT, RED, and yCPK but also of other five secondary metabolite biosynthetic clusters. In addition, a number of primary metabolism-related genes in the ΔdraR-K mutant, such as ureA/B/C/D/G/F, the pstSCAB operon, and the chb gene, exhibited altered expression, which might enable the organism to balance the C/N/P ratio under the condition of a high concentration of glutamine. We also found that the expression of many developmental genes, including ramR, chpA/D/E, and the whiE gene cluster, was affected by the draR-K deletion. Furthermore, the direct role of DraR-K on the transcription of several genes, including chb and pepA/pepA2, was validated using electrophoretic mobility shift assays (EMSAs). In summary, our transcriptomic analyses revealed that DraR-K plays global regulatory roles in the physiological and morphological differentiation of S. coelicolor.
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Affiliation(s)
- Zhenyu Yu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China
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GlnR negatively regulates the transcription of the alanine dehydrogenase encoding gene ald in Amycolatopsis mediterranei U32 under nitrogen limited conditions via specific binding to its major transcription initiation site. PLoS One 2014; 9:e104811. [PMID: 25144373 PMCID: PMC4140684 DOI: 10.1371/journal.pone.0104811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/14/2014] [Indexed: 11/25/2022] Open
Abstract
Ammonium assimilation is catalyzed by two enzymatic pathways, i.e., glutamine synthetase/glutamate synthase (GS/GOGAT) and alanine dehydrogenase (AlaDH) in Amycolatopsis mediterranei U32. Under nitrogen-rich conditions, the AlaDH pathway is the major route for ammonium assimilation, while the GS/GOGAT pathway takes over when the extracellular nitrogen supply is limited. The global nitrogen regulator GlnR was previously characterized to activate the transcription of the GS encoding gene glnA in response to nitrogen limitation and is demonstrated in this study as a repressor for the transcription of the AlaDH encoding gene ald, whose regulation is consistent with the switch of the ammonium assimilation pathways from AlaDH to GS/GOGAT responding to nitrogen limitation. Three transcription initiation sites (TISs) of ald were determined with primer extension assay, among which transcription from aldP2 contributed the major transcripts under nitrogen-rich conditions but was repressed to an undetectable level in response to nitrogen limitation. Through DNase I footprinting assay, two separate regions were found to be protected by GlnR within ald promoter, within which three GlnR binding sites (a1, b1 sites in region I and a2 site in region II) were defined. Interestingly, the major TIS aldP2 is located in the middle of a2 site within region II. Therefore, one may easily conclude that GlnR represses the transcription of ald via specific binding to the GlnR binding sites, which obviously blocks the transcription initiation from aldP2 and therefore reduces ald transcripts.
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Lin W, Wang Y, Han X, Zhang Z, Wang C, Wang J, Yang H, Lu Y, Jiang W, Zhao GP, Zhang P. Atypical OmpR/PhoB subfamily response regulator GlnR of actinomycetes functions as a homodimer, stabilized by the unphosphorylated conserved Asp-focused charge interactions. J Biol Chem 2014; 289:15413-25. [PMID: 24733389 DOI: 10.1074/jbc.m113.543504] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp(50) residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-β5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called "phosphorylation pocket" is not conserved, with its space being occupied by an Arg(52) from the β3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp(50) with the highly conserved Arg(52) and Thr(9) in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.
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Affiliation(s)
- Wei Lin
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Ying Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, the State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaobiao Han
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Zilong Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Chengyuan Wang
- State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jin Wang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Huaiyu Yang
- the Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinhua Lu
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Weihong Jiang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology
| | - Guo-Ping Zhao
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, the State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China, the Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China, the Department of Microbiology and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China, and
| | - Peng Zhang
- From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,
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Genetic variants in the genes of the stress hormone signalling pathway and depressive symptoms during and after pregnancy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:469278. [PMID: 24741566 PMCID: PMC3972848 DOI: 10.1155/2014/469278] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 11/29/2022]
Abstract
Purpose. The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in genes of the stress hormone signaling pathway, specifically FKBP5, NR3C1, and CRHR1, are associated with depressive symptoms during and after pregnancy. Methods. The Franconian Maternal Health Evaluation Study (FRAMES) recruited healthy pregnant women prospectively for the assessment of maternal and fetal health including the assessment of depressiveness. The German version of the 10-item Edinburgh Postnatal Depression Scale (EPDS) was completed at three time points in this prospective cohort study. Visit 1 was at study entry in the third trimester of the pregnancy, visit 2 was shortly after birth, and visit 3 was 6–8 months after birth. Germline DNA was collected from 361 pregnant women. Nine SNPs in the above mentioned genes were genotyped. After construction of haplotypes for each gene, a multifactorial linear mixed model was performed to analyse the depression values over time. Results. EPDS values were within expected ranges and comparable to previously published studies. Neither did the depression scores differ for comparisons among haplotypes at fixed time points nor did the change over time differ among haplotypes for the examined genes. No haplotype showed significant associations with depressive symptoms severity during pregnancy or the postpartum period. Conclusion. The analysed candidate haplotypes in FKBP5, NR3C1, and CRHR1 did not show an association with depression scores as assessed by EPDS in this cohort of healthy unselected pregnant women.
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Jenkins VA, Barton GR, Robertson BD, Williams KJ. Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis. BMC Genomics 2013; 14:301. [PMID: 23642041 PMCID: PMC3662644 DOI: 10.1186/1471-2164-14-301] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/29/2013] [Indexed: 11/24/2022] Open
Abstract
Background Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. Results We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. Conclusions We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions.
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Affiliation(s)
- Victoria A Jenkins
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington, London SW7 2AZ, UK
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Three of four GlnR binding sites are essential for GlnR-mediated activation of transcription of the Amycolatopsis mediterranei nas operon. J Bacteriol 2013; 195:2595-602. [PMID: 23543714 DOI: 10.1128/jb.00182-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Amycolatopsis mediterranei U32, genes responsible for nitrate assimilation formed one operon, nasACKBDEF, whose transcription is induced by the addition of nitrate. Here, we characterized GlnR as a direct transcriptional activator for the nas operon. The GlnR-protected DNA sequences in the promoter region of the nas operon were characterized by DNase I footprinting assay, the previously deduced Streptomyces coelicolor double 22-bp GlnR binding consensus sequences comprising a1, b1, a2, and b2 sites were identified, and the sites were then mutated individually to test their roles in both the binding of GlnR in vitro and the GlnR-mediated transcriptional activation in vivo. The results clearly showed that only three GlnR binding sites (a1, b1, and b2 sites) were required by GlnR for its specific binding to the nas promoter region and efficient activation of the transcription of the nas operon in U32, while the a2 site seemed unnecessary.
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Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB. J Bacteriol 2012; 194:5237-44. [PMID: 22821977 DOI: 10.1128/jb.00989-12] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription of amtB in Streptomyces coelicolor has been proposed to be counter-regulated by GlnR (a global regulator for nitrogen metabolism) and PhoP (a global regulator for phosphate metabolism). However, the GlnR-protected region, which was deduced to be two 22-bp GlnR binding boxes (gTnAc-n6-GaAAc-n6-GtnAC-n6-GAAAc-n6, abbreviated as a1-b1 and a2-b2), was separated from the PhoP-protected region in the promoter of amtB, leaving the mechanism for this regulation undefined. In this study, another 22-bp GlnR binding box, which consisted of a3-site-n6-b3-site (a3-b3) overlapping with the PhoP-binding sequences, was identified in the promoter region of amtB by a DNase I footprinting assay. An electrophoretic mobility shift assay (EMSA) using purified recombinant GlnR and the synthetic amtB promoter fragments with the three GlnR binding boxes individually mutated demonstrated that every box was involved in GlnR binding in vitro. Further in vivo assays using the egfp reporter gene fused to various kinds of mutated promoter regions of amtB demonstrated that all of the three GlnR binding boxes were required for GlnR-mediated activation of amtB transcription under the nitrogen-limited condition. The results of EMSA using the amtB promoter with mixtures of recombinant His-tagged GlnR and Trx-His-S-tagged PhoP inferred that PhoP might compete against GlnR from binding at the a3-b3 site, attributable to the PhoP/GlnR counter-regulatory function subjected to further experimental proof.
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McCormick JR, Flärdh K. Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 2012; 36:206-31. [PMID: 22092088 PMCID: PMC3285474 DOI: 10.1111/j.1574-6976.2011.00317.x] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 10/29/2011] [Accepted: 10/30/2011] [Indexed: 12/16/2022] Open
Abstract
Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in the production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae first to form specialized aerial hyphae and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from '-omics' studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve.
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Affiliation(s)
| | - Klas Flärdh
- Department of Biology, Lund University, Lund, Sweden
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Waldvogel E, Herbig A, Battke F, Amin R, Nentwich M, Nieselt K, Ellingsen TE, Wentzel A, Hodgson DA, Wohlleben W, Mast Y. The PII protein GlnK is a pleiotropic regulator for morphological differentiation and secondary metabolism in Streptomyces coelicolor. Appl Microbiol Biotechnol 2011; 92:1219-36. [PMID: 22033567 DOI: 10.1007/s00253-011-3644-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/26/2011] [Accepted: 10/12/2011] [Indexed: 01/04/2023]
Abstract
GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.
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Affiliation(s)
- Eva Waldvogel
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Germany
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Jankevics A, Merlo ME, de Vries M, Vonk RJ, Takano E, Breitling R. Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2). Proteomics 2011; 11:4622-31. [PMID: 21956891 DOI: 10.1002/pmic.201100254] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 08/12/2011] [Accepted: 09/13/2011] [Indexed: 01/09/2023]
Abstract
The global analysis of metabolism by liquid chromatography coupled to mass spectrometry is often hampered by a large amount of biological and technical variability. Here, we introduce an experimental and analytical strategy that can produce robust metabolome profiles in the face of this challenge. By applying a new computational approach based on concordance analysis to an extremely large number of analytical replicates, we are able to show that the overexpression of an antisense non-coding RNA targeting glutamine synthetase I results in a major reorganization of the metabolism of Streptomyces coelicolor, the model species of antibiotic-producing bacteria. We identified 97 metabolites with statistically significant reproducible dynamic behavior across the time series. The observed metabolic changes are very rapid, specific and widespread across metabolism, but focus on the nitrogen assimilation pathways. Our results demonstrate the power of highly replicated experimental designs for the robust characterization of metabolite dynamics. The identified global rearrangement of metabolism suggests the usefulness of RNA interference as an efficient strategy to manipulate the physiology of bacteria with wider biotechnological applicability in microorganisms.
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Affiliation(s)
- Andris Jankevics
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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