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Droste J, Rückert C, Kalinowski J, Hamed MB, Anné J, Simoens K, Bernaerts K, Economou A, Busche T. Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Front Microbiol 2021; 12:604034. [PMID: 33935985 PMCID: PMC8079986 DOI: 10.3389/fmicb.2021.604034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5'-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5' untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5'-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5'-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.
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Affiliation(s)
- Julian Droste
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Mohamed Belal Hamed
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokii, Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Kenneth Simoens
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Kim JN, Jeong Y, Yoo JS, Roe JH, Cho BK, Kim BG. Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor. BMC Genomics 2015; 16:116. [PMID: 25766138 PMCID: PMC4340878 DOI: 10.1186/s12864-015-1311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. Recent study revealed that NdgR is one of the regulatory targets of SigR, an oxidative stress response sigma factor, suggesting that the NdgR plays an important physiological role in response to environmental stresses. Although the regulatory functions of NdgR were partly characterized, determination of its regulon is required for better understanding of the transcriptional regulatory network related with the oxidative stress response. RESULTS We determined genome-wide binding loci of NdgR by using chromatin immunoprecipitation coupled with sequencing (ChIP-seq) and explored its physiological roles. The ChIP-seq profiles revealed 19 direct binding loci with a 15-bp imperfect palindromic motif, including 34 genes in their transcription units. Most genes in branched-chain amino acid and cysteine biosynthesis pathways were involved in the NdgR regulon. We proved that ndgR is induced by SigR under the thiol oxidation, and that an ndgR mutant strain is sensitive to the thiol oxidizing agent, diamide. Through the expression test of NdgR and the target genes for NdgR under diamide treatment, regulatory motifs were suggested. Interestingly, NdgR constitutes two regulatory motifs, coherent and incoherent feed-forward loops (FFL), in order to control its regulon under the diamide treatment. Using the regulatory motifs, NdgR regulates cysteine biosynthesis in response to thiol oxidative stress, enabling cells to maintain sulfur assimilation with homeostasis under stress conditions. CONCLUSIONS Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain amino acids biosynthesis and sulphur assimilation. The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing amino acid biosynthesis in the context of stress responses in S. coelicolor.
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Affiliation(s)
- Ji-Nu Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Korea.
| | - Yujin Jeong
- Department of Biological Sciences and KAIST institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
| | - Ji Sun Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 151-742, Korea.
| | - Jung-Hye Roe
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 151-742, Korea.
| | - Byung-Kwan Cho
- Department of Biological Sciences and KAIST institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Korea.
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Cheng JS, Liang YQ, Ding MZ, Cui SF, Lv XM, Yuan YJ. Metabolic analysis reveals the amino acid responses of Streptomyces lydicus to pitching ratios during improving streptolydigin production. Appl Microbiol Biotechnol 2013; 97:5943-54. [DOI: 10.1007/s00253-013-4790-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/02/2013] [Accepted: 02/18/2013] [Indexed: 11/25/2022]
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Lopatovskaya KV, Seliverstov AV, Lyubetsky VA. Attenuation regulation of the amino acid and aminoacyl-tRNA biosynthesis operons in bacteria: A comparative genomic analysis. Mol Biol 2010. [DOI: 10.1134/s0026893310010164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yang YH, Song E, Kim EJ, Lee K, Kim WS, Park SS, Hahn JS, Kim BG. NdgR, an IclR-like regulator involved in amino-acid-dependent growth, quorum sensing, and antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol 2008; 82:501-11. [PMID: 19083232 DOI: 10.1007/s00253-008-1802-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 11/17/2008] [Accepted: 11/18/2008] [Indexed: 12/01/2022]
Abstract
NdgR (regulator for nitrogen source-dependent growth and antibiotic production), an IclR-like regulator, has been initially identified as a binding protein to the promoters of doxorubicin biosynthetic genes in Streptomyces peucetius by DNA affinity capture assay method. NdgR is well conserved throughout the Streptomyces species and many other bacteria such as Mycobacteria and Corynebacteria. In Streptomyces coelicolor, ndgR deletion mutant showed slow cell growth and defects in differentiation and enhances the production of actinorhodin (ACT) in minimal media containing certain amino acids where wild-type strain could not produce ACT. Although deletion mutant of ndgR showed different antibiotic production in minimal media containing Leu or Gln, it only showed reduced mRNA expression levels of the genes involved in leucine metabolism. Neither NdgR-dependent expression of glnA nor direct binding of NdgR protein to glnA, glnII, and glnR promoters was observed. However, ScbR, which is governed by NdgR shown by gel mobility shift assay, binds to promoter of glnR, suggesting indirect regulation of glutamine metabolism by NdgR. NdgR protein binds to intergenic region of ndgR-leuC, and scbR-scbA involved in gamma-butyrolactone. Two-dimensional gel analysis has shown a global effect of ndgR deletion in protein expression, including up-regulated proteins involved in ACT synthesis and down-regulation of chaperones such as GroEL, GroES, and DnaK. These results suggest a global regulatory role for NdgR in amino acid metabolisms, quorum sensing, morphological changes, antibiotic production, and expression of chaperonines in S. coelicolor.
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Affiliation(s)
- Yung-Hun Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
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Expression Regulation of the Amino Acid Biosynthesis and Aminoacyl-tRNA Synthase Genes in Actinobacteria. Mol Biol 2005. [DOI: 10.1007/s11008-005-0116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Seliverstov AV, Putzer H, Gelfand MS, Lyubetsky VA. Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol 2005; 5:54. [PMID: 16202131 PMCID: PMC1262725 DOI: 10.1186/1471-2180-5-54] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 10/03/2005] [Indexed: 01/25/2023] Open
Abstract
Background Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria. Results Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria. Conclusion The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box.
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Affiliation(s)
- Alexander V Seliverstov
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia
| | - Harald Putzer
- Institut de Biologie Physico-Chimique, CNRS UPR9073, 13, rue P. et M. Curie, 75005 Paris, France
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia
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