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Abanoz-Seçgin B, Otur Ç, Okay S, Kurt-Kızıldoğan A. The regulatory role of Fur-encoding SCLAV_3199 in iron homeostasis in Streptomyces clavuligerus. Gene 2023:147594. [PMID: 37364696 DOI: 10.1016/j.gene.2023.147594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/09/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Iron homeostasis is strictly regulated by complex cascades connected with secondary metabolism in bacteria. Ferric uptake regulators ('Fur's), siderophores, efflux systems, and two-component signal transduction systems are the leading players in response stimuli. However, these regulatory mechanisms remain to be elucidated in Streptomyces clavuligerus. Our study focused on unraveling a possible role of SCLAV_3199 which encodes a Fur family transcriptional regulator, particularly in iron regulation and at the global level in this species. We deleted the SCLAV_3199 gene in S. clavuligerus and compared gene expression differences with the wild-type strain based on iron availability by RNA-seq. We found a potential regulatory effect of SCLAV_3199 on many transcriptional regulators and transporters. Besides, the genes encoding iron sulfur binding proteins were overexpressed in the mutant in the presence of iron. Notably, catechol (SCLAV_5397), and hydroxamate-type (SCLAV_1952, SCLAV_4680) siderophore-related genes were upregulated in the mutant strain in iron scarcity. Concomitantly, S. clavuligerus Δ3199 produced 1.65 and 1.9 times more catechol and hydroxamate-type siderophores, respectively, than that of the wild type strain under iron depletion. Iron containing chemically defined medium did not favor antibiotic production in S. clavuligerus Δ3199 while fermentation in starch-asparagine medium led to improved cephamycin C (2.23-fold) and clavulanic acid (2.56-fold) production in the mutant compared to the control. However, better tunicamycin yield (2.64-fold) was obtained in trypticase soy broth-grown cultures of S. clavuligerus Δ3199. Our findings demonstrate that the SCLAV_3199 gene plays a significant role in regulating both iron homeostasis and secondary metabolite biosynthesis in S. clavuligerus.
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Affiliation(s)
- Büşra Abanoz-Seçgin
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Çiğdem Otur
- Department of Agricultural Biotechnology, Ondokuz Mayıs University, Samsun 55139, Türkiye
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, 06230, Türkiye
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Nitric Oxide Signaling for Aerial Mycelium Formation in Streptomyces coelicolor A3(2) M145. Appl Environ Microbiol 2022; 88:e0122222. [PMID: 36354316 PMCID: PMC9746327 DOI: 10.1128/aem.01222-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitric oxide (NO) is a well-known signaling molecule in various organisms. Streptomyces undergoes complex morphological differentiation, similar to that of fungi. A recent study revealed a nitrogen oxide metabolic cycle that forms NO in Streptomyces coelicolor A3(2) M145. Further, endogenously produced NO serves as a signaling molecule. Here, we report that endogenously produced NO regulates cyclic 3',5'-diguanylate (c-di-GMP) levels and controls aerial mycelium formation through the c-di-GMP-binding transcriptional regulator BldD in S. coelicolor A3(2) M145. These observations provide important insights into the mechanisms regulating morphological differentiation. This is the first study to demonstrate a link between NO and c-di-GMP in S. coelicolor A3(2) M145. Morphological differentiation is closely linked to the initiation of secondary metabolism in actinomycetes. Thus, the NO signaling-based regulation of aerial mycelium formation has potential applications in the fermentation industry employing useful actinomycetes. IMPORTANCE Eukaryotic and prokaryotic cells utilize nitric oxide (NO) to regulate physiological functions. Besides its role as a producer of different bioactive substances, Streptomyces is suggested to be involved in mycelial development regulated by endogenously produced NO. However, the regulatory mechanisms are unclear. In this study, we proposed that NO signaling is involved in aerial mycelium formation in S. coelicolor A3(2) M145. NO serves as a signaling molecule for the regulation of intracellular cyclic 3',5'-diguanylate (c-di-GMP) levels, resulting in aerial mycelium formation controlled by a c-di-GMP receptor, BldD. As the abundant production of valuable secondary metabolites is closely related to the initiation of morphological differentiation in Streptomyces, NO may provide value for application in industrial fermentation by serving as a tool for regulating secondary metabolism.
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Zorro-Aranda A, Escorcia-Rodríguez JM, González-Kise JK, Freyre-González JA. Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor. Sci Rep 2022; 12:2840. [PMID: 35181703 PMCID: PMC8857197 DOI: 10.1038/s41598-022-06658-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. Even though S. coelicolor has an outstanding variety of regulators among bacteria, little effort to globally study its transcription has been made. We manually curated 29 years of literature and databases to assemble a meta-curated experimentally-validated gene regulatory network (GRN) with 5386 genes and 9707 regulatory interactions (~ 41% of the total expected interactions). This provides the most extensive and up-to-date reconstruction available for the regulatory circuitry of this organism. Only ~ 6% (534/9707) are supported by experiments confirming the binding of the transcription factor to the upstream region of the target gene, the so-called “strong” evidence. While for the remaining interactions there is no confirmation of direct binding. To tackle network incompleteness, we performed network inference using several methods (including two proposed here) for motif identification in DNA sequences and GRN inference from transcriptomics. Further, we contrasted the structural properties and functional architecture of the networks to assess the reliability of the predictions, finding the inference from DNA sequence data to be the most trustworthy approach. Finally, we show two applications of the inferred and the curated networks. The inference allowed us to propose novel transcription factors for the key Streptomyces antibiotic regulatory proteins (SARPs). The curated network allowed us to study the conservation of the system-level components between S. coelicolor and Corynebacterium glutamicum. There we identified the basal machinery as the common signature between the two organisms. The curated networks were deposited in Abasy Atlas (https://abasy.ccg.unam.mx/) while the inferences are available as Supplementary Material.
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Affiliation(s)
- Andrea Zorro-Aranda
- Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomics Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, 62210, Cuernavaca, Morelos, México.,Bioprocess Research Group, Department of Chemical Engineering, Universidad de Antioquia, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomics Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - José Kenyi González-Kise
- Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomics Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, 62210, Cuernavaca, Morelos, México.,Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomics Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, 62210, Cuernavaca, Morelos, México.
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Nitric Oxide Signaling for Actinorhodin Production in Streptomyces coelicolor A3(2) via the DevS/R Two-Component System. Appl Environ Microbiol 2021; 87:e0048021. [PMID: 33990302 DOI: 10.1128/aem.00480-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitric oxide (NO) is an important signaling molecule in eukaryotic and prokaryotic cells. A previous study revealed an NO synthase-independent NO production metabolic cycle in which the three nitrogen oxides, nitrate (NO3-), nitrite (NO2-), and NO, were generated in the actinobacterium Streptomyces coelicolor A3(2). NO was suggested to act as a signaling molecule, functioning as a hormone that regulates secondary metabolism. Here, we demonstrate the NO-mediated regulation of the production of the blue-pigmented antibiotic actinorhodin (ACT), via the heme-based DevS/R two-component system (TCS). Intracellular NO controls the stabilization or inactivation of DevS, depending on the NO concentration. An electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR analysis revealed the direct binding between DevR and the promoter region of actII-ORF4, resulting in gene expression. Our results indicate that NO regulates the DevS/R TCS, thereby strictly controlling the secondary metabolism of S. coelicolor A3(2). IMPORTANCE Diverse organisms, such as mammals, plants, and bacteria, utilize NO via well-known signal transduction mechanisms. Many useful secondary metabolite-producing bacteria of the Streptomyces genus had been also suggested for the metabolism regulated by endogenously produced NO; however, the regulatory mechanisms remain to be elucidated. In this study, we demonstrated the molecular mechanism by which endogenously produced NO regulates antibiotic production via the DevS/R TCS in S. coelicolor A3(2). NO serves as both a stabilizer and a repressor in the regulation of antibiotic production. This report shows the mechanism by which Streptomyces utilizes endogenously produced NO to modulate its normal life cycle. Moreover, this study implies that studying NO signaling in actinobacteria can help in the development of both clinical strategies against pathogenic actinomycetes and the actinobacterial industries.
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Ünsaldı E, Kurt-Kızıldoğan A, Özcan S, Becher D, Voigt B, Aktaş C, Özcengiz G. Proteomic analysis of a hom-disrupted, cephamycin C overproducing Streptomyces clavuligerus. Protein Pept Lett 2021; 28:205-220. [PMID: 32707026 DOI: 10.2174/0929866527666200723163655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Streptomyces clavuligerus is prolific producer of cephamycin C, a medically important antibiotic. In our former study, cephamycin C titer was 2-fold improved by disrupting homoserine dehydrogenase (hom) gene of aspartate pahway in Streptomyces clavuligerus NRRL 3585. OBJECTIVE In this article, we aimed to provide a comprehensive understanding at the proteome level on potential complex metabolic changes as a consequence of hom disruption in Streptomyces clavuligerus AK39. METHODS A comparative proteomics study was carried out between the wild type and its hom disrupted AK39 strain by 2 Dimensional Electrophoresis-Matrix Assisted Laser Desorption and Ionization Time-Of-Flight Mass Spectrometry (2DE MALDI-TOF/MS) and Nanoscale Liquid Chromatography- Tandem Mass Spectrometry (nanoLC-MS/MS) analyses. Clusters of Orthologous Groups (COG) database was used to determine the functional categories of the proteins. The theoretical pI and Mw values of the proteins were calculated using Expasy pI/Mw tool. RESULTS "Hypothetical/Unknown" and "Secondary Metabolism" were the most prominent categories of the differentially expressed proteins. Upto 8.7-fold increased level of the positive regulator CcaR was a key finding since CcaR was shown to bind to cefF promoter thereby direcly controlling its expression. Consistently, CeaS2, the first enzyme of CA biosynthetic pathway, was 3.3- fold elevated. There were also many underrepresented proteins associated with the biosynthesis of several Non-Ribosomal Peptide Synthases (NRPSs), clavams, hybrid NRPS/Polyketide synthases (PKSs) and tunicamycin. The most conspicuously underrepresented protein of amino acid metabolism was 4-Hydroxyphenylpyruvate dioxygenase (HppD) acting in tyrosine catabolism. The levels of a Two Component System (TCS) response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain as well as DNA-binding protein HU were elevated while a TetR-family transcriptional regulator was underexpressed. CONCLUSION The results obtained herein will aid in finding out new targets for further improvement of cephamycin C production in Streptomyces clavuligerus.
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Affiliation(s)
- Eser Ünsaldı
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | | | - Servet Özcan
- Department of Biology, Erciyes University, Kayseri 38280, Turkey
| | - Dörte Becher
- Institute of Microbiology, Ernst- Moritz-Arndt-University of Greifswald, Greifswald D-17487, Germany
| | - Birgit Voigt
- Institute of Microbiology, Ernst- Moritz-Arndt-University of Greifswald, Greifswald D-17487, Germany
| | - Caner Aktaş
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
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Baş L, Otur Ç, Kurt-Kızıldoğan A. Enhanced Tunicamycin Biosynthesis in BldG Overexpressed Streptomyces clavuligerus. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s000368382004002x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Homologous expression of lysA encoding diaminopimelic acid (DAP) decarboxylase reveals increased antibiotic production in Streptomyces clavuligerus. Braz J Microbiol 2019; 51:547-556. [PMID: 31833007 DOI: 10.1007/s42770-019-00202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022] Open
Abstract
lysA gene encoding meso-diaminopimelic acid (DAP) decarboxylase enzyme that catalyzes L-lysine biosynthesis in the aspartate pathway in Streptomyces clavuligerus was overexpressed, and its effects on cephamycin C (CephC), clavulanic acid (CA), and tunicamycin productions were investigated. Multicopy expression of lysA gene under the control of glpF promoter (glpFp) in S. clavuligerus pCOlysA led to higher expression levels ranging from 2- to 6-fold increase at both lysA gene and CephC biosynthetic gene cluster at T36 and T48 of TSBG fermentation. These results accorded well with CephC production. Thus, 1.86- and 3.14-fold higher volumetric as well as 1.26- and 1.71-fold increased specific CephC yields were recorded in S. clavuligerus pCOlysA in comparison with the wild-type and its control strain, respectively, at 48th h. Increasing the expression of lysA provided 4.3 times more tunicamycin yields in the recombinant strain. These findings suggested that lysA overexpression in S. clavuligerus made the strain more productive for CephC and tunicamycin. The results also supported the presence of complex interactions among antibiotic biosynthesis pathways in S. clavuligerus.
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Martínez-Burgo Y, Santos-Aberturas J, Rodríguez-García A, Barreales EG, Tormo JR, Truman AW, Reyes F, Aparicio JF, Liras P. Activation of Secondary Metabolite Gene Clusters in Streptomyces clavuligerus by the PimM Regulator of Streptomyces natalensis. Front Microbiol 2019; 10:580. [PMID: 30984130 PMCID: PMC6448028 DOI: 10.3389/fmicb.2019.00580] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/06/2019] [Indexed: 11/13/2022] Open
Abstract
Expression of non-native transcriptional activators may be a powerful general method to activate secondary metabolites biosynthetic pathways. PAS-LuxR regulators, whose archetype is PimM, activate the biosynthesis of polyene macrolide antifungals and other antibiotics, and have been shown to be functionally preserved across multiple Streptomyces strains. In this work we show that constitutive expression of pimM in Streptomyces clavuligerus ATCC 27064 significantly affected its transcriptome and modifies secondary metabolism. Almost all genes in three secondary metabolite clusters were overexpressed, including the clusters responsible for the biosynthesis of the clinically important clavulanic acid and cephamycin C. In comparison to a control strain, this resulted in 10- and 7-fold higher production levels of these metabolites, respectively. Metabolomic and bioactivity studies of S. clavuligerus::pimM also revealed deep metabolic changes. Antifungal activity absent in the control strain was detected in S. clavuligerus::pimM, and determined to be the result of a fivefold increase in the production of the tunicamycin complex.
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Affiliation(s)
| | | | - Antonio Rodríguez-García
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain.,Institute of Biotechnology of León, INBIOTEC, León, Spain
| | - Eva G Barreales
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - José Rubén Tormo
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Fernando Reyes
- Centre of Excellence for Research into Innovative Medicine, Health Sciences Technology, MEDINA, Granada, Spain
| | - Jesús F Aparicio
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
| | - Paloma Liras
- Microbiology Section, Department of Molecular Biology, University of León, León, Spain
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Fu J, Zong G, Zhang P, Zhao Z, Ma J, Pang X, Cao G. XdhR negatively regulates actinorhodin biosynthesis in Streptomyces coelicolor M145. FEMS Microbiol Lett 2017; 364:4563580. [DOI: 10.1093/femsle/fnx226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jiafang Fu
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, Jingshi Road 18877, Jinan 250062, Shandong, China
| | - Gongli Zong
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, Jingshi Road 18877, Jinan 250062, Shandong, China
| | - Peipei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan 250100, China
| | - Zhilong Zhao
- School of Phaemacy, Linyi University, Linyi, China
| | - Junxia Ma
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, Jingshi Road 18877, Jinan 250062, Shandong, China
| | - Xiuhua Pang
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan 250100, China
| | - Guangxiang Cao
- Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, Jingshi Road 18877, Jinan 250062, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan 250100, China
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Yukioka Y, Tanahashi T, Shida K, Oguchi H, Ogawa S, Saito C, Yajima S, Ito S, Ohsawa K, Shoun H, Sasaki Y. A role of nitrite reductase (NirBD) for NO homeostatic regulation in Streptomyces coelicolor A3(2). FEMS Microbiol Lett 2016; 364:fnw241. [PMID: 27797866 DOI: 10.1093/femsle/fnw241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/27/2016] [Accepted: 10/17/2016] [Indexed: 12/23/2022] Open
Abstract
Although nitric oxide (NO) is an important signaling molecule in bacteria and higher organisms, excessive intracellular NO is highly reactive and dangerous. Therefore, living cells need strict regulation systems for cellular NO homeostasis. Recently, we discovered that Streptomyces coelicolor A3(2) retains the nitrogen oxide cycle (NO3-→NO2-→NO→NO3-) and nitrite removal system. The nitrogen oxide cycle regulates cellular NO levels, thereby controlling secondary metabolism initiation (red-pigmented antibiotic, RED production) and morphological differentiation. Nitrite induces gene expression in neighboring cells, suggesting another role for this cycle as a producer of transmittable intercellular communication molecules. Here, we demonstrated that ammonium-producing nitrite reductase (NirBD) is involved in regulating NO homeostasis in S. coelicolor A3(2). NirBD was constitutively produced in culture independently of GlnR, a known transcriptional factor. NirBD cleared the accumulated nitrite from the medium. Nir deletion mutants showed increased NO-dependent gene expression at later culture stages, whereas the wild-type M145 showed decreased expression, suggesting that high NO concentration was maintained in the mutant. Moreover, the nir deletion mutant produced more RED than that produced by the wild-type M145. These results suggest that NO2- removal by NirBD is important to regulate NO homeostasis and to complete NO signaling in S. coelicolor.
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Affiliation(s)
- Yuriya Yukioka
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Tsukiko Tanahashi
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Keisuke Shida
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Haruka Oguchi
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Shota Ogawa
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Chiaki Saito
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinsaku Ito
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Kanju Ohsawa
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Shoun
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka Setagaya-ku, Tokyo 156-8502, Japan
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Nitrogen oxide cycle regulates nitric oxide levels and bacterial cell signaling. Sci Rep 2016; 6:22038. [PMID: 26912114 PMCID: PMC4766573 DOI: 10.1038/srep22038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
Nitric oxide (NO) signaling controls various metabolic pathways in bacteria and higher eukaryotes. Cellular enzymes synthesize and detoxify NO; however, a mechanism that controls its cellular homeostasis has not been identified. Here, we found a nitrogen oxide cycle involving nitrate reductase (Nar) and the NO dioxygenase flavohemoglobin (Fhb), that facilitate inter-conversion of nitrate, nitrite, and NO in the actinobacterium Streptomyces coelicolor. This cycle regulates cellular NO levels, bacterial antibiotic production, and morphological differentiation. NO down-regulates Nar and up-regulates Fhb gene expression via the NO-dependent transcriptional factors DevSR and NsrR, respectively, which are involved in the auto-regulation mechanism of intracellular NO levels. Nitrite generated by the NO cycles induces gene expression in neighboring cells, indicating an additional role of the cycle as a producer of a transmittable inter-cellular communication molecule.
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The Pathway-Specific Regulator ClaR of Streptomyces clavuligerus Has a Global Effect on the Expression of Genes for Secondary Metabolism and Differentiation. Appl Environ Microbiol 2015; 81:6637-48. [PMID: 26187955 DOI: 10.1128/aem.00916-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 07/08/2015] [Indexed: 12/11/2022] Open
Abstract
Streptomyces clavuligerus claR::aph is a claR-defective mutant, but in addition to its claR defect it also carries fewer copies of the resident linear plasmids pSCL2 and pSCL4 (on the order of 4 × 10(5)-fold lower than the wild-type strain), as shown by qPCR. To determine the function of ClaR without potential interference due to plasmid copy number, a new strain, S. clavuligerus ΔclaR::aac, with claR deleted and carrying the wild-type level of plasmids, was constructed. Transcriptomic analyses were performed in S. clavuligerus ΔclaR::aac and S. clavuligerus ATCC 27064 as the control strain. The new ΔclaR mutant did not produce clavulanic acid (CA) and showed a partial expression of genes for the early steps of the CA biosynthesis pathway and a very poor expression (1 to 8%) of the genes for the late steps of the CA pathway. Genes for cephamycin C biosynthesis were weakly upregulated (1.7-fold at 22.5 h of culture) in the ΔclaR mutant, but genes for holomycin biosynthesis were expressed at levels from 3- to 572-fold higher than in the wild-type strain, supporting the observed overproduction of holomycin by S. clavuligerus ΔclaR::aac. Interestingly, three secondary metabolites produced by gene clusters SMCp20, SMCp22, and SMCp24, encoding still-cryptic compounds, had partially or totally downregulated their genes in the mutant, suggesting a regulatory role for ClaR wider than previously reported. In addition, the amfR gene was downregulated, and consequently, the mutant did not produce aerial mycelium. Expression levels of about 100 genes in the genome were partially up- or downregulated in the ΔclaR mutant, many of them related to the upregulation of the sigma factor-encoding rpoE gene.
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Martínez-Burgo Y, Álvarez-Álvarez R, Pérez-Redondo R, Liras P. Heterologous expression of Streptomyces clavuligerus ATCC 27064 cephamycin C gene cluster. J Biotechnol 2014; 186:21-9. [DOI: 10.1016/j.jbiotec.2014.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 12/13/2022]
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Mikulík K, Bobek J, Zídková J, Felsberg J. 6S RNA modulates growth and antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol 2014; 98:7185-97. [DOI: 10.1007/s00253-014-5806-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/26/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
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Role of the twin arginine protein transport pathway in the assembly of the Streptomyces coelicolor cytochrome bc1 complex. J Bacteriol 2013; 196:50-9. [PMID: 24142258 DOI: 10.1128/jb.00776-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cytochrome bc1-cytochrome aa3 complexes together comprise one of the major branches of the bacterial aerobic respiratory chain. In actinobacteria, the cytochrome bc1 complex shows a number of unusual features in comparison to other cytochrome bc1 complexes. In particular, the Rieske iron-sulfur protein component of this complex, QcrA, is a polytopic rather than a monotopic membrane protein. Bacterial Rieske proteins are usually integrated into the membrane in a folded conformation by the twin arginine protein transport (Tat) pathway. In this study, we show that the activity of the Streptomyces coelicolor M145 cytochrome bc1 complex is dependent upon an active Tat pathway. However, the polytopic Rieske protein is still integrated into the membrane in a ΔtatC mutant strain, indicating that a second protein translocation machinery also participates in its assembly. Difference spectroscopy indicated that the cytochrome c component of the complex was correctly assembled in the absence of the Tat machinery. We show that the intact cytochrome bc1 complex can be isolated from S. coelicolor M145 membranes by affinity chromatography. Surprisingly, a stable cytochrome bc1 complex containing the Rieske protein can be isolated from membranes even when the Tat system is inactive. These findings strongly suggest that the additional transmembrane segments of the S. coelicolor Rieske protein mediate hydrophobic interactions with one or both of the cytochrome subunits.
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Alvarez-Álvarez R, Martínez-Burgo Y, Pérez-Redondo R, Braña AF, Martín JF, Liras P. Expression of the endogenous and heterologous clavulanic acid cluster in Streptomyces flavogriseus: why a silent cluster is sleeping. Appl Microbiol Biotechnol 2013; 97:9451-63. [PMID: 23974366 DOI: 10.1007/s00253-013-5148-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
Abstract
Clusters for clavulanic acid (CA) biosynthesis are present in the actinomycetes Streptomyces flavogriseus ATCC 33331 and Saccharomonospora viridis DSM 43017. These clusters, which are silent, contain blocks of conserved genes in the same order as those of the Streptomyces clavuligerus CA cluster but assembled in a different organization. S. flavogriseus was grown in nine different media, but clavulanic acid production was undetectable using bioassays or by high-performance liquid chromatography analyses. Reverse-transcriptase polymerase chain reaction (RT-PCR) of S. flavogriseus CA biosynthesis genes showed that the regulatory genes ccaR and claR and some biosynthetic genes were expressed whereas expression of cyp, orf12, orf13, and oppA2 was undetectable. The ccaR gene of S. clavuligerus was unable to switch on CA production in S. flavogriseus::[Pfur-ccaR C], but insertion of a cosmid carrying the S. clavuligerus CA cluster (not including the ccaR gene) conferred clavulanic acid production on S. flavogriseus::[SCos-CA] particularly in TBO and YEME media; these results suggests that some of the S. flavogriseus CA genes are inactive. The known heptameric sequences recognized by CcaR in S. clavuligerus are poorly or not conserved in S. flavogriseus. Quantitative RT-PCR analysis of the CA gene clusters of S. clavuligerus and S. flavogriseus showed that the average expression value of the expressed genes in the former strain was in the order of 1.68-fold higher than in the later. The absence of CA production by S. flavogriseus can be traced to the lack of expression of the essential genes cyp, orf12, orf13, orf14, and oppA2. Heterologous expression of S. clavuligerus CA gene cluster in S. flavogriseus::[SCos-CA] was 11- to 14-fold lower than in the parental strain, suggesting that the genetic background of the host strain is important for optimal production of CA in Streptomyces.
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Affiliation(s)
- R Alvarez-Álvarez
- Microbiology Section, Department of Molecular Biology, Faculty of Biology and Environmental Sciences, Vegazana Campus, University of León, León, 24071, Spain,
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Kurt A, Álvarez-Álvarez R, Liras P, Özcengiz G. Role of the cmcH–ccaR intergenic region and ccaR overexpression in cephamycin C biosynthesis in Streptomyces clavuligerus. Appl Microbiol Biotechnol 2013; 97:5869-80. [DOI: 10.1007/s00253-013-4721-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 01/08/2023]
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Reverse biological engineering of hrdB to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis. Proc Natl Acad Sci U S A 2010; 107:11250-4. [PMID: 20534557 DOI: 10.1073/pnas.1006085107] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Avermectin and its analogues are produced by the actinomycete Streptomyces avermitilis and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene, aveR, were up-regulated in the high-producing strain. The upstream promoter region of aveR was predicted and proved to be directly recognized by sigma(hrdB) in vitro. A mutant library of hrdB gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved hrdB expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of aveR was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the hrdB gene can not only elicit the overexpression of aveR but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems.
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Wang G, Tanaka Y, Ochi K. The G243D mutation (afsB mutation) in the principal sigma factor sigmaHrdB alters intracellular ppGpp level and antibiotic production in Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2010; 156:2384-2392. [PMID: 20488875 DOI: 10.1099/mic.0.039834-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Deficient antibiotic production in an afsB mutant, BH5, of Streptomyces coelicolor A3(2) was recently shown to be due to a mutation (G243D) in region 1.2 of the primary sigma factor sigma(HrdB). Here we show that intracellular ppGpp levels during growth, as well as after amino acid depletion, in the mutant BH5 are lower than those of the afsB(+) parent strain. The introduction of certain rifampicin resistance (rif) mutations, which bypassed the requirement of ppGpp for transcription of pathway-specific regulatory genes, actII-ORF4 and redD, for actinorhodin and undecylprodigiosin, respectively, completely restored antibiotic production by BH5. Antibiotic production was restored also by introduction of a new class of thiostrepton-resistance (tsp) mutations, which provoked aberrant accumulation of intracellular ppGpp. Abolition of ppGpp synthesis in the afsB tsp mutant Tsp33 again abolished antibiotic production. These results indicate that intracellular ppGpp level is finely tuned for successful triggering of antibiotic production in the wild-type strain, and that this fine tuning was absent from the afsB mutant BH5, resulting in a failure to initiate antibiotic production in this strain.
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Affiliation(s)
- Guojun Wang
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Yukinori Tanaka
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Kozo Ochi
- Hiroshima Institute of Technology, Department of Health Science, Faculty of Applied Information Science, Miyake 2-1-1, Saeki-ku, Hiroshima 731-5193, Japan.,National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
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Lopez-Garcia MT, Santamarta I, Liras P. Morphological differentiation and clavulanic acid formation are affected in a Streptomyces clavuligerus adpA-deleted mutant. Microbiology (Reading) 2010; 156:2354-2365. [DOI: 10.1099/mic.0.035956-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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21
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Le TBK, Fiedler HP, den Hengst CD, Ahn SK, Maxwell A, Buttner MJ. Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus. Mol Microbiol 2009; 72:1462-74. [PMID: 19460097 DOI: 10.1111/j.1365-2958.2009.06735.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because most antibiotics are potentially lethal to the producing organism, there must be mechanisms to ensure that the machinery responsible for export of the mature antibiotic is in place at the time of biosynthesis. Simocyclinone D8 is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü 6040. Within the simocyclinone biosynthetic cluster are two divergently transcribed genes, simR and simX, encoding proteins that resemble the TetR/TetA repressor-efflux pump pair that cause widespread resistance to clinically important tetracyclines. Engineered expression of simX from a strong, heterologous promoter conferred high level simocyclinone D8 resistance on Streptomyces lividans, showing that simX encodes a simocyclinone efflux pump. Transcription of simX is controlled by SimR, which directly represses the simX and simR promoters by binding to two operator sites in the simX-simR intergenic region. Simocyclinone D8 abolishes DNA binding by SimR, providing a mechanism that couples the biosynthesis of simocyclinone to its export. In addition, an intermediate in the biosynthetic pathway, simocyclinone C4, which is essentially inactive as a DNA gyrase inhibitor, also induces simX expression in vivo and relieves simX repression by SimR in vitro.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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A new TetR family transcriptional regulator required for morphogenesis in Streptomyces coelicolor. J Bacteriol 2007; 190:61-7. [PMID: 17965158 DOI: 10.1128/jb.01316-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both morphogenesis and antibiotic production in the streptomycetes are initiated in response to starvation, and these events are coupled. We previously described a transposon-generated mutant in Streptomyces coelicolor, SE293, that resulted in a bld strain that overproduced the antibiotic actinorhodin. The SCO1135 open reading frame identified by the insertion encodes a member of the TetR family of transcriptional regulators. Here we show that a constructed deletion of the SCO1135 open reading frame resulted in the same morphological and antibiotic production phenotype as the insertion mutant. The constructed deletion also resulted in constitutive expression of SCO1135 transcript, as well as that of the gene cluster immediately adjacent to it, SCO1134-1132, which encodes a putative molybdopterin binding complex. A His6-tagged version of the SCO1135 protein product was shown to bind the intergenic region between SCO1135 and SCO1134, which contains the apparent transcription start sites for each gene mapped by primer extension analysis. Increased expression of the SCO1134-1132 transcript in the SCO1135 deletion mutant also resulted in increased expression of xanthine dehydrogenase activity, confirming the predictions about these open reading framed based on protein similarity. We have designated the SCO1134-1142 gene cluster xdhABC and the regulator encoded by SCO1135 xdhR. We speculate that the inappropriate expression of xanthine dehydrogenase affects purine salvaging pathways at the onset of development, creating artificially high concentrations of both GTP and ppGpp and perturbing the pathways these molecules participate in for the initiation of morphogenesis and antibiotic production.
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Williamson NR, Fineran PC, Leeper FJ, Salmond GPC. The biosynthesis and regulation of bacterial prodiginines. Nat Rev Microbiol 2006; 4:887-99. [PMID: 17109029 DOI: 10.1038/nrmicro1531] [Citation(s) in RCA: 359] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The red-pigmented prodiginines are bioactive secondary metabolites produced by both Gram-negative and Gram-positive bacteria. Recently, these tripyrrole molecules have received renewed attention owing to reported immunosuppressive and anticancer properties. The enzymes involved in the biosynthetic pathways for the production of two of these molecules, prodigiosin and undecylprodigiosin, are now known. However, the biochemistry of some of the reactions is still poorly understood. The physiology and regulation of prodiginine production in Serratia and Streptomyces are now well understood, although the biological role of these pigments in the producer organisms remains unclear. However, research into the biology of pigment production will stimulate interest in the bioengineering of strains to synthesize useful prodiginine derivatives.
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Affiliation(s)
- Neil R Williamson
- Department of Biochemistry, Tennis Court Road, University of Cambridge, UK
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Arabolaza A, Banchio C, Gramajo H. Transcriptional regulation of the macs1-fadD1 operon encoding two acyl-CoA synthases involved in the physiological differentiation of Streptomyces coelicolor. MICROBIOLOGY-SGM 2006; 152:1427-1439. [PMID: 16622059 DOI: 10.1099/mic.0.28553-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The long-chain acyl-CoA synthase (ACS) FadD1 plays an important role in timing the levels of antibiotic production in Streptomyces coelicolor. fadD1 and macs1, encoding a putative medium-chain ACS, are part of a two-gene operon, whose expression is induced during the stationary phase of growth. Here it is reported that transcription of the macs1-fadD1 operon is positively regulated by AcsR, a LuxR-type transcriptional regulator. In an acsR mutant, expression of the macs1-fadD1 genes loses its normal up-regulation and the mutant becomes deficient in antibiotic production, in a clear correlation with the phenotype shown by a fadD1 null mutant. The absence of macs1-fadD1 induction in the acsR mutant was restored by complementation with a wild-type copy of the acsR gene, showing a strict link between AcsR and induction of the macs1-fadD1 operon. Gel mobility shift assays and DNase I footprinting indicated that AcsR binds to specific sequences about +162 nucleotides downstream of the macs1 transcriptional start site. In the putative operator sequence three almost identical direct tandem repeats of seven nucleotides were identified where the central sequence is essential for AcsR recognition and binding. Transcriptional fusions of the divergent pacsR and pmacs1 promoters indicated that AcsR does not regulate its own transcription, and that it binds to the operator region to control exclusively the growth-phase induction of the macs1-fadD1 operon.
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Affiliation(s)
- Ana Arabolaza
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
| | - Claudia Banchio
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
| | - Hugo Gramajo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
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Uguru GC, Stephens KE, Stead JA, Towle JE, Baumberg S, McDowall KJ. Transcriptional activation of the pathway-specific regulator of the actinorhodin biosynthetic genes in Streptomyces coelicolor. Mol Microbiol 2006; 58:131-50. [PMID: 16164554 DOI: 10.1111/j.1365-2958.2005.04817.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Streptomyces produce a plethora of secondary metabolites including antibiotics and undergo a complex developmental cycle. As a means of establishing the pathways that regulate secondary metabolite production by this important bacterial genus, the model species Streptomyces coelicolor and its relatives have been the subject of several genetic screens. However, despite the identification and characterization of numerous genes that affect antibiotic production, there is still no overall understanding of the network that integrates the various environmental and growth signals to bring about changes in the expression of biosynthetic genes. To establish new links, we are taking a biochemical approach to identify transcription factors that regulate antibiotic production in S. coelicolor. Here we describe the identification and characterization of a transcription factor, designated AtrA, that regulates transcription of actII-ORF4, the pathway-specific activator of the actinorhodin biosynthetic gene cluster in S. coelicolor. Disruption of the corresponding atrA gene, which is not associated with any antibiotic gene cluster, reduced the production of actinorhodin, but had no detectable effect on the production of undecylprodigiosin or the calcium-dependent antibiotic. These results indicate that atrA has specificity with regard to the biosynthetic genes it influences. An orthologue of atrA is present in the genome of Streptomyces avermitilis, the only other streptomycete for which there is a publicly available complete sequence. We also show that S. coelicolor AtrA can bind in vitro to the promoter of strR, a transcriptional activator unrelated to actII-ORF4 that is the final regulator of streptomycin production in Streptomyces griseus. These findings provide further evidence that the path leading to the expression of pathway-specific activators of antibiotic biosynthesis genes in disparate Streptomyces may share evolutionarily conserved components in at least some cases, even though the final activators are not related, and suggests that the regulation of streptomycin production, which serves an important paradigm, may be more complex than represented by current models.
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Affiliation(s)
- Gabriel C Uguru
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev 2005; 69:326-56. [PMID: 15944459 PMCID: PMC1197418 DOI: 10.1128/mmbr.69.2.326-356.2005] [Citation(s) in RCA: 832] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a general profile for the proteins of the TetR family of repressors. The stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix DNA binding motif and adjacent regions in the three-dimensional structures of TetR, QacR, CprB, and EthR, four family members for which the function and three-dimensional structure are known. We have detected a set of 2,353 nonredundant proteins belonging to this family by screening genome and protein databases with the TetR profile. Proteins of the TetR family have been found in 115 genera of gram-positive, alpha-, beta-, and gamma-proteobacteria, cyanobacteria, and archaea. The set of genes they regulate is known for 85 out of the 2,353 members of the family. These proteins are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which the family member is involved can be simple, as in TetR (i.e., TetR bound to the target operator represses tetA transcription and is released in the presence of tetracycline), or more complex, involving a series of regulatory cascades in which either the expression of the TetR family member is modulated by another regulator or the TetR family member triggers a cell response to react to environmental insults. Based on what has been learned from the cocrystals of TetR and QacR with their target operators and from their three-dimensional structures in the absence and in the presence of ligands, and based on multialignment analyses of the conserved stretch of 47 amino acids in the 2,353 TetR family members, two groups of residues have been identified. One group includes highly conserved positions involved in the proper orientation of the helix-turn-helix motif and hence seems to play a structural role. The other set of less conserved residues are involved in establishing contacts with the phosphate backbone and target bases in the operator. Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org.
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Affiliation(s)
- Juan L Ramos
- Department of Plant Biochemistry and Molecular and Cellular Biology, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas, Granada, Spain.
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27
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Takano E, Kinoshita H, Mersinias V, Bucca G, Hotchkiss G, Nihira T, Smith CP, Bibb M, Wohlleben W, Chater K. A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor. Mol Microbiol 2005; 56:465-79. [PMID: 15813737 DOI: 10.1111/j.1365-2958.2005.04543.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gamma-butyrolactone signalling molecules are produced by many Streptomyces species, and several have been shown to regulate antibiotic production. In Streptomyces coelicolor A3(2) at least one gamma-butyrolactone (SCB1) has been shown to stimulate antibiotic production, and genes encoding proteins that are involved in its synthesis (scbA) and binding (scbR) have been characterized. Expression of these genes is autoregulated by a complex mechanism involving the gamma-butyrolactone. In this study, additional genes influenced by ScbR were identified by DNA microarray analysis, and included a cryptic cluster of genes for a hypothetical type I polyketide. Further analysis of this gene cluster revealed that the pathway-specific regulatory gene, kasO, is a direct target for regulation by ScbR. Gel retardation and DNase I footprinting analyses identified two potential binding sites for ScbR, one at -3 to -35 nt and the other at -222 to -244 nt upstream of the kasO transcriptional start site. Addition of SCB1 eliminated the DNA binding activity of ScbR at both sites. The expression of kasO was growth phase regulated in the parent (maximal during transition phase), undetectable in a scbA null mutant, and constitutively expressed in a scbR null mutant. Addition of SCB1 to the scbA mutant restored the expression of kasO, indicating that ScbR represses kasO until transition phase, when presumably SCB1 accumulates in sufficient quantity to relieve kasO repression. Expression of the cryptic antibiotic gene cluster was undetectable in a kasO deletion mutant. This is the first report with comprehensive in vivo and in vitro data to show that a gamma-butyrolactone-binding protein directly regulates a secondary metabolite pathway-specific regulatory gene in Streptomyces.
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Affiliation(s)
- Eriko Takano
- Mikrobiologie/Biotechnologie, Eberhard-Karls-Universität Tübingen, auf der Morgenstelle 28, 72076 Tübingen, Germany.
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28
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Takano E, Tao M, Long F, Bibb MJ, Wang L, Li W, Buttner MJ, Bibb MJ, Deng ZX, Chater KF. A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor. Mol Microbiol 2003; 50:475-86. [PMID: 14617172 DOI: 10.1046/j.1365-2958.2003.03728.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptomycetes are mycelial bacteria that produce sporulating aerial hyphae on solid media. Bald (bld) mutants fail to form aerial mycelium under at least some conditions. bldA encodes the only tRNA species able to read the leucine codon UUA efficiently, implying the involvement of a TTA-containing gene in initiating aerial growth. One candidate for such a gene was bldH, because the bldH109 mutant of Streptomyces coelicolor resembles bldA mutants in some aspects. In the work reported here, adpAc, an S. coelicolor gene similar to the Streptomyces griseus A factor-regulated adpAg, was found to complement the bldH109 mutant partially at both single and multiple copies. The sequence of adpAc from the bldH109 mutant revealed a frameshift. A constructed in frame deletion of adpAc conferred a bald colony phenotype, and the mutant behaved like bldA mutants and bldH109 in its pattern of extracellular signal exchange. Both adpAc and adpAg contain a TTA codon. A TTA-free version of adpAc was engineered by replacing the TTA leucine codon with a cognate TTG leucine codon. The adpA(TTATTG) gene could partially restore aerial mycelium formation to a bldA mutant when it was followed in cis by the gene ornA, as in the natural chromosomal arrangement. This indicated that the UUA codon in adpAc mRNA is the principal target through which bldA influences morphological differentiation. It also implied that translational arrest at the UUA codon in adpAc mRNA caused a polar effect on the downstream ornA, and that the poor translation of both genes contributes extensively to the deficiency of aerial mycelium formation in bldA mutants. Unlike the situation in S. griseus, adpAc transcription does not depend on the host's -butyrolactone signalling system, at least in liquid cultures. In addition, sigma factor BldN, which is the homologue of an S. griseus sigma factor AdsA that is absent from adpAg mutants of S. griseus, was present in the constructed adpAc null mutant of S. coelicolor.
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Affiliation(s)
- E Takano
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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Okamoto S, Lezhava A, Hosaka T, Okamoto-Hosoya Y, Ochi K. Enhanced expression of S-adenosylmethionine synthetase causes overproduction of actinorhodin in Streptomyces coelicolor A3(2). J Bacteriol 2003; 185:601-9. [PMID: 12511507 PMCID: PMC145329 DOI: 10.1128/jb.185.2.601-609.2003] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We found that a 46-kDa protein is highly expressed in an actinorhodin-overproducing Streptomyces coelicolor A3(2) mutant (KO-179), which exhibited a low-level resistance to streptomycin. The protein was identified as S-adenosylmethionine (SAM) synthetase, which is a product of the metK gene. Enzyme assay revealed that SAM synthetase activity in strain KO-179 was 5- to 10-fold higher than in wild-type cells. The elevation of SAM synthetase activity was found to be associated with an increase in the level of intracellular SAM. RNase protection assay revealed that the metK gene was transcribed from two distinct promoters (p1 and p2) and that enhanced expression of the MetK protein in the mutant strain KO-179 was attributed to elevated transcription from metKp2. Strikingly, the introduction of a high-copy-number plasmid containing the metK gene into wild-type cells resulted in a precocious hyperproduction of actinorhodin. Furthermore, the addition of SAM to the culture medium induced Act biosynthesis in wild-type cells. Overexpression of metK stimulated the expression of the pathway-specific regulatory gene actII-ORF4, as demonstrated by the RNase protection assay. The addition of SAM also caused hyperproduction of streptomycin in Streptomyces griseus. These findings implicate the significant involvement of intracellular SAM in initiating the onset of secondary metabolism in STREPTOMYCES:
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Affiliation(s)
- Susumu Okamoto
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
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Hu H, Zhang Q, Ochi K. Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase beta subunit) of Streptomyces lividans. J Bacteriol 2002; 184:3984-91. [PMID: 12081971 PMCID: PMC135172 DOI: 10.1128/jb.184.14.3984-3991.2002] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We found that the biosynthesis of actinorhodin (Act), undecylprodigiosin (Red), and calcium-dependent antibiotic (CDA) are dramatically activated by introducing certain mutations into the rpoB gene that confer resistance to rifampin to Streptomyces lividans 66, which produces less or no antibiotics under normal growth conditions. Activation of Act and/or Red biosynthesis by inducing mutations in the rpoB gene was shown to be dependent on the mutation's position and the amino acid species substituted in the beta-subunit of the RNA polymerase. Mutation analysis identified 15 different kinds of point mutations, which are located in region I, II, or III of the rpoB gene and, in addition, two novel mutations (deletion of nucleotides 1287 to 1289 and a double substitution at nucleotides 1309 and 1310) were also found. Western blot analyses and S1 mapping analyses demonstrated that the expression of actII-ORF4 and redD, which are pathway-specific regulatory genes for Act and Red, respectively, was activated in the mutants able to produce Act and Red. The ActIV-ORF1 protein (an enzyme for Act biosynthesis) and the RedD protein were produced just after the upregulation of ActII-ORF4 and RedZ, respectively. These results indicate that the mutation in the rpoB gene of S. lividans, resulting in the activation of Act and/or Red biosynthesis, functions at the transcription level by activating directly or indirectly the key regulatory genes, actII-ORF4 and redD. We propose that the mutated RNA polymerase may function by mimicking the ppGpp-bound form in activating the onset of secondary metabolism in STREPTOMYCES:
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Affiliation(s)
- Haifeng Hu
- National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
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Baldwin NE, Dombroski AJ. Isolation and characterization of mutations in region 1.2 of Escherichia coli sigma70. Mol Microbiol 2001; 42:427-37. [PMID: 11703665 DOI: 10.1046/j.1365-2958.2001.02642.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eubacterial RNA polymerase uses the sigma (sigma) subunit for recognition of and transcription initiation from promoter DNA sequences. One family of sigma factors includes those related to the primary sigma factor from Escherichia coli, sigma70. Members of the sigma70 family have four highly conserved domains, of which regions 2 to 4 are present in all members. Region 1 can be subdivided into regions 1.1 and 1.2. Region 1.1 affects DNA binding by sigma70 alone, as well as transcription initiation by holoenzyme. Region 1.2, present and highly conserved in most sigma factors, has not yet been assigned a putative function, although previous work has demonstrated that it is not required for either association with the core subunits of RNA polymerase or promoter-specific binding by holoenzyme. We generated random single amino acid substitutions targeted to region 1.2 of E. coli sigma70 as well as a deletion of region 1.2, and characterized the behaviour of the mutant sigma factors both in vivo and in vitro to investigate the function of region 1.2 during transcription initiation. In this study, we show that mutations in region 1.2 can affect promoter binding, open complex and initiated complex formation and the transition from abortive transcription to elongation.
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Affiliation(s)
- N E Baldwin
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, 6431 Fannin JFB 1.765, Houston, TX 77030, USA
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Takano E, Chakraburtty R, Nihira T, Yamada Y, Bibb MJ. A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol 2001; 41:1015-28. [PMID: 11555283 DOI: 10.1046/j.1365-2958.2001.02562.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many streptomycetes produce extracellular gamma-butyrolactones. In several cases, these have been shown to act as signals for the onset of antibiotic production. Synthesis of these molecules appears to require a member of the AfsA family of proteins (AfsA is required for A-factor synthesis of the gamma-butyrolactone A-factor and consequently for streptomycin production in Streptomyces griseus). An afsA homologue, scbA, was identified in Streptomyces coelicolor A3(2) and was found to lie adjacent to a divergently transcribed gene, scbR, which encodes a gamma-butyrolactone binding protein. Gel retardation assays and DNase I footprinting studies revealed DNA binding sites for ScbR at - 4 to - 33 nt with respect to the scbA transcriptional start site, and at - 42 to - 68 nt with respect to the scbR transcriptional start site. Addition of the gamma-butyrolactone SCB1 of S. coelicolor resulted in loss of the DNA-binding ability of ScbR. A scbA mutant produced no gamma-butyrolactones, yet overproduced two antibiotics, actinorhodin (Act) and undecylprodigiosin (Red), whereas a deletion mutant of scbR also failed to make gamma-butyrolactones and showed delayed Red production. These phenotypes differ markedly from those expected by analogy with the S. griseus A-factor system. Furthermore, transcription of scbR increased, and that of scbA was abolished, in an scbR mutant, indicating that ScbR represses its own expression while activating that of scbA. In the scbA mutant, expression of both genes was greatly reduced. Addition of SCB1 to the scbA mutant induced transcription of scbR, but did not restore scbA expression, indicating that the deficiency in scbA transcription in the scbA mutant is not solely due to the inability to produce SCB1, and that ScbA is a positive autoregulator in addition to being required for gamma-butyrolactone production. Overall, these results indicate a complex mechanism for gamma-butyrolactone-mediated regulation of antibiotic biosynthesis in S. coelicolor.
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Affiliation(s)
- E Takano
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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Hesketh A, Sun J, Bibb M. Induction of ppGpp synthesis in Streptomyces coelicolor A3(2) grown under conditions of nutritional sufficiency elicits actII-ORF4 transcription and actinorhodin biosynthesis. Mol Microbiol 2001; 39:136-44. [PMID: 11123695 DOI: 10.1046/j.1365-2958.2001.02221.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Production of ppGpp in Streptomyces coelicolor A3(2) was achieved independently of amino acid limitation by placing N-terminal segments of the ppGpp synthetase gene, relA, under the control of a thiostrepton-inducible promoter (tipAp). S1 nuclease protection experiments indicated that induced ppGpp concentrations of 6-12 pmol mg(-1) dry weight in late-exponential phase cultures caused activation of transcription of actII-ORF4, the pathway-specific activator gene for actinorhodin production. This level of ppGpp had no effect on growth rate, implying a causal role for ppGpp in activating actII-ORF4 transcription. No effect was observed on the transcription of the corresponding and homologous activator gene for undecylprodigiosin production, redD, reflecting a requirement for additional regulatory factors for activation of its transcription. This work provides the most compelling evidence yet for the activation of an antibiotic biosynthetic pathway by the stringent factor ppGpp.
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Affiliation(s)
- A Hesketh
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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