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Du G, Yang X, Wu Z, Pan M, Dong Z, Zhang Y, Xiang W, Li S. Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis. BIOLOGY 2024; 13:344. [PMID: 38785828 PMCID: PMC11118972 DOI: 10.3390/biology13050344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.
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Affiliation(s)
- Guozhong Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Xue Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Zhengxiong Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Minghui Pan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Zhuoxu Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China; (G.D.); (X.Y.); (Z.W.); (M.P.); (Z.D.); (Y.Z.)
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2
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Pei X, Lei Y, Zhang H. Transcriptional regulators of secondary metabolite biosynthesis in Streptomyces. World J Microbiol Biotechnol 2024; 40:156. [PMID: 38587708 DOI: 10.1007/s11274-024-03968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
In the post-genome era, great progress has been made in metabolic engineering using recombinant DNA technology to enhance the production of high-value products by Streptomyces. With the development of microbial genome sequencing techniques and bioinformatic tools, a growing number of secondary metabolite (SM) biosynthetic gene clusters in Streptomyces and their biosynthetic logics have been uncovered and elucidated. In order to increase our knowledge about transcriptional regulators in SM of Streptomyces, this review firstly makes a comprehensive summary of the characterized factors involved in enhancing SM production and awakening SM biosynthesis. Future perspectives on transcriptional regulator engineering for new SM biosynthesis by Streptomyces are also provided.
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Affiliation(s)
- Xinwei Pei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yunyun Lei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
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Tian J, Li Y, Zhang C, Su J, Lu W. Characterization of a pleiotropic regulator MtrA in Streptomyces avermitilis controlling avermectin production and morphological differentiation. Microb Cell Fact 2024; 23:103. [PMID: 38584273 PMCID: PMC11000389 DOI: 10.1186/s12934-024-02331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/11/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND The macrolide antibiotic avermectin, a natural product derived from Streptomyces avermitilis, finds extensive applications in agriculture, animal husbandry and medicine. The mtrA (sav_5063) gene functions as a transcriptional regulator belonging to the OmpR family. As a pleiotropic regulator, mtrA not only influences the growth, development, and morphological differentiation of strains but also modulates genes associated with primary metabolism. However, the regulatory role of MtrA in avermectin biosynthesis remains to be elucidated. RESULTS In this study, we demonstrated that MtrA, a novel OmpR-family transcriptional regulator in S. avermitilis, exerts global regulator effects by negatively regulating avermectin biosynthesis and cell growth while positively controlling morphological differentiation. The deletion of the mtrA gene resulted in an increase in avermectin production, accompanied by a reduction in biomass and a delay in the formation of aerial hyphae and spores. The Electrophoretic Mobility Shift Assay (EMSA) revealed that MtrA exhibited binding affinity towards the upstream region of aveR, the intergenic region between aveA1 and aveA2 genes, as well as the upstream region of aveBVIII in vitro. These findings suggest that MtrA exerts a negative regulatory effect on avermectin biosynthesis by modulating the expression of avermectin biosynthesis cluster genes. Transcriptome sequencing and fluorescence quantitative PCR analysis showed that mtrA deletion increased the transcript levels of the cluster genes aveR, aveA1, aveA2, aveC, aveE, aveA4 and orf-1, which explains the observed increase in avermectin production in the knockout strain. Furthermore, our findings demonstrate that MtrA positively regulates the cell division and differentiation genes bldM and ssgC, while exerting a negative regulatory effect on bldD, thereby modulating the primary metabolic processes associated with cell division, differentiation and growth in S. avermitilis, consequently impacting avermectin biosynthesis. CONCLUSIONS In this study, we investigated the negative regulatory effect of the global regulator MtrA on avermectin biosynthesis and its effects on morphological differentiation and cell growth, and elucidated its transcriptional regulatory mechanism. Our findings indicate that MtrA plays crucial roles not only in the biosynthesis of avermectin but also in coordinating intricate physiological processes in S. avermitilis. These findings provide insights into the synthesis of avermectin and shed light on the primary and secondary metabolism of S. avermitilis mediated by OmpR-family regulators.
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Affiliation(s)
- Jinpin Tian
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Yue Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China
| | - Jianyu Su
- Key Laboratory of the Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Yinchuan, 750021, China.
- College of Life Science, Ningxia University, Yinchuan, 750021, Ningxia, China.
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, People's Republic of China.
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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Li C, Urem M, Du C, Zhang L, van Wezel GP. Systems-wide analysis of the ROK-family regulatory gene rokL6 and its role in the control of glucosamine toxicity in Streptomyces coelicolor. Appl Environ Microbiol 2023; 89:e0167423. [PMID: 37982622 PMCID: PMC10734537 DOI: 10.1128/aem.01674-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Central metabolism plays a key role in the control of growth and antibiotic production in streptomycetes. Specifically, aminosugars act as signaling molecules that affect development and antibiotic production, via metabolic interference with the global repressor DasR. While aminosugar metabolism directly connects to other major metabolic routes such as glycolysis and cell wall synthesis, several important aspects of their metabolism are yet unresolved. Accumulation of N-acetylglucosamine 6-phosphate or glucosamine 6-phosphate is lethal to many bacteria, a yet unresolved phenomenon referred to as "aminosugar sensitivity." We made use of this concept by selecting for suppressors in genes related to glucosamine toxicity in nagB mutants, which showed that the gene pair of rok-family regulatory gene rokL6 and major facilitator superfamily transporter gene sco1448 forms a cryptic rescue mechanism. Inactivation of rokL6 resulted in the expression of sco1448, which then prevents the toxicity of amino sugar-derived metabolites in Streptomyces. The systems biology of RokL6 and its transcriptional control of sco1448 shed new light on aminosugar metabolism in streptomycetes and on the response of bacteria to aminosugar toxicity.
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Affiliation(s)
- Chao Li
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
| | - Mia Urem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Chao Du
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
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6
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Wang R, Zhao J, Chen L, Ye J, Wu H, Zhang H. LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023; 107:7501-7514. [PMID: 37768348 DOI: 10.1007/s00253-023-12756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The Actinomycetes Streptomyces lincolnensis is the producer of lincosamide-type antibiotic lincomycin, a widely utilized drug against Gram-positive bacteria and protozoans. In this work, through gene knockout, complementation, and overexpression experiments, we identified LcbR1 (SLINC_1595), a GntR family transcriptional regulator, as a repressor for lincomycin biosynthesis. Deletion of lcbR1 boosted lincomycin production by 3.8-fold, without obvious change in morphological development or cellular growth. The homologues of LcbR1 are widely distributed in Streptomyces. Heterologous expression of SCO1410 from Streptomyces coelicolor resulted in the reduction of lincomycin yield, implying that the function of LcbR1 is conserved across different species. Alignment among sequences upstream of lcbR1 and their homologues revealed a conserved 16-bp palindrome (-TTGAACGATCCTTCAA-), which was further proven to be the recognition motif of LcbR1 by electrophoretic mobility shift assays (EMSAs). Via this motif, LcbR1 suppressed the transcription of lcbR1 and SLINC_1596 sharing the same bi-directional promoter. SLINC_1596, one important target of LcbR1, exerted a positive effect on lincomycin production. As detected by quantitative real-time PCR (qRT-PCR) analyses, the expressions of all selected structural (lmbA, lmbC, lmbJ, lmbV, and lmbW), resistance (lmrA and lmrB) and regulatory genes (lmrC and lmbU) from lincomycin biosynthesis cluster were upregulated in deletion strain ΔlcbR1 at 48 h of fermentation, while the mRNA amounts of bldD, glnR, ramR, SLCG_Lrp, and SLCG_2919, previously characterized as the regulators on lincomycin production, were decreased in strain ΔlcbR1, although the regulatory effects of LcbR1 on the above differential expression genes seemed to be indirect. Besides, indicated by EMSAs, the expression of lcbR1 might be regulated by GlnR, SLCG_Lrp, and SLCG_2919, which shows the complexity of the regulatory network on lincomycin biosynthesis. KEY POINTS: • LcbR1 is a novel and conservative GntR family regulator regulating lincomycin production. • LcbR1 modulates the expressions of lcbR1 and SLINC_1596 through a palindromic motif. • GlnR, SLCG_Lrp, and SLCG_2919 can control the expression of lcbR1.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Lei Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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7
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Wang R, Zhao J, Chen L, Ye J, Wu H, Zhang H. LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023. [DOI: doi.org/10.1007/s00253-023-12756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 10/09/2023]
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8
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Cuervo L, Malmierca MG, García-Salcedo R, Méndez C, Salas JA, Olano C, Ceniceros A. Co-Expression of Transcriptional Regulators and Housekeeping Genes in Streptomyces spp.: A Strategy to Optimize Metabolite Production. Microorganisms 2023; 11:1585. [PMID: 37375086 DOI: 10.3390/microorganisms11061585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The search for novel bioactive compounds to overcome resistance to current therapeutics has become of utmost importance. Streptomyces spp. are one of the main sources of bioactive compounds currently used in medicine. In this work, five different global transcriptional regulators and five housekeeping genes, known to induce the activation or overproduction of secondary metabolites in Streptomyces coelicolor, were cloned in two separated constructs and expressed in 12 different strains of Streptomyces spp. from the in-house CS collection. These recombinant plasmids were also inserted into streptomycin and rifampicin resistant Streptomyces strains (mutations known to enhance secondary metabolism in Streptomyces). Different media with diverse carbon and nitrogen sources were selected to assess the strains' metabolite production. Cultures were then extracted with different organic solvents and analysed to search for changes in their production profiles. An overproduction of metabolites already known to be produced by the biosynthesis wild-type strains was observed such as germicidin by CS113, collismycins by CS149 and CS014, or colibrimycins by CS147. Additionally, the activation of some compounds such as alteramides in CS090a pSETxkBMRRH and CS065a pSETxkDCABA or inhibition of the biosynthesis of chromomycins in CS065a in pSETxkDCABA when grown in SM10 was demonstrated. Therefore, these genetic constructs are a relatively simple tool to manipulate Streptomyces metabolism and explore their wide secondary metabolites production potential.
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Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Raúl García-Salcedo
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - José A Salas
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Ana Ceniceros
- Functional Biology Department, University of Oviedo, 33006 Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A.), University of Oviedo, 33006 Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
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9
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Li GH, Zhang KQ. Natural nematicidal metabolites and advances in their biocontrol capacity on plant parasitic nematodes. Nat Prod Rep 2023; 40:646-675. [PMID: 36597965 DOI: 10.1039/d2np00074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: 2010 to 2021Natural nematicidal metabolites are important sources of nematode control. This review covers the isolation and structural determination of nematicidal metabolites from 2010 to 2021. We summarise chemical structures, bioactivity, metabolic regulation and biosynthesis of potential nematocides, and structure-activity relationship and application potentiality of natural metabolites in plant parasitic nematodes' biocontrol. In doing so, we aim to provide a comprehensive overview of the potential roles that natural metabolites can play in anti-nematode strategies.
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Affiliation(s)
- Guo-Hong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650091, China.
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650091, China.
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10
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Zhang H, Chen W, Wang X, Li Y, Zhu Z. Positive regulation of MarR-type regulator slnO and improving salinomycin production of Streptomyces albus by multiple transcriptional regulations. Can J Microbiol 2022; 68:157-163. [PMID: 34982582 DOI: 10.1139/cjm-2021-0342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of this study is to explore the function of MarR-family regulator slnO. In addition, the high-yield strain of salinomycin was constructed by using combined regulation strategies. Firstly the slnO gene over-expression strain (GO) was constructed in Streptomyces albus. Compared to wild type (WT) strain,salinomycin production in GO strain was increased about 28%. Electrophoretic mobility gel shift assays (EMSAs) confirmed that SlnO protein can bind specifically to the intergenic region of slnN-slnO, slnQ-slnA1 and slnF-slnT. qRT-PCR experiments also showed that slnA1, slnF, and slnT1 were significantly up-regulated, while the expression level of the slnN gene was down-regulated in GO strain. Secondly, slnN gene deletion strain (slnNDM) was used as the starting strain, and the pathway specific gene slnR in salinomycin gene cluster was over expressed in slnNDM. The new strain was named ZJUS01. The yield of salinomycin in ZJUS01 strain was 25% and 56% higher than that in slnNDM strain and WT strain. Above results indicate that the slnO gene has a positive regulation effect on the biosynthesis of salinomycin. Meanwhile, the yield of salinomycin could be greatly increased by manipulating multiple transcriptional regulations.
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Affiliation(s)
- Hongrui Zhang
- Zhejiang Chinese Medical University, 70571, Hangzhou, China;
| | - Weiwei Chen
- Zhejiang Chinese Medical University, 70571, Hangzhou, China;
| | - Xinyi Wang
- Zhejiang Chinese Medical University, 70571, Hangzhou, China;
| | - Yongquan Li
- Zhejiang University, 12377, Hangzhou, China, 310058;
| | - Zhenhong Zhu
- Zhejiang Chinese Medical University, 70571, Hangzhou, China, 310053;
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Liu Y, Khan S, Wu P, Li B, Liu L, Ni J, Zhang H, Chen K, Wu H, Zhang B. Uncovering and Engineering a Mini-Regulatory Network of the TetR-Family Regulator SACE_0303 for Yield Improvement of Erythromycin in Saccharopolyspora erythraea. Front Bioeng Biotechnol 2021; 9:692901. [PMID: 34595157 PMCID: PMC8476842 DOI: 10.3389/fbioe.2021.692901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/14/2021] [Indexed: 02/03/2023] Open
Abstract
Erythromycins produced by Saccharopolyspora erythraea have broad-spectrum antibacterial activities. Recently, several TetR-family transcriptional regulators (TFRs) were identified to control erythromycin production by multiplex control modes; however, their regulatory network remains poorly understood. In this study, we report a novel TFR, SACE_0303, positively correlated with erythromycin production in Sac. erythraea. It directly represses its adjacent gene SACE_0304 encoding a MarR-family regulator and indirectly stimulates the erythromycin biosynthetic gene eryAI and resistance gene ermE. SACE_0304 negatively regulates erythromycin biosynthesis by directly inhibiting SACE_0303 as well as eryAI and indirectly repressing ermE. Then, the SACE_0303 binding site within the SACE_0303-SACE_0304 intergenic region was defined. Through genome scanning combined with in vivo and in vitro experiments, three additional SACE_0303 target genes (SACE_2467 encoding cation-transporting ATPase, SACE_3156 encoding a large transcriptional regulator, SACE_5222 encoding α-ketoglutarate permease) were identified and proved to negatively affect erythromycin production. Finally, by coupling CRISPRi-based repression of those three targets with SACE_0304 deletion and SACE_0303 overexpression, we performed stepwise engineering of the SACE_0303-mediated mini-regulatory network in a high-yield strain, resulting in enhanced erythromycin production by 67%. In conclusion, the present study uncovered the regulatory network of a novel TFR for control of erythromycin production and provides a multiplex tactic to facilitate the engineering of industrial actinomycetes for yield improvement of antibiotics.
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Affiliation(s)
- Ying Liu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Sabir Khan
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Panpan Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Bowen Li
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Lanlan Liu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Jingshu Ni
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Hongxia Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Ketao Chen
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Hang Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Buchang Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China
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12
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Heat Shock Repressor HspR Directly Controls Avermectin Production, Morphological Development, and H 2O 2 Stress Response in Streptomyces avermitilis. Appl Environ Microbiol 2021; 87:e0047321. [PMID: 34160269 DOI: 10.1128/aem.00473-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heat shock response (HSR) is a universal cellular response that promotes survival following temperature increase. In filamentous Streptomyces, which accounts for ∼70% of commercial antibiotic production, HSR is regulated by transcriptional repressors; in particular, the widespread MerR-family regulator HspR has been identified as a key repressor. However, functions of HspR in other biological processes are unknown. The present study demonstrates that HspR pleiotropically controls avermectin production, morphological development, and heat shock and H2O2 stress responses in the industrially important species Streptomyces avermitilis. HspR directly activated ave structural genes (aveA1 and aveA2) and H2O2 stress-related genes (katA1, catR, katA3, oxyR, ahpC, and ahpD), whereas it directly repressed heat shock genes (HSGs) (the dnaK1-grpE1-dnaJ1-hspR operon, clpB1p, clpB2p, and lonAp) and developmental genes (wblB, ssgY, and ftsH). HspR interacted with PhoP (response regulator of the widespread PhoPR two-component system) at dnaK1p to corepress the important dnaK1-grpE1-dnaJ1-hspR operon. PhoP exclusively repressed target HSGs (htpG, hsp18_1, and hsp18_2) different from those of HspR (clpB1p, clpB2p, and lonAp). A consensus HspR-binding site, 5'-TTGANBBNNHNNNDSTSHN-3', was identified within HspR target promoter regions, allowing prediction of the HspR regulon involved in broad cellular functions. Taken together, our findings demonstrate a key role of HspR in the coordination of a variety of important biological processes in Streptomyces species. IMPORTANCE Our findings are significant to clarify the molecular mechanisms underlying HspR function in Streptomyces antibiotic production, development, and H2O2 stress responses through direct control of its target genes associated with these biological processes. HspR homologs described to date function as transcriptional repressors but not as activators. The results of the present study demonstrate that HspR acts as a dual repressor/activator. PhoP cross talks with HspR at dnaK1p to coregulate the heat shock response (HSR), but it also has its own specific target heat shock genes (HSGs). The novel role of PhoP in the HSR further demonstrates the importance of this regulator in Streptomyces. Overexpression of hspR strongly enhanced avermectin production in Streptomyces avermitilis wild-type and industrial strains. These findings provide new insights into the regulatory roles and mechanisms of HspR and PhoP and facilitate methods for antibiotic overproduction in Streptomyces species.
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13
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Liu J, Li L, Wang Y, Li B, Cai X, Tang L, Dong S, Yang E, Wu H, Zhang B. Joint engineering of SACE_Lrp and its target MarR enhances the biosynthesis and export of erythromycin in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2021; 105:2911-2924. [PMID: 33760930 DOI: 10.1007/s00253-021-11228-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 11/24/2022]
Abstract
The Lrp and MarR families are two groups of transcriptional regulators widely distributed among prokaryotes. However, the hierarchical-regulatory relationship between the Lrp family and the MarR family remains unknown. Our previous study found that an Lrp (SACE_Lrp) from Saccharopolyspora erythraea indirectly repressed the biosynthesis of erythromycin. In this study, we characterized a novel MarR family protein (SACE_6745) from S. erythraea, which is controlled by SACE_Lrp and plays a direct regulatory role in erythromycin biosynthesis and export. SACE_Lrp directly regulated the expression of marR by specifically binding a precise site OM (5'-CTCCGGGAACCATT-3'). Gene disruption of marR increased the production of erythromycin by 45% in S. erythraea A226. We found that MarR has direct DNA-binding activity for the promoter regions of the erythromycin biosynthetic genes, as well as an ABC exporter SACE_2701-2702 which was genetically proved to be responsible for erythromycin efflux. Disruption of SACE_Lrp in industrial S. erythraea WB was an efficient strategy to enhance erythromycin production. Herein, we jointly engineered SACE_Lrp and its target MarR by deleting marR in WBΔSACE_Lrp, resulting in 20% increase in erythromycin yield in mutant WBΔLrpΔmarR compared to WBΔSACE_Lrp, and 39% to WB. Overall, our findings provide new insights into the hierarchical-regulatory relationship of Lrp and MarR proteins and new avenues for coordinating antibiotic biosynthesis and export by joint engineering regulators in actinomycetes. KEY POINTS: • The hierarchical-regulatory relationship between SACE_Lrp and MarR was identified. • MarR directly controlled the expression of erythromycin biosynthesis and export genes. • Joint engineering of SACE_Lrp-MarR regulatory element enhanced erythromycin production.
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Affiliation(s)
- Jing Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Long Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Bowen Li
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Xinlu Cai
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Lijuan Tang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shengnan Dong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Endong Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hang Wu
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
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14
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Liu Z, Zhao Y, Huang C, Luo Y. Recent Advances in Silent Gene Cluster Activation in Streptomyces. Front Bioeng Biotechnol 2021; 9:632230. [PMID: 33681170 PMCID: PMC7930741 DOI: 10.3389/fbioe.2021.632230] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.
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Affiliation(s)
- Zhenyu Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yatong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chaoqun Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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15
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Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Streptomyces is a significant source of natural products that are used as therapeutic antibiotics, anticancer and antitumor agents, pesticides, and dyes. Recently, with the advances in metabolite analysis, many new secondary metabolites have been characterized. Moreover, genome mining approaches demonstrate that many silent and cryptic biosynthetic gene clusters (BGCs) and many secondary metabolites are produced in very low amounts under laboratory conditions. One strain many compounds (OSMAC), overexpression/deletion of regulatory genes, ribosome engineering, and promoter replacement have been utilized to activate or enhance the production titer of target compounds. Hence, the heterologous expression of BGCs by transferring to a suitable production platform has been successfully employed for the detection, characterization, and yield quantity production of many secondary metabolites. In this review, we introduce the systematic approach for the heterologous production of secondary metabolites from Streptomyces in Streptomyces and other hosts, the genome analysis tools, the host selection, and the development of genetic control elements for heterologous expression and the production of secondary metabolites.
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16
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Dolzhenko T, Burkova L, Dolzhenko O, Laptiev A. Biorational insectoacaricides based on avermectins to protect grapes. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213404010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The article presents an assessment of the biological effectiveness of biorational insectoacaricides based on abamectin and emamectin benzoate – metabolites of soil actinomycetes, to protect grapes from pests. We studied the effectiveness of new drugs: Mekar, ME (18 g/l abamectin) and Mabet, EC (18 g/l abamectin) against Schizotetranychus pruni; Yunona, ME (50 g/l emamectin benzoate), Emakleim, VRG (50 g/l emamectin benzoate) and Proclame Fit, WDG (400 g/kg lufenuron + 50 g/kg emamectin) against Lobesia botrana in the Krasnodar Region. According to the research results, the drugs Mekar, ME (18 g/l), Yunona, ME (50 g/l) and Proclame Fit, WDG (400 g/kg + 50 g/kg) are included in the State Catalog of Pesticides and Agrochemicals Permitted for Use on the territory of the Russian Federation and can be used in biologized and adaptively integrated grape protection systems.
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17
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Kißling L, Schneider C, Seibel K, Dorjjugder N, Busche T, Kalinowski J, Mack M. The roseoflavin producer
Streptomyces davaonensis
has a high catalytic capacity and specific genetic adaptations with regard to the biosynthesis of riboflavin. Environ Microbiol 2020; 22:3248-3265. [DOI: 10.1111/1462-2920.15066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/10/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Lena Kißling
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Carmen Schneider
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Katharina Seibel
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Nasanjargal Dorjjugder
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
| | - Tobias Busche
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Jörn Kalinowski
- Center for Biotechnology Bielefeld University Bielefeld 33594 Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of Biotechnology Mannheim University of Applied Sciences Mannheim 68163 Germany
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18
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Lu X, Liu X, Chen Z, Li J, van Wezel GP, Chen W, Wen Y. The ROK-family regulator Rok7B7 directly controls carbon catabolite repression, antibiotic biosynthesis, and morphological development in Streptomyces avermitilis. Environ Microbiol 2020; 22:5090-5108. [PMID: 32452104 DOI: 10.1111/1462-2920.15094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/10/2020] [Accepted: 05/19/2020] [Indexed: 11/30/2022]
Abstract
Carbon catabolite repression (CCR) is a common phenomenon in bacteria that modulates expression of genes involved in uptake of alternative carbon sources. In the filamentous streptomycetes, which produce half of all known antibiotics, the precise mechanism of CCR is yet unknown. We report here that the ROK-family regulator Rok7B7 pleiotropically controls xylose and glucose uptake, CCR, development, as well as production of the macrolide antibiotics avermectin and oligomycin A in Streptomyces avermitilis. Rok7B7 directly repressed structural genes for avermectin biosynthesis, whereas it activated olmRI, the cluster-situated activator gene for oligomycin A biosynthesis. Rok7B7 also directly repressed the xylose uptake operon xylFGH, whose expression was induced by xylose and repressed by glucose. Both xylose and glucose served as Rok7B7 ligands. rok7B7 deletion led to enhancement and reduction of avermectin and oligomycin A production, respectively, relieved CCR of xylFGH, and increased co-uptake efficiency of xylose and glucose. A consensus Rok7B7-binding site, 5'-TTKAMKHSTTSAV-3', was identified within aveA1p, olmRIp, and xylFp, which allowed prediction of the Rok7B7 regulon and confirmation of 11 additional targets involved in development, secondary metabolism, glucose uptake, and primary metabolic processes. Our findings will facilitate methods for strain improvement, antibiotic overproduction, and co-uptake of xylose and glucose in Streptomyces species.
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Affiliation(s)
- Xiaorui Lu
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xingchao Liu
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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19
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Deng X, Li M, Liu L, Zhang J, Zhang Y, Guo J, Zhao T, Cao S, Li Z, Zhang H. Functional analysis of Bucella reveals transcriptional regulation of MarR. Microb Pathog 2020; 144:104201. [PMID: 32325238 DOI: 10.1016/j.micpath.2020.104201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Brucellosis is a zoonotic infectious disease caused by Brucella infection. MarR-family transcription factors are closely related to diverse physiological functions necessary for many pathogens adaptation to environmental changes. However, whether the MarR-family transcription factors are involved in virulence, mediated inflammatory responses and regulated virulence gene expression in the intracellular pathogen Brucella are still unknown. Therefore, we created a 2308ΔMarR6 mutant of B. abortus 2308 (S2308). Virulence and inflammatory cytokines assays were performed using a murine macrophage cell line (RAW 264.7). We also performed chromatin immunoprecipitation of MarR6 followed by next-generation sequencing (ChIP-seq). The results showed that 2308ΔMarR6 was significantly reduced survival capability in RAW 264.7. After the macrophages were infected with 2308ΔMarR6, the levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-12 (IL-12), interferon-gamma (IFN-γ) and macrophage chemoattractant protein-1 (MCP-1) were decreased and were significantly lower than that for the S2308-infected group, indicating that the 2308ΔMarR6 mutant could reduce the secretion of inflammatory cytokines. Furthermore, we detected 122 intergenic ChIP-seq peaks of MarR6 binding distributed across the Brucella genome. Taken together, the research has recorded valuable data about MarR6. Our findings are of great significance in elucidating the function of MarR6.
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Affiliation(s)
- Xingmei Deng
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Min Li
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Liangbo Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Jing Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Yu Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Jia Guo
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Tianyi Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Shuzhu Cao
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China
| | - Zhiqiang Li
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, Henan Province, China.
| | - Hui Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang Province, China.
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20
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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21
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Hiraide Y, Yamamoto H, Kawajiri Y, Yamakawa H, Wada K, Fujita Y. Super-activator variants of the cyanobacterial transcriptional regulator ChlR essential for tetrapyrrole biosynthesis under low oxygen conditions. Biosci Biotechnol Biochem 2020; 84:481-490. [DOI: 10.1080/09168451.2019.1687281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
ChlR is a MarR-type transcriptional regulator that activates the transcription of the chlAII-ho2-hemN operon in response to low oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803. Upon exposure to low oxygen conditions, ChlR activates transcription of the operon that encodes enzymes critical to tetrapyrrole biosynthesis under low oxygen conditions. We previously identified a super-activator variant, D35H, of ChlR that constitutively activates transcription of the operon. To gain insight into the low-oxygen induced activation of ChlR, we obtained eight additional super-activator variants of ChlR including D35H from pseudorevertants of a chlAI-disrupted mutant. Most substitutions were located in the N-terminal region of ChlR. Mapping of the substituted amino acid residues provided valuable structural insights that uncovered the activation mechanism of ChlR.
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Affiliation(s)
- Yuto Hiraide
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yasushi Kawajiri
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hisanori Yamakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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22
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The evolution of MarR family transcription factors as counter-silencers in regulatory networks. Curr Opin Microbiol 2020; 55:1-8. [PMID: 32044654 DOI: 10.1016/j.mib.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 11/21/2022]
Abstract
Gene duplication facilitates the evolution of biological complexity, as one copy of a gene retains its original function while a duplicate copy can acquire mutations that would otherwise diminish fitness. Duplication has played a particularly important role in the evolution of regulatory networks by permitting novel regulatory interactions and responses to stimuli. The diverse MarR family of transcription factors (MFTFs) illustrate this concept, ranging from highly specific repressors of single operons to pleiotropic global regulators controlling hundreds of genes. MFTFs are often genetically and functionally linked to antimicrobial efflux systems. However, the SlyA MFTF lineage in the Enterobacteriaceae plays little or no role in regulating efflux but rather functions as transcriptional counter-silencers, which alleviate xenogeneic silencing of horizontally acquired genes and facilitate bacterial evolution by horizontal gene transfer. This review will explore recent advances in our understanding of MFTF traits that have contributed to their functional evolution.
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23
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Yan H, Lu X, Sun D, Zhuang S, Chen Q, Chen Z, Li J, Wen Y. BldD, a master developmental repressor, activates antibiotic production in two Streptomyces species. Mol Microbiol 2019; 113:123-142. [PMID: 31628680 DOI: 10.1111/mmi.14405] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 02/07/2023]
Abstract
BldD generally functions as a repressor controlling morphological development of Streptomyces. In this work, evidences that BldD also activates antibiotic production are provided. In Streptomyces roseosporus (which produces daptomycin widely used for treatment of human infections), deletion of bldD notably reduced daptomycin production, but enhanced sporulation. BldD stimulated daptomycin production by directly activating transcription of dpt structural genes and dptR3 (which encodes an indirect activator of daptomycin production), and repressed its own gene. BldD-binding sites on promoter regions of dptE, dptR3, and bldD were all found to contain BldD box-like sequences, facilitating prediction of new BldD targets. Two Streptomyces global regulatory genes, adpA and afsR, were confirmed to be directly activated by BldD. The protein AfsR was shown to act as an activator of daptomycin production, but a repressor of development. BldD directly represses nine key developmental genes. In Streptomyces avermitilis (which produces effective anthelmintic agents avermectins), BldD homolog (BldDsav) directly activates avermectin production through ave structural genes and cluster-situated activator gene aveR. This is the first report that BldD activates antibiotic biosynthesis both directly and via a cascade mechanism. BldD homologs are widely distributed among Streptomyces, our findings suggest that BldD may activate antibiotic production in other Streptomyces species.
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Affiliation(s)
- Hao Yan
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaorui Lu
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Di Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shuai Zhuang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiong Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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24
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McLean TC, Wilkinson B, Hutchings MI, Devine R. Dissolution of the Disparate: Co-ordinate Regulation in Antibiotic Biosynthesis. Antibiotics (Basel) 2019; 8:E83. [PMID: 31216724 PMCID: PMC6627628 DOI: 10.3390/antibiotics8020083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Discovering new antibiotics is vital to combat the growing threat of antimicrobial resistance. Most currently used antibiotics originate from the natural products of actinomycete bacteria, particularly Streptomyces species, that were discovered over 60 years ago. However, genome sequencing has revealed that most antibiotic-producing microorganisms encode many more natural products than previously thought. Biosynthesis of these natural products is tightly regulated by global and cluster situated regulators (CSRs), most of which respond to unknown environmental stimuli, and this likely explains why many biosynthetic gene clusters (BGCs) are not expressed under laboratory conditions. One approach towards novel natural product discovery is to awaken these cryptic BGCs by re-wiring the regulatory control mechanism(s). Most CSRs bind intergenic regions of DNA in their own BGC to control compound biosynthesis, but some CSRs can control the biosynthesis of multiple natural products by binding to several different BGCs. These cross-cluster regulators present an opportunity for natural product discovery, as the expression of multiple BGCs can be affected through the manipulation of a single regulator. This review describes examples of these different mechanisms, including specific examples of cross-cluster regulation, and assesses the impact that this knowledge may have on the discovery of novel natural products.
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Affiliation(s)
- Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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Characterization and engineering of the Lrp/AsnC family regulator SACE_5717 for erythromycin overproduction in Saccharopolyspora erythraea. J Ind Microbiol Biotechnol 2019; 46:1013-1024. [PMID: 31016583 DOI: 10.1007/s10295-019-02178-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
In this work, we found that the Lrp/AsnC family protein SACE_5717 negatively regulated erythromycin biosynthesis in S. erythraea. Disruption of SACE_5717 led to a 27% improvement in the yield of erythromycin in S. erythraea A226. SACE_5717 directly repressed its own gene expression, as well as that of the adjacent gene SACE_5716 by binding to the target sequence 5'-GAACGTTCGCCGTCACGCC-3'. The predicted LysE superfamily protein SACE_5716 directly influenced the export of lysine, histidine, threonine and glycine in S. erythraea. Arginine, tyrosine and tryptophan were characterized as the effectors of SACE_5717 by weakening the binding affinity of SACE_5717. In the industrial S. erythraea WB strain, deletion of SACE_5717 (WBΔSACE_5717) increased erythromycin yield by 20%, and by 36% when SACE_5716 was overexpressed in WBΔSACE_5717 (WBΔSACE_5717/5716). In large-scale 5-L fermentation experiment, erythromycin yield in the engineered strain WBΔSACE_5717/5716 reached 4686 mg/L, a 41% enhancement over 3323 mg/L of the parent WB strain.
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26
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Wei J, He L, Niu G. Regulation of antibiotic biosynthesis in actinomycetes: Perspectives and challenges. Synth Syst Biotechnol 2018; 3:229-235. [PMID: 30417136 PMCID: PMC6215055 DOI: 10.1016/j.synbio.2018.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/27/2018] [Accepted: 10/17/2018] [Indexed: 02/08/2023] Open
Abstract
Actinomycetes are the main sources of antibiotics. The onset and level of production of each antibiotic is subject to complex control by multi-level regulators. These regulators exert their functions at hierarchical levels. At the lower level, cluster-situated regulators (CSRs) directly control the transcription of neighboring genes within the gene cluster. Higher-level pleiotropic and global regulators exert their functions mainly through modulating the transcription of CSRs. Advances in understanding of the regulation of antibiotic biosynthesis in actinomycetes have inspired us to engineer these regulators for strain improvement and antibiotic discovery.
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Affiliation(s)
- Junhong Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Lang He
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
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