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Thakur M, Kumar P, Rajput D, Yadav V, Dhaka N, Shukla R, Kumar Dubey K. Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories. BIORESOURCE TECHNOLOGY 2023; 376:128836. [PMID: 36898554 DOI: 10.1016/j.biortech.2023.128836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008 Kazakhstan
| | - Deepanshi Rajput
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rishikesh Shukla
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura- 281406, U.P., India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Jin S, Hui M, Lu Y, Zhao Y. An overview on the two-component systems of Streptomyces coelicolor. World J Microbiol Biotechnol 2023; 39:78. [PMID: 36645528 DOI: 10.1007/s11274-023-03522-6] [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: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The two-component system (TCS) found in various organisms is a regulatory system, which is involved in the response by the organism to stimuli, thereby regulating the internal behavior of the cell. It is commonly found in prokaryotes and is an important signaling system in bacteria. TCSs are involved in the regulation of physiological and morphological differentiation of the industrially important microbes from the genus Streptomyces, which produce a vast array of bioactive secondary metabolites (SMs). Genetic engineering of TCSs can substantially increase the yield of target SMs, which is valuable for industrial-scale production. Research on TCS has mainly been completed in the model strain Streptomyces coelicolor. In this review, we summarize the recent advances in the functional identification and elucidation of the regulatory mechanisms of various TCSs in S. coelicolor, with a focus on their roles in the biosynthesis of important SMs.
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Affiliation(s)
- Shangping Jin
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Ming Hui
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, 200234, Shanghai, China.
| | - Yawei Zhao
- College of Bioengineering, Henan University of Technology, 100 Lianhua Street, 450001, Zhengzhou, China.
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Sánchez de la Nieta R, Santamaría RI, Díaz M. Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled. Int J Mol Sci 2022; 23:ijms232315085. [PMID: 36499414 PMCID: PMC9739842 DOI: 10.3390/ijms232315085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria of the Streptomyces genus constitute an authentic biotech gold mine thanks to their ability to produce a myriad of compounds and enzymes of great interest at various clinical, agricultural, and industrial levels. Understanding the physiology of these organisms and revealing their regulatory mechanisms is essential for their manipulation and application. Two-component systems (TCSs) constitute the predominant signal transduction mechanism in prokaryotes, and can detect a multitude of external and internal stimuli and trigger the appropriate cellular responses for adapting to diverse environmental conditions. These global regulatory systems usually coordinate various biological processes for the maintenance of homeostasis and proper cell function. Here, we review the multiple TCSs described and characterized in Streptomyces coelicolor, one of the most studied and important model species within this bacterial group. TCSs are involved in all cellular processes; hence, unravelling the complex regulatory network they form is essential for their potential biotechnological application.
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Tong LL, Wang Y, Du YH, Yuan L, Liu MZ, Mu XY, Chen ZL, Zhang YD, He SJ, Li XJ, Guo DS. Transcriptomic Analysis of Morphology Regulatory Mechanisms of Microparticles to Paraisaria dubia in Submerged Fermentation. Appl Biochem Biotechnol 2022; 194:4333-4347. [PMID: 35083705 DOI: 10.1007/s12010-022-03820-z] [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] [Accepted: 12/31/2021] [Indexed: 11/25/2022]
Abstract
Liquid submerged fermentation is an effective strategy to achieve large-scale production of active ingredients by macrofungi, and controlling mycelium morphology is a key factor restricting the development of this technology. Mining for superior morphological regulatory factors and elucidation of their regulatory mechanisms are vital for the further development of macrofungal fermentation technology. In this study, microparticles were used to control the morphology of Paraisaria dubia (P. dubia) in submerged fermentation, and the underlying regulatory mechanisms were revealed by transcriptomic. The relative frequency of S-type pellet diameter increased significantly from 7.14 to 88.31%, and biomass increased 1.54 times when 15 g/L talc was added. Transcriptome analysis showed that the morphological regulation of filamentous fungi was a complex biological process, which involved signal transduction, mycelium polar growth, cell wall synthesis and cell division, etc. It also showed a positive impact on the basic and secondary metabolism of P. dubia. We provided a theoretical basis for controlling the mycelium morphology of P. dubia in submerged fermentation, which will promote the development of macrofungal fermentation technology.
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Affiliation(s)
- Ling-Ling Tong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Yue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Yuan-Hang Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Li Yuan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Meng-Zhen Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Xin-Ya Mu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Zi-Lei Chen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Yi-Dan Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Shao-Jie He
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Xiu-Juan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China.
| | - Dong-Sheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210023, People's Republic of China.
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80, Changjiang Road, Nanyang, 210023, People's Republic of China.
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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