1
|
Han R, Xiang R, Li J, Wang F, Wang C. High-level production of microbial prodigiosin: A review. J Basic Microbiol 2021; 61:506-523. [PMID: 33955034 DOI: 10.1002/jobm.202100101] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/11/2022]
Abstract
Prodigiosin is a natural red pigment derived primarily from secondary metabolites of microorganisms, especially Serratia marcescens. It can also be chemically synthesized. Prodigiosin has been proven to have antitumor, antibacterial, antimalaria, anti-insect, antialgae, and immunosuppressive activities, and is gaining increasing important in the global market because of its great potential application value in clinical medicine development, environmental treatment, preparation of food additives, and so on. Due to the low efficiency of prodigiosin chemical synthesis, high-level prodigiosin of production by microorganisms are necessary for prodigiosin applications. In this paper, the production of prodigiosin by microorganism in recent decades is reviewed. The methods and strategies for increasing the yield of prodigiosin are discussed from the aspects of medium composition, additives, factors affecting production conditions, strain modification, and fermentation methods.
Collapse
Affiliation(s)
- Rui Han
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Roujin Xiang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Jinglin Li
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Fengqing Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Chuan Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| |
Collapse
|
2
|
Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin. Appl Microbiol Biotechnol 2019; 103:1667-1680. [PMID: 30637495 DOI: 10.1007/s00253-018-09611-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
Collapse
Affiliation(s)
- Chee-Hoo Yip
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Orr Yarkoni
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - James Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| |
Collapse
|
3
|
Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES. Genome engineering for microbial natural product discovery. Curr Opin Microbiol 2018; 45:53-60. [PMID: 29510374 DOI: 10.1016/j.mib.2018.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 11/16/2022]
Abstract
The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design.
Collapse
Affiliation(s)
- Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea.
| |
Collapse
|
4
|
Identification of the streptothricin and tunicamycin biosynthetic gene clusters by genome mining in Streptomyces sp. strain fd1-xmd. Appl Microbiol Biotechnol 2018; 102:2621-2633. [DOI: 10.1007/s00253-018-8748-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 10/18/2022]
|
5
|
Metabolic engineering of Streptomyces coelicolor for enhanced prodigiosins (RED) production. SCIENCE CHINA-LIFE SCIENCES 2017; 60:948-957. [DOI: 10.1007/s11427-017-9117-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/06/2017] [Indexed: 12/14/2022]
|
6
|
RifZ (AMED_0655) Is a Pathway-Specific Regulator for Rifamycin Biosynthesis in Amycolatopsis mediterranei. Appl Environ Microbiol 2017; 83:AEM.03201-16. [PMID: 28159794 DOI: 10.1128/aem.03201-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Rifamycin and its derivatives are particularly effective against the pathogenic mycobacteria Mycobacterium tuberculosis and Mycobacterium leprae Although the biosynthetic pathway of rifamycin has been extensively studied in Amycolatopsis mediterranei, little is known about the regulation in rifamycin biosynthesis. Here, an in vivo transposon system was employed to identify genes involved in the regulation of rifamycin production in A. mediterranei U32. In total, nine rifamycin-deficient mutants were isolated, among which three mutants had the transposon inserted in AMED_0655 (rifZ, encoding a LuxR family regulator). The rifZ gene was further knocked out via homologous recombination, and the transcription of genes in the rifamycin biosynthetic gene cluster (rif cluster) was remarkably reduced in the rifZ null mutant. Based on the cotranscription assay results, genes within the rif cluster were grouped into 10 operons, sharing six promoter regions. By use of electrophoretic mobility shift assay and DNase I footprinting assay, RifZ was proved to specially bind to all six promoter regions, which was consistent with the fact that RifZ regulated the transcription of the whole rif cluster. The binding consensus sequence was further characterized through alignment using the RifZ-protected DNA sequences. By use of bionformatic analysis, another five promoters containing the RifZ box (CTACC-N8-GGATG) were identified, among which the binding of RifZ to the promoter regions of both rifK and orf18 (AMED_0645) was further verified. As RifZ directly regulates the transcription of all operons within the rif cluster, we propose that RifZ is a pathway-specific regulator for the rif cluster.IMPORTANCE To this day, rifamycin and its derivatives are still the first-line antituberculosis drugs. The biosynthesis of rifamycin has been extensively studied, and most biosynthetic processes have been characterized. However, little is known about the regulation of the transcription of the rifamycin biosynthetic gene cluster (rif cluster), and no regulator has been characterized. Through the employment of transposon screening, we here characterized a LuxR family regulator, RifZ, as a direct transcriptional activator for the rif cluster. As RifZ directly regulates the transcription of the entire rif cluster, it is considered a pathway-specific regulator for rifamycin biosynthesis. Therefore, as the first regulator characterized for direct regulation of rif cluster transcription, RifZ may provide a new clue for further engineering of high-yield industrial strains.
Collapse
|
7
|
Wang X, Tang B, Ye Y, Mao Y, Lei X, Zhao G, Ding X. Bxb1 integrase serves as a highly efficient DNA recombinase in rapid metabolite pathway assembly. Acta Biochim Biophys Sin (Shanghai) 2017; 49:44-50. [PMID: 27864282 DOI: 10.1093/abbs/gmw115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/24/2016] [Indexed: 11/13/2022] Open
Abstract
Phage-encoded serine integrases are widely used in genetic engineering. They also have the potential to serve as efficient DNA assemblers, demonstrated by the method of site-specific recombination-based tandem assembly (SSRTA) that can combine biological parts into devices, pathways, and systems. Here, four serine integrases, ϕBT1, TG1, ϕRv1, and Bxb1, were investigated to ascertain their in vitro DNA assembly activities. Bxb1 integrase displayed the highest efficiency to obtain final products. Thus, we conclude that Bxb1 integrase is an excellent choice for DNA assembly in vitro Using this enzyme and its recognition sites, BioBrick standards were designed that are compatible with the SSRTA method for module addition. A rapid and efficient procedure was developed for the assembly of a multigene metabolic pathway in one step, directly from non-cutting plasmids containing the gene fragments. This technique is easy and convenient, and would be of interest to the synthetic biology community.
Collapse
Affiliation(s)
- Xianwei Wang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Biao Tang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yu Ye
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yayi Mao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolai Lei
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guoping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| |
Collapse
|
8
|
Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
Collapse
Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | | | | | | |
Collapse
|
9
|
Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 2015; 43:343-70. [PMID: 26364200 DOI: 10.1007/s10295-015-1682-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/28/2015] [Indexed: 12/18/2022]
Abstract
Actinomycetes continue to be important sources for the discovery of secondary metabolites for applications in human medicine, animal health, and crop protection. With the maturation of actinomycete genome mining as a robust approach to identify new and novel cryptic secondary metabolite gene clusters, it is critical to continue developing methods to activate and enhance secondary metabolite biosynthesis for discovery, development, and large-scale manufacturing. This review covers recent reports on promising new approaches and further validations or technical improvements of existing approaches to strain improvement applicable to a wide range of Streptomyces species and other actinomycetes.
Collapse
|
10
|
Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. New applications for phage integrases. J Mol Biol 2014; 426:2703-16. [PMID: 24857859 PMCID: PMC4111918 DOI: 10.1016/j.jmb.2014.05.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision. The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors. Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro. Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers. Serine integrases are increasingly being exploited for synthetic biology applications.
Collapse
Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Sean Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh EH9 3JR, UK
| | - Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
| |
Collapse
|
11
|
Iterative marker excision system. Appl Microbiol Biotechnol 2014; 98:4557-70. [DOI: 10.1007/s00253-014-5523-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/03/2014] [Accepted: 01/05/2014] [Indexed: 10/25/2022]
|