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Lee Y, Hwang S, Kim W, Kim JH, Palsson BO, Cho BK. CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces. J Ind Microbiol Biotechnol 2024; 51:kuae009. [PMID: 38439699 PMCID: PMC10949845 DOI: 10.1093/jimb/kuae009] [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: 01/18/2024] [Accepted: 03/02/2024] [Indexed: 03/06/2024]
Abstract
The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production. ONE-SENTENCE SUMMARY This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.
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Affiliation(s)
- Yongjae Lee
- Department of Biological Sciences, 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
| | - Woori Kim
- Department of Biological Sciences, 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
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center 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
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate school of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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Mao Y, Zhang X, Zhou T, Hou B, Ye J, Wu H, Wang R, Zhang H. Three new LmbU targets outside lmb cluster inhibit lincomycin biosynthesis in Streptomyces lincolnensis. Microb Cell Fact 2024; 23:3. [PMID: 38172890 PMCID: PMC10763038 DOI: 10.1186/s12934-023-02284-y] [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: 08/04/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Antibiotics biosynthesis is usually regulated by the cluster-situated regulatory gene(s) (CSRG(s)), which directly regulate the genes within the corresponding biosynthetic gene cluster (BGC). Previously, we have demonstrated that LmbU functions as a cluster-situated regulator (CSR) of lincomycin. And it has been found that LmbU regulates twenty non-lmb genes through comparative transcriptomic analysis. However, the regulatory mode of CSRs' targets outside the BGC remains unknown. RESULTS We screened the targets of LmbU in the whole genome of Streptomyces lincolnensis and found fourteen candidate targets, among which, eight targets can bind to LmbU by electrophoretic mobility shift assays (EMSA). Reporter assays in vivo revealed that LmbU repressed the transcription of SLINC_0469 and SLINC_1037 while activating the transcription of SLINC_8097. In addition, disruptions of SLINC_0469, SLINC_1037, and SLINC_8097 promoted the production of lincomycin, and qRT-PCR showed that SLINC_0469, SLINC_1037, and SLINC_8097 inhibited transcription of the lmb genes, indicating that all the three regulators can negatively regulate lincomycin biosynthesis. CONCLUSIONS LmbU can directly regulate genes outside the lmb cluster, and these genes can affect both lincomycin biosynthesis and the transcription of lmb genes. Our results first erected the cascade regulatory circuit of LmbU and regulators outside lmb cluster, which provides the theoretical basis for the functional research of LmbU family proteins.
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Affiliation(s)
- Yue Mao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xianyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Tianyu Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
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Lin CY, Ru Y, Jin Y, Lin Q, Zhao GR. PAS domain containing regulator SLCG_7083 involved in morphological development and glucose utilization in Streptomyces lincolnensis. Microb Cell Fact 2023; 22:257. [PMID: 38093313 PMCID: PMC10717218 DOI: 10.1186/s12934-023-02263-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Streptomyces lincolnensis is well known for producing the clinically important antimicrobial agent lincomycin. The synthetic and regulatory mechanisms on lincomycin biosynthesis have been deeply explored in recent years. However, the regulation involved in primary metabolism have not been fully addressed. RESULTS SLCG_7083 protein contains a Per-Arnt-Sim (PAS) domain at the N-terminus, whose homologous proteins are highly distributed in Streptomyces. The inactivation of the SLCG_7083 gene indicated that SLCG_7083 promotes glucose utilization, slows mycelial growth and affects sporulation in S. lincolnensis. Comparative transcriptomic analysis further revealed that SLCG_7083 represses eight genes involved in sporulation, cell division and lipid metabolism, and activates two genes involved in carbon metabolism. CONCLUSIONS SLCG_7083 is a PAS domain-containing regulator on morphological development and glucose utilization in S. lincolnensis. Our results first revealed the regulatory function of SLCG_7083, and shed new light on the transcriptional effects of SLCG_7083-like family proteins in Streptomyces.
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Affiliation(s)
- Chun-Yan Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China
| | - Yixian Ru
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China
| | - Yanchao Jin
- College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou, Fujian, 350117, China
| | - Qi Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China.
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen, 518055, China.
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Zou J, Mao Y, Hou B, Kang Y, Wang R, Wu H, Ye J, Zhang H. DeoR regulates lincomycin production in Streptomyces lincolnensis. World J Microbiol Biotechnol 2023; 39:332. [DOI: doi.org/10.1007/s11274-023-03788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
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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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Zou J, Mao Y, Hou B, Kang Y, Wang R, Wu H, Ye J, Zhang H. DeoR regulates lincomycin production in Streptomyces lincolnensis. World J Microbiol Biotechnol 2023; 39:332. [PMID: 37801155 DOI: 10.1007/s11274-023-03788-w] [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: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Regulators belonging to the DeoR family are widely distributed among the bacteria. Few studies have reported that DeoR family proteins regulate secondary metabolism of Streptomyces. This study explored the function of DeoR (SLINC_8027) in Streptomyces lincolnensis. Deletion of deoR in NRRL 2936 led to an increase in cell growth. The lincomycin production of the deoR deleted strain ΔdeoR was 3.4-fold higher than that of the wild strain. This trait can be recovered to a certain extent in the deoR complemented strain ΔdeoR::pdeoR. According to qRT-PCR analysis, DeoR inhibited the transcription of all detectable genes in the lincomycin biosynthesis cluster and repressed the expression of glnR, bldD, and SLCG_Lrp, which encode regulators outside the cluster. DeoR also inhibited the transcription of itself, as revealed by the XylE reporter. Furthermore, we demonstrated that DeoR bound directly to the promoter region of deoR, lmbA, lmbC-D, lmbJ-K, lmrA, lmrC, glnR, and SLCG_Lrp, by recognizing the 5'-CGATCR-3' motif. This study found that versatile regulatory factor DeoR negatively regulates lincomycin biosynthesis and cellular growth in S. lincolnensis, which expanded the regulatory network of lincomycin biosynthesis.
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Affiliation(s)
- Jingyun Zou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yue Mao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, 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, 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, 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, East China University of Science and Technology, Shanghai, 200237, China
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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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Wu W, Kang Y, Hou B, Ye J, Wang R, Wu H, Zhang H. Characterization of a TetR-type positive regulator AtrA for lincomycin production in Streptomyces lincolnensis. Biosci Biotechnol Biochem 2023; 87:786-795. [DOI: doi.org/10.1093/bbb/zbad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
ABSTRACT
AtrA belongs to the TetR family and has been well characterized for its roles in antibiotic biosynthesis regulation. Here, we identified an AtrA homolog (AtrA-lin) in Streptomyces lincolnensis. Disruption of atrA-lin resulted in reduced lincomycin production, whereas the complement restored the lincomycin production level to that of the wild-type. In addition, atrA-lin disruption did not affect cell growth and morphological differentiation. Furthermore, atrA-lin disruption hindered the transcription of regulatory gene lmbU, structural genes lmbA and lmbW inside the lincomycin biosynthesis gene cluster, and 2 other regulatory genes, adpA and bldA. Completement of atrA-lin restored the transcription of these genes to varying degrees. Notably, we found that AtrA-lin directly binds to the promoter region of lmbU. Collectively, AtrA-lin positively modulated lincomycin production via both pathway-specific and global regulators. This study offers further insights into the functional diversity of AtrA homologs and the mechanism of lincomycin biosynthesis regulation.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
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Adsorption of lincomycin on microwave activated biochar: Batch and dynamic adsorption. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.08.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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