101
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Jiang YH, Liu YF, Wang K, Zhou JY, Guo F, Zhao QW, Mao XM. Fine-Tuning Cas9 Activity with a Cognate Inhibitor AcrIIA4 to Improve Genome Editing in Streptomyces. ACS Synth Biol 2021; 10:2833-2841. [PMID: 34734710 DOI: 10.1021/acssynbio.1c00141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient enabling technology is required for synthetic biology in Streptomyces due to its natural product reservoir. Though the CRISPR-Cas9 system is powerful for genome editing in this genus, the proposed Cas9 toxicity has limited its application. Here on the basis of previous inducible Cas9 expression at the transcriptional and translational levels coupled with atpD overexpression, a Cas9 cognate inhibitor AcrIIA4 was further introduced to fine-tune the Cas9 activity. In both laboratory and industrial Streptomyces species, we showed that, compared to the constitutively expressed Cas9, incorporating AcrIIA4 increased the conjugation efficiency from 700- to 7000-fold before induction, while a comparable 65%-90% editing efficiency was obtained even on multiple loci for simultaneous deletion after Cas9 expression was induced, along with no significant off-targets. Thus, AcrIIA4 could be a modulator to control Cas9 activity to significantly improve genome editing, and this new toolkit would be widely adaptable and fasten genetic engineering in Streptomyces.
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Affiliation(s)
- Yu-Hang Jiang
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Fan Liu
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Kai Wang
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Jing-Yi Zhou
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Fengzhu Guo
- Zhejiang Silver-Elephant Bio-engineering Co., Ltd. No 18 Shifeng Road E., Fuxi Sub-district, Tiantai 317200, Zhejiang Province China
| | - Qing-Wei Zhao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xu-Ming Mao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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102
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Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X. Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria. Nucleic Acids Res 2021; 50:e15. [PMID: 34792175 PMCID: PMC8860599 DOI: 10.1093/nar/gkab1076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
Recombineering assisted multiplex genome editing generally uses single-stranded oligonucleotides for site directed mutational changes. It has proven highly efficient for functional screens and to optimize microbial cell factories. However, this approach is limited to relatively small mutational changes. Here, we addressed the challenges involved in the use of double-stranded DNA substrates for multiplex genome engineering. Recombineering is mediated by phage single-strand annealing proteins annealing ssDNAs into the replication fork. We apply this insight to facilitate the generation of ssDNA from the dsDNA substrate and to alter the speed of replication by elevating the available deoxynucleoside triphosphate (dNTP) levels. Intracellular dNTP concentration was elevated by ribonucleotide reductase overexpression or dNTP addition to establish double-stranded DNA Recombineering-assisted Multiplex Genome Engineering (dReaMGE), which enables rapid and flexible insertional and deletional mutagenesis at multiple sites on kilobase scales in diverse bacteria without the generation of double-strand breaks or disturbance of the mismatch repair system. dReaMGE can achieve combinatorial genome engineering works, for example, alterations to multiple biosynthetic pathways, multiple promoter or gene insertions, variations of transcriptional regulator combinations, within a few days. dReaMGE adds to the repertoire of bacterial genome engineering to facilitate discovery, functional genomics, strain optimization and directed evolution of microbial cell factories.
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Affiliation(s)
- Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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103
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Tsutsumi H, Katsuyama Y, Tezuka T, Miyano R, Inahashi Y, Takahashi Y, Nakashima T, Ohnishi Y. Identification and Analysis of the Biosynthetic Gene Cluster for the Indolizidine Alkaloid Iminimycin in Streptomyces griseus. Chembiochem 2021; 23:e202100517. [PMID: 34767291 DOI: 10.1002/cbic.202100517] [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: 09/27/2021] [Revised: 10/27/2021] [Indexed: 11/06/2022]
Abstract
Indolizidine alkaloids, which have versatile bioactivities, are produced by various organisms. Although the biosynthesis of some indolizidine alkaloids has been studied, the enzymatic machinery for their biosynthesis in Streptomyces remains elusive. Here, we report the identification and analysis of the biosynthetic gene cluster for iminimycin, an indolizidine alkaloid with a 6-5-3 tricyclic system containing an iminium cation from Streptomyces griseus. The gene cluster has 22 genes, including four genes encoding polyketide synthases (PKSs), which consist of eight modules in total. In vitro analysis of the first module revealed that its acyltransferase domain selects malonyl-CoA, although predicted to select methylmalonyl-CoA. Inactivation of seven tailoring enzyme-encoding genes and structural elucidation of four compounds accumulated in mutants provided important insights into iminimycin biosynthesis, although some of these compounds appeared to be shunt products. This study expands our knowledge of the biosynthetic machinery of indolizidine alkaloids and the enzymatic chemistry of PKS.
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Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Rei Miyano
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yoko Takahashi
- Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Takuji Nakashima
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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104
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In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens. Microorganisms 2021; 9:microorganisms9112297. [PMID: 34835423 PMCID: PMC8625390 DOI: 10.3390/microorganisms9112297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.
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105
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Ji CH, Kim H, Je HW, Kwon H, Lee D, Kang HS. Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus. Metab Eng 2021; 69:40-49. [PMID: 34737068 DOI: 10.1016/j.ymben.2021.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022]
Abstract
Secondary metabolites are produced at low titers by native producers due to tight regulations of their productions in response to environmental conditions. Synthetic biology provides a rational engineering principle for transcriptional optimization of secondary metabolite BGCs (biosynthetic gene clusters). Here, we demonstrate the use of synthetic biology principles for the development of a high-titer strain of the clinically important antibiotic daptomycin. Due to the presence of large NRPS (non-ribosomal peptide synthetase) genes with multiple direct repeats, we employed a top-down approach that allows transcriptional optimization of genes in daptomycin BGC with the minimum inputs of synthetic DNAs. The repeat-free daptomycin BGC was created through partial codon-reprogramming of a NRPS gene and cloned into a shuttle BAC vector, allowing BGC refactoring in a host with a powerful recombination system. Then, transcriptions of functionally divided operons were sequentially optimized through three rounds of DBTL (design-build-test-learn) cycles that resulted in up to ~2300% improvement in total lipopeptide titers compared to the wild-type strain. Upon decanoic acid feeding, daptomycin accounted for ∼ 40% of total lipopeptide production. To the best of our knowledge, this is the highest improvement of daptomycin titer ever achieved through genetic engineering of S. roseosporus. The top-down engineering approach we describe here could be used as a general strategy for the development of high-titer industrial strains of secondary metabolites produced by BGCs containing genes of large multi-modular NRPS and PKS enzymes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Haeun Kwon
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Dongho Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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106
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Gomez-Escribano JP, Algora Gallardo L, Bozhüyük KAJ, Kendrew SG, Huckle BD, Crowhurst NA, Bibb MJ, Collis AJ, Micklefield J, Herron PR, Wilkinson B. Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus. Microb Genom 2021; 7:000669. [PMID: 34747689 PMCID: PMC8743545 DOI: 10.1099/mgen.0.000669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/09/2021] [Indexed: 12/28/2022] Open
Abstract
Streptomyces clavuligerus is an industrially important actinomycete whose genetic manipulation is limited by low transformation and conjugation efficiencies, low levels of recombination of introduced DNA, and difficulty in obtaining consistent sporulation. We describe the construction and application of versatile vectors for Cas9-mediated genome editing of this strain. To design spacer sequences with confidence, we derived a highly accurate genome assembly for an isolate of the type strain (ATCC 27064). This yielded a chromosome assembly (6.75 Mb) plus assemblies for pSCL4 (1795 kb) and pSCL2 (149 kb). The strain also carries pSCL1 (12 kb), but its small size resulted in only partial sequence coverage. The previously described pSCL3 (444 kb) is not present in this isolate. Using our Cas9 vectors, we cured pSCL4 with high efficiency by targeting the plasmid's parB gene. Five of the resulting pSCL4-cured isolates were characterized and all showed impaired sporulation. Shotgun genome sequencing of each of these derivatives revealed large deletions at the ends of the chromosomes in all of them, and for two clones sufficient sequence data was obtained to show that the chromosome had circularized. Taken together, these data indicate that pSCL4 is essential for the structural stability of the linear chromosome.
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Affiliation(s)
- Juan Pablo Gomez-Escribano
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: Department of Bioresources for Bioeconomy and Health Research, Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Lis Algora Gallardo
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Kenan A. J. Bozhüyük
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Steven G. Kendrew
- Biotechnology and Environmental Shared Service, GlaxoSmithKline, Southdown View Way, Worthing BN14 8QH, UK
- Engineered Biodesign Limited, Cambridge CB1 3SN, UK
| | - Benjamin D. Huckle
- Biotechnology and Environmental Shared Service, GlaxoSmithKline, Southdown View Way, Worthing BN14 8QH, UK
| | - Nicola A. Crowhurst
- Biotechnology and Environmental Shared Service, GlaxoSmithKline, Southdown View Way, Worthing BN14 8QH, UK
| | - Mervyn J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Andrew J. Collis
- Biotechnology and Environmental Shared Service, GlaxoSmithKline, Southdown View Way, Worthing BN14 8QH, UK
| | - Jason Micklefield
- Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Paul R. Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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107
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Racharaks R, Arnold W, Peccia J. Development of CRISPR-Cas9 knock-in tools for free fatty acid production using the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. J Microbiol Methods 2021; 189:106315. [PMID: 34454980 DOI: 10.1016/j.mimet.2021.106315] [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: 07/06/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cyanobacteria and the reliance on unique antibiotic resistance markers. CRISPR-Cas9 has emerged as an effective and versatile editing platform in a wide variety of organisms, but its application for cyanobacterial engineering is limited by the inherent toxicity of Cas9 resulting in poor transformation efficiencies. Here, we demonstrated that a single-plasmid CRISPR-Cas9 system, pCRISPOmyces-2, can effectively knock-in a truncated thioesterase gene from Escherichia coli to generate free fatty acid (FFA) producing mutants of Syn2973. To do so, three parameters were evaluated on the effect of generating recipient colonies after conjugation with pCRISPOmyces-2-based plasmids: 1) a modified conjugation protocol termed streaked conjugation, 2) the deletion of the gene encoding RecJ exonuclease, and 3) single guide RNA (sgRNA) sequence. With the use of the streaked conjugation protocol and a ΔrecJ mutant strain of Syn2973, the conjugation efficiency for the pCRISPomyces-2 plasmid could be improved by 750-fold over the wildtype (WT) for a conjugation efficiency of 2.0 × 10-6 transconjugants/recipient cell. While deletion of the RecJ exonuclease alone increased the conjugation efficiency by 150-fold over the WT, FFA generation was impaired in FFA-producing mutants with the ΔrecJ background, and the large number of poor FFA-producing isolates indicated the potential increase in spontaneous mutation rates. The sgRNA sequence was found to be critical in achieving the desired CRISPR-Cas9-mediated knock-in mutation as the sgRNA impacts conjugation efficiency, likelihood of homogenous recombinants, and free fatty acid production in engineered strains.
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Affiliation(s)
- Ratanachat Racharaks
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Wyatt Arnold
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA.
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108
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Kim DR, Kwak YS. A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4. THE PLANT PATHOLOGY JOURNAL 2021; 37:389-395. [PMID: 34365750 PMCID: PMC8357572 DOI: 10.5423/ppj.nt.03.2021.0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 06/13/2023]
Abstract
Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus) and IALS, Gyeongsang National University, Jinju 52828, Korea
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109
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Lee HJ, Lee SJ. Advances in Accurate Microbial Genome-Editing CRISPR Technologies. J Microbiol Biotechnol 2021; 31:903-911. [PMID: 34261850 PMCID: PMC9723281 DOI: 10.4014/jmb.2106.06056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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110
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Beck C, Blin K, Gren T, Jiang X, Mohite OS, Palazzotto E, Tong Y, Charusanti P, Weber T. Metabolic Engineering of Filamentous Actinomycetes. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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111
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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112
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Cibichakravarthy B, Jose PA. Biosynthetic Potential of Streptomyces Rationalizes Genome-Based Bioprospecting. Antibiotics (Basel) 2021; 10:antibiotics10070873. [PMID: 34356794 PMCID: PMC8300671 DOI: 10.3390/antibiotics10070873] [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: 05/18/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Streptomyces are the most prolific source of structurally diverse microbial natural products. Advancing genome-based analysis reveals the previously unseen potential of Streptomyces to produce numerous novel secondary metabolites, which allows us to take natural product discovery to the next phase. However, at present there is a huge disproportion between the rate of genome reports and discovery of new compounds. From this perspective of harnessing the enduring importance of Streptomyces, we discuss the recent genome-directed advancements inspired by hidden biosynthetic wealth that provide hope for future antibiotics.
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Affiliation(s)
- Balasubramanian Cibichakravarthy
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761000, Israel;
| | - Polapass Arul Jose
- Department of Entomology and Plant Pathology & Microbiology, The Hebrew University of Jerusalem, POB 12, Rehovot 761000, Israel
- Correspondence:
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113
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, 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, 2800 Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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114
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Ren CY, Liu Y, Wei WP, Dai J, Ye BC. Reconstruction of Secondary Metabolic Pathway to Synthesize Novel Metabolite in Saccharopolyspora erythraea. Front Bioeng Biotechnol 2021; 9:628569. [PMID: 34277577 PMCID: PMC8283810 DOI: 10.3389/fbioe.2021.628569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Natural polyketides play important roles in clinical treatment, agriculture, and animal husbandry. Compared to natural hosts, heterologous chassis (especially Actinomycetes) have many advantages in production of polyketide compounds. As a widely studied model Actinomycete, Saccharopolyspora erythraea is an excellent host to produce valuable heterologous polyketide compounds. However, many host factors affect the expression efficiency of heterologous genes, and it is necessary to modify the host to adapt heterologous production. In this study, the CRISPR-Cas9 system was used to knock out the erythromycin biosynthesis gene cluster of Ab (erythromycin high producing stain). A fragment of 49491 bp in genome (from SACE_0715 to SACE_0733) was deleted, generating the recombinant strain AbΔery in which erythromycin synthesis was blocked and synthetic substrates methylmalonyl-CoA and propionyl-CoA accumulated enormously. Based on AbΔery as heterologous host, three genes, AsCHS, RgTAL, and Sc4CL, driven by strong promoters Pj23119, PermE, and PkasO, respectively, were introduced to produce novel polyketide by L-tyrosine and methylmalonyl-CoA. The product (E)-4-hydroxy-6-(4-hydroxystyryl)-3,5-dimethyl-2H-pyrone was identified in fermentation by LC-MS. High performance liquid chromatography analysis showed that knocking out ery BGC resulted in an increase of methylmalonyl-CoA by 142% and propionyl-CoA by 57.9% in AbΔery compared to WT, and the yield of heterologous product in AbΔery:AsCHS-RgTAL-Sc4CL was higher than WT:AsCHS-RgTAL-Sc4CL. In summary, this study showed that AbΔery could potentially serve as a precious heterologous host to boost the synthesis of other valuable polyketone compounds using methylmalonyl-CoA and propionyl-CoA in the future.
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Affiliation(s)
- Chong-Yang Ren
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yong Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Ping Wei
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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115
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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116
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Gomez-Escribano JP, Holmes NA, Schlimpert S, Bibb MJ, Chandra G, Wilkinson B, Buttner MJ, Bibb MJ. Streptomyces venezuelae NRRL B-65442: genome sequence of a model strain used to study morphological differentiation in filamentous actinobacteria. J Ind Microbiol Biotechnol 2021; 48:6294913. [PMID: 34100946 PMCID: PMC8788739 DOI: 10.1093/jimb/kuab035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
For over a decade, Streptomyces venezuelae has been used to study the molecular mechanisms that control morphological development in streptomycetes and it is now a well-established model strain. Its rapid growth and ability to sporulate in a near-synchronised manner in liquid culture, unusual among streptomycetes, greatly facilitates the application of modern molecular techniques such as ChIP-seq and RNA-seq, as well as fluorescence time-lapse imaging of the complete Streptomyces life cycle. Here we describe a high-quality genome sequence of our isolate of the strain (NRRL B-65442) consisting of an 8.2 Mb chromosome and a 158 kb plasmid, pSVJI1, which had not been reported previously. Surprisingly, while NRRL B-65442 yields green spores on MYM agar, the ATCC type strain 10712 (from which NRRL B-65442 was derived) produces grey spores. While comparison of the genome sequences of the two isolates revealed almost total identity, it did reveal a single nucleotide substitution in a gene, vnz_33525, likely to be involved in spore pigment biosynthesis. Replacement of the vnz_33525 allele of ATCC 10712 with that of NRRL B-65442 resulted in green spores, explaining the discrepancy in spore pigmentation. We also applied CRISPR-Cas9 to delete the essential parB of pSVJI1 to cure the plasmid from the strain without obvious phenotypic consequences.
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Affiliation(s)
| | - Neil A Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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117
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Goel N, Fatima SW, Kumar S, Sinha R, Khare SK. Antimicrobial resistance in biofilms: Exploring marine actinobacteria as a potential source of antibiotics and biofilm inhibitors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00613. [PMID: 33996521 PMCID: PMC8105627 DOI: 10.1016/j.btre.2021.e00613] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is one of the serious global public health threats that require immediate action. With the emergence of new resistance mechanisms in infection-causing microorganisms such as bacteria, fungi, and viruses, AMR threatens the effective prevention and treatment of diseases caused by them. This has resulted in prolonged illness, disability, and death. It has been predicted that AMR will lead to over ten million deaths by 2050. The rapid spread of multidrug-resistant bacteria is also causing old antibiotics to become ineffective. Among the diverse factors contributing to AMR, intrinsic biofilm development has been highlighted as an essential contributing facet. Moreover, biofilm-derived antibiotic tolerance leads to serious recurrent chronic infections. Therefore, the discovery of novel bioactive molecules is a potential solution that can help combat AMR. To achieve this, sustained mining of novel antimicrobial leads from actinobacteria, particularly marine actinobacteria, can be a promising strategy. Given their vast diversity and different habitats, the extraordinary capacity of actinobacteria can be tapped to synthesize new antibiotics or bioactive molecules for biofilm inhibition. Advanced screening strategies and novel approaches in the field of modern biochemical and molecular biology can be used to detect such new compounds. In view of this, the present review focuses on understanding some of the recent strategies to inhibit biofilm formation and explores the potential role of marine actinobacteria as sources of novel antibiotics and biofilm inhibitor molecules.
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Affiliation(s)
- Nikky Goel
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sumit Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sunil K. Khare
- Department of Chemistry, Indian Institute of Technology Delhi, India
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118
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Li YP, Bu QT, Li JF, Xie H, Su YT, Du YL, Li YQ. Genome-based rational engineering of Actinoplanes deccanensis for improving fidaxomicin production and genetic stability. BIORESOURCE TECHNOLOGY 2021; 330:124982. [PMID: 33743279 DOI: 10.1016/j.biortech.2021.124982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Microbial fermentation is currently still the major way to produce structural complicated clinical drugs. Yet, the low productivity and genetic instability of producing strains remain the bottlenecks in microbial pharmaceutical industry. Fidaxomicin is a microbial drug against the Clostridium difficile infection. Here, a genome-based combinatorial engineering strategy was established to improve both fidaxomicin production and the genetic stability of Actinoplanes deccanensis YP-1. Guided by genomic analysis, several genetic instability-associated elements were cumulatively deleted, generating a more genetically stable mutant. Further rational engineering approaches including elimination of a pigment pathway, duplication of the fidaxomicin gene cluster, overexpression of a positive regulator and optimization of the fermentation medium, led to an overall 27-folds improvement in fidaxomicin production. Taken together, the genome-based rational combinatorial engineering strategy was efficient to enhance the fidaxomicin production and ameliorate the genetic stability of YP-1, it can also be widely used in other industrial actinomycetes for strain improvement.
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Affiliation(s)
- Yue-Ping Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Ji-Feng Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Huang Xie
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ting Su
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ling Du
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China.
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119
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Zhang Y, Yun K, Huang H, Tu R, Hua E, Wang M. Antisense RNA Interference-Enhanced CRISPR/Cas9 Base Editing Method for Improving Base Editing Efficiency in Streptomyces lividans 66. ACS Synth Biol 2021; 10:1053-1063. [PMID: 33720688 DOI: 10.1021/acssynbio.0c00563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CRISPR/Cas9-mediated base editors, based on cytidine deaminase or adenosine deaminase, are emerging genetic technologies that facilitate genomic manipulation in many organisms. Since base editing is free from DNA double-strand breaks (DSBs), it has certain advantages, such as a lower toxicity, compared to the traditional DSB-based genome engineering technologies. In terms of Streptomyces, a base editing method has been successfully applied in several model and non-model species, such as Streptomyces coelicolor and Streptomyces griseofuscus. In this study, we first proved that BE2 (rAPOBEC1-dCas9-UGI) and BE3 (rAPOBEC1-nCas9-UGI) were functional base editing tools in Streptomyces lividans 66, albeit with a much lower editing efficiency compared to that of S. coelicolor. Uracil generated in deamination is a key intermediate in the base editing process, and it can be hydrolyzed by uracil DNA glycosidase (UDG) involved in the intracellular base excision repair, resulting in a low base editing efficiency. By knocking out two endogenous UDGs (UDG1 and UDG2), we managed to improve the base editing efficiency by 3.4-67.4-fold among different loci. However, the inactivation of UDG is detrimental to the genome stability and future application of engineered strains. Therefore, we finally developed antisense RNA interference-enhanced CRISPR/Cas9 Base Editing method (asRNA-BE) to transiently disrupt the expression of uracil DNA glycosidases during base editing, leading to a 2.8-65.8-fold enhanced editing efficiency and better genome stability. Our results demonstrate that asRNA-BE is a much better editing tool for base editing in S. lividans 66 and might be beneficial for improving the base editing efficiency and genome stability in other Streptomyces strains.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Kaiyue Yun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Huamei Huang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ran Tu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Erbing Hua
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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120
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Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor. mBio 2021; 12:mBio.00794-21. [PMID: 34006658 PMCID: PMC8262882 DOI: 10.1128/mbio.00794-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of bacteria are known to differentiate into cells with distinct phenotypic traits during processes such as biofilm formation or the development of reproductive structures. These cell types, by virtue of their specialized functions, embody a division of labor. However, how bacteria build spatial patterns of differentiated cells is not well understood. Here, we examine the factors that drive spatial patterns in divisions of labor in colonies of Streptomyces coelicolor, a multicellular bacterium capable of synthesizing an array of antibiotics and forming complex reproductive structures (e.g., aerial hyphae and spores). Using fluorescent reporters, we demonstrate that the pathways for antibiotic biosynthesis and aerial hypha formation are activated in distinct waves of gene expression that radiate outwards in S. coelicolor colonies. We also show that the spatiotemporal separation of these cell types depends on a key activator in the developmental pathway, AdpA. Importantly, when we manipulated local gradients by growing competing microbes nearby, or through physical disruption, expression in these pathways could be decoupled and/or disordered, respectively. Finally, the normal spatial organization of these cell types was partially restored with the addition of a siderophore, a public good made by these organisms, to the growth medium. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of physiological gradients and regulatory network architecture, key factors that also drive patterns of cellular differentiation in multicellular eukaryotic organisms.
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121
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The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem 2021; 65:261-275. [PMID: 33956071 DOI: 10.1042/ebc20200132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.
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122
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Calvelo VY, Crisante D, Elliot M, Nodwell JR. The ARC2 response in Streptomcyes coelicolor requires the global regulatory genes afsR and afsS. MICROBIOLOGY-SGM 2021; 167. [PMID: 33945461 DOI: 10.1099/mic.0.001047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ARC2 is a synthetic compound, related in structure and mechanism to the antibiotic triclosan, that activates the production of many specialized metabolites in the Streptomyces genus of bacteria. In this work, we demonstrate that the addition of ARC2 to Streptomyces coelicolor cultures results in considerable alterations in overall gene expression including most notably the specialized metabolic genes. Using actinorhodin production as a model system, we show that the effect of ARC2 depends on the pleiotropic regulators afsR and afsS but not afsK. We find that the constitutive expression of afsS can bypass the need for afsR but not the reverse, while the constitutive expression of afsK had no effect on actinorhodin production. These data are consistent with a model in which ARC2 activates a cell stress response that depends on AfsR activating the expression of the afsS gene such that AfsS then triggers the production of actinorhodin.
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Affiliation(s)
- Vanessa Yoon Calvelo
- Department of Biochemistry University of Toronto MaRS Discovery District 661 University Avenue Toronto, Ontario CANADA M5G 1M1, Canada
| | - David Crisante
- Department of Biology McMaster University 1280 Main Street West Hamilton, Ontario CANADA L8S 4K1, Canada
| | - Marie Elliot
- Department of Biology McMaster University 1280 Main Street West Hamilton, Ontario CANADA L8S 4K1, Canada
| | - Justin Rea Nodwell
- Department of Biochemistry University of Toronto MaRS Discovery District 661 University Avenue Toronto, Ontario CANADA M5G 1M1, Canada
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123
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [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: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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124
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Tsevelkhoroloo M, Shim SH, Lee CR, Hong SK, Hong YS. LacI-Family Transcriptional Regulator DagR Acts as a Repressor of the Agarolytic Pathway Genes in Streptomyces coelicolor A3(2). Front Microbiol 2021; 12:658657. [PMID: 33889146 PMCID: PMC8055832 DOI: 10.3389/fmicb.2021.658657] [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: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 11/15/2022] Open
Abstract
Actinobacteria utilize various polysaccharides in the soil as carbon source by degrading them via extracellular hydrolytic enzymes. Agarose, a marine algal polysaccharide composed of D-galactose and 3,6-anhydro-L-galactose (AHG), is one of the carbon sources used by S. coelicolor A3(2). However, little is known about agar hydrolysis in S. coelicolor A3(2), except that the regulation of agar hydrolysis metabolism is strongly inhibited by glucose as in the catabolic pathways of other polysaccharides. In this study, we elucidated the role of DagR in regulating the expression of three agarase genes (dagA, dagB, and dagC) in S. coelicolor A3(2) by developing a dagR-deletion mutant (Δsco3485). We observed that the Δsco3485 mutant had increased mRNA level of the agarolytic pathway genes and 1.3-folds higher agarase production than the wild type strain, indicating that the dagR gene encodes a cluster-suited repressor. Electrophoretic mobility shift assay revealed that DagR bound to the upstream regions of the three agarase genes. DNase 1 footprinting analysis demonstrated that a palindromic sequence present in the upstream region of the three agarase genes was essential for DagR-binding. Uniquely, the DNA-binding activity of DagR was inhibited by AHG, one of the final degradation products of agarose. AHG-induced agarase production was not observed in the Δsco3485 mutant, as opposed to that in the wild type strain. Therefore, DagR acts as a repressor that binds to the promoter region of the agarase genes, inhibits gene expression at the transcriptional level, and is derepressed by AHG. This is the first report on the regulation of gene expression regarding agar metabolism in S. coelicolor A3(2).
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Affiliation(s)
- Maral Tsevelkhoroloo
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - So Heon Shim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
| | - Chang-Ro Lee
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
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125
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Cao M, Zheng C, Yang D, Kalkreuter E, Adhikari A, Liu YC, Rateb ME, Shen B. Cryptic Sulfur Incorporation in Thioangucycline Biosynthesis. Angew Chem Int Ed Engl 2021; 60:7140-7147. [PMID: 33465268 PMCID: PMC7969429 DOI: 10.1002/anie.202015570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Sulfur incorporation into natural products is a critical area of biosynthetic studies. Recently, a subset of sulfur-containing angucyclines has been discovered, and yet, the sulfur incorporation step is poorly understood. In this work, a series of thioether-bridged angucyclines were discovered, and a cryptic epoxide Michael acceptor intermediate was revealed en route to thioangucyclines (TACs) A and B. However, systematic gene deletion of the biosynthetic gene cluster (BGC) by CRISPR/Cas9 could not identify any gene responsible for the conversion of the epoxide intermediate to TACs. Instead, a series of in vitro and in vivo experiments conclusively showed that the conversion is the result of two non-enzymatic steps, possibly mediated by endogenous hydrogen sulfide. Therefore, the TACs are proposed to derive from a detoxification process. These results are expected to contribute to the study of both angucyclines and the utilization of inorganic sulfur in natural product biosynthesis.
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Affiliation(s)
| | | | - Dong Yang
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Edward Kalkreuter
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ajeeth Adhikari
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yu-Chen Liu
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Mostafa E. Rateb
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
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Cao M, Zheng C, Yang D, Kalkreuter E, Adhikari A, Liu Y, Rateb ME, Shen B. Cryptic Sulfur Incorporation in Thioangucycline Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mingming Cao
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Chengjian Zheng
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Dong Yang
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Edward Kalkreuter
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Ajeeth Adhikari
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Yu‐Chen Liu
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Mostafa E. Rateb
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Ben Shen
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
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Heng E, Tan LL, Zhang MM, Wong FT. CRISPR-Cas strategies for natural product discovery and engineering in actinomycetes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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128
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Synefiaridou D, Veening JW. Harnessing CRISPR-Cas9 for Genome Editing in Streptococcus pneumoniae D39V. Appl Environ Microbiol 2021; 87:e02762-20. [PMID: 33397704 PMCID: PMC8105017 DOI: 10.1128/aem.02762-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by the detection and cleavage of invading foreign DNA. Modified versions of this system can be exploited as a biotechnological tool for precise genome editing at a targeted locus. Here, we developed a replicative plasmid that carries the CRISPR-Cas9 system for RNA-programmable genome editing by counterselection in the opportunistic human pathogen Streptococcus pneumoniae Specifically, we demonstrate an approach for making targeted markerless gene knockouts and large genome deletions. After a precise double-stranded break (DSB) is introduced, the cells' DNA repair mechanism of homology-directed repair (HDR) is exploited to select successful transformants. This is achieved through the transformation of a template DNA fragment that will recombine in the genome and eliminate recognition of the target of the Cas9 endonuclease. Next, the newly engineered strain can be easily cured from the plasmid, which is temperature sensitive for replication, by growing it at the nonpermissive temperature. This allows for consecutive rounds of genome editing. Using this system, we engineered a strain with three major virulence factors deleted. The approaches developed here could potentially be adapted for use with other Gram-positive bacteria.IMPORTANCEStreptococcus pneumoniae (the pneumococcus) is an important opportunistic human pathogen killing more than 1 million people each year. Having the availability of a system capable of easy genome editing would significantly facilitate drug discovery and efforts to identify new vaccine candidates. Here, we introduced an easy-to-use system to perform multiple rounds of genome editing in the pneumococcus by putting the CRISPR-Cas9 system on a temperature-sensitive replicative plasmid. The approaches used here will advance genome editing projects in this important human pathogen.
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Affiliation(s)
- Dimitra Synefiaridou
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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129
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Portable CRISPR-Cas9 N System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei. Appl Environ Microbiol 2021; 87:AEM.02669-20. [PMID: 33397707 DOI: 10.1128/aem.02669-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Diverse Lactobacillus strains are widely used as probiotic cultures in the dairy and dietary supplement industries, and specific strains, such as Lactobacillus acidophilus NCFM, have been engineered for the development of biotherapeutics. To expand the Lactobacillus manipulation toolbox with enhanced efficiency and ease, we present here a CRISPR (clustered regularly interspaced palindromic repeats)-SpyCas9D10A nickase (Cas9N)-based system for programmable engineering of L. acidophilus NCFM, a model probiotic bacterium. Successful single-plasmid delivery system was achieved with the engineered pLbCas9N vector harboring cas9 N under the regulation of a Lactobacillus promoter and a cloning region for a customized single guide RNA (sgRNA) and editing template. The functionality of the pLbCas9N system was validated in NCFM with targeted chromosomal deletions ranging between 300 bp and 1.9 kb at various loci (rafE, lacS, and ltaS), yielding 35 to 100% mutant recovery rates. Genome analysis of the mutants confirmed precision and specificity of the pLbCas9N system. To showcase the versatility of this system, we also inserted an mCherry fluorescent-protein gene downstream of the pgm gene to create a polycistronic transcript. The pLbCas9N system was further deployed in other species to generate a concurrent single-base substitution and gene deletion in Lactobacillus gasseri ATCC 33323 and an in-frame gene deletion in Lactobacillus paracasei Lpc-37, highlighting the portability of the system in phylogenetically distant Lactobacillus species, where its targeting activity was not interfered with by endogenous CRISPR-Cas systems. Collectively, these editing outcomes illustrate the robustness and versatility of the pLbCas9N system for genome manipulations in diverse lactobacilli and open new avenues for the engineering of health-promoting lactic acid bacteria.IMPORTANCE This work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three Lactobacillus species belonging to the lactic acid bacteria (LAB), which are commonly known for their long history of use in food fermentations and as indigenous members of healthy microbiotas and for their emerging roles in human and animal commercial health-promoting applications. We exploited the established CRISPR-SpyCas9 nickase for flexible and precise genome editing applications in Lactobacillus acidophilus and further demonstrated the efficacy of this universal system in two distantly related Lactobacillus species. This versatile Cas9-based system facilitates genome engineering compared to conventional gene replacement systems and represents a valuable gene editing modality in species that do not possess native CRISPR-Cas systems. Overall, this portable tool contributes to expanding the genome editing toolbox of LAB for studying their health-promoting mechanisms and engineering of these beneficial microbes as next-generation vaccines and designer probiotics.
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130
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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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131
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Song C, Luan J, Li R, Jiang C, Hou Y, Cui Q, Cui T, Tan L, Ma Z, Tang YJ, Stewart AF, Fu J, Zhang Y, Wang H. RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters. Nucleic Acids Res 2021; 48:e130. [PMID: 33119745 PMCID: PMC7736807 DOI: 10.1093/nar/gkaa956] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022] Open
Abstract
Biosynthesis reprograming is an important way to diversify chemical structures. The large repetitive DNA sequences existing in polyketide synthase genes make seamless DNA manipulation of the polyketide biosynthetic gene clusters extremely challenging. In this study, to replace the ethyl group attached to the C-21 of the macrolide insecticide spinosad with a butenyl group by refactoring the 79-kb gene cluster, we developed a RedEx method by combining Redαβ mediated linear-circular homologous recombination, ccdB counterselection and exonuclease mediated in vitro annealing to insert an exogenous extension module in the polyketide synthase gene without any extra sequence. RedEx was also applied for seamless deletion of the rhamnose 3′-O-methyltransferase gene in the spinosad gene cluster to produce rhamnosyl-3′-desmethyl derivatives. The advantages of RedEx in seamless mutagenesis will facilitate rational design of complex DNA sequences for diverse purposes.
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Affiliation(s)
- Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Yu Hou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tianqi Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Long Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zaichao Ma
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, 266237, China
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132
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Devine R, McDonald HP, Qin Z, Arnold CJ, Noble K, Chandra G, Wilkinson B, Hutchings MI. Re-wiring the regulation of the formicamycin biosynthetic gene cluster to enable the development of promising antibacterial compounds. Cell Chem Biol 2021; 28:515-523.e5. [PMID: 33440167 PMCID: PMC8062789 DOI: 10.1016/j.chembiol.2020.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022]
Abstract
The formicamycins are promising antibiotics first identified in Streptomyces formicae KY5, which produces the compounds at low levels. Here, we show that by understanding the regulation of the for biosynthetic gene cluster (BGC), we can rewire the BGC to increase production levels. The for BGC consists of 24 genes expressed on nine transcripts. The MarR regulator ForJ represses expression of seven transcripts encoding the major biosynthetic genes as well as the ForGF two-component system that initiates biosynthesis. We show that overexpression of forGF in a ΔforJ background increases formicamycin production 10-fold compared with the wild-type. De-repression, by deleting forJ, also switches on biosynthesis in liquid culture and induces the production of additional, previously unreported formicamycin congeners. Furthermore, combining de-repression with mutations in biosynthetic genes leads to biosynthesis of additional bioactive precursors. Formicamycin biosynthesis requires 24 genes expressed on nine transcripts Deleting the MarR regulator ForJ increases formicamycin biosynthesis De-repressing formicamycin biosynthesis induces production in liquid culture Re-wiring regulation and biosynthesis results in the production of new congeners
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Affiliation(s)
- Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Hannah P McDonald
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Corinne J Arnold
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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133
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Bao XR, Pan Y, Lee CM, Davis TH, Bao G. Tools for experimental and computational analyses of off-target editing by programmable nucleases. Nat Protoc 2021; 16:10-26. [PMID: 33288953 PMCID: PMC8049448 DOI: 10.1038/s41596-020-00431-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Genome editing using programmable nucleases is revolutionizing life science and medicine. Off-target editing by these nucleases remains a considerable concern, especially in therapeutic applications. Here we review tools developed for identifying potential off-target editing sites and compare the ability of these tools to properly analyze off-target effects. Recent advances in both in silico and experimental tools for off-target analysis have generated remarkably concordant results for sites with high off-target editing activity. However, no single tool is able to accurately predict low-frequency off-target editing, presenting a bottleneck in therapeutic genome editing, because even a small number of cells with off-target editing can be detrimental. Therefore, we recommend that at least one in silico tool and one experimental tool should be used together to identify potential off-target sites, and amplicon-based next-generation sequencing (NGS) should be used as the gold standard assay for assessing the true off-target effects at these candidate sites. Future work to improve off-target analysis includes expanding the true off-target editing dataset to evaluate new experimental techniques and to train machine learning algorithms; performing analysis using the particular genome of the cells in question rather than the reference genome; and applying novel NGS techniques to improve the sensitivity of amplicon-based off-target editing quantification.
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Affiliation(s)
- X Robert Bao
- ILISATech, Houston, TX, USA
- Arsenal Biosciences, South San Francisco, CA, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M Lee
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA.
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134
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Qiao Y, Zhang Q, Chen D, Liu M, Liu W. Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202105035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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135
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Zhang D, Wang X, Ye Y, He Y, He F, Tian Y, Luo Y, Liang S. Label-free proteomic dissection on dptP-deletion mutant uncovers dptP involvement in strain growth and daptomycin tolerance of Streptomyces roseosporus. Microb Biotechnol 2020; 14:708-725. [PMID: 33369164 PMCID: PMC7936300 DOI: 10.1111/1751-7915.13736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/07/2020] [Indexed: 02/05/2023] Open
Abstract
Daptomycin (DAP) is a novel microbial lipopeptide antibiotic synthesized by the DAP biosynthetic gene cluster dpt of Streptomyces roseosporus (S. roseosporus). DptP gene locates upstream of dpt and confers DAP resistance to Streptomyces ambofaciens (S. ambofaciens). So far, the biological functions of dptP gene for S. roseosporus growth are still completely uncovered. We performed label‐free quantification proteomic dissections with loss‐ and gain‐of‐function experiments to decipher dptP‐involved functions. Deletion of dptP gene activated energy metabolism and metabolism of secondary metabolites pathways and enhanced the transcription levels and protein abundance of key members of the dpt cluster. Whereas dptP deletion inhibited transport/signal transduction and drug resistance pathways and protein abundance of cell division‐relative proteins, subsequently decreased mycelia cell growth rate. S. roseosporus strain with dptP deletion was more sensitive to DAP treatment compared to the wild type. In contrast, overexpression of dptP gene decreased transcription levels of DAP biosynthetic genes and enhanced growth rate of Streptomcyes strain upon elevated culture temperature and DAP supplementation. Taken together, dptP gene contributes to Streptomcyes primary growth under elevated temperature and DAP treatment, whereas it plays negative roles on metabolism of secondary metabolites and transcription of DAP biosynthetic genes.
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Affiliation(s)
- Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Ye
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu He
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Fuqiang He
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, 610065, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
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136
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Liu Z, Zhu Z, Tang J, He H, Wan Q, Luo Y, Huang W, Yu Z, Hu Y, Ding X, Xia L. RNA-Seq-Based Transcriptomic Analysis of Saccharopolyspora spinosa Revealed the Critical Function of PEP Phosphonomutase in the Replenishment Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14660-14669. [PMID: 33258371 DOI: 10.1021/acs.jafc.0c04443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of novel biological insecticides. Although the complete genome sequence of S. spinosa has been published, the transcriptome of S. spinosa remains poorly characterized. In this study, high-throughput RNA sequencing (RNA-seq) technology was applied to dissect the transcriptome of S. spinosa. Through transcriptomic analysis of different periods of S. spinosa growth, we found large numbers of differentially expressed genes and classified them according to their different functions. Based on the RNA-seq data, the CRISPR-Cas9 method was used to knock out the PEP phosphonomutase gene (orf 06952-4171). The yield of spinosyns A and D in S. spinosa-ΔPEP was 178.91 mg/L and 42.72 mg/L, which was 2.14-fold and 1.76-fold higher than that in the wild type (83.51 and 24.34 mg/L), respectively. The analysis of the mutant strains also verified the validity of the transcriptome data. The deletion of the PEP phosphonomutase gene leads to an increase in pyruvate content and affects the biosynthesis of spinosad. The replenishment of phosphoenol pyruvate in S. spinosa provides the substrate for the production of spinosad. We envision that these transcriptomic analysis results will contribute to the further study of secondary metabolites in actinomycetes.
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Affiliation(s)
- Zhudong Liu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zirong Zhu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Jianli Tang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Haocheng He
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Qianqian Wan
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yuewen Luo
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Weitao Huang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Ziquan Yu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yibo Hu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Liqiu Xia
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
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137
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Nishida K, Kondo A. CRISPR-derived genome editing technologies for metabolic engineering. Metab Eng 2020; 63:141-147. [PMID: 33307189 DOI: 10.1016/j.ymben.2020.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022]
Abstract
In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms includingindustrially relevant ones. Targeted DNA cleavage by CRISPR-Cas provides variousgenome engineering modes such as indels, replacements, large deletions, knock-in and chromosomal rearrangements, while host-dependent differences in repair pathways need to be considered. The versatility of the CRISPR system has given rise to derivative technologies that complement nuclease-based editing, which causes cytotoxicity especially in microorganisms. Deaminase-mediated base editing installs targeted point mutations with much less toxicity. CRISPRi and CRISPRa can temporarily control gene expression without changing the genomic sequence. Multiplex, combinatorial and large scale editing are made possible by streamlined design and construction of gRNA libraries to further accelerates comprehensive discovery, evaluation and building of metabolic pathways. This review summarizes the technical basis and recent advances in CRISPR-related genome editing tools applied for metabolic engineering purposes, with representative examples of industrially relevant eukaryotic and prokaryotic organisms.
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Affiliation(s)
- Keiji Nishida
- Engineering Biology Research Center, Kobe University, Japan; Graduate School of Science, Technology and Innovation, Kobe University, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, Japan; Graduate School of Science, Technology and Innovation, Kobe University, Japan.
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138
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Dey A. CRISPR/Cas genome editing to optimize pharmacologically active plant natural products. Pharmacol Res 2020; 164:105359. [PMID: 33285226 DOI: 10.1016/j.phrs.2020.105359] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/15/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
Since time immemorial, human use medicinal plants as sources of food, therapy and industrial purpose. Classical biotechnology and recent next-generation sequencing (NGS) techniques have been successfully used to optimize plant-derived natural-products of biomedical significance. Earlier, protein based editing tools viz. zinc-finger nucleases (ZFNs) and transcription activator-like endonucleases (TALENs) have been popularized for transcriptional level genome manipulation. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is an efficient, robust and selective site-directed mutagenesis strategy for RNA-guided genome-editing. CRISPR/Cas9 genome-editing tool employs designed guide-RNAs that identifies a 3 base-pair protospacer adjacent motif (PAM) sequence occurring downstream of the target-DNA. The present review comprehensively complies the recent literature (2010-2020) retrieved from scientific-databases on the application of CRISPR/Cas9-editing-tools as potent genome-editing strategies in medicinal-plants discussing the recent developments, challenges and future-perspectives with notes on broader applicability of the technique in plants and lower-organisms. In plants, CRISPR/Cas-editing has been implemented successfully in relation to crop-yield and stress-tolerance. However, very few medicinal plants have been edited using CRISPR/Cas genome tool owing to the lack of whole-genome and mRNA-sequences and shortfall of suitable transformation and regeneration strategies. However, recently a number of plant secondary metabolic-pathways (viz. alkaloid, terpenoid, flavonoids, phenolic, saponin etc.) have been engineered employing CRISPR/Cas-editing via knock-out, knock-in, point-mutation, fine-tuning of gene-expression and targeted-mutagenesis. This genome-editing tool further extends its applicability incorporating the tools of synthetic- and systems-biology, functional-genomics and NGS to produce genetically-engineered medicinal-crops with advanced-traits facilitating the production of pharmaceuticals and nutraceuticals.
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Affiliation(s)
- Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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139
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Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, Hao YH, Zhao Y, Tan Z. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res 2020; 48:11706-11720. [PMID: 33045726 PMCID: PMC7672459 DOI: 10.1093/nar/gkaa841] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Jia-yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Juan-nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yong Zhao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P.R. China
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140
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Droste J, Kulisch M, Wolf T, Schaffert L, Schneiker-Bekel S, Pühler A, Kalinowski J. A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110. Appl Microbiol Biotechnol 2020; 104:9283-9294. [PMID: 32989516 PMCID: PMC7567727 DOI: 10.1007/s00253-020-10923-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
Actinoplanes sp. SE50/110 is the industrially relevant producer of acarbose, which is used in the treatment of diabetes mellitus. Recent studies elucidated the expression dynamics in Actinoplanes sp. SE50/110 during growth. From these data, we obtained a large genomic region (ACSP50_3900 to ACSP50_3950) containing 51 genes, of which 39 are transcribed in the same manner. These co-regulated genes were found to be stronger transcribed on maltose compared with glucose as a carbon source. The transcriptional regulator MalT was identified as an activator of this maltose-regulated large genomic region (MRLGR). Since most of the genes are poorly annotated, the function of this region is farther unclear. However, comprehensive BLAST analyses indicate similarities to enzymes involved in amino acid metabolism. We determined a conserved binding motif of MalT overlapping the -35 promoter region of 17 transcription start sites inside the MRLGR. The corresponding sequence motif 5'-TCATCC-5nt-GGATGA-3' displays high similarities to reported MalT binding sites in Escherichia coli and Klebsiella pneumoniae, in which MalT is the activator of mal genes. A malT deletion and an overexpression mutant were constructed. Differential transcriptome analyses revealed an activating effect of MalT on 40 of the 51 genes. Surprisingly, no gene of the maltose metabolism is affected. In contrast to many other bacteria, MalT is not the activator of mal genes in Actinoplanes sp. SE50/110. Finally, the MRLGR was found partly in other closely related bacteria of the family Micromonosporaceae. Even the conserved MalT binding site was found upstream of several genes inside of the corresponding regions. KEY POINTS : • MalT is the maltose-dependent activator of a large genomic region in ACSP50_WT. • The consensus binding motif is similar to MalT binding sites in other bacteria. • MalT is not the regulator of genes involved in maltose metabolism in ACSP50_WT.
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Affiliation(s)
- Julian Droste
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Martin Kulisch
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Timo Wolf
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Lena Schaffert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Alfred Pühler
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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141
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Meaker GA, Hair EJ, Gorochowski TE. Advances in engineering CRISPR-Cas9 as a molecular Swiss Army knife. Synth Biol (Oxf) 2020; 5:ysaa021. [PMID: 33344779 PMCID: PMC7737000 DOI: 10.1093/synbio/ysaa021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-guided endonuclease system CRISPR-Cas9 has been extensively modified since its discovery, allowing its capabilities to extend far beyond double-stranded cleavage to high fidelity insertions, deletions and single base edits. Such innovations have been possible due to the modular architecture of CRISPR-Cas9 and the robustness of its component parts to modifications and the fusion of new functional elements. Here, we review the broad toolkit of CRISPR-Cas9-based systems now available for diverse genome-editing tasks. We provide an overview of their core molecular structure and mechanism and distil the design principles used to engineer their diverse functionalities. We end by looking beyond the biochemistry and toward the societal and ethical challenges that these CRISPR-Cas9 systems face if their transformative capabilities are to be deployed in a safe and acceptable manner.
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Affiliation(s)
- Grace A Meaker
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Emma J Hair
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, UK
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142
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Liao Z, Song Z, Xu J, Ma Z, Bechthold A, Yu X. Identification of a gene from Streptomyces rimosus M527 negatively affecting rimocidin biosynthesis and morphological differentiation. Appl Microbiol Biotechnol 2020; 104:10191-10202. [PMID: 33057790 DOI: 10.1007/s00253-020-10955-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022]
Abstract
The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, was found to be highly effective against a broad range of fungal plant pathogens. Current understanding of the regulatory mechanism of rimocidin biosynthesis and morphological differentiation in S. rimosus M527 is limited. NsdA is considered a negative regulator involved in morphological differentiation and biosynthesis of secondary metabolites in some Streptomyces species. In this study, nsdAsr was cloned from S. rimosus M527. The role of nsdAsr in rimocidin biosynthesis and morphological differentiation was investigated by gene deletion, complementation, and over-expression. A ΔnsdAsr mutant was obtained using CRISPR/Cas9. The mutant produced more rimocidin (46%) and accelerated morphological differentiation than the wild-type strain. Over-expression of nsdAsr led to a decrease in rimocidin production and impairment of morphological differentiation. Quantitative RT-PCR analysis revealed that transcription of rim genes responsible for rimocidin biosynthesis was upregulated in the ΔnsdAsr mutant but downregulated in the nsdAsr over-expression strain. Similar effects have been described for Streptomyces coelicolor M145 and the industrial toyocamycin-producing strain Streptomyces diastatochromogenes 1628. KEY POINTS: • A negative regulator for sporulation and rimocidin production was identified. • The CRISPR/Cas9 system was used for gene deletion in S. rimosus M527.
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Affiliation(s)
- Zhijun Liao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Zhangqing Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Jie Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China.
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China.
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143
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Hou SY, Zhang MY, Wang HD, Zhang YX. Biosynthesis Gene Cluster and Oxazole Ring Formation Enzyme for Inthomycins in Streptomyces sp. Strain SYP-A7193. Appl Environ Microbiol 2020; 86:e01388-20. [PMID: 32801183 PMCID: PMC7531957 DOI: 10.1128/aem.01388-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022] Open
Abstract
Inthomycins belong to a growing family of oxazole-containing polyketides and exhibit a broad spectrum of anti-oomycete and herbicidal activities. In this study, we purified inthomycins A and B from the metabolites of Streptomyces sp. strain SYP-A7193 and determined their chemical structures. Genome sequencing, comparative genomic analysis, and gene disruption of Streptomyces sp. SYP-A7193 showed that the inthomycin biosynthetic gene cluster (itm) belonged to the hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system. Functional domain comparison and disruption/complementation experiments of itm12 resulted in the complete loss of inthomycins A and B and the subsequent restoration of their production, confirming that itm12 encodes a discrete acyltransferase (AT), and hence, itm was considered to belong to the trans-AT type I PKS system. Moreover, the disruption/complementation experiments of itm15 also resulted in the loss and restoration of inthomycin A and B formation. Further gene cloning, expression, purification, and activity verification of itm15 revealed that Itm15 is a cyclodehydratase that catalyzes a straight-chain dehydration reaction to form an oxazole ring for the biosynthesis of inthomycins A and B. Thus, we discovered a novel enzyme that catalyzes oxazole ring formation and elucidated the complete biosynthetic pathway of inthomycins.IMPORTANCEStreptomyces species produce numerous secondary metabolites with diverse structures and pharmacological activities that are beneficial for human health and have several applications in agriculture. In this study, hybrid nonribosomal peptide synthetase/polyketide synthase metabolites inthomycins A and B were isolated from after fermenting Streptomyces sp. SYP-A7193. Genome sequencing, gene disruption, gene complementation, heterologous expression, and activity assay revealed that the biosynthesis gene assembly line of inthomycins A and B was a 95.3-kb trans-AT type I PKS system in the strain SYP-A7193. More importantly, Itm15, a cyclodehydratase, was identified to be an oxazole ring formation enzyme required for the biosynthesis of inthomycins A and B; it is significant to discover this catalyzation reaction in the PKS/NRPS system in the field of microbiology. Our findings could provide further insights into the diversity of trans-AT type I PKS systems and the mechanism of oxazole cyclization involved in the biosynthesis of natural products.
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Affiliation(s)
- Shao-Yang Hou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Hong-Da Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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144
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Cao Z, Yu J, Wang W, Lu H, Xia X, Xu H, Yang X, Bao L, Zhang Q, Wang H, Zhang S, Zhang L. Multi-scale data-driven engineering for biosynthetic titer improvement. Curr Opin Biotechnol 2020; 65:205-212. [DOI: 10.1016/j.copbio.2020.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/18/2020] [Accepted: 04/17/2020] [Indexed: 11/29/2022]
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145
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He X, Ren Y, Meng W, Yu X, Zhou X. Knocking out Analysis of the CpxP gene using Crispr/Cas9 in Escherichia coli MG1655. AMB Express 2020; 10:172. [PMID: 32979149 PMCID: PMC7519928 DOI: 10.1186/s13568-020-01099-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022] Open
Abstract
Based on the analysis of cpxP genes among Escherichia coli strains, cpxP gene-targeting short guide RNA (sgRNA) was designed and inserted into the pGL3-MGP-RNA. The donor sequences (MG-HR) for homologous repair were designed and cloned by PCR. MG-HR and pGL3-MGP-RNA were transformed into E. coli MG1655 (pCas9). The cpxP gene expression cassette was amplified by PCR and subcloned into pBBR1MCS-2. Then the pBBR-cpxP was independently transformed into E. coli MG1655. The results of motility experiment suggest that cpxP gene had a significant effect on the movement ability of E. coli strain. The CpxP protein had a significant inhibition of bacterial activity. The lastest 81 CpxP proteins sequences were selected and analyzed by multi-sequence alignment and molecular cluster. The CpxP proteins were roughly divided into three categories. Our results suggest that the CpxP protein was involved in bacterial motility, infection and pathogenicity.
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146
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pSETT4, an Improved φC31-Based Integrative Vector System for Actinoplanes sp. SE50/110. Microbiol Resour Announc 2020; 9:9/39/e00596-20. [PMID: 32972929 PMCID: PMC7516140 DOI: 10.1128/mra.00596-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pSETT4 vector integrates into the Actinoplanes sp. SE50/110 chromosome via the bacteriophage φC31 integrase and allows cloning of a gene of interest by Golden Gate assembly (BsaI). T4 terminators surround the expression cassette to isolate the transcriptional unit and to prevent antisense transcription. The system can be used in other Actinomycetales by exchanging the promoter.
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147
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CRISPR-Cas-mediated gene editing in lactic acid bacteria. Mol Biol Rep 2020; 47:8133-8144. [PMID: 32926267 DOI: 10.1007/s11033-020-05820-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/05/2020] [Indexed: 12/12/2022]
Abstract
The high efficiency, convenience and diversity of clustered regular interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are driving a technological revolution in the gene editing of lactic acid bacteria (LAB). Cas-RNA cassettes have been adopted as tools to perform gene deletion, insertion and point mutation in several species of LAB. In this article, we describe the basic mechanisms of the CRISPR-Cas system, and the current gene editing methods available, focusing on the CRISPR-Cas models developed for LAB. We also compare the different types of CRISPR-Cas-based genomic manipulations classified according to the different Cas proteins and the type of recombineering, and discuss the rapidly evolving landscape of CRISPR-Cas application in LAB.
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148
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Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microb Cell Fact 2020; 19:172. [PMID: 32883277 PMCID: PMC7470686 DOI: 10.1186/s12934-020-01431-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
As important genome editing tools, CRISPR/Cas systems, especially those based on type II Cas9 and type V Cas12a, are widely used in genetic and metabolic engineering of bacteria. However, the intrinsic toxicity of Cas9 and Cas12a-mediated CRISPR/Cas tools can lead to cell death in some strains, which led to the development of endogenous type I and III CRISPR/Cas systems. However, these systems are hindered by complicated development and limited applications. Thus, further development and optimization of CRISPR/Cas systems is needed. Here, we briefly summarize the mechanisms of different types of CRISPR/Cas systems as genetic manipulation tools and compare their features to provide a reference for selecting different CRISPR/Cas tools. Then, we show the use of CRISPR/Cas technology for bacterial strain evolution and metabolic engineering, including genome editing, gene expression regulation and the base editor tool. Finally, we offer a view of future directions for bacterial CRISPR/Cas technology.
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Affiliation(s)
- Zhenquan Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Lina Cong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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149
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Hao W, Suo F, Lin Q, Chen Q, Zhou L, Liu Z, Cui W, Zhou Z. Design and Construction of Portable CRISPR-Cpf1-Mediated Genome Editing in Bacillus subtilis 168 Oriented Toward Multiple Utilities. Front Bioeng Biotechnol 2020; 8:524676. [PMID: 32984297 PMCID: PMC7492563 DOI: 10.3389/fbioe.2020.524676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Bacillus subtilis is an important Gram-positive bacterium for industrial biotechnology, which has been widely used to produce diverse high-value added chemicals and industrially and pharmaceutically relevant proteins. Robust and versatile toolkits for genome editing in B. subtilis are highly demanding to design higher version chassis. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 has been extensively adapted for genome engineering of multiple bacteria, it has many defects, such as higher molecular weight which leads to higher carrier load, low deletion efficiency and complexity of sgRNA construction for multiplex genome editing. Here, we designed a CRISPR-Cpf1-based toolkit employing a type V Cas protein, Cpf1 from Francisella novicida. Using this platform, we precisely deleted single gene and gene cluster in B. subtilis with high editing efficiency, such as sacA, ganA, ligD & ligV, and bac operon. Especially, an extremely large gene cluster of 38 kb in B. subtilis genome was accurately deleted from the genome without introducing any unexpected mutations. Meanwhile, the synthetic platform was further upgraded to a version for multiplex genome editing, upon which two genes sacA and aprE were precisely and efficiently deleted using only one plasmid harboring two targeting sequences. In addition, we successfully inserted foreign genes into the genome of the chassis using the CRISPR-Cpf1 platform. Our work highlighted the availability of CRISPR-Cpf1 to gene manipulation in B. subtilis, including the flexible deletion of a single gene and multiple genes or a gene cluster, and gene knock-in. The designed genome-editing platform was easily and broadly applicable to other microorganisms. The novel platforms we constructed in this study provide a promising tool for efficient genome editing in diverse bacteria.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiao Lin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiaoqing Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangnan University (Rugao) Food Biotechnology Research Institute, Jiangsu, China
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150
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Chen H, Li D, Cai Y, Wu LF, Song T. Bacteriophytochrome from Magnetospirillum magneticum affects phototactic behavior in response to light. FEMS Microbiol Lett 2020; 367:5895327. [PMID: 32821904 DOI: 10.1093/femsle/fnaa142] [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] [Received: 04/12/2020] [Accepted: 08/19/2020] [Indexed: 01/03/2023] Open
Abstract
Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.
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Affiliation(s)
- Haitao Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China.,School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Dandan Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yao Cai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Long-Fei Wu
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS, F-13402 Marseille, France.,LCB, Aix Marseille University, CNRS, F-13402 Marseille, France
| | - Tao Song
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China.,School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
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