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Zhu Z, Ding X, Rang J, Xia L. Application and research progress of ARTP mutagenesis in actinomycetes breeding. Gene 2024; 929:148837. [PMID: 39127415 DOI: 10.1016/j.gene.2024.148837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.
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Affiliation(s)
- Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jie Rang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China.
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Wang S, Zeng X, Jiang Y, Wang W, Bai L, Lu Y, Zhang L, Tan GY. Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing. Nat Prod Rep 2024; 41:1441-1455. [PMID: 38888887 DOI: 10.1039/d4np00010b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.
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Affiliation(s)
- Shuliu Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Xiaoqian Zeng
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Yue Jiang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
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Wang W, Chen X, Ma J, Li W, Long Y. Activity of Streptomyces globosus OPF-9 against the important pathogen Alternaria longipes and biocontrol mechanisms revealed by multi-omic analyses. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 204:106094. [PMID: 39277405 DOI: 10.1016/j.pestbp.2024.106094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/13/2024] [Accepted: 08/17/2024] [Indexed: 09/17/2024]
Abstract
Plant diseases caused by fungal pathogens represent main threats to the yield and quality of agricultural products, and Alternaria longipes is one of the most important pathogens in agricultural systems. Biological control is becoming increasingly prevalent in the management of plant diseases due to its environmental compatibility and sustainability. In the present study, a bacterial strain, designated as OPF-9, was shown to effectively inhibit the pathogen A. longipes, which was identified as Streptomyces globosus. The culture conditions for OPF-9 were optimized through a stepwise approach and the fermentation broth acquired displayed an excellent inhibitory activity against A. longipes in vitro and in vivo. Further investigations suggested that the fermentation broth exhibited strong stability under a range of adverse environmental conditions. To reveal the molecular bases of OPF-9 in inhibiting pathogens, the whole-genome sequencing and assembly were conducted on this strain. It showed that the genome size of OPF-9 was 7.668 Mb, containing a chromosome and two plasmids. Multiple clusters of secondary metabolite synthesis genes were identified by genome annotation analysis. In addition, the fermentation broth of strain OPF-9 was analyzed by LC-MS/MS non-target metabolomic assay and the activity of potential antifungal substances was determined. Among the five compounds evaluated, pyrogallol displayed the most pronounced inhibitory activity against A. longipes, which was found to effectively inhibit the mycelial growth of this pathogen. Overall, this study reported, for the first time, a strain of S. globosus that effectively inhibits A. longipes and revealed the underlying biocontrol mechanisms by genomic and metabolomic analyses.
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Affiliation(s)
- Weizhen Wang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xuetang Chen
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Jiling Ma
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Wenzhi Li
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Youhua Long
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China.
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Sang Z, Li X, Yan H, Wang W, Wen Y. Development of a group II intron-based genetic manipulation tool for Streptomyces. Microb Biotechnol 2024; 17:e14472. [PMID: 38683679 PMCID: PMC11057498 DOI: 10.1111/1751-7915.14472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces. Moreover, by repressing the potential competition of RecA-dependent homologous recombination, we enhanced site-specific insertion efficiency of this tool to 2.38%. Subsequently, we demonstrated the application of this tool by screening and characterizing the secondary metabolite biosynthetic gene cluster (BGC) responsible for synthesizing the red pigment in Streptomyces roseosporus. Accompanied with identifying and inactivating this BGC, we observed that the impair of this cluster promoted cell growth and daptomycin production. Additionally, we applied this tool to activate silent jadomycin BGC in Streptomyces venezuelae. Overall, this work demonstrates the potential of this method as an alternative tool for genetic engineering and cryptic natural product mining in Streptomyces species.
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Affiliation(s)
- Ziwei Sang
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xingwang Li
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Wen
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
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Vojnovic S, Aleksic I, Ilic-Tomic T, Stevanovic M, Nikodinovic-Runic J. Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes. Appl Microbiol Biotechnol 2024; 108:185. [PMID: 38289383 PMCID: PMC10827964 DOI: 10.1007/s00253-023-12900-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 02/01/2024]
Abstract
The application of enzymes is expanding across diverse industries due to their nontoxic and biodegradable characteristics. Another advantage is their cost-effectiveness, reflected in reduced processing time, water, and energy consumption. Although Gram-positive bacteria, Bacillus, and Streptomyces spp. are successfully used for production of industrially relevant enzymes, they still lag far behind Escherichia coli as hosts for recombinant protein production. Generally, proteins secreted by Bacillus and Streptomyces hosts are released into the culture medium; their native conformation is preserved and easier recovery process enabled. Given the resilience of both hosts in harsh environmental conditions and their spore-forming capability, a deeper understanding and broader use of Bacillus and Streptomyces as expression hosts could significantly enhance the robustness of industrial bioprocesses. This mini-review aims to compare two expression hosts, emphasizing their specific advantages in industrial surroundings such are chemical, detergent, textile, food, animal feed, leather, and paper industries. The homologous sources, heterologous hosts, and molecular tools used for the production of recombinant proteins in these hosts are discussed. The potential to use both hosts as biocatalysts is also evaluated. Undoubtedly, Bacillus and Streptomyces spp. as production hosts possess the potential to take on a more substantial role, providing superior (bio-based) process robustness and flexibility. KEY POINTS: • Bacillus and Streptomyces spp. as robust hosts for enzyme production. • Industrially relevant enzyme groups for production in alternative hosts highlighted. • Molecular biology techniques are enabling easier utilization of both hosts.
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Affiliation(s)
- Sandra Vojnovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
| | - Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
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Li JY, Liang JY, Liu ZY, Yi YZ, Zhao J, Huang ZY, Chen J. Multicopy Chromosome Integration and Deletion of Negative Global Regulators Significantly Increased the Heterologous Production of Aborycin in Streptomyces coelicolor. Mar Drugs 2023; 21:534. [PMID: 37888469 PMCID: PMC10608281 DOI: 10.3390/md21100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Aborycin is a type I lasso peptide with a stable interlocked structure, offering a favorable framework for drug development. The aborycin biosynthetic gene cluster gul from marine sponge-associated Streptomyces sp. HNS054 was cloned and integrated into the chromosome of S. coelicolor hosts with different copies. The three-copy gul-integration strain S. coelicolor M1346::3gul showed superior production compared to the one-copy or two-copy gul-integration strains, and the total titer reached approximately 10.4 mg/L, i.e., 2.1 times that of the native strain. Then, five regulatory genes, phoU (SCO4228), wblA (SCO3579), SCO1712, orrA (SCO3008) and gntR (SCO1678), which reportedly have negative effects on secondary metabolism, were further knocked out from the M1346::3gul genome by CRISPR/Cas9 technology. While the ΔSCO1712 mutant showed a significant decrease (4.6 mg/L) and the ΔphoU mutant showed no significant improvement (12.1 mg/L) in aborycin production, the ΔwblA, ΔorrA and ΔgntR mutations significantly improved the aborycin titers to approximately 23.6 mg/L, 56.3 mg/L and 48.2 mg/L, respectively, which were among the highest heterologous yields for lasso peptides in both Escherichia coli systems and Streptomyces systems. Thus, this study provides important clues for future studies on enhancing antibiotic production in Streptomyces systems.
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Affiliation(s)
- Jia-Yi Li
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Jun-Yu Liang
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Zhao-Yuan Liu
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Yue-Zhao Yi
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
| | - Jing Zhao
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Zhi-Yong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jun Chen
- Department of Marine Biological Science & Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (J.-Y.L.); (J.-Y.L.); (Z.-Y.L.); (Y.-Z.Y.); (J.Z.)
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
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Sword TT, Barker JW, Spradley M, Chen Y, Petzold CJ, Bailey CB. Expression of blue pigment synthetase a from Streptomyces lavenduale reveals insights on the effects of refactoring biosynthetic megasynthases for heterologous expression in Escherichia coli. Protein Expr Purif 2023; 210:106317. [PMID: 37286066 PMCID: PMC10330848 DOI: 10.1016/j.pep.2023.106317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 06/09/2023]
Abstract
High GC bacteria from the genus Streptomyces harbor expansive secondary metabolism. The expression of biosynthetic proteins and the characterization and identification of biological "parts" for synthetic biology purposes from such pathways are of interest. However, the high GC content of proteins from actinomycetes in addition to the large size and multi-domain architecture of many biosynthetic proteins (such as non-ribosomal peptide synthetases; NRPSs, and polyketide synthases; PKSs often called "megasynthases") often presents issues with full-length translation and folding. Here we evaluate a non-ribosomal peptide synthetase (NRPS) from Streptomyces lavenduale, a multidomain "megasynthase" gene that comes from a high GC (72.5%) genome. While a preliminary step in revealing differences, to our knowledge this presents the first head-to-head comparison of codon-optimized sequences versus a native sequence of proteins of streptomycete origin heterologously expressed in E. coli. We found that any disruption in co-translational folding from codon mismatch that reduces the titer of indigoidine is explainable via the formation of more inclusion bodies as opposed to compromising folding or posttranslational modification in the soluble fraction. This result supports that one could apply any refactoring strategies that improve soluble expression in E. coli without concern that the protein that reaches the soluble fraction is differentially folded.
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Affiliation(s)
- Tien T Sword
- Department of Chemistry University of Tennessee-Knoxville, Knoxville, TN, USA
| | - J William Barker
- Department of Chemistry University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Madeline Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Yan Chen
- Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Christopher J Petzold
- Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Constance B Bailey
- Department of Chemistry University of Tennessee-Knoxville, Knoxville, TN, USA.
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Buyuklyan JA, Zakalyukina YV, Osterman IA, Biryukov MV. Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes. Acta Naturae 2023; 15:4-16. [PMID: 37908767 PMCID: PMC10615194 DOI: 10.32607/actanaturae.23426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/19/2023] [Indexed: 11/02/2023] Open
Abstract
Representatives of the phylum Actinomycetota are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous "rediscovery" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.
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Affiliation(s)
- J A Buyuklyan
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
| | - Yu V Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
| | - I A Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025 Russian Federation
| | - M V Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
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Hu M, Chen S, Ni Y, Wei W, Mao W, Ge M, Qian X. CRISPR/Cas9-mediated genome editing in vancomycin-producing strain Amycolatopsis keratiniphila. Front Bioeng Biotechnol 2023; 11:1141176. [PMID: 36937767 PMCID: PMC10020181 DOI: 10.3389/fbioe.2023.1141176] [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: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Amycolatopsis is an important source of diverse valuable bioactive natural products. The CRISPR/Cas-mediated gene editing tool has been established in some Amycolatopsis species and has accomplished the deletion of single gene or two genes. The goal of this study was to develop a high-efficient CRISPR/Cas9-mediated genome editing system in vancomycin-producing strain A. keratiniphila HCCB10007 and enhance the production of vancomycin by deleting the large fragments of ECO-0501 BGC. By adopting the promoters of gapdhp and ermE*p which drove the expressions of scocas9 and sgRNA, respectively, the all-in-one editing plasmid by homology-directed repair (HDR) precisely deleted the single gene gtfD and inserted the gene eGFP with the efficiency of 100%. Furthermore, The CRISPR/Cas9-mediated editing system successfully deleted the large fragments of cds13-17 (7.7 kb), cds23 (12.7 kb) and cds22-23 (21.2 kb) in ECO-0501 biosynthetic gene cluster (BGC) with high efficiencies of 81%-97% by selecting the sgRNAs with a suitable PAM sequence. Finally, a larger fragment of cds4-27 (87.5 kb) in ECO-0501 BGC was deleted by a dual-sgRNA strategy. The deletion of the ECO-0501 BGCs revealed a noticeable improvement of vancomycin production, and the mutants, which were deleted the ECO-0501 BGCs of cds13-17, cds22-23 and cds4-27, all achieved a 30%-40% increase in vancomycin yield. Therefore, the successful construction of the CRISPR/Cas9-mediated genome editing system and its application in large fragment deletion in A. keratiniphila HCCB10007 might provide a powerful tool for other Amycolatopsis species.
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Affiliation(s)
- Mengyi Hu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Ni
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Wenwei Mao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Xiuping Qian
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
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10
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Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces species. METHODS IN MICROBIOLOGY 2022; 200:106545. [DOI: 10.1016/j.mimet.2022.106545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
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11
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Wadler CS, Wolters JF, Fortney NW, Throckmorton KO, Zhang Y, Miller CR, Schneider RM, Wendt-Pienkowski E, Currie CR, Donohue TJ, Noguera DR, Hittinger CT, Thomas MG. Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:70. [PMID: 35751080 PMCID: PMC9233362 DOI: 10.1186/s13068-022-02168-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.
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Affiliation(s)
- Caryn S Wadler
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - John F Wolters
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Nathaniel W Fortney
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Kurt O Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Yaoping Zhang
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Caroline R Miller
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Rachel M Schneider
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Evelyn Wendt-Pienkowski
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Daniel R Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Chris Todd Hittinger
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA.
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12
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Li M, Huo YX, Guo S. CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes. BIOLOGY 2022; 11:571. [PMID: 35453770 PMCID: PMC9024924 DOI: 10.3390/biology11040571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 12/23/2022]
Abstract
Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.
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Affiliation(s)
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
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13
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Lee EG, Kwak JS, Kim KH. CRISPR/Cas9-mediated generation of auxotrophic Edwardsiella piscicida mutants and immunization in olive flounder (Paralichthys olivaceus). FISH & SHELLFISH IMMUNOLOGY 2022; 122:98-105. [PMID: 35114359 DOI: 10.1016/j.fsi.2022.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/06/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Edwardsiella piscicida has been a cause of mass mortality in cultured fish. In this study, to produce auxotrophic E. piscicida mutants, a CRISPR/Cas9 system was used instead of the traditional sacB-based allelic exchange method. Under the optimal CRISPR engineering condition, we could efficiently produce either alr or asd gene knockout E. piscicida auxotrophic mutants, and this genome editing process was much simpler and faster than the allelic exchange method. The simultaneous knockout of double auxotrophic genes (alr and asd) and the insertion of a foreign gene expression cassette in E. piscicida chromosome were also successfully performed using the established CRISPR/Cas9 system. Furthermore, to enhance the possibility to get permission as a commercial vaccine, we produced an auxotrophic E. piscicida mutant having only one nucleotide-deleted alr gene (E. piscicida △alr-1). Olive flounder (Paralichthys olivaceus) fingerlings immunized with 1 × 106 and 1 × 105 CFU/fish of E. piscicida △alr-1 showed the superior ability in the induction of serum agglutination activity and in the protection against E. piscicida compared to killed E. piscicida. However, olive flounder immunized with 1 × 107 CFU/fish of E. piscicida △alr-1 showed high mortality far before the challenge, and the isolated E. piscicida from moribund and dead fish had the wild type alr gene, suggesting the reversion of one base-deleted alr gene to original form by a second mutation in olive flounder. Therefore, investigation on the minimum number of edited nucleotide for stable maintenance of E. piscicida mutants should be further conducted.
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Affiliation(s)
- Eun Gyeong Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea
| | - Jun Soung Kwak
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea.
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14
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Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:515. [PMID: 35082289 PMCID: PMC8792006 DOI: 10.1038/s41467-022-27955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combine multiple, state-of-the-art approaches to reprogram the stambomycin PKS by deleting seven internal modules. One system produces the target 37-membered mini-stambomycin metabolites − a reduction in chain length of 14 carbons relative to the 51-membered parental compounds − but also substantial quantities of shunt metabolites. Our data also support an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain of the PKS. The mini-stambomycin yields are reduced relative to wild type, likely reflecting the poor tolerance of the modules downstream of the modified interfaces to the non-native substrates. Overall, we identify factors contributing to the productivity of engineered whole assembly lines, but our findings also highlight the need for further research to increase production titers. Genetic engineering of the type I polyketide synthases (PKSs) to produce desirable analogous remains largely inefficient. Here, the authors leverage multiple approaches to delete seven internal modules from the stambomycin PKS and generate 37-membered mini-stambomycin macrolactones.
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15
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Massicard JM, Su L, Jacob C, Weissman KJ. Engineering Modular Polyketide Biosynthesis in Streptomyces Using CRISPR/Cas: A Practical Guide. Methods Mol Biol 2022; 2489:173-200. [PMID: 35524051 DOI: 10.1007/978-1-0716-2273-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The CRISPR/Cas system, which has been widely applied to organisms ranging from microbes to animals, is currently being adapted for use in Streptomyces bacteria. In this case, it is notably applied to rationally modify the biosynthetic pathways giving rise to the polyketide natural products, which are heavily exploited in the medical and agricultural arenas. Our aim here is to provide the potential user with a practical guide to exploit this approach for manipulating polyketide biosynthesis, by treating key experimental aspects including vector choice, design of the basic engineering components, and trouble-shooting.
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Affiliation(s)
- Jean-Malo Massicard
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France
| | - Li Su
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France
| | - Christophe Jacob
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France.
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France.
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16
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Abstract
Natural products have traditionally been a fruitful source of chemical matter that has been developed into novel therapeutics. Actinomycetes and several other bacterial taxa are especially gifted in biosynthesizing natural products. However, many decades of intense bioactivity-based screening led to a large rediscovery problem, rendering industrial natural product discovery pipelines uneconomical. Numerous methods for circumventing the rediscovery problem have been developed, among them various chemistry-focused strategies, including reactivity-based screening. Emerging from the field of chemical proteomics, reactivity-based screening relies on a reactive probe that chemoselectively modifies a functional group of interest in the context of a complex biological sample. Reactivity-based probes for several distinct functional groups have been deployed to discover new polyketide and peptidic natural products. This chapter describes the protocols to conduct a reactivity-based screening campaign, including bacteria cultivation and screening of cellular extracts with phenylglyoxal-, tetrazine-, thiol-, and aminooxy-functionalized probes, which respectively target primary uriedo, electron-rich olefins, Michael acceptors, and reactive carbonyls. In addition, a recent case study is presented that employs reactivity-based screening as a component of a forward genetics screen to identify a previously unknown peptidyl arginine deiminase. We anticipate that these methods will be useful for those interested in discovering natural products that evade detection by traditional, bioassay-guided methods and others who wish to rapidly connect metabolic chemotype with genotype.
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Affiliation(s)
- Lonnie A. Harris
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois, Urbana, IL, United States,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States,Department of Microbiology, University of Illinois, Urbana, IL, United States,Corresponding Author: 600 S. Mathews Avenue, Roger Adams Laboratory, Rm. 361, University of Illinois, Urbana, IL 61801, 217-333-1345,
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17
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Ouyang H, Hong J, Malroy J, Zhu X. An E. coli-Based Biosynthetic Platform Expands the Structural Diversity of Natural Benzoxazoles. ACS Synth Biol 2021; 10:2151-2158. [PMID: 34530615 DOI: 10.1021/acssynbio.1c00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Benzoxazoles are frequently found in synthetic pharmaceuticals and medicinally active natural products. To facilitate benzoxazole-based drug development, an eco-friendly and rapid platform for benzoxazole production is required. In this study, we have completed the biosynthesis of benzoxazoles in E. coli by coexpressing the minimal set of enzymes required for their biosynthesis. Moreover, by coupling this E. coli-based platform with precursor-directed biosynthesis, we have shown that the benzoxazole biosynthetic system is highly promiscuous in incorporating fluorine, chlorine, nitrile, picolinic, and alkyne functionalities into the scaffold. Our E. coli-based system thus paves the way for straightforward generation of novel benzoxazole analogues through future protein engineering and combinatorial biosynthesis.
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Affiliation(s)
- Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua Hong
- Department of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Jeshua Malroy
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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18
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Wang X, Fu Y, Wang M, Niu G. Synthetic Cellobiose-Inducible Regulatory Systems Allow Tight and Dynamic Controls of Gene Expression in Streptomyces. ACS Synth Biol 2021; 10:1956-1965. [PMID: 34347449 DOI: 10.1021/acssynbio.1c00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Precise control of microbial gene expression is crucial for synthetic biotechnological applications. This is particularly true for the bacterial genus Streptomyces, major producers of diverse natural products including many antibiotics. Although a plethora of genetic tools have been developed for Streptomyces, there is still an urgent need for effective gene induction systems. We herein created two novel cellobiose-inducible regulatory systems referred to as Cel-RS1 and Cel-RS2. The regulatory systems are based upon the well-characterized repressor/operator pair CebR/cebO from Streptomyces scabies and the well-defined constitutive kasO* promoter. Both Cel-RS1 and Cel-RS2 exhibit a high level of induced reporter activity and virtually no leaky expression in three model Streptomyces species, which are commonly used as surrogate hosts for expression of natural product biosynthetic gene clusters. Cel-RS2 has been proven successful for programmable control of gene expression and controllable production of specialized metabolites in multiple Streptomyces species. The strategy can be used to expand the toolkit of inducible regulatory systems that will be broadly applicable to various Streptomyces.
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Affiliation(s)
- Xia Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yudie Fu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Meiyan Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
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19
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Liu Z, Zhao Y, Huang C, Luo Y. Recent Advances in Silent Gene Cluster Activation in Streptomyces. Front Bioeng Biotechnol 2021; 9:632230. [PMID: 33681170 PMCID: PMC7930741 DOI: 10.3389/fbioe.2021.632230] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.
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Affiliation(s)
- Zhenyu Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yatong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chaoqun Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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20
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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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21
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Recent Advances of Actinomycetes. Biomolecules 2021; 11:biom11020134. [PMID: 33494267 PMCID: PMC7909820 DOI: 10.3390/biom11020134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
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22
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Majumder MAA, Rahman S, Cohall D, Bharatha A, Singh K, Haque M, Gittens-St Hilaire M. Antimicrobial Stewardship: Fighting Antimicrobial Resistance and Protecting Global Public Health. Infect Drug Resist 2020; 13:4713-4738. [PMID: 33402841 PMCID: PMC7778387 DOI: 10.2147/idr.s290835] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health. It increases morbidity and mortality, and is associated with high economic costs due to its health care burden. Infections with multidrug-resistant (MDR) bacteria also have substantial implications on clinical and economic outcomes. Moreover, increased indiscriminate use of antibiotics during the COVID-19 pandemic will heighten bacterial resistance and ultimately lead to more deaths. This review highlights AMR's scale and consequences, the importance, and implications of an antimicrobial stewardship program (ASP) to fight resistance and protect global health. Antimicrobial stewardship (AMS), an organizational or system-wide health-care strategy, is designed to promote, improve, monitor, and evaluate the rational use of antimicrobials to preserve their future effectiveness, along with the promotion and protection of public health. ASP has been very successful in promoting antimicrobials' appropriate use by implementing evidence-based interventions. The "One Health" approach, a holistic and multisectoral approach, is also needed to address AMR's rising threat. AMS practices, principles, and interventions are critical steps towards containing and mitigating AMR. Evidence-based policies must guide the "One Health" approach, vaccination protocols, health professionals' education, and the public's awareness about AMR.
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Affiliation(s)
- Md Anwarul Azim Majumder
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Sayeeda Rahman
- School of Medicine, American University of Integrative Sciences, Bridgetown, Barbados
| | - Damian Cohall
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Ambadasu Bharatha
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Keerti Singh
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
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