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Wang X, Chen N, Cruz-Morales P, Zhong B, Zhang Y, Wang J, Xiao Y, Fu X, Lin Y, Acharya S, Li Z, Deng H, Sun Y, Bai L, Tang X, Keasling JD, Luo X. Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis. Nat Metab 2024; 6:933-946. [PMID: 38609677 DOI: 10.1038/s42255-024-01024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 03/06/2024] [Indexed: 04/14/2024]
Abstract
Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we proposed that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the 'coenzyme' category have been examined, including a gene cluster encoding for the cofactor pyrroloquinoline quinone. When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides an innovative engineering strategy for improving polyketide production and finding previously unidentified BGCs.
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Affiliation(s)
- Xinran Wang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ningxin Chen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Biming Zhong
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yangming Zhang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jian Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Yifan Xiao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinnan Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Lin
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Suneil Acharya
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhibo Li
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Jay D Keasling
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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Wen Y, Zhang B, Zhang G, Wu M, Chen X, Chen T, Liu G, Zhang W. Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks. Antonie Van Leeuwenhoek 2023; 116:1407-1419. [PMID: 37847451 DOI: 10.1007/s10482-023-01882-5] [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: 04/11/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
A novel Streptomyces strain, designated 3_2T, was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2T, compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2T possessed MK-9 (H6) and MK-9 (H8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C16:0 (23.6%) and anteiso-C15:0 (10.4%). The fermentation products of strain 3_2T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2T (= JCM 34935T = GDMCC 4.217T).
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Affiliation(s)
- Ying Wen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
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Thakur M, Kumar P, Rajput D, Yadav V, Dhaka N, Shukla R, Kumar Dubey K. Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories. BIORESOURCE TECHNOLOGY 2023; 376:128836. [PMID: 36898554 DOI: 10.1016/j.biortech.2023.128836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.
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Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Punit Kumar
- Department of Morphology and Physiology, Karaganda Medical University, Karaganda 100008 Kazakhstan
| | - Deepanshi Rajput
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh 123031, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh 123031, India
| | - Rishikesh Shukla
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura- 281406, U.P., India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
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Landscape of Post-Transcriptional tRNA Modifications in Streptomyces albidoflavus J1074 as Portrayed by Mass Spectrometry and Genomic Data Mining. J Bacteriol 2023; 205:e0029422. [PMID: 36468867 PMCID: PMC9879100 DOI: 10.1128/jb.00294-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Actinobacterial genus Streptomyces (streptomycetes) represents one of the largest cultivable group of bacteria famous for their ability to produce valuable specialized (secondary) metabolites. Regulation of secondary metabolic pathways inextricably couples the latter to essential cellular processes that determine levels of amino acids, carbohydrates, phosphate, etc. Post-transcriptional tRNA modifications remain one of the least studied aspects of streptomycete physiology, albeit a few of them were recently shown to impact antibiotic production. In this study, we describe the diversity of post-transcriptional tRNA modifications in model strain Streptomyces albus (albidoflavus) J1074 by combining mass spectrometry and genomic data. Our results show that J1074 can produce more chemically distinct tRNA modifications than previously thought. An in silico approach identified orthologs for enzymes governing most of the identified tRNA modifications. Yet, genetic control of certain modifications remained elusive, suggesting early divergence of tRNA modification pathways in Streptomyces from the better studied model bacteria, such as Escherichia coli and Bacillus subtilis. As a first point in case, our data point to the presence of a non-canonical MiaE enzyme performing hydroxylation of prenylated adenosines. A further finding concerns the methylthiotransferase MiaB, which requires previous modification of adenosines by MiaA to i6A for thiomethylation to ms2i6A. We show here that the J1074 ortholog, when overexpressed, yields ms2A in a ΔmiaA background. Our results set the working ground for and justify a more detailed studies of biological significance of tRNA modification pathways in streptomycetes. IMPORTANCE Post-transcriptional tRNA modifications (PTTMs) play an important role in maturation and functionality of tRNAs. Little is known about tRNA modifications in the antibiotic-producing actinobacterial genus Streptomyces, even though peculiar tRNA-based regulatory mechanisms operate in this taxon. We provide a first detailed description of the chemical diversity of PTTMs in the model species, S. albidoflavus J1074, and identify most plausible genes for these PTTMs. Some of the PTTMs are described for the first time for Streptomyces. Production of certain PTTMs in J1074 appears to depend on enzymes that show no sequence similarity to known PTTM enzymes from model species. Our findings are of relevance for interrogation of genetic basis of PTTMs in pathogenic actinobacteria, such as M. tuberculosis.
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