1
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Zhu Y, Lu T, Zhang H, Liu M, Pang X. SVEN_5003 is a Major Developmental Regulator in Streptomyces venezuelae. Curr Microbiol 2024; 81:166. [PMID: 38724665 DOI: 10.1007/s00284-024-03688-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/03/2024] [Indexed: 05/15/2024]
Abstract
Many regulatory genes that affect cellular development in Streptomyces, such as the canonical bld genes, have already been identified. However, in this study, we identified sven_5003 in Streptomyces venezuelae as a major new developmental regulatory gene, the deletion of which leads to a bald phenotype, typical of bld mutants, under multiple growth conditions. Our data indicated that disruption of sven_5003 also has a differential impact on the production of the two antibiotics jadomycin and chloramphenicol. Enhanced production of jadomycin but reduced production of chloramphenicol were detected in our sven_5003 mutant strain (S. venezuelae D5003). RNA-Seq analysis indicated that SVEN_5003 impacts expression of hundreds of genes, including genes involved in development, primary and secondary metabolism, and genes of unknown function, a finding confirmed by real-time PCR analysis. Transcriptional analysis indicated that sven_5003 is an auto-regulatory gene, repressing its own expression. Despite the evidence indicating that SVEN_5003 is a regulatory factor, a putative DNA-binding domain was not predicted from its primary amino acid sequence, implying an unknown regulatory mechanism by SVEN_5003. Our findings revealed that SVEN_5003 is a pleiotropic regulator with a critical role in morphological development in S. venezuelae.
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Affiliation(s)
- Yanping Zhu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ting Lu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hanlei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Liu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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2
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Rukthanapitak P, Saito K, Kobayashi R, Kaweewan I, Kodani S. Heterologous production of a new lanthipeptide boletupeptin using a cryptic biosynthetic gene cluster of the myxobacterium Melittangium boletus. J Biosci Bioeng 2024; 137:354-359. [PMID: 38458885 DOI: 10.1016/j.jbiosc.2024.02.001] [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: 11/30/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/10/2024]
Abstract
Myxobacteria have comparatively large genomes that contain many biosynthetic genes with the potential to produce secondary metabolites. Based on genome mining, we discovered a new biosynthetic gene cluster of class III lanthipeptide in the genome of the myxobacterium Melittangium boletus. The biosynthetic gene cluster contained a precursor peptide-coding gene bolA, and a class III lanthipeptide synthetase-coding gene bolKC. The expression vector containing bolA and bolKC was constructed using synthetic DNA with codon-optimized sequences based on the commercially available vector pET29b. Co-expression of the two genes in the host Escherichia coli BL21(DE3) yielded a new class III lanthipeptide named boletupeptin. The structure of boletupeptin was proposed to have one unit of labionin, as determined by mass spectrometry experiments after reductive cleavage. This is the first report of a class III lanthipeptide from a myxobacterial origin.
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Affiliation(s)
- Pratchaya Rukthanapitak
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ryo Kobayashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Medicine, Chiang Mai University, Inthawarorot Rd., Sri Phum, Muang, Chiang Mai 50200, Thailand
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
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3
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Zhang C, Seyedsayamdost MR. Widespread Peptide Surfactants with Post-translational C-methylations Promote Bacterial Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576971. [PMID: 38328144 PMCID: PMC10849626 DOI: 10.1101/2024.01.23.576971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Bacteria produce a variety of peptides to mediate nutrient acquisition, microbial interactions, and other physiological processes. Of special interest are surface-active peptides that aid in growth and development. Herein, we report the structure and characterization of clavusporins, unusual and hydrophobic ribosomal peptides with multiple C-methylations at unactivated carbon centers, which help drastically reduce the surface tension of water and thereby aid in Streptomyces development. The peptides are synthesized by a previously uncharacterized protein superfamily, termed DUF5825, in conjunction with a vitamin B12-dependent radical S-adenosylmethionine metalloenzyme. The operon encoding clavusporin is wide-spread among actinomycete bacteria, suggesting a prevalent role for clavusporins as morphogens in erecting aerial hyphae and thereby advancing sporulation and proliferation.
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Affiliation(s)
- Chen Zhang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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4
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Hernandez Garcia A, Nair SK. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. ACS CENTRAL SCIENCE 2023; 9:1944-1956. [PMID: 37901177 PMCID: PMC10604976 DOI: 10.1021/acscentsci.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/31/2023]
Abstract
In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent β-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.
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Affiliation(s)
- Andrea Hernandez Garcia
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
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5
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Schlimpert S, Elliot MA. The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development. J Bacteriol 2023; 205:e0015323. [PMID: 37347176 PMCID: PMC10367585 DOI: 10.1128/jb.00153-23] [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: 06/23/2023] Open
Abstract
Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.
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Affiliation(s)
- Susan Schlimpert
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marie A. Elliot
- Department of Biology and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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6
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Saito K, Mukai K, Kaweewan I, Nakagawa H, Hosaka T, Kodani S. Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense. J Microbiol 2023; 61:641-648. [PMID: 37306831 DOI: 10.1007/s12275-023-00059-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023]
Abstract
Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.
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Affiliation(s)
- Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Keiichiro Mukai
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO), Ibaraki, 305-8642, Japan
| | - Takeshi Hosaka
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
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7
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Li Y, Ma Y, Xia Y, Zhang T, Sun S, Gao J, Yao H, Wang H. Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks. Nat Commun 2023; 14:2944. [PMID: 37221219 DOI: 10.1038/s41467-023-38517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Cyclic peptide natural products represent an important class of bioactive compounds and clinical drugs. Enzymatic side-chain macrocyclization of ribosomal peptides is a major strategy developed by nature to generate these chemotypes, as exemplified by the superfamily of ribosomally synthesized and post-translational modified peptides. Despite the diverse types of side-chain crosslinks in this superfamily, the participation of histidine residues is rare. Herein, we report the discovery and biosynthesis of bacteria-derived tricyclic lanthipeptide noursin, which is constrained by a tri amino acid labionin crosslink and an unprecedented histidine-to-butyrine crosslink, named histidinobutyrine. Noursin displays copper-binding ability that requires the histidinobutyrine crosslink and represents the first copper-binding lanthipeptide. A subgroup of lanthipeptide synthetases, named LanKCHbt, were identified to catalyze the formation of both the labionin and the histidinobutyrine crosslinks in precursor peptides and produce noursin-like compounds. The discovery of the histidinobutyrine-containing lanthipeptides expands the scope of post-translational modifications, structural diversity and bioactivity of ribosomally synthesized and post-translational modified peptides.
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Affiliation(s)
- Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yeying Ma
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yinzheng Xia
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Tao Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Shuaishuai Sun
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China.
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8
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Nofiani R, Ardiningsih P, Zahra STA, Sukito A, Weisberg AJ, Chang JH, Mahmud T. Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2. Arch Microbiol 2023; 205:244. [PMID: 37209150 DOI: 10.1007/s00203-023-03556-2] [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: 01/09/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/22/2023]
Abstract
Streptomyces sp. RS2 was isolated from an unidentified sponge collected around Randayan Island, Indonesia. The genome of Streptomyces sp. RS2 consists of a linear chromosome of 9,391,717 base pairs with 71.9% of G + C content, 8270 protein-coding genes, as well as 18 rRNA and 85 tRNA loci. Twenty-eight putative secondary metabolites biosynthetic gene clusters (BGCs) were identified in the genome sequence. Nine of them have 100% similarity to BGCs for albaflavenone, α-lipomycin, coelibactin, coelichelin, ectoine, geosmin, germicidin, hopene, and lanthionine (SapB). The remaining 19 BGCs have low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. Biological activity assays of extracts from 21 different cultures of the RS2 strain showed that SCB ASW was the best medium for the production of antimicrobial and cytotoxic compounds. Streptomyces sp. RS2 has great potential to be a producer of novel secondary metabolites, particularly those with antimicrobial and antitumor activities.
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Affiliation(s)
- Risa Nofiani
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia.
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.
| | - Puji Ardiningsih
- Department of Chemistry, Universitas Tanjungpura, Pontianak, 78124, Indonesia
| | | | - Agus Sukito
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16458, Indonesia
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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9
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Barona-Gómez F, Chevrette MG, Hoskisson PA. On the evolution of natural product biosynthesis. Adv Microb Physiol 2023; 83:309-349. [PMID: 37507161 DOI: 10.1016/bs.ampbs.2023.05.001] [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: 07/30/2023]
Abstract
Natural products are the raw material for drug discovery programmes. Bioactive natural products are used extensively in medicine and agriculture and have found utility as antibiotics, immunosuppressives, anti-cancer drugs and anthelminthics. Remarkably, the natural role and what mechanisms drive evolution of these molecules is relatively poorly understood. The exponential increase in genome and chemical data in recent years, coupled with technical advances in bioinformatics and genetics have enabled progress to be made in understanding the evolution of biosynthetic gene clusters and the products of their enzymatic machinery. Here we discuss the diversity of natural products, incorporating the mechanisms that govern evolution of metabolic pathways and how this can be applied to biosynthetic gene clusters. We build on the nomenclature of natural products in terms of primary, integrated, secondary and specialised metabolism and place this within an ecology-evolutionary-developmental biology framework. This eco-evo-devo framework we believe will help to clarify the nature and use of the term specialised metabolites in the future.
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Affiliation(s)
| | - Marc G Chevrette
- Department of Microbiology and Cell Sciences, University of Florida, Museum Drive, Gainesville, FL, United States; University of Florida Genetics Institute, University of Florida, Mowry Road, Gainesville, FL, United States
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Cathedral Street, Glasgow, United Kingdom.
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10
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Wu Y, Ma J, Shi J, Cao S, Luo J, Zheng T, Wang M. iTRAQ-Based Quantitative Proteomic Analysis of Arthrobacter simplex in Response to Cortisone Acetate and Its Mutants with Improved Δ 1-Dehydrogenation Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6376-6388. [PMID: 37043686 DOI: 10.1021/acs.jafc.3c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arthrobacter simplex is extensively used for cortisone acetate (CA) biotransformation in industry, but the Δ1-dehydrogenation molecular fundamental remains unclear. Herein, the comparative proteome revealed several proteins with the potential role in this reaction, which were mainly involved in lipid or amino acid transport and metabolism, energy production and conversion, steroid degradation, and transporter. The influences of six proteins were further confirmed, where pps, MceGA, yrbE4AA, yrbE4BA, and hyp2 showed positive impacts, while hyp1 exhibited a negative effect. Additionally, KsdD5 behaved as the best catalytic enzyme. By the combined manipulation in multiple genes under the control of a stronger promoter, an optimal strain with better catalytic enzyme activity, substrate transportation, and cell stress tolerance was created. After biotechnology optimization, the production peak and productivity were, respectively, boosted by 4.1- and 4.0-fold relative to the initial level. Our work broadens the understanding of the Δ1-dehydrogenation mechanism, also providing effective strategies for excellent steroid-transforming strains.
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Affiliation(s)
- Yan Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jianan Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jinghui Shi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuting Cao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jianmei Luo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Tingting Zheng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
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11
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Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
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12
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Lei Y, Asamizu S, Ishizuka T, Onaka H. Regulation of Multidrug Efflux Pumps by TetR Family Transcriptional Repressor Negatively Affects Secondary Metabolism in Streptomyces coelicolor A3(2). Appl Environ Microbiol 2023; 89:e0182222. [PMID: 36790176 PMCID: PMC10056966 DOI: 10.1128/aem.01822-22] [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: 11/10/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Streptomyces spp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs, Streptomyces spp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants of Streptomyces coelicolor that show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture with Tsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of the sco1718 gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs in Streptomyces coelicolor A3(2). In the genome of S. coelicolor A3(2), two other sets of TFR and two-component ATP-binding cassette (ABC) transporter genes (sco4358-4360 and sco5384-5382) were found which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. An electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that TFRs repressed the expression of each adjacent two-component ABC transporter genes by binding to the operator sequence. Notably, the Δsco1718 mutant showed increased resistance to several antibiotics of other actinomycete origin. Our results imply the switching of cell metabolism to direct offense (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem. IMPORTANCE The bacterial metabolic potential to synthesize diverse secondary metabolites in the environment has been revealed by recent (meta)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment. Streptomyces spp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, including Streptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes in Streptomyces coelicolor A3(2). We found that each TFR controlled the expression of respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome of Streptomyces species, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.
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Affiliation(s)
- Yukun Lei
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Tokyo, Japan
| | - Takumi Ishizuka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Tokyo, Japan
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13
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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14
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Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40. BIOLOGY 2023; 12:biology12030345. [PMID: 36979037 PMCID: PMC10044865 DOI: 10.3390/biology12030345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Streptomyces are factories of antimicrobial secondary metabolites. We isolated a Streptomyces species associated with the Pelargonium graveolens rhizosphere. Its total metabolic extract exhibited potent antibacterial and antifungal properties against all the tested pathogenic microbes. Whole genome sequencing and genome analyses were performed to take a look at its main characteristics and to reconstruct the metabolic pathways that can be associated with biotechnologically useful traits. AntiSMASH was used to identify the secondary metabolite gene clusters. In addition, we searched for known genes associated with plant growth-promoting characteristics. Finally, a comparative and pan-genome analysis with three closely related genomes was conducted. It was identified as Streptomyces vinaceusdrappus strain AC-40. Genome mining indicated the presence of several secondary metabolite gene clusters. Some of them are identical or homologs to gene clusters of known metabolites with antimicrobial, antioxidant, and other bioactivities. It also showed the presence of several genes related to plant growth promotion traits. The comparative genome analysis indicated that at least five of these gene clusters are highly conserved through rochei group genomes. The genotypic and phenotypic characteristics of S. vinaceusdrappus strain AC-40 indicate that it is a promising source of beneficial secondary metabolites with pharmaceutical and biotechnological applications.
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15
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Sass P. Antibiotics: Precious Goods in Changing Times. Methods Mol Biol 2023; 2601:3-26. [PMID: 36445576 DOI: 10.1007/978-1-0716-2855-3_1] [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: 06/16/2023]
Abstract
Antibiotics represent a first line of defense of diverse microorganisms, which produce and use antibiotics to counteract natural enemies or competitors for nutritional resources in their nearby environment. For antimicrobial activity, nature has invented a great variety of antibiotic modes of action that involve the perturbation of essential bacterial structures or biosynthesis pathways of macromolecules such as the bacterial cell wall, DNA, RNA, or proteins, thereby threatening the specific microbial lifestyle and eventually even survival. However, along with highly inventive modes of antibiotic action, nature also developed a comparable set of resistance mechanisms that help the bacteria to circumvent antibiotic action. Microorganisms have evolved specific adaptive responses that allow to appropriately react to the presence of antimicrobial agents, thereby ensuring survival during antimicrobial stress. In times of rapid development and spread of antibiotic (multi-)resistance, new resistance-breaking strategies to counteract bacterial infections are desperately needed. This chapter is an update to Chapter 1 of the first edition of this book and intends to give an overview of common antibiotics and their target pathways. It will also present examples for new antibiotics with novel modes of action, illustrating that nature's repertoire of innovative new antimicrobial agents has not been fully exploited yet, and we still might find new drugs that help to evade established antimicrobial resistance strategies.
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Affiliation(s)
- Peter Sass
- Interfaculty Institute for Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany.
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16
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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17
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Abstract
The three-dimensional structure of natural products is critical for their biological activities and, as such, enzymes have evolved that specifically generate active stereoisomers. Lanthipeptides are post-translationally modified peptidic natural products that contain macrocyclic thioethers featuring lanthionine (Lan) and/or methyllanthionine (MeLan) residues with defined stereochemistry. In this report, we compare two class I lanthipeptide biosynthetic gene clusters (BGCs), coi and olv, that represent two families of lanthipeptide gene clusters found in Actinobacteria. The precursor peptides and BGCs are quite similar with genes encoding a dehydratase, cyclase, and methyltransferase (MT). We illustrate that the precursor peptide CoiA1 is converted by these enzymes into a polymacrocyclic product, mCoiA1, that contains an analogous ring pattern to the previously characterized post-translationally modified OlvA peptide (mOlvA). However, a clear distinction between the two BGCs is an additional Thr-glutamyl lyase (GL) domain that is fused to the MT, CoiSA, which results in divergence of the product stereochemistry for the coi BGC. Two out of three MeLan rings of mCoiA1 contain different stereochemistry than the corresponding residues in mOlvA, with the most notable difference being a rare d-allo-l-MeLan residue, the formation of which is guided by CoiSA. This study illustrates how nature utilizes a distinct GL to control natural product stereochemistry in lanthipeptide biosynthesis.
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Affiliation(s)
- Raymond Sarksian
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States,Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States,. Tel: 217 244 5360
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18
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Pei ZF, Zhu L, Sarksian R, van der Donk WA, Nair SK. Class V Lanthipeptide Cyclase Directs the Biosynthesis of a Stapled Peptide Natural Product. J Am Chem Soc 2022; 144:17549-17557. [PMID: 36107785 PMCID: PMC9621591 DOI: 10.1021/jacs.2c06808] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lanthipeptides are a class of cyclic peptides characterized by the presence of one or more lanthionine (Lan) or methyllanthionine (MeLan) thioether rings. These cross-links are produced by α,β-unsaturation of Ser or Thr residues in peptide substrates by dehydration, followed by a Michael-type conjugate addition of Cys residues onto the dehydroamino acids. Lanthipeptides may be broadly classified into at least five different classes, and the biosynthesis of classes I-IV lanthipeptides requires catalysis by LanC cyclases that control both the site-specificity and the stereochemistry of the conjugate addition. In contrast, there are no current examples of LanCs that occur in class V biosynthetic clusters, despite the presence of lanthionine rings in these compounds. In this work, bioinformatics-guided co-occurrence analysis identifies more than 240 putative class V lanthipeptide clusters that contain a LanC cyclase. Reconstitution studies demonstrate that the cyclase-catalyzed product is notably distinct from the product formed spontaneously. Stereochemical analysis shows that the cyclase diverts the final product to a configuration that is distinct from one that is energetically favored. Structural characterization of the final product by multi-dimensional NMR spectroscopy reveals that it forms a helical stapled peptide. Mutational analysis identified a plausible order for cyclization and suggests that enzymatic rerouting to the final structure is largely directed by the construction of the first lanthionine ring. These studies show that lanthipeptide cyclases are needed for the biosynthesis of some constrained peptides, the formations of which would otherwise be energetically unfavored.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Raymond Sarksian
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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19
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Wang R, Cao Y, Kong F, Hou B, Zhao J, Kang Y, Ye J, Wu H, Zhang H. Developmental regulator RamRsl controls both morphological development and lincomycin biosynthesis in Streptomyces lincolnensis. J Appl Microbiol 2022; 133:400-409. [DOI: doi.org/10.1111/jam.15568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Abstract
Aims
Assessing the role of ramRsl, a gene absent in a lincomycin over-producing strain, in the regulation of morphological development and lincomycin biosynthesis in Streptomyces lincolnensis.
Methods and Results
The gene ramRsl was deleted from the wild-type strain NRRL 2936 and the ΔramR mutant strain was characterized by a slower growth rate and a delayed morphological differentiation compared to the original strain NRRL 2936. Furthermore, the ΔramR produced 2.6-fold more lincomycin than the original strain, and consistently the level of expression of all lincomycin cluster located genes was enhanced at 48 and 96 h in the ΔramR. Complementation of ΔramR with an intact copy of ramRsl restored all wild-type features, whereas the over-expression of ramRsl led to a reduction of 33% of the lincomycin yield. Furthermore, the level of expression of glnR, bldA and SLCG_2919, three of known lincomycin biosynthesis regulators, was lower in the ΔramR than in the original strain at the early stage of fermentation and we demonstrated, using electrophoretic mobility shift assay and XylE reporter assay, that glnR is a novel direct target of RamR.
Conclusions
Altogether, these results indicated that, beyond promoting the morphological development, RamR regulates negatively lincomycin biosynthesis and positively the expression of the nitrogen regulator GlnR.
Significance and Impact of the Study
We demonstrated that RamR plays a negative role in the regulation of lincomycin biosynthesis in S. lincolnensis. Interestingly, the deletion of this gene in other antibiotic-producing Streptomyces strains might also increase their antibiotic-producing abilities.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Yuan Cao
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Fanjing Kong
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
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20
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Wang M, Li J, Cong W, Zhang J. Antimicrobial Mechanism and Secondary Metabolite Profiles of Biocontrol Agent Streptomyces lydicus M01 Based on Ultra-High-Performance Liquid Chromatography Connected to a Quadrupole Time-of-Flight Mass Spectrometer Analysis and Genome Sequencing. Front Microbiol 2022; 13:908879. [PMID: 35711789 PMCID: PMC9194905 DOI: 10.3389/fmicb.2022.908879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/04/2022] [Indexed: 11/15/2022] Open
Abstract
Streptomyces lydicus was used as biopesticide for crop protection in agriculture, however, the antimicrobial mechanism remains unclear and no systematic research on the secondary metabolites of S. lydicus has been reported. In this study, the extract of S. lydicus M01 culture was used to treat plant pathogen Alternaria alternata and morphological changes in the plasma membrane and cell wall of hyphae and conidia were observed. Fluorescence microscopy combined with different dyes showed that the accumulation of reactive oxygen species and cell death were also induced. To investigate the secondary metabolites in the culture filtrate, an online detection strategy of ultra-high-performance liquid chromatography connected to a quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF-MS) was used for identification. The results revealed an excess of 120 metabolites, mainly consisted of fungicides, antibacterial agents, herbicides, insecticides, and plant growth regulators, such as IAA. Among which the five dominant components were oxadixyl, chloreturon, S-metolachlor, fentrazamide, and bucarpolate. On the other hand, the complete genome of S. lydicus M01 was sequenced and a number of key function gene clusters that contribute to the biosynthesis of active secondary metabolites were revealed. This is the first systematic characterization of S. lydicus secondary metabolites, and these results offer novel and valuable evidence for a comprehensive understanding of the biocontrol agent S. lydicus and its application in agriculture.
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Affiliation(s)
- Mingxuan Wang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jing Li
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenjie Cong
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jianguo Zhang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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21
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Wang R, Cao Y, Kong F, Hou B, Zhao J, Kang Y, Ye J, Wu H, Zhang H. Developmental regulator RamR sl controls both morphological development and lincomycin biosynthesis in Streptomyces lincolnensis. J Appl Microbiol 2022; 133:400-409. [PMID: 35384192 DOI: 10.1111/jam.15568] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
AIMS Assessing the role of ramRsl , a gene absent in a lincomycin over-producing strain, in the regulation of morphological development and lincomycin biosynthesis in S. lincolnensis. METHODS AND RESULTS The gene ramRsl was deleted from the wild type strain NRRL 2936 and the ΔramR mutant strain was characterized by a slower growth rate and a delayed morphological differentiation compared to the original strain NRRL 2936. Furthermore, the ΔramR produced 2.6-fold more lincomycin than the original strain, and consistently the level of expression of all lincomycin cluster located genes was enhanced at 48 h and 96 h in the ΔramR. Complementation of ΔramR with an intact copy of ramRsl restored all wild type features whereas the over-expression of ramRsl led to a reduction of 33% of the lincomycin yield. Furthermore, the level of expression of glnR, bldA, and SLCG_2919, three of known lincomycin biosynthesis regulators, was lower in the ΔramR than in the original strain at the early stage of fermentation and we demonstrated, using EMSA and XylE reporter assay, that glnR is a novel direct target of RamR. CONCLUSIONS Altogether these results indicated that, beyond promoting the morphological development, RamR regulates negatively lincomycin biosynthesis and positively the expression of the nitrogen regulator GlnR. SIGNIFICANCE AND IMPACT OF THE STUDY We demonstrated that RamR plays a negative role in the regulation of lincomycin biosynthesis in S. lincolnensis. Interestingly, the deletion of this gene in other antibiotic producing Streptomyces strains might also increase their antibiotic producing abilities.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuan Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Fanjing Kong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
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22
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Sarksian R, Hegemann JD, Simon MA, Acedo JZ, van der Donk WA. Unexpected Methyllanthionine Stereochemistry in the Morphogenetic Lanthipeptide SapT. J Am Chem Soc 2022; 144:6373-6382. [PMID: 35352944 PMCID: PMC9011353 DOI: 10.1021/jacs.2c00517] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Lanthipeptides are
polycyclic peptides characterized by the presence
of lanthionine (Lan) and/or methyllanthionine (MeLan). They are members
of the ribosomally synthesized and post-translationally modified peptides (RiPPs). The stereochemical
configuration of (Me)Lan cross-links is important for the bioactivity
of lanthipeptides. To date, MeLan residues in characterized lanthipeptides
have either the 2S,3S or 2R,3R stereochemistry. Herein, we reconstituted
in Escherichia coli the biosynthetic pathway toward
SapT, a class I lanthipeptide that exhibits morphogenetic activity.
Through the synthesis of standards, the heterologously produced peptide
was shown to possess three MeLan residues with the 2S,3R stereochemistry (d-allo-l-MeLan), the first time such stereochemistry has been
observed in a lanthipeptide. Bioinformatic analysis of the biosynthetic
enzymes suggests this stereochemistry may also be present in other
lanthipeptides. Analysis of another gene cluster in Streptomyces
coelicolor that is widespread in actinobacteria confirmed
another example of d-allo-l-MeLan
and verified the bioinformatic prediction. We propose a mechanism
for the origin of the unexpected stereochemistry and provide support
using site-directed mutagenesis.
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Affiliation(s)
- Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Max A Simon
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
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23
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Hamry SR, Thibodeaux CJ. Biochemical and biophysical investigation of the HalM2 lanthipeptide synthetase using mass spectrometry. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid emergence of antimicrobial resistance in clinical settings has called for renewed efforts to discover and develop new antimicrobial compounds. Lanthipeptides present a promising, genetically encoded molecular scaffold for the engineering of structurally complex, biologically active peptides. These peptide natural products are constructed by enzymes (lanthipeptide synthetases) with relaxed substrate specificity that iteratively modify the precursor lanthipeptide to generate structures with defined sets of thioether macrocycles. The mechanistic features that guide the maturation of lanthipeptides into their proper, fully modified forms are obscured by the complexity of the multistep maturation and the large size and dynamic structures of the synthetases and precursor peptides. Over the past several years, our lab has been developing a suite of mass spectrometry-based techniques that are ideally suited to untangling the complex reaction sequences and molecular interactions that define lanthipeptide biosynthesis. This review focuses on our development and application of these mass spectrometry-based techniques to investigate the biochemical, kinetic, and biophysical properties of the haloduracin β class II lanthipeptide synthetase, HalM2.
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Affiliation(s)
- Sally R. Hamry
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Christopher J. Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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24
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Liu B, Wei Q, Yang M, Shi L, Zhang K, Ge B. Effect of toyF on wuyiencin and toyocamycin production by Streptomyces albulus CK-15. World J Microbiol Biotechnol 2022; 38:65. [PMID: 35229201 DOI: 10.1007/s11274-022-03234-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces albulus CK-15 produces various secondary metabolites, including the antibiotics wuyiencin and toyocamycin, which can reportedly control a broad range of plant fungal diseases. The production of these nucleoside antibiotics in CK-15 is regulated by two biosynthesis gene clusters. To investigate the potential effect of toyocamycin biosynthesis on wuyiencin production, we herein generated S. albulus strains in which a key gene in the toyocamycin biosynthesis gene cluster, namely toyF, was either deleted or overexpressed. The toyF deletion mutant ∆toyF did not produce toyocamycin, while the production of wuyiencin increased by 23.06% in comparison with that in the wild-type (WT) strain. In addition, ΔtoyF reached the highest production level of wuyiencin 4 h faster than the WT strain (60 h vs. and 64 h). Further, toyocamycin production by the toyF overexpression strain was two-fold higher than by the WT strain, while wuyiencin production was reduced by 29.10%. qRT-PCR showed that most genes in the toyocamycin biosynthesis gene cluster were expressed at lower levels in ∆toyF as compared with those in the WT strain, while the expression levels of genes in the wuyiencin biosynthesis gene cluster were upregulated. Finally, the growth rate of ∆toyF was much faster than that of the WT strain when cultured on solid or liquid medium. Based on our findings, we report that in industrial fermentation processes, ∆toyF has the potential to increase the production of wuyiencin and reduce the timeframe of fermentation.
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Affiliation(s)
- Binghua Liu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Qiuhe Wei
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaoling Yang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liming Shi
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kecheng Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Beibei Ge
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins. mBio 2022; 13:e0278121. [PMID: 35012331 PMCID: PMC8749437 DOI: 10.1128/mbio.02781-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. IMPORTANCE Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood. Here, we show that the population structure of a ubiquitous Streptomyces species complex matches its habitat distribution and can be defined by gene flow discontinuities. Using comparative genomics and physiological assays, we reveal that gains and losses of specific genomic traits play a significant role in the transition between free-living and host-associated lifestyles, driving speciation of the species. These results provide new insights into the evolutionary trajectory of Streptomyces and the notion of species.
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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Zin NM, Ismail A, Mark DR, Westrop G, Schniete JK, Herron PR. Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42. Front Bioeng Biotechnol 2021; 9:740722. [PMID: 34712653 PMCID: PMC8545861 DOI: 10.3389/fbioe.2021.740722] [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: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.
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Affiliation(s)
- Noraziah M Zin
- School of Diagnostic and Applied Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aishah Ismail
- School of Diagnostic and Applied Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Gareth Westrop
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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Arulprakasam KR, Dharumadurai D. Genome mining of biosynthetic gene clusters intended for secondary metabolites conservation in actinobacteria. Microb Pathog 2021; 161:105252. [PMID: 34662717 DOI: 10.1016/j.micpath.2021.105252] [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: 07/02/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
Evolution of genome sequencing technology, on the one hand, and advancement of computational genome mining tools, on the other hand, paves way for improvement in predicting secondary metabolites. In past, numerous efforts were made concerning genome mining for recognizing secondary metabolites within the genus, but only a negligible quantity of comparative genomic reports had carried out among species of different genera. In this study, we explored potential of 24 actinobacteria species belonging to the genera, including Streptomyces, Nocardia, Micromonospora, and Saccharomonospora, to traverse diversity and distribution of Biosynthetic Gene Clusters (BGCs). Investigating results obtained from antiSMASH (Antibiotics and Secondary Metabolites Analysis Shell), NaPDoS (Natural Product Domain Seeker), and NP.searcher revealed conservation of genus-specific gene clusters among various species. E.g., NAGGN (n-acetyl glutaminyl glutamine amide) is present in Micromonospora, furan in Nocardia, melanin, and lassopeptide occur in Streptomyces. Bioactive compounds like alkyl-O-dihydro geranyl methoxy hydroquinone, SapB, desferrioxamine E, 2-Methylisoborneol, mayamycin, cyclodipeptide synthase, diisonitrile, salinichelin, hopene, ectoine and isorenieratene are highly conserved among diverse genera. Furthermore, pharmacological activity of actinobacterial derived metabolites against bacterial and fungal pathogens were illustrated. We need to accomplish large-scale analysis of natural products, including various genera of actinobacteria to deliver comprehensive intuition to overcome antibiotic resistance.
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Affiliation(s)
- Karthick Raja Arulprakasam
- Department of Microbiology, School of Life Sciences Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Dhanasekaran Dharumadurai
- Department of Microbiology, School of Life Sciences Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
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Vela Gurovic MS, Díaz ML, Gallo CA, Dietrich J. Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species. Mol Genet Genomics 2021; 296:1299-1311. [PMID: 34564766 DOI: 10.1007/s00438-021-01823-9] [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: 05/14/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022]
Abstract
A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.
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Affiliation(s)
- María Soledad Vela Gurovic
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina. .,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina.
| | - Marina Lucía Díaz
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
| | - Cristian Andres Gallo
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina
| | - Julián Dietrich
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
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Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach. Antonie van Leeuwenhoek 2021; 114:1483-1496. [PMID: 34355285 PMCID: PMC8448680 DOI: 10.1007/s10482-021-01609-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/23/2021] [Indexed: 11/04/2022]
Abstract
Strain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.
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Zerouki C, Bensalah F, Kuittinen S, Pappinen A, Turunen O. Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara. BMC Genomics 2021; 22:578. [PMID: 34315408 PMCID: PMC8317367 DOI: 10.1186/s12864-021-07866-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective. RESULTS Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. CONCLUSION The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.
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Affiliation(s)
- Chahira Zerouki
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland.
- Laboratory of Microbial Genetics, Department of Biology, University ORAN 1, 31000, Oran, Algeria.
| | - Farid Bensalah
- Laboratory of Microbial Genetics, Department of Biology, University ORAN 1, 31000, Oran, Algeria
| | - Suvi Kuittinen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Ari Pappinen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
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Bothwell IR, Caetano T, Sarksian R, Mendo S, van der Donk WA. Structural Analysis of Class I Lanthipeptides from Pedobacter lusitanus NL19 Reveals an Unusual Ring Pattern. ACS Chem Biol 2021; 16:1019-1029. [PMID: 34085816 PMCID: PMC9845027 DOI: 10.1021/acschembio.1c00106] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide natural products characterized by the presence of lanthionine and methyllanthionine cross-linked amino acids formed by dehydration of Ser/Thr residues followed by conjugate addition of Cys to the resulting dehydroamino acids. Class I lanthipeptide dehydratases utilize glutamyl-tRNAGlu as a cosubstrate to glutamylate Ser/Thr followed by glutamate elimination. A vast majority of lanthipeptides identified from class I synthase systems have been from Gram-positive bacteria. Herein, we report the heterologous expression and modification in Escherichia coli of two lanthipeptides from the Gram-negative Bacteroidetes Pedobacter lusitanus NL19. These peptides are representative of a group of compounds frequently encoded in Pedobacter genomes. Structural characterization of the lanthipeptides revealed a novel ring pattern as well as an unusual ll-lanthionine stereochemical configuration and a cyclase that lacks the canonical zinc ligands found in most LanC enzymes.
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Affiliation(s)
- Ian R. Bothwell
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Tânia Caetano
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Raymond Sarksian
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Sónia Mendo
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
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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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36
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Uggowitzer KA, Habibi Y, Wei W, Moitessier N, Thibodeaux CJ. Mutations in Dynamic Structural Elements Alter the Kinetics and Fidelity of the Multifunctional Class II Lanthipeptide Synthetase, HalM2. Biochemistry 2021; 60:412-430. [PMID: 33507068 DOI: 10.1021/acs.biochem.0c00919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Class II lanthipeptide synthetases (LanM enzymes) catalyze the multistep post-translational modification of genetically encoded precursor peptides into macrocyclic (often antimicrobial) lanthipeptides. The reaction sequence involves dehydration of serine/threonine residues, followed by intramolecular addition of cysteine thiols onto the nascent dehydration sites to construct thioether bridges. LanMs utilize two separate active sites in an iterative yet highly coordinated manner to maintain a remarkable level of regio- and stereochemical control over the multistep maturation. The mechanisms underlying this biosynthetic fidelity remain enigmatic. We recently demonstrated that proper function of the haloduracin β synthetase (HalM2) requires dynamic structural elements scattered across the surface of the enzyme. Here, we perform kinetic simulations, structural analysis of reaction intermediates, hydrogen-deuterium exchange mass spectrometry studies, and molecular dynamics simulations to investigate the contributions of these dynamic HalM2 structural elements to biosynthetic efficiency and fidelity. Our studies demonstrate that a large, conserved loop (HalM2 residues P349-P405) plays essential roles in defining the precursor peptide binding site, facilitating efficient peptide dehydration, and guiding the order of thioether ring formation. Moreover, mutations near the interface of the HalM2 dehydratase and cyclase domains perturb cyclization fidelity and result in aberrant thioether topologies that cannot be corrected by the wild type enzyme, suggesting an element of kinetic control in the normal cyclization sequence. Overall, this work provides the most comprehensive correlation of the structural and functional properties of a LanM enzyme reported to date and should inform mechanistic studies of the biosynthesis of other ribosomally synthesized and post-translationally modified peptide natural products.
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Draft Genome Sequence of Terrestrial Streptomyces sp. Strain VITNK9, Isolated from Vellore, Tamil Nadu, India, Exhibiting Antagonistic Activity against Fish Pathogens. Microbiol Resour Announc 2021; 10:10/1/e01282-20. [PMID: 33414310 PMCID: PMC8407733 DOI: 10.1128/mra.01282-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of Streptomyces sp. strain VITNK9, isolated from a soil sample collected in Vellore District (12.9165°N, 79.1325°E), Tamil Nadu, India, with an assembly size of 7,920,076 bp and 72.7% GC content.
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38
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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Tenconi E, Traxler M, Tellatin D, van Wezel GP, Rigali S. Prodiginines Postpone the Onset of Sporulation in Streptomyces coelicolor. Antibiotics (Basel) 2020; 9:E847. [PMID: 33256178 PMCID: PMC7760128 DOI: 10.3390/antibiotics9120847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
Bioactive natural products are typically secreted by the producer strain. Besides that, this allows the targeting of competitors, also filling a protective role, reducing the chance of self-killing. Surprisingly, DNA-degrading and membrane damaging prodiginines (PdGs) are only produced intracellularly, and are required for the onset of the second round of programmed cell death (PCD) in Streptomyces coelicolor. In this work, we investigated the influence of PdGs on the timing of the morphological differentiation of S. coelicolor. The deletion of the transcriptional activator gene redD that activates the red cluster for PdGs or nutrient-mediated reduction of PdG synthesis both resulted in the precocious appearance of mature spore chains. Transcriptional analysis revealed an accelerated expression of key developmental genes in the redD null mutant, including bldN for the developmental σ factor BldN which is essential for aerial mycelium formation. In contrast, PdG overproduction due to the enhanced copy number of redD resulted in a delay or block in sporulation. In addition, confocal fluorescence microscopy revealed that the earliest aerial hyphae do not produce PdGs. This suggests that filaments that eventually differentiate into spore chains and are hence required for survival of the colony, are excluded from the second round of PCD induced by PdGs. We propose that one of the roles of PdGs would be to delay the entrance of S. coelicolor into the dormancy state (sporulation) by inducing the leakage of the intracellular content of dying filaments thereby providing nutrients for the survivors.
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Affiliation(s)
- Elodie Tenconi
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
- Hedera-22, Boulevard du rectorat 27b, B-4000 Liège, Belgium
| | - Matthew Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA;
| | - Déborah Tellatin
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands;
| | - Sébastien Rigali
- InBioS—Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000 Liège, Belgium; (E.T.); (D.T.)
- Hedera-22, Boulevard du rectorat 27b, B-4000 Liège, Belgium
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40
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Sánchez de la Nieta R, Antoraz S, Alzate JF, Santamaría RI, Díaz M. Antibiotic Production and Antibiotic Resistance: The Two Sides of AbrB1/B2, a Two-Component System of Streptomyces coelicolor. Front Microbiol 2020; 11:587750. [PMID: 33162964 PMCID: PMC7581861 DOI: 10.3389/fmicb.2020.587750] [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: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Antibiotic resistance currently presents one of the biggest threats to humans. The development and implementation of strategies against the spread of superbugs is a priority for public health. In addition to raising social awareness, approaches such as the discovery of new antibiotic molecules and the elucidation of resistance mechanisms are common measures. Accordingly, the two-component system (TCS) of Streptomyces coelicolor AbrB1/B2, offer amenable ways to study both antibiotic production and resistance. Global transcriptomic comparisons between the wild-type strain S. coelicolor M145 and the mutant ΔabrB, using RNA-Seq, showed that the AbrB1/B2 TCS is implicated in the regulation of different biological processes associated with stress responses, primary and secondary metabolism, and development and differentiation. The ΔabrB mutant showed the up-regulation of antibiotic biosynthetic gene clusters and the down-regulation of the vancomycin resistance gene cluster, according to the phenotypic observations of increased antibiotic production of actinorhodin and undecylprodigiosin, and greater susceptibility to vancomycin. The role of AbrB1/B2 in vancomycin resistance has also been shown by an in silico analysis, which strongly indicates that AbrB1/B2 is a homolog of VraR/S from Staphylococcus aureus and LiaR/S from Enterococcus faecium/Enterococcus faecalis, both of which are implied in vancomycin resistance in these pathogenic organisms that present a serious threat to public health. The results obtained are interesting from a biotechnological perspective since, on one hand, this TCS is a negative regulator of antibiotic production and its high degree of conservation throughout Streptomyces spp. makes it a valuable tool for improving antibiotic production and the discovery of cryptic metabolites with antibiotic action. On the other hand, AbrB1/B2 contributes to vancomycin resistance and is a homolog of VraR/S and LiaR/S, important regulators in clinically relevant antibiotic-resistant bacteria. Therefore, the study of AbrB1/B2 could provide new insight into the mechanism of this type of resistance.
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Affiliation(s)
- Ricardo Sánchez de la Nieta
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Sergio Antoraz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Ramón I Santamaría
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
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41
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Benaud N, Edwards RJ, Amos TG, D'Agostino PM, Gutiérrez-Chávez C, Montgomery K, Nicetic I, Ferrari BC. Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics. Environ Microbiol 2020; 23:3646-3664. [PMID: 33140504 DOI: 10.1111/1462-2920.15300] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short-read technologies. We sequenced 17 Antarctic soil bacteria from multi-genome libraries, employing the long-read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold-adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non-ribosomal peptide and polyketide-encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella, while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant-like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
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Affiliation(s)
- Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Paul M D'Agostino
- Technische Universität Dresden, Chair of Technical Biochemistry, Bergstraße 66, 01602 Dresden, Germany
| | | | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Iskra Nicetic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
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42
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Pipiya SO, Terekhov SS, Mokrushina YA, Knorre VD, Smirnov IV, Gabibov AG. Engineering Artificial Biodiversity of Lantibiotics to Expand Chemical Space of DNA-Encoded Antibiotics. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1319-1334. [PMID: 33280576 DOI: 10.1134/s0006297920110048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The discovery of antibiotics was one of the fundamental stages in the development of humanity, leading to a dramatic increase in the life expectancy of millions of people all over the world. The uncontrolled use of antibiotics resulted in the selection of resistant strains of bacteria, limiting the effectiveness of antimicrobial therapy nowadays. Antimicrobial peptides (AMPs) were considered promising candidates for next-generation antibiotics for a long time. However, the practical application of AMPs is restricted by their low therapeutic indices, impaired pharmacokinetics, and pharmacodynamics, which is predetermined by their peptide structure. Nevertheless, the DNA-encoded nature of AMPs enables creating broad repertoires of artificial biodiversity of antibiotics, making them versatile templates for the directed evolution of antibiotic activity. Lantibiotics are a unique class of AMPs with an expanded chemical space. A variety of post-translational modifications, mechanisms of action on bacterial membranes, and DNA-encoded nature make them a convenient molecular template for creating highly representative libraries of antimicrobial compounds. Isolation of new drug candidates from this synthetic biodiversity is extremely attractive but requires high-throughput screening of antibiotic activity. The combination of synthetic biology and ultrahigh-throughput microfluidics allows implementing the concept of directed evolution of lantibiotics for accelerated creation of new promising drug candidates.
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Affiliation(s)
- S O Pipiya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S S Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yu A Mokrushina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - V D Knorre
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - I V Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A G Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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43
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Smits SHJ, Schmitt L, Beis K. Self-immunity to antibacterial peptides by ABC transporters. FEBS Lett 2020; 594:3920-3942. [PMID: 33040342 DOI: 10.1002/1873-3468.13953] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/22/2020] [Accepted: 10/05/2020] [Indexed: 01/17/2023]
Abstract
Bacteria produce under certain stress conditions bacteriocins and microcins that display antibacterial activity against closely related species for survival. Bacteriocins and microcins exert their antibacterial activity by either disrupting the membrane or inhibiting essential intracellular processes of the bacterial target. To this end, they can lyse bacterial membranes and cause subsequent loss of their integrity or nutrients, or hijack membrane receptors for internalisation. Both bacteriocins and microcins are ribosomally synthesised and several are posttranslationally modified, whereas others are not. Such peptides are also toxic to the producer bacteria, which utilise immunity proteins or/and dedicated ATP-binding cassette (ABC) transporters to achieve self-immunity and peptide export. In this review, we discuss the structure and mechanism of self-protection that is conferred by these ABC transporters.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany.,Center for Structural Studies, Heinrich-Heine-University, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, UK.,Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
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44
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Hegemann JD, Süssmuth RD. Matters of class: coming of age of class III and IV lanthipeptides. RSC Chem Biol 2020; 1:110-127. [PMID: 34458752 PMCID: PMC8341899 DOI: 10.1039/d0cb00073f] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
Lanthipeptides belong to the superfamily of ribosomally-synthesized and posttranslationally-modified peptides (RiPPs). Despite the fact that they represent one of the longest known RiPP subfamilies, their youngest members, classes III and IV, have only been described more recently. Since then, a plethora of studies furthered the understanding of their biosynthesis. While there are commonalities between classes III and IV due to the similar domain architectures of their processing enzymes, there are also striking differences that allow their discrimination. In this concise review article, we summarize what is known about the underlying biosynthetic principles of these lanthipeptides and discuss open questions for future research.
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Affiliation(s)
- Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
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45
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Russell AH, Truman AW. Genome mining strategies for ribosomally synthesised and post-translationally modified peptides. Comput Struct Biotechnol J 2020; 18:1838-1851. [PMID: 32728407 PMCID: PMC7369419 DOI: 10.1016/j.csbj.2020.06.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/14/2023] Open
Abstract
Genome mining is a computational method for the automatic detection and annotation of biosynthetic gene clusters (BGCs) from genomic data. This approach has been increasingly utilised in natural product (NP) discovery due to the large amount of sequencing data that is now available. Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of structurally complex NP with diverse bioactivities. RiPPs have recently been shown to occupy a much larger expanse of genomic and chemical space than previously appreciated, indicating that annotation of RiPP BGCs in genomes may have been overlooked in the past. This review provides an overview of the genome mining tools that have been specifically developed to aid in the discovery of RiPP BGCs, which have been built from an increasing knowledgebase of RiPP structures and biosynthesis. Given these recent advances, the application of targeted genome mining has great potential to accelerate the discovery of important molecules such as antimicrobial and anticancer agents whilst increasing our understanding about how these compounds are biosynthesised in nature.
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Affiliation(s)
- Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
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46
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Lagedroste M, Reiners J, Knospe CV, Smits SHJ, Schmitt L. A Structural View on the Maturation of Lanthipeptides. Front Microbiol 2020; 11:1183. [PMID: 32582108 PMCID: PMC7296275 DOI: 10.3389/fmicb.2020.01183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/08/2020] [Indexed: 01/16/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides, which display diverse bioactivities (e.g., antifungal, antimicrobial, and antiviral). One characteristic of these lanthipeptides is the presence of thioether bonds, which are termed (methyl-) lanthionine rings. These modifications are installed by corresponding modification enzymes in a two-step modality. First, serine and threonine residues are dehydrated followed by a subsequent catalyzed cyclization reaction, in which the dehydrated serine and threonine residues are undergoing a Michael-type addition with cysteine residues. The dedicated enzymes are encoded by one or two genes and the classification of lanthipeptides is pending on this. The modification steps form the basis of distinguishing the different classes of lanthipeptides and furthermore reflect also important mechanistic differences. Here, we will summarize recent insights into the mechanisms and the structures of the participating enzymes, focusing on the two core modification steps - dehydration and cyclization.
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Affiliation(s)
- Marcel Lagedroste
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - C Vivien Knospe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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47
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Walker MC, Eslami SM, Hetrick KJ, Ackenhusen SE, Mitchell DA, van der Donk WA. Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. BMC Genomics 2020; 21:387. [PMID: 32493223 PMCID: PMC7268733 DOI: 10.1186/s12864-020-06785-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of genes encoding characteristic enzymes involved in the post-translational modification process, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide biosynthesis. To address this challenge, we enhanced the predictive capabilities of Rapid ORF Description & Evaluation Online (RODEO) to identify members of all four known classes of lanthipeptides. Results Using RODEO, we mined over 100,000 bacterial and archaeal genomes in the RefSeq database. We identified nearly 8500 lanthipeptide precursor peptides. These precursor peptides were identified in a broad range of bacterial phyla as well as the Euryarchaeota phylum of archaea. Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. A number of these precursor peptides are similar to those of previously characterized lanthipeptides, but even more were not, including potential antibiotics. One such new antimicrobial lanthipeptide was purified and characterized. Additionally, examination of the biosynthetic gene clusters revealed that enzymes installing secondary post-translational modifications are more widespread than initially thought. Conclusion Lanthipeptide biosynthetic gene clusters are more widely distributed and the precursor peptides encoded within these clusters are more diverse than previously appreciated, demonstrating that the lanthipeptide sequence-function space remains largely underexplored.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Chemical Biology, University of New Mexico, 346 Clark Hall, 300 Terrace St. NE, Albuquerque, NM, 87131, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
| | - Sara M Eslami
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Kenton J Hetrick
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Sarah E Ackenhusen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
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48
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Guerrero-Garzón JF, Zehl M, Schneider O, Rückert C, Busche T, Kalinowski J, Bredholt H, Zotchev SB. Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products. Front Microbiol 2020; 11:437. [PMID: 32256483 PMCID: PMC7093587 DOI: 10.3389/fmicb.2020.00437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/02/2020] [Indexed: 01/25/2023] Open
Abstract
Actinomycete bacteria from marine environments represent a potential source for new antibiotics and anti-tumor drugs. Ten strains belonging to the genus Streptomyces isolated from the marine sponge Antho dichotoma collected at the bottom of the Trondheim fjord (Norway) were screened for antibiotic activity. Since only few isolates proved to be bioactive in the conditions tested, we decided to gain an insight into their biosynthetic potential using genome sequencing and analysis. Draft genomes were analyzed for the presence of secondary metabolite biosynthesis gene clusters (BGCs) using antiSMASH software. BGCs specifying both known and potentially novel secondary metabolites were identified, suggesting that these isolates might be sources for new bioactive compounds. The results of this analysis also implied horizontal transfer of several gene clusters between the studied isolates, which was especially evident for the lantibiotic- and thiopeptide-encoding BGCs. The latter implies the significance of particular secondary metabolites for the adaptation of Streptomyces to the spatially enclosed marine environments such as marine sponges. Two bioactive isolates, one showing activity against both yeast and Bacillus subtilis, and one only against yeast were analyzed in details, leading to the identification of cycloheximide, linearmycins, and echinomycins that are presumably responsible for the observed bioactivities.
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Affiliation(s)
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Olha Schneider
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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49
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Wang X, Gu Q, Breukink E. Non-lipid II targeting lantibiotics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183244. [PMID: 32126235 DOI: 10.1016/j.bbamem.2020.183244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, China
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.
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50
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Caetano T, van der Donk W, Mendo S. Bacteroidetes can be a rich source of novel lanthipeptides: The case study of Pedobacter lusitanus. Microbiol Res 2020; 235:126441. [PMID: 32109689 DOI: 10.1016/j.micres.2020.126441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022]
Abstract
Lanthipeptides are intriguing peptides known since 1928, the year of penicillin's discovery. At that time, they were known as lantibiotics due to their (methyl)lanthionine amino acids and antibacterial activity. Their body of knowledge expanded tremendously over the last few years. Our analysis reveals that Bacteroidetes has a high state of clusters encoding the biosynthesis of class I lanthipeptides. We show that some strains of Pedobacter have a number of LanBs/genome comparable to that of some Actinobacteria. The case study selected was Pedobacter lusitanus NL19. Its clusters identified encode LanBs associated with LanCs as well as orphan LanBs. The first are concomitant with LanT transporters typical of class II lanthipeptides (and not class I), making their clusters into a hybrid class I and class II type. So far, this kind of operon was described only once and is involved in the production of pinensins, the first lanthipeptide with antifungal activity. A particular feature of pinensins is their splitted LanBs and we found that these enzymes are also widely encoded in Bacteroides. The function of a high percentage of proteins predicted to play a role in the production of Pedobacter lanthipeptides is unknown. Other major fraction of these proteins is expected to be enrolled in signal-transduction pathways. We demonstrate that the occurrence of lanthipeptides clusters in the genomes of Gram-negative bacteria is higher than previously reported. More importantly, we show that their genetic background is highly diverse, which is an undeniable foreshadowing of novel peptide structures, biochemistry and biological function.
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Affiliation(s)
- Tânia Caetano
- Department of Biology and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Wilfred van der Donk
- Howard Hughes Medical Institute, Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, United States
| | - Sónia Mendo
- Department of Biology and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
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