1
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Yi Y, Liang L, de Jong A, Kuipers OP. A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems. Genomics 2024; 116:110880. [PMID: 38857812 DOI: 10.1016/j.ygeno.2024.110880] [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: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.
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Affiliation(s)
- Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | | | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands.
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2
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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3
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Luo XY, Hu CM, Yin Q, Zhang XM, Liu ZZ, Zhou CK, Zhang JG, Chen W, Yang YJ. Dual-Mechanism Peptide SR25 has Broad Antimicrobial Activity and Potential Application for Healing Bacteria-infected Diabetic Wounds. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401793. [PMID: 38874469 DOI: 10.1002/advs.202401793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/12/2024] [Indexed: 06/15/2024]
Abstract
The rise of antibiotic resistance poses a significant public health crisis, particularly due to limited antimicrobial options for the treatment of infections with Gram-negative pathogens. Here, an antimicrobial peptide (AMP) SR25 is characterized, which effectively kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism without detectable resistance. Meanwhile, an SR25-functionalized hydrogel is developed for the efficient treatment of infected diabetic wounds. SR25 is obtained through genome mining from an uncultured bovine enteric actinomycete named Nonomuraea Jilinensis sp. nov. Investigations reveal that SR25 has two independent cellular targets, disrupting bacterial membrane integrity and restraining the activity of succinate:quinone oxidoreductase (SQR). In a diabetic mice wound infection model, the SR25-incorporated hydrogel exhibits high efficacy against mixed infections of Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA), accelerating wound healing. Overall, these findings demonstrate the therapeutic potential of SR25 and highlight the value of mining drugs with multiple mechanisms from uncultured animal commensals for combating challenging bacterial pathogens.
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Affiliation(s)
- Xue-Yue Luo
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Chun-Mei Hu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Qi Yin
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Xiao-Mei Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Zhen-Zhen Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Cheng-Kai Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Jian-Gang Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Wei Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
| | - Yong-Jun Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin, 130062, P. R. China
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4
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Nuhamunada M, Mohite OS, Phaneuf P, Palsson B, Weber T. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res 2024; 52:5478-5495. [PMID: 38686794 PMCID: PMC11162802 DOI: 10.1093/nar/gkae314] [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: 06/29/2023] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.
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Affiliation(s)
- Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Patrick V Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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5
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MacIntyre LW, Koirala B, Rosenzweig A, Morales-Amador A, Brady SF. Cinnamosyn, a Cinnamoylated Synthetic-Bioinformatic Natural Product with Cytotoxic Activity. Org Lett 2024; 26:4433-4437. [PMID: 38767867 DOI: 10.1021/acs.orglett.4c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Most biosynthetic gene clusters (BGCs) are functionally inaccessible by using fermentation methods. Bioinformatic-coupled total synthesis provides an alternative approach for accessing BGC-encoded bioactivities. To date, synthetic bioinformatic natural product (synBNP) methods have focused on lipopeptides containing simple lipids. Here we increase the bioinformatic and synthetic complexity of the synBNP approach by targeting BGCs that encode N-cinnamoyl lipids. This led to our synthesis of cinnamosyn, a 10-mer N-cinnamoyl-containing peptide that is cytotoxic to human cells.
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Affiliation(s)
- Logan W MacIntyre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Bimal Koirala
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adam Rosenzweig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Adrián Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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6
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Wu S, Zhou H, Chen D, Lu Y, Li Y, Qiao J. Multi-omic analysis tools for microbial metabolites prediction. Brief Bioinform 2024; 25:bbae264. [PMID: 38859767 PMCID: PMC11165163 DOI: 10.1093/bib/bbae264] [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: 02/03/2024] [Revised: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
How to resolve the metabolic dark matter of microorganisms has long been a challenging problem in discovering active molecules. Diverse omics tools have been developed to guide the discovery and characterization of various microbial metabolites, which make it gradually possible to predict the overall metabolites for individual strains. The combinations of multi-omic analysis tools effectively compensates for the shortcomings of current studies that focus only on single omics or a broad class of metabolites. In this review, we systematically update, categorize and sort out different analysis tools for microbial metabolites prediction in the last five years to appeal for the multi-omic combination on the understanding of the metabolic nature of microbes. First, we provide the general survey on different updated prediction databases, webservers, or software that based on genomics, transcriptomics, proteomics, and metabolomics, respectively. Then, we discuss the essentiality on the integration of multi-omics data to predict metabolites of different microbial strains and communities, as well as stressing the combination of other techniques, such as systems biology methods and data-driven algorithms. Finally, we identify key challenges and trends in developing multi-omic analysis tools for more comprehensive prediction on diverse microbial metabolites that contribute to human health and disease treatment.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Haonan Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Danlei Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yutong Lu
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yanni Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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7
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Luo P, Huang JH, Lv JM, Wang GQ, Hu D, Gao H. Biosynthesis of fungal terpenoids. Nat Prod Rep 2024; 41:748-783. [PMID: 38265076 DOI: 10.1039/d3np00052d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.
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Affiliation(s)
- Pan Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
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8
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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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9
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Han T, Miao G. Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites. Molecules 2024; 29:2106. [PMID: 38731602 PMCID: PMC11085123 DOI: 10.3390/molecules29092106] [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: 03/08/2024] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.
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Affiliation(s)
- Taotao Han
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan 232038, China
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10
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Frey B, Aiesi M, Rast BM, Rüthi J, Julmi J, Stierli B, Qi W, Brunner I. Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach. PLoS One 2024; 19:e0300503. [PMID: 38578779 PMCID: PMC10997104 DOI: 10.1371/journal.pone.0300503] [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: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024] Open
Abstract
Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.
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Affiliation(s)
- Beat Frey
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Margherita Aiesi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Facoltà de Science Agrarie e Alimentari, University Degli Studi di Milano, Milano, Italy
| | - Basil M. Rast
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Joel Rüthi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jérôme Julmi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Ivano Brunner
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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11
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McBee DP, Hulsey ZN, Hedges MR, Baccile JA. Biological Demands and Toxicity of Isoprenoid Precursors in Bacillus Subtilis Through Cell-Permeant Analogs of Isopentenyl Pyrophosphate and Dimethylallyl Pyrophosphate. Chembiochem 2024:e202400064. [PMID: 38568158 DOI: 10.1002/cbic.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Bacterial isoprenoids are necessary for many biological processes, including maintaining membrane integrity, facilitating intercellular communication, and preventing oxidative damage. All bacterial isoprenoids are biosynthesized from two five carbon structural isomers, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are cell impermeant. Herein, we demonstrate exogenous delivery of IPP and DMAPP into Bacillus subtilis by utilizing a self-immolative ester (SIE)-caging approach. We initially evaluated native B. subtilis esterase activity, which revealed a preference for short straight chain esters. We then examined the viability of the SIE-caging approach in B. subtilis and demonstrate that the released caging groups are well tolerated and the released IPP and DMAPP are bioavailable, such that isoprenoid biosynthesis can be rescued in the presence of pathway inhibitors. We further show that IPP and DMAPP are both toxic and inhibit growth of B. subtilis at the same concentration. Lastly, we establish the optimal ratio of IPP to DMAPP (5 : 1) for B. subtilis growth and find that, surprisingly, DMAPP alone is insufficient to rescue isoprenoid biosynthesis under high concentrations of fosmidomycin. These findings showcase the potential of the SIE-caging approach in B. subtilis and promise to both aid in novel isoprenoid discovery and to inform metabolic engineering efforts in bacteria.
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Affiliation(s)
- Dillon P McBee
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Zackary N Hulsey
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Makayla R Hedges
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
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12
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Seo HW, Wassano NS, Amir Rawa MS, Nickles GR, Damasio A, Keller NP. A Timeline of Biosynthetic Gene Cluster Discovery in Aspergillus fumigatus: From Characterization to Future Perspectives. J Fungi (Basel) 2024; 10:266. [PMID: 38667937 PMCID: PMC11051388 DOI: 10.3390/jof10040266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
In 1999, the first biosynthetic gene cluster (BGC), synthesizing the virulence factor DHN melanin, was characterized in Aspergillus fumigatus. Since then, 19 additional BGCs have been linked to specific secondary metabolites (SMs) in this species. Here, we provide a comprehensive timeline of A. fumigatus BGC discovery and find that initial advances centered around the commonly expressed SMs where chemical structure informed rationale identification of the producing BGC (e.g., gliotoxin, fumigaclavine, fumitremorgin, pseurotin A, helvolic acid, fumiquinazoline). Further advances followed the transcriptional profiling of a ΔlaeA mutant, which aided in the identification of endocrocin, fumagillin, hexadehydroastechrome, trypacidin, and fumisoquin BGCs. These SMs and their precursors are the commonly produced metabolites in most A. fumigatus studies. Characterization of other BGC/SM pairs required additional efforts, such as induction treatments, including co-culture with bacteria (fumicycline/neosartoricin, fumigermin) or growth under copper starvation (fumivaline, fumicicolin). Finally, four BGC/SM pairs were discovered via overexpression technologies, including the use of heterologous hosts (fumicycline/neosartoricin, fumihopaside, sphingofungin, and sartorypyrone). Initial analysis of the two most studied A. fumigatus isolates, Af293 and A1160, suggested that both harbored ca. 34-36 BGCs. However, an examination of 264 available genomes of A. fumigatus shows up to 20 additional BGCs, with some strains showing considerable variations in BGC number and composition. These new BGCs present a new frontier in the future of secondary metabolism characterization in this important species.
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Affiliation(s)
- Hye-Won Seo
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Natalia S. Wassano
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Mira Syahfriena Amir Rawa
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
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13
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Arif Y, Mir AR, Zieliński P, Hayat S, Bajguz A. Microplastics and nanoplastics: Source, behavior, remediation, and multi-level environmental impact. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120618. [PMID: 38508005 DOI: 10.1016/j.jenvman.2024.120618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/21/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Plastics introduced into the natural environment persist, degrade, and fragment into smaller particles due to various environmental factors. Microplastics (MPs) (ranging from 1 μm to 5 mm) and nanoplastics (NPs) (less than 1 μm) have emerged as pollutants posing a significant threat to all life forms on Earth. Easily ingested by living organisms, they lead to ongoing bioaccumulation and biomagnification. This review summarizes existing studies on the sources of MPs and NPs in various environments, highlighting their widespread presence in air, water, and soil. It primarily focuses on the sources, fate, degradation, fragmentation, transport, and ecotoxicity of MPs and NPs. The aim is to elucidate their harmful effects on marine organisms, soil biota, plants, mammals, and humans, thereby enhancing the understanding of the complex impacts of plastic particles on the environment. Additionally, this review highlights remediation technologies and global legislative and institutional measures for managing waste associated with MPs and NPs. It also shows that effectively combating plastic pollution requires the synergization of diverse management, monitoring strategies, and regulatory measures into a comprehensive policy framework.
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Affiliation(s)
- Yamshi Arif
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Anayat Rasool Mir
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Piotr Zieliński
- Department of Water Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245, Bialystok, Poland
| | - Shamsul Hayat
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Andrzej Bajguz
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245, Bialystok, Poland.
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14
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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15
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Chioti VT, Clark KA, Ganley JG, Han EJ, Seyedsayamdost MR. N-Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster. J Am Chem Soc 2024; 146:7313-7323. [PMID: 38452252 PMCID: PMC11062405 DOI: 10.1021/jacs.3c11740] [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] [Indexed: 03/09/2024]
Abstract
DUF692 multinuclear iron oxygenases (MNIOs) are an emerging family of tailoring enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Three members, MbnB, TglH, and ChrH, have been characterized to date and shown to catalyze unusual and complex transformations. Using a co-occurrence-based bioinformatic search strategy, we recently generated a sequence similarity network of MNIO-RiPP operons that encode one or more MNIOs adjacent to a transporter. The network revealed >1000 unique gene clusters, evidence of an unexplored biosynthetic landscape. Herein, we assess an MNIO-RiPP cluster from this network that is encoded in Proteobacteria and Actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes a 23-residue precursor peptide, two MNIOs, a RiPP recognition element, and a transporter. Using both in vivo and in vitro methods, we show that one MNIO, homologous to MbnB, installs an oxazolone-thioamide at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO catalyzes N-Cα bond cleavage of the penultimate Asn to generate a C-terminally amidated peptide. This transformation expands the reaction scope of the enzyme family, marks the first example of an MNIO-catalyzed modification that does not involve Cys, and sets the stage for future exploration of other MNIO-RiPPs.
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Affiliation(s)
- Vasiliki T Chioti
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jack G Ganley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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16
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Zou Z, Ji Y, Schwaneberg U. Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2024; 63:e202310910. [PMID: 38081121 DOI: 10.1002/anie.202310910] [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: 07/31/2023] [Indexed: 12/23/2023]
Abstract
Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Yu Ji
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
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17
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Zhang Y, Feng L, Hemu X, Tan NH, Wang Z. OSMAC Strategy: A promising way to explore microbial cyclic peptides. Eur J Med Chem 2024; 268:116175. [PMID: 38377824 DOI: 10.1016/j.ejmech.2024.116175] [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: 09/18/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Microbial secondary metabolites are pivotal for the development of novel drugs. However, conventional culture techniques, have left a vast array of unexpressed biosynthetic gene clusters (BGCs) in microorganisms, hindering the discovery of metabolites with distinct structural features and diverse biological functions. To address this limitation, several innovative strategies have been emerged. The "One Strain Many Compounds" (OSMAC) strategy, which involves altering microbial culture conditions, has proven to be particularly effective in mining numerous novel secondary metabolites for the past few years. Among these, microbial cyclic peptides stand out. These peptides often comprise rare amino acids, unique chemical structures, and remarkable biological function. With the advancement of the OSMAC strategy, a plethora of new cyclic peptides have been identified from diverse microbial genera. This work reviews the progress in mining novel compounds using the OSMAC strategy and the applications of this strategy in discovering 284 microbial cyclic peptides from 63 endophytic strains, aiming to offer insights for the further explorations into novel active cyclic peptides.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Feng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xinya Hemu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ning-Hua Tan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Zhe Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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18
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Sonowal S, Gogoi U, Buragohain K, Nath R. Endophytic fungi as a potential source of anti-cancer drug. Arch Microbiol 2024; 206:122. [PMID: 38407579 DOI: 10.1007/s00203-024-03829-4] [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: 11/02/2023] [Revised: 12/24/2023] [Accepted: 01/01/2024] [Indexed: 02/27/2024]
Abstract
Endophytes are considered one of the major sources of bioactive compounds used in different aspects of health care including cancer treatment. When colonized, they either synthesize these bioactive compounds as a part of their secondary metabolite production or augment the host plant machinery in synthesising such bioactive compounds. Hence, the study of endophytes has drawn the attention of the scientific community in the last few decades. Among the endophytes, endophytic fungi constitute a major portion of endophytic microbiota. This review deals with a plethora of anti-cancer compounds derived from endophytic fungi, highlighting alkaloids, lignans, terpenes, polyketides, polyphenols, quinones, xanthenes, tetralones, peptides, and spirobisnaphthalenes. Further, this review emphasizes modern methodologies, particularly omics-based techniques, asymmetric dihydroxylation, and biotic elicitors, showcasing the dynamic and evolving landscape of research in this field and describing the potential of endophytic fungi as a source of anticancer drugs in the future.
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Affiliation(s)
- Sukanya Sonowal
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Urvashee Gogoi
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Kabyashree Buragohain
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Ratul Nath
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India.
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, 786004, India.
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19
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Sehnal L, Lo Presti L, Ziemert N. Discovering cryptic natural products by substrate manipulation. Nat Chem 2024; 16:149-151. [PMID: 38267538 DOI: 10.1038/s41557-023-01433-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Affiliation(s)
- Ludek Sehnal
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Libera Lo Presti
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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20
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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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21
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Kwon T, Hovde BT. Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures. Sci Rep 2024; 14:1534. [PMID: 38233413 PMCID: PMC10794256 DOI: 10.1038/s41598-023-50095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.
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Affiliation(s)
- Taehyung Kwon
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Blake T Hovde
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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22
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Blin K, Shaw S, Medema MH, Weber T. The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more. Nucleic Acids Res 2024; 52:D586-D589. [PMID: 37904617 PMCID: PMC10767862 DOI: 10.1093/nar/gkad984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Many microorganisms produce natural products that are frequently used in the development of medicines and crop protection agents. Genome mining has evolved into a prominent method to access this potential. antiSMASH is the most popular tool for this task. Here we present version 4 of the antiSMASH database, providing biosynthetic gene clusters detected by antiSMASH 7.1 in publicly available, dereplicated, high-quality microbial genomes via an interactive graphical user interface. In version 4, the database contains 231 534 high quality BGC regions from 592 archaeal, 35 726 bacterial and 236 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.
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Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, 6708PB, The Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
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23
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Silva SG, Nabhan Homsi M, Keller-Costa T, Rocha U, Costa R. Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon. mSystems 2023; 8:e0064323. [PMID: 38018967 PMCID: PMC10734526 DOI: 10.1128/msystems.00643-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.
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Affiliation(s)
- Sandra Godinho Silva
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Masun Nabhan Homsi
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Tina Keller-Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
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24
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Talukdar A, Kundu P, Bhattacharjee S, Dey S, Dey A, Biswas JK, Chaudhuri P, Bhattacharya S. Microplastics in mangroves with special reference to Asia: Occurrence, distribution, bioaccumulation and remediation options. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166165. [PMID: 37574065 DOI: 10.1016/j.scitotenv.2023.166165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/15/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Microplastics (MPs) are a new and lesser-known pollutant that has intrigued the interest of scientists all over the world in recent decades. MP (<5mm in size) can enter marine environments such as mangrove forests in a variety of ways, interfering with the health of the environment and organisms. Mangroves are now getting increasingly exposed to microplastic contamination due to their proximity to human activities and their position as critical transitional zones between land and sea. The present study reviews the status of MPs contamination specifically in mangrove ecosystems situated in Asia. Different sources and characteristics of MPs, subsequent deposition of MPs in mangrove water and sediments, bioaccumulation in different organisms are discussed in this context. MP concentrations in sediments and organisms were higher in mangrove forests exposed to fishing, coastal tourism, urban, and industrial wastewater than in pristine areas. The distribution of MPs varies from organism to organism in mangrove ecosystems, and is significantly influenced by their morphometric characteristics, feeding habits, dwelling environment etc. Mangrove plants can accumulate microplastics in their roots, stem and leaves through absorption, adsorption and entrapment helping in reducing abundance of microplastic in the surrounding environment. Several bacterial and fungal species are reported from these mangrove ecosystems, which are capable of degrading MPs. The bioremediation potential of mangrove plants offers an innovative and sustainable approach to mitigate microplastic pollution. Diverse mechanisms of MP biodegradation by mangrove dwelling organisms are discussed in this context. Biotechnological applications can be utilized to explore the genetic potential of the floral and faunal species found in the Asian mangroves. Detailed studies are required to monitor, control, and evaluate MP pollution in sediments and various organisms in mangrove ecosystems in Asia as well as in other parts of the world.
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Affiliation(s)
| | - Pritha Kundu
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India
| | - Shrayan Bhattacharjee
- Ecosystem and Ecology Laboratory, Post-graduate Department of Zoology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India
| | - Satarupa Dey
- Department of Botany, Shyampur Siddheswari Mahavidyalaya, Howrah 711301, West Bengal, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Jayanta Kumar Biswas
- Enviromicrobiology, Ecotoxicology & Ecotechnology Research Laboratory (3E-MicroToxTech Lab), Department of Ecological Studies, and International Centre for Ecological Engineering, University of Kalyani, Nadia, West Bengal 741235, India
| | - Punarbasu Chaudhuri
- Department of Environmental Science, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Sayan Bhattacharya
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India.
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25
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Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
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Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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26
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Wang X, Hu S, Wang J, Zhang T, Ye K, Wen A, Zhu G, Vegas A, Zhang L, Yan W, Liu X, Liu P. Biochemical and Structural Characterization of OvoA Th2: A Mononuclear Nonheme Iron Enzyme from Hydrogenimonas thermophila for Ovothiol Biosynthesis. ACS Catal 2023; 13:15417-15426. [PMID: 38058600 PMCID: PMC10696552 DOI: 10.1021/acscatal.3c04026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Ovothiol A and ergothioneine are thiol-histidine derivatives with sulfur substitutions at the δ-carbon or ε-carbon of the l-histidine imidazole ring, respectively. Both ovothiol A and ergothioneine have protective effects on many aging-related diseases, and the sulfur substitution plays a key role in determining their chemical and biological properties, while factors governing sulfur incorporation regioselectivities in ovothiol and ergothioneine biosynthesis in the corresponding enzymes (OvoA, Egt1, or EgtB) are not yet known. In this study, we have successfully obtained the first OvoA crystal structure, which provides critical information to explain their C-S bond formation regioselectivity. Furthermore, OvoATh2 exhibits several additional activities: (1) ergothioneine sulfoxide synthase activity akin to Egt1 in ergothioneine biosynthesis; (2) cysteine dioxygenase activity using l-cysteine and l-histidine analogues as substrates; (3) cysteine dioxygenase activity upon mutation of an active site tyrosine residue (Y406). The structural insights and diverse chemistries demonstrated by OvoATh2 pave the way for future comprehensive structure-function correlation studies.
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Affiliation(s)
- Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Sha Hu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Tao Zhang
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Ke Ye
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Aiwen Wen
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Arturo Vegas
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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27
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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28
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Zhou Z, Zhuo L, Fu X, Zou Q. Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs. Brief Bioinform 2023; 25:bbad483. [PMID: 38171927 PMCID: PMC10764208 DOI: 10.1093/bib/bbad483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Exploring microbial stress responses to drugs is crucial for the advancement of new therapeutic methods. While current artificial intelligence methodologies have expedited our understanding of potential microbial responses to drugs, the models are constrained by the imprecise representation of microbes and drugs. To this end, we combine deep autoencoder and subgraph augmentation technology for the first time to propose a model called JDASA-MRD, which can identify the potential indistinguishable responses of microbes to drugs. In the JDASA-MRD model, we begin by feeding the established similarity matrices of microbe and drug into the deep autoencoder, enabling to extract robust initial features of both microbes and drugs. Subsequently, we employ the MinHash and HyperLogLog algorithms to account intersections and cardinality data between microbe and drug subgraphs, thus deeply extracting the multi-hop neighborhood information of nodes. Finally, by integrating the initial node features with subgraph topological information, we leverage graph neural network technology to predict the microbes' responses to drugs, offering a more effective solution to the 'over-smoothing' challenge. Comparative analyses on multiple public datasets confirm that the JDASA-MRD model's performance surpasses that of current state-of-the-art models. This research aims to offer a more profound insight into the adaptability of microbes to drugs and to furnish pivotal guidance for drug treatment strategies. Our data and code are publicly available at: https://github.com/ZZCrazy00/JDASA-MRD.
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Affiliation(s)
- Zhecheng Zhou
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, 325000, Wenzhou, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, 325000, Wenzhou, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, 410012, Changsha, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 611730, Chengdu, China
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29
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Riera N, Davyt D, Durán R, Iraola G, Lemanceau P, Bajsa N. An antibiotic produced by Pseudomonas fluorescens CFBP2392 with antifungal activity against Rhizoctonia solani. Front Microbiol 2023; 14:1286926. [PMID: 38033591 PMCID: PMC10682437 DOI: 10.3389/fmicb.2023.1286926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Pseudomonas fluorescens CFBP2392 has been recognized as a potential biocontrol agent due to its ability to suppress damping-off and root rot disease. This isolate has antibacterial activity in vitro as many other strains from the Pseudomonas fluorescens complex. In this work, the antibacterial and antifungal activity of the strain were explored. Dual culture assays evidenced the antifungal activity of the strain against different phytopathogens: Alternaria sp., Pythium ultimun, Fusarium oxysporum, and Rhizoctonia solani. Purification of an antifungal fraction was performed by preparative HPLC from the chemical extraction of growth media. The fraction showed altered R. solani growth and ultrastructure. Transmission electron microscopy revealed the purified compound induced hypertrophied mitochondria, membranous vesicles, and a higher number of vacuoles in R. salani cytoplasm. In addition, co-cultivation of P. fluorescens CFBP2392 with R. solani resulted in an enlarged and deformed cell wall. To gain genomic insights on this inhibition, the complete genome of P. fluorescens CFBP2392 was obtained with Oxford Nanopore technology. Different biosynthetic gene clusters (BGCs) involved in specialized metabolites production including a lokisin-like and a koreenceine-like cluster were identified. In accordance with the putative BGCs identified, sequence phylogeny analysis of the MacB transporter in the lokisin-like cluster further supports the similarity with other transporters from the amphisin family. Our results give insights into the cellular effects of the purified microbial metabolite in R. solani ultrastructure and provide a genomic background to further explore the specialized metabolite potential.
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Affiliation(s)
- Nadia Riera
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Danilo Davyt
- Laboratorio de Química Farmacéutica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Rosario Durán
- Unidad Mixta de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Gregorio Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Philippe Lemanceau
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne—Université de Bourgogne Franche-Comté, Dijon, France
| | - Natalia Bajsa
- Laboratorio de Ecología Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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30
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Hibbard T, McLellan RM, Stevenson LJ, Richardson AT, Nicholson MJ, Parker EJ. Functional Crosstalk between Discrete Indole Terpenoid Gene Clusters in Tolypocladium album. Org Lett 2023; 25:7470-7475. [PMID: 37797949 PMCID: PMC10595974 DOI: 10.1021/acs.orglett.3c02412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 10/07/2023]
Abstract
Indole terpenoids make up a large group of secondary metabolites that display an enticing array of bioactivities. While indole diterpene (IDT) and rarely indole sesquiterpene (IST) pathways have been found individually in filamentous fungi, here we show that both cluster types are encoded within the genome of Tolypocladium album. Through heterologous reconstruction, we demonstrate the SES cluster encodes for IST biosynthesis and can tailor IDT substrates produced by the TER cluster.
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Affiliation(s)
- Taylor
R. Hibbard
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Rose M. McLellan
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Luke J. Stevenson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Alistair T. Richardson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Matthew J. Nicholson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Wellington
UniVentures, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Emily J. Parker
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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31
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Cumsille A, Serna-Cardona N, González V, Claverías F, Undabarrena A, Molina V, Salvà-Serra F, Moore ERB, Cámara B. Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution. BMC Genomics 2023; 24:622. [PMID: 37858045 PMCID: PMC10588199 DOI: 10.1186/s12864-023-09694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
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Affiliation(s)
- Andrés Cumsille
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Néstor Serna-Cardona
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina González
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Fernanda Claverías
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Agustina Undabarrena
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Vania Molina
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Beatriz Cámara
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile.
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32
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Miranda KJ, Jaber S, Atoum D, Arjunan S, Ebel R, Jaspars M, Edrada-Ebel R. Pseudomonassin, a New Bioactive Ribosomally Synthesised and Post-Translationally Modified Peptide from Pseudomonas sp. SST3. Microorganisms 2023; 11:2563. [PMID: 37894221 PMCID: PMC10609385 DOI: 10.3390/microorganisms11102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Genome mining and metabolomics have become valuable tools in natural products research to evaluate and identify potential new chemistry from bacteria. In the search for new compounds from the deep-sea organism, Pseudomonas sp. SST3, from the South Shetland Trough, Antarctica, a co-cultivation with a second deep-sea Pseudomonas zhaodongensis SST2, was undertaken to isolate pseudomonassin, a ribosomally synthesised and post-translationally modified peptide (RiPP) that belongs to a class of RiPP called lasso peptides. Pseudomonassin was identified using a genome-mining approach and isolated by means of mass spectrometric guided isolation. Extensive metabolomics analysis of the co-cultivation of Pseudomonas sp. SST3 and P. zhaodongensis SST2, Pseudomonas sp. SST3 and Escherichia coli, and P. zhaodongensis SST2 and E. coli were performed using principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA), which revealed potential new metabolites in the outlier regions of the co-cultivation, with other metabolites identified previously from other species of Pseudomonas. The sequence of pseudomonassin was completely deduced using high collision dissociation tandem mass spectrometry (HCD-MS/MS). Preliminary studies on its activity against the pathogenic P. aeruginosa and its biofilm formation have been assessed and produced a minimum inhibitory concentration (MIC) of 63 μg/mL and 28 μg/mL, respectively.
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Affiliation(s)
- Kevin Jace Miranda
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
- College of Pharmacy and Graduate School, Adamson University, 900 San Marcelino Street, Ermita, Manila 1000, Philippines
| | - Saif Jaber
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (S.J.); (R.E.-E.)
| | - Dana Atoum
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Subha Arjunan
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (S.J.); (R.E.-E.)
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33
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Manochkumar J, Cherukuri AK, Kumar RS, Almansour AI, Ramamoorthy S, Efferth T. A critical review of machine-learning for "multi-omics" marine metabolite datasets. Comput Biol Med 2023; 165:107425. [PMID: 37696182 DOI: 10.1016/j.compbiomed.2023.107425] [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: 05/30/2023] [Revised: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.
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Affiliation(s)
- Janani Manochkumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Aswani Kumar Cherukuri
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014, India
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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34
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Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat Biotechnol 2023; 41:1416-1423. [PMID: 36782070 PMCID: PMC10423304 DOI: 10.1038/s41587-023-01675-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2023] [Indexed: 02/15/2023]
Abstract
The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
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Affiliation(s)
| | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Changzhou Medical Center, Nanjing Medical University, Changzhou, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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35
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Covas C, Figueiredo G, Gomes M, Santos T, Mendo S, Caetano TS. The Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential. Microorganisms 2023; 11:2445. [PMID: 37894103 PMCID: PMC10609062 DOI: 10.3390/microorganisms11102445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard, Pedobacter spp. have recently gained attention, not only for their role as plant growth promoters but also for their potential in producing antimicrobials. This study focuses on the genomic analysis of Pedobacter spp. to unveil the diversity of the SMs encoded in their genomes. Among the 41 genomes analyzed, a total of 233 biosynthetic gene clusters (BGCs) were identified, revealing the potential for the production of diverse SMs, including RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Overall, BGC distribution did not correlate with phylogenetic lineage and most of the BGCs showed no significant hits in the MIBiG database, emphasizing the uniqueness of the compounds that Pedobacter spp. can produce. Of all the species examined, P. cryoconitis and P. lusitanus stood out for having the highest number and diversity of BGCs. Focusing on their applicability and ecological functions, we investigated in greater detail the BGCs responsible for siderophore and terpenoid production in these species and their relatives. Our findings suggest that P. cryoconitis and P. lusitanus have the potential to produce novel mixtures of siderophores, involving bifunctional IucAC/AcD NIS synthetases, as well as carotenoids and squalene. This study highlights the biotechnological potential of Pedobacter spp. in medicine, agriculture and other industries, emphasizing the need for a continued exploration of its SMs and their applications.
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Affiliation(s)
| | | | | | | | | | - Tânia S. Caetano
- CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.C.); (G.F.); (S.M.)
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36
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Sharma A, Singh RN, Song XP, Singh RK, Guo DJ, Singh P, Verma KK, Li YR. Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery. Front Microbiol 2023; 14:1229955. [PMID: 37808307 PMCID: PMC10556750 DOI: 10.3389/fmicb.2023.1229955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023] Open
Abstract
Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely "Squalene." Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.
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Affiliation(s)
- Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- State Key Laboratory of Conservation and Utilization of Subtropical, College of Agriculture, Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement, Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXXAS), Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- State Key Laboratory of Conservation and Utilization of Subtropical, College of Agriculture, Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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38
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Dong H, Ming D. A Comprehensive Self-Resistance Gene Database for Natural-Product Discovery with an Application to Marine Bacterial Genome Mining. Int J Mol Sci 2023; 24:12446. [PMID: 37569821 PMCID: PMC10419868 DOI: 10.3390/ijms241512446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
In the world of microorganisms, the biosynthesis of natural products in secondary metabolism and the self-resistance of the host always occur together and complement each other. Identifying resistance genes from biosynthetic gene clusters (BGCs) helps us understand the self-defense mechanism and predict the biological activity of natural products synthesized by microorganisms. However, a comprehensive database of resistance genes is still lacking, which hinders natural product annotation studies in large-scale genome mining. In this study, we compiled a resistance gene database (RGDB) by scanning the four available databases: CARD, MIBiG, NCBIAMR, and UniProt. Every resistance gene in the database was annotated with resistance mechanisms and possibly involved chemical compounds, using manual annotation and transformation from the resource databases. The RGDB was applied to analyze resistance genes in 7432 BGCs in 1390 genomes from a marine microbiome project. Our calculation showed that the RGDB successfully identified resistance genes for more than half of the BGCs, suggesting that the database helps prioritize BGCs that produce biologically active natural products.
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Affiliation(s)
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing 211816, China
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Qiu S, Yang A, Zeng H. Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook. PLoS Comput Biol 2023; 19:e1011391. [PMID: 37619239 PMCID: PMC10449171 DOI: 10.1371/journal.pcbi.1011391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.
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Affiliation(s)
- Sizhe Qiu
- School of Food and Health, Beijing Technology and Business University, Bejing, China
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Hong Zeng
- School of Food and Health, Beijing Technology and Business University, Bejing, China
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40
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Zdouc MM, van der Hooft JJJ, Medema MH. Metabolome-guided genome mining of RiPP natural products. Trends Pharmacol Sci 2023; 44:532-541. [PMID: 37391295 DOI: 10.1016/j.tips.2023.06.004] [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: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a chemically diverse class of metabolites. Many RiPPs show potent biological activities that make them attractive starting points for drug development. A promising approach for the discovery of new classes of RiPPs is genome mining. However, the accuracy of genome mining is hampered by the lack of signature genes shared across different RiPP classes. One way to reduce false-positive predictions is by complementing genomic information with metabolomics data. In recent years, several new approaches addressing such integrative genomics and metabolomics analyses have been developed. In this review, we provide a detailed discussion of RiPP-compatible software tools that integrate paired genomics and metabolomics data. We highlight current challenges in data integration and identify opportunities for further developments targeting new classes of bioactive RiPPs.
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Affiliation(s)
- Mitja M Zdouc
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands; Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.
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41
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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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42
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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43
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Wang X, Zhou N, Wang B. Bacterial synthetic biology: tools for novel drug discovery. Expert Opin Drug Discov 2023; 18:1087-1097. [PMID: 37482696 DOI: 10.1080/17460441.2023.2239704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
INTRODUCTION Bacterial synthetic biology has provided powerful tools to revolutionize the drug discovery process. These tools can be harnessed to generate bacterial novel pharmaceutical compounds with enhanced bioactivity and selectivity or to create genetically modified microorganisms as living drugs. AREAS COVERED This review provides a current overview of the state-of-the-art in bacterial synthetic biology tools for novel drug discovery. The authors discuss the application of these tools including bioinformatic tools, CRISPR tools, engineered bacterial transcriptional regulators, and synthetic biosensors for novel drug discovery. Additionally, the authors present the recent progress on reprogramming bacteriophages as living drugs to fight against antibiotic-resistant pathogens. EXPERT OPINION The field of using bacterial synthetic biology tools for drug discovery is rapidly advancing. However, challenges remain in developing reliable and robust methods to engineer bacteria. Further advancements in synthetic biology hold promise to speed up drug discovery, facilitating the development of novel therapeutics against various diseases.
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Affiliation(s)
- Xiyan Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Nan Zhou
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, China
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44
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Santiago BCF, de Souza ID, Cavalcante JVF, Morais DAA, da Silva MB, Pasquali MADB, Dalmolin RJS. Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions. Microorganisms 2023; 11:1668. [PMID: 37512841 PMCID: PMC10386303 DOI: 10.3390/microorganisms11071668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.
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Affiliation(s)
- Bianca C F Santiago
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Iara D de Souza
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - João Vitor F Cavalcante
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Mikaelly B da Silva
- Food Engineering Department, Federal University of Campina Grande, Campina Grande 58401-490, Brazil
| | | | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
- Department of Biochemistry-CB, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
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45
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Rios-Martinez C, Bhattacharya N, Amini AP, Crawford L, Yang KK. Deep self-supervised learning for biosynthetic gene cluster detection and product classification. PLoS Comput Biol 2023; 19:e1011162. [PMID: 37220151 DOI: 10.1371/journal.pcbi.1011162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 05/07/2023] [Indexed: 05/25/2023] Open
Abstract
Natural products are chemical compounds that form the basis of many therapeutics used in the pharmaceutical industry. In microbes, natural products are synthesized by groups of colocalized genes called biosynthetic gene clusters (BGCs). With advances in high-throughput sequencing, there has been an increase of complete microbial isolate genomes and metagenomes, from which a vast number of BGCs are undiscovered. Here, we introduce a self-supervised learning approach designed to identify and characterize BGCs from such data. To do this, we represent BGCs as chains of functional protein domains and train a masked language model on these domains. We assess the ability of our approach to detect BGCs and characterize BGC properties in bacterial genomes. We also demonstrate that our model can learn meaningful representations of BGCs and their constituent domains, detect BGCs in microbial genomes, and predict BGC product classes. These results highlight self-supervised neural networks as a promising framework for improving BGC prediction and classification.
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Affiliation(s)
- Carolina Rios-Martinez
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Nicholas Bhattacharya
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
- Department of Mathematics, University of California, Berkeley, Berkeley, California, United States of America
| | - Ava P Amini
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Lorin Crawford
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Kevin K Yang
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
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46
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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47
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Yılmaz TM, Mungan MD, Berasategui A, Ziemert N. FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. Nucleic Acids Res 2023:7173779. [PMID: 37207330 DOI: 10.1093/nar/gkad386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
There is an urgent need to diversify the pipeline for discovering novel natural products due to the increase in multi-drug resistant infections. Like bacteria, fungi also produce secondary metabolites that have potent bioactivity and rich chemical diversity. To avoid self-toxicity, fungi encode resistance genes which are often present within the biosynthetic gene clusters (BGCs) of the corresponding bioactive compounds. Recent advances in genome mining tools have enabled the detection and prediction of BGCs responsible for the biosynthesis of secondary metabolites. The main challenge now is to prioritize the most promising BGCs that produce bioactive compounds with novel modes of action. With target-directed genome mining methods, it is possible to predict the mode of action of a compound encoded in an uncharacterized BGC based on the presence of resistant target genes. Here, we introduce the 'fungal bioactive compound resistant target seeker' (FunARTS) available at https://funarts.ziemertlab.com. This is a specific and efficient mining tool for the identification of fungal bioactive compounds with interesting and novel targets. FunARTS rapidly links housekeeping and known resistance genes to BGC proximity and duplication events, allowing for automated, target-directed mining of fungal genomes. Additionally, FunARTS generates gene cluster networking by comparing the similarity of BGCs from multi-genomes.
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Affiliation(s)
- Turgut Mesut Yılmaz
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mehmet Direnç Mungan
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Aileen Berasategui
- University of Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Nadine Ziemert
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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48
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Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023:7151336. [PMID: 37140036 DOI: 10.1093/nar/gkad344] [Citation(s) in RCA: 245] [Impact Index Per Article: 245.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Microorganisms produce small bioactive compounds as part of their secondary or specialised metabolism. Often, such metabolites have antimicrobial, anticancer, antifungal, antiviral or other bio-activities and thus play an important role for applications in medicine and agriculture. In the past decade, genome mining has become a widely-used method to explore, access, and analyse the available biodiversity of these compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org/) has supported researchers in their microbial genome mining tasks, both as a free to use web server and as a standalone tool under an OSI-approved open source licence. It is currently the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in archaea, bacteria, and fungi. Here, we present the updated version 7 of antiSMASH. antiSMASH 7 increases the number of supported cluster types from 71 to 81, as well as containing improvements in the areas of chemical structure prediction, enzymatic assembly-line visualisation and gene cluster regulation.
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Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Hannah E Augustijn
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics. Frankfurt am Main, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Artem Fetter
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - William W Metcalf
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics. Frankfurt am Main, Germany
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs.Lyngby, Denmark
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49
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Yee DA, Niwa K, Perlatti B, Chen M, Li Y, Tang Y. Genome mining for unknown-unknown natural products. Nat Chem Biol 2023; 19:633-640. [PMID: 36702957 PMCID: PMC10159913 DOI: 10.1038/s41589-022-01246-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/20/2022] [Indexed: 01/27/2023]
Abstract
Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. Here we focused on a conserved fungal biosynthetic pathway that lacks a canonical core enzyme and used heterologous expression to identify the associated natural product, a highly modified cyclo-arginine-tyrosine dipeptide. Biochemical characterization of the pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein and has no sequence homology to non-ribosomal peptide synthetase or bacterial cyclodipeptide synthase. RCDPS homologs are widely encoded in fungal genomes; other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides, and characterization of a cyclo-arginine-tryptophan RCDPS showed that the enzyme is aminoacyl-tRNA dependent. Further characterization of the biosynthetic pathway led to discovery of new compounds whose structures would not have been predicted without knowledge of RCDPS function.
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Affiliation(s)
- Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Kanji Niwa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bruno Perlatti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Yuqing Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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50
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Luo C, Chen M, Luo K, Yin X, Onchari MM, Wang X, Zhang J, Zhong H, Tian B. Genome Sequencing and Genetic Engineering Reveal the Contribution of Bacitracin Produced by Bacillus paralicheniformis CPL618 to Anti-Staphylococcus aureus Activity. Curr Microbiol 2023; 80:135. [PMID: 36913050 DOI: 10.1007/s00284-023-03196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/19/2023] [Indexed: 03/14/2023]
Abstract
Staphylococcus aureus is one of the important pathogens causing human diseases, especially its treatment has great challenges due to its resistance to methicillin and vancomycin. The Bacillus strains are known to be major sources of second metabolites that can function as drugs. Therefore, it is of great value to excavate metabolites with good inhibitory activity against S. aureus from Bacillus strains. In this study, a strain Bacillus paralicheniformis CPL618 with good antagonistic activity against S. aureus was isolated and genome analysis showed that the size was 4,447,938 bp and contained four gene clusters fen, bac, dhb, and lch which are potentially responsible for four cyclic peptides fengycin, bacitracin, bacillibactin, and lichenysin biosynthesis, respectively. These gene clusters were knockout by homologous recombination. The bacteriostatic experiment results showed that the antibacterial activity of ∆bac decreased 72.3% while Δfen, Δdhb, and ΔlchA did not significantly changed as that of wild type. Interestingly, the maximum bacitracin yield was up to 92 U/mL in the LB medium, which was extremely unusual in wild type strains. To further improve the production of bacitracin, transcription regulators abrB and lrp were knocked out, the bacitracin produced by ΔabrB, Δlrp, and ΔabrB + lrp was 124 U/mL, 112 U/mL, and 160 U/ml, respectively. Although no new anti-S. aureus compounds was found by using genome mining in this study, the molecular mechanisms of high yield of bacitracin and anti-S. aureus in B. paralicheniformis CPL618 were clarified. Moreover, B. paralicheniformis CPL618 was further genetically engineered for industrial production of bacitracin.
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Affiliation(s)
- Chuping Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China.
| | - Meilin Chen
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Kecheng Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Xiulian Yin
- Key Laboratory for Palygorskite Science and Applied Technology of Jiangsu Province, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Mary M Onchari
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Xiaohua Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Jinfeng Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Haijing Zhong
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China
| | - Baoxia Tian
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin, Institute of Technology, Huaian, 223003, China.
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