201
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p-Aminophenylalanine Involved in the Biosynthesis of Antitumor Dnacin B1 for Quinone Moiety Formation. Molecules 2020; 25:molecules25184186. [PMID: 32932689 PMCID: PMC7570522 DOI: 10.3390/molecules25184186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/04/2022] Open
Abstract
Actinosynnema species produce diverse natural products with important biological activities, which represent an important resource of antibiotic discovery. Advances in genome sequencing and bioinformatics tools have accelerated the exploration of the biosynthetic gene clusters (BGCs) encoding natural products. Herein, the completed BGCs of dnacin B1 were first discovered in two Actinosynnema pretiosum subsp. auranticum strains DSM 44131T (hereafter abbreviated as strain DSM 44131T) and X47 by comparative genome mining strategy. The BGC for dnacin B1 contains 41 ORFs and spans a 66.9 kb DNA region in strain DSM 44131T. Its involvement in dnacin B1 biosynthesis was identified through the deletion of a 9.7 kb region. Based on the functional gene analysis, we proposed the biosynthetic pathway for dnacin B1. Moreover, p-amino-phenylalanine (PAPA) unit was found to be the dnacin B1 precursor for the quinone moiety formation, and this was confirmed by heterologous expression of dinV, dinE and dinF in Escherichia coli. Furthermore, nine potential PAPA aminotransferases (APAT) from the genome of strain DSM 44131T were explored and expressed. Biochemical evaluation of their amino group transformation ability was carried out with p-amino-phenylpyruvic acid (PAPP) or PAPA as the substrate for the final product formation. Two of those, APAT4 and APAT9, displayed intriguing aminotransferase ability for the formation of PAPA. The proposed dnacin B1 biosynthetic machinery and PAPA biosynthetic investigations not only enriched the knowledge of tetrahydroisoquinoline (THIQ) biosynthesis, but also provided PAPA building blocks to generate their structurally unique homologues.
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202
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Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
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203
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Lee AJ, Einarsson GG, Gilpin DF, Tunney MM. Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis? Front Pharmacol 2020; 11:569821. [PMID: 33013411 PMCID: PMC7509435 DOI: 10.3389/fphar.2020.569821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
The advent of high-throughput multi-omics technologies has underpinned the expansion in lung microbiome research, increasing our understanding of the nature, complexity and significance of the polymicrobial communities harbored by people with CF (PWCF). Having established that structurally complex microbial communities exist within the airways, the focus of recent research has now widened to investigating the function and dynamics of the resident microbiota during disease as well as in health. With further refinement, multi-omics approaches present the opportunity to untangle the complex interplay between microbe-microbe and microbe-host interactions in the lung and the relationship with respiratory disease progression, offering invaluable opportunities to discover new therapeutic approaches for our management of airway infection in CF.
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Affiliation(s)
- Andrew J. Lee
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Gisli G. Einarsson
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Deirdre F. Gilpin
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| | - Michael M. Tunney
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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204
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Kusuma AB, Nouioui I, Klenk HP, Goodfellow M. Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil. Int J Syst Evol Microbiol 2020; 70:4874-4882. [PMID: 32821037 PMCID: PMC7656270 DOI: 10.1099/ijsem.0.004346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/06/2020] [Indexed: 01/17/2023] Open
Abstract
A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces. Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus, Streptomyces griseomycini, Streptomyces griseostramineus, Streptomyces labedae, Streptomyces lomondensis and Streptomyces spinoverrucosus. A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA-DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.
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Affiliation(s)
- Ali Budhi Kusuma
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Indonesian Centre for Extremophile Bioresources and Biotechnology (ICEBB), Faculty of Biotechnology, Sumbawa University of Technology, Sumbawa Besar, 84371, Indonesia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Leibniz-Institut DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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205
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Zhong Z, He B, Li J, Li YX. Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). Synth Syst Biotechnol 2020; 5:155-172. [PMID: 32637669 PMCID: PMC7327761 DOI: 10.1016/j.synbio.2020.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity. Recent advances in genomics and synthetic biology, are facilitating us to discover a large number of new ribosomal natural products, including lanthipeptides, lasso peptides, sactipeptides, thiopeptides, microviridins, cyanobactins, linear thiazole/oxazole-containing peptides and so on. In this review, we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters (BGCs) encoding RiPPs, and the genome mining-guided discovery of novel RiPPs. We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future, especially the discovery of RiPPs from dominant but uncultivated microbes, which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.
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Affiliation(s)
- Zheng Zhong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Beibei He
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
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206
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Newman DJ, Cragg GM. Plant Endophytes and Epiphytes: Burgeoning Sources of Known and "Unknown" Cytotoxic and Antibiotic Agents? PLANTA MEDICA 2020; 86:891-905. [PMID: 32023633 DOI: 10.1055/a-1095-1111] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In the last 20 or so years, the influence of endophytes and, quite recently, epiphytes of plants upon the compounds found in those plants, which were usually assumed to be phytochemicals produced by the plant for a variety of reasons, often as a defense against predators, is becoming more evident, in particular in the case of antitumor agents originally isolated from plant sources, though antibiotic agents might also be found, particularly from epiphytes. In this review, we started with the first report in 1993 of a taxol-producing endophyte and then expanded the compounds discussed to include camptothecin, the vinca alkaloids, podophyllotoxin, and homoharringtonine from endophytic microbes and then the realization that maytansine is not a plant secondary metabolite at all, and that even such a well-studied plant such as Arabidopsis thaliana has a vast repertoire of potential bioactive agents in its leaf epiphytic bacteria. We have taken data from a variety of sources, including a reasonable history of these discoveries that were not given in recent papers by us, nor in other papers covering this topic. The sources included the Scopus database, but we also performed other searches using bibliographic tools, thus, the majority of the papers referenced are the originals, though we note some very recent papers that have built on previous results. We concluded with a discussion of the more modern techniques that can be utilized to "persuade" endophytes and epiphytes to switch on silent biosynthetic pathways and how current analytical techniques may aid in evaluating such programs. We also comment at times on some findings, particularly in the case of homoharringtonine, where there are repetitious data reports differing by a few years claiming the same endophyte as the producer.
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Affiliation(s)
- David J Newman
- NIH Special Volunteer, NCI Natural Products Branch, Wayne, PA, USA
| | - Gordon M Cragg
- NIH Special Volunteer, NCI Natural Products Branch, Gaithersburg, MD, USA
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207
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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208
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Raps FC, Fäseke VC, Häussinger D, Sparr C. Catalyst‐Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides. Angew Chem Int Ed Engl 2020; 59:18390-18394. [DOI: 10.1002/anie.202005733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Daniel Häussinger
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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209
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Zwick CR, Renata H. Harnessing the biocatalytic potential of iron- and α-ketoglutarate-dependent dioxygenases in natural product total synthesis. Nat Prod Rep 2020; 37:1065-1079. [PMID: 32055818 PMCID: PMC7426249 DOI: 10.1039/c9np00075e] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to the end of 2019Iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGs) represent a versatile and intriguing enzyme family by virtue of their ability to directly functionalize unactivated C-H bonds at the cost of αKG and O2. Fe/αKGs play an important role in the biosynthesis of natural products, valuable biologically active secondary metabolites frequently pursued as drug leads. The field of natural product total synthesis seeks to contruct these molecules as effeciently as possible, although natural products continue to challenge chemists due to their intricate structural complexity. Chemoenzymatic approaches seek to remedy the shortcomings of traditional synthetic methodology by combining Nature's biosynthetic machinery with traditional chemical methods to efficiently construct natural products. Although other oxygenase families have been widely employed for this purpose, Fe/αKGs remain underutilized. The following review will cover recent chemoenzymatic total syntheses involving Fe/αKG enzymes. Additionally, related information involving natural product biosynthesis, methods development, and non-chemoenzymatic total syntheses will be discussed to inform retrosynthetic logic and synthetic design.
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Affiliation(s)
- Christian R Zwick
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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210
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From Ocean to Medicine: Pharmaceutical Applications of Metabolites from Marine Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9080455. [PMID: 32731464 PMCID: PMC7460513 DOI: 10.3390/antibiotics9080455] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/17/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022] Open
Abstract
Oceans cover seventy percent of the planet's surface and besides being an immense reservoir of biological life, they serve as vital sources for human sustenance, tourism, transport and commerce. Yet, it is estimated by the National Oceanic and Atmospheric Administration (NOAA) that eighty percent of the oceans remain unexplored. The untapped biological resources present in oceans may be fundamental in solving several of the world's public health crises of the 21st century, which span from the rise of antibiotic resistance in bacteria, pathogenic fungi and parasites, to the rise of cancer incidence and viral infection outbreaks. In this review, health risks as well as how marine bacterial derived natural products may be tools to fight them will be discussed. Moreover, an overview will be made of the research pipeline of novel molecules, from identification of bioactive bacterial crude extracts to the isolation and chemical characterization of the molecules within the framework of the One Health approach. This review highlights information that has been published since 2014, showing the current relevance of marine bacteria for the discovery of novel natural products.
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211
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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212
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Begrem S, Ivaniuk F, Gigout-Chevalier F, Kolypczuk L, Bonnetot S, Leroi F, Grovel O, Delbarre-Ladrat C, Passerini D. New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses. Microorganisms 2020; 8:microorganisms8071093. [PMID: 32708353 PMCID: PMC7409045 DOI: 10.3390/microorganisms8071093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 12/26/2022] Open
Abstract
Carnobacteriummaltaromaticum and Carnobacteriumdivergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.
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Affiliation(s)
- Simon Begrem
- University of Nantes, 44035 Nantes Cedex 1, France; (S.B.); (O.G.)
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Flora Ivaniuk
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Frédérique Gigout-Chevalier
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Laetitia Kolypczuk
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Sandrine Bonnetot
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Françoise Leroi
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Olivier Grovel
- University of Nantes, 44035 Nantes Cedex 1, France; (S.B.); (O.G.)
| | - Christine Delbarre-Ladrat
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
| | - Delphine Passerini
- IFREMER, BRM, EM3B Laboratory, 44300 Nantes Cedex 3, France; (F.I.); (F.G.-C.); (L.K.); (S.B.); (F.L.); (C.D.-L.)
- Correspondence:
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213
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Oni FE, Geudens N, Adiobo A, Omoboye OO, Enow EA, Onyeka JT, Salami AE, De Mot R, Martins JC, Höfte M. Biosynthesis and Antimicrobial Activity of Pseudodesmin and Viscosinamide Cyclic Lipopeptides Produced by Pseudomonads Associated with the Cocoyam Rhizosphere. Microorganisms 2020; 8:microorganisms8071079. [PMID: 32698413 PMCID: PMC7409209 DOI: 10.3390/microorganisms8071079] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas cyclic lipopeptides (CLPs) are encoded non-ribosomally by biosynthetic gene clusters (BGCs) and possess diverse biological activities. In this study, we conducted chemical structure and BGC analyses with antimicrobial activity assays for two CLPs produced by Pseudomonas strains isolated from the cocoyam rhizosphere in Cameroon and Nigeria. LC-MS and NMR analyses showed that the Pseudomonas sp. COR52 and A2W4.9 produce pseudodesmin and viscosinamide, respectively. These CLPs belong to the Viscosin group characterized by a nonapeptidic moiety with a 7-membered macrocycle. Similar to other Viscosin-group CLPs, the initiatory non-ribosomal peptide synthetase (NRPS) gene of the viscosinamide BGC is situated remotely from the other two NRPS genes. In contrast, the pseudodesmin genes are all clustered in a single genomic locus. Nano- to micromolar levels of pseudodesmin and viscosinamide led to the hyphal distortion and/or disintegration of Rhizoctonia solani AG2-2 and Pythium myriotylum CMR1, whereas similar levels of White Line-Inducing Principle (WLIP), another member of the Viscosin group, resulted in complete lysis of both soil-borne phytopathogens. In addition to the identification of the biosynthetic genes of these two CLPs and the demonstration of their interaction with soil-borne pathogens, this study provides further insights regarding evolutionary divergence within the Viscosin group.
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Affiliation(s)
- Feyisara E. Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, 2520 Potchefstroom, South Africa
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute of Agricultural Research for Development (IRAD), Ekona, P. M. B 25 Buea, Cameroon;
| | - Olumide O. Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Department of Microbiology, Obafemi Awolowo University, 220005 Ile-Ife, Osun State, Nigeria
| | - Elsie A. Enow
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
| | - Joseph T. Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), 440001 Umudike, Abia State, Nigeria;
| | - Ayodeji E. Salami
- Faculty of Agriculture, Department of Crop, Horticulture and Landscape Design, Ekiti State University (EKSU), 360211 Ado-Ekiti, Nigeria;
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, 3001 Heverlee, Belgium;
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium; (N.G.); (J.C.M.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (F.E.O.); (O.O.O.); (E.A.E.)
- Correspondence: ; Tel.: +32-9-264-6017
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214
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Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
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Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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215
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El-Sayed AS, El-Sayed MT, Rady AM, Zein N, Enan G, Shindia A, El-Hefnawy S, Sitohy M, Sitohy B. Exploiting the Biosynthetic Potency of Taxol from Fungal Endophytes of Conifers Plants; Genome Mining and Metabolic Manipulation. Molecules 2020; 25:E3000. [PMID: 32630044 PMCID: PMC7412027 DOI: 10.3390/molecules25133000] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 11/17/2022] Open
Abstract
Endophytic fungi have been considered as a repertoire for bioactive secondary metabolites with potential application in medicine, agriculture and food industry. The biosynthetic pathways by fungal endophytes raise the argument of acquisition of these machineries of such complex metabolites from the plant host. Diterpenoids "Taxol" is the most effective anticancer drug with highest annual sale, since its discovery in 1970 from the Pacific yew tree, Taxus brevifolia. However, the lower yield of Taxol from this natural source (bark of T. brevifolia), availability and vulnerability of this plant to unpredicted fluctuation with the ecological and environmental conditions are the challenges. Endophytic fungi from Taxus spp. opened a new avenue for industrial Taxol production due to their fast growth, cost effectiveness, independence on climatic changes, feasibility of genetic manipulation. However, the anticipation of endophytic fungi for industrial Taxol production has been challenged by the loss of its productivity, due to the metabolic reprograming of cells, downregulating the expression of its encoding genes with subculturing and storage. Thus, the objectives of this review were to (1) Nominate the endophytic fungal isolates with the Taxol producing potency from Taxaceae and Podocarpaceae; (2) Emphasize the different approaches such as molecular manipulation, cultural optimization, co-cultivation for enhancing the Taxol productivities; (3) Accentuate the genome mining of the rate-limiting enzymes for rapid screening the Taxol biosynthetic machinery; (4) Triggering the silenced rate-limiting genes and transcriptional factors to activates the biosynthetic gene cluster of Taxol.
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Affiliation(s)
- Ashraf S.A. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt; (M.T.E.-S.); (G.E.); (A.S.); (S.E.-H.)
| | - Manal T. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt; (M.T.E.-S.); (G.E.); (A.S.); (S.E.-H.)
| | - Amgad M. Rady
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Cairo 12566, Egypt;
| | - Nabila Zein
- Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Gamal Enan
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt; (M.T.E.-S.); (G.E.); (A.S.); (S.E.-H.)
| | - Ahmed Shindia
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt; (M.T.E.-S.); (G.E.); (A.S.); (S.E.-H.)
| | - Sara El-Hefnawy
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt; (M.T.E.-S.); (G.E.); (A.S.); (S.E.-H.)
| | - Mahmoud Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt;
| | - Basel Sitohy
- Department of Clinical Microbiology, Infection and Immunology, Umeå University, SE-90185 Umeå, Sweden
- Department of Radiation Sciences, Oncology, Umeå University, SE-90185 Umeå, Sweden
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216
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Russell AH, Truman AW. Genome mining strategies for ribosomally synthesised and post-translationally modified peptides. Comput Struct Biotechnol J 2020; 18:1838-1851. [PMID: 32728407 PMCID: PMC7369419 DOI: 10.1016/j.csbj.2020.06.032] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/14/2023] Open
Abstract
Genome mining is a computational method for the automatic detection and annotation of biosynthetic gene clusters (BGCs) from genomic data. This approach has been increasingly utilised in natural product (NP) discovery due to the large amount of sequencing data that is now available. Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of structurally complex NP with diverse bioactivities. RiPPs have recently been shown to occupy a much larger expanse of genomic and chemical space than previously appreciated, indicating that annotation of RiPP BGCs in genomes may have been overlooked in the past. This review provides an overview of the genome mining tools that have been specifically developed to aid in the discovery of RiPP BGCs, which have been built from an increasing knowledgebase of RiPP structures and biosynthesis. Given these recent advances, the application of targeted genome mining has great potential to accelerate the discovery of important molecules such as antimicrobial and anticancer agents whilst increasing our understanding about how these compounds are biosynthesised in nature.
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Affiliation(s)
- Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
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217
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Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK. Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 2020; 18:1548-1556. [PMID: 32637051 PMCID: PMC7327026 DOI: 10.1016/j.csbj.2020.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 01/04/2023] Open
Abstract
Streptomyces are a large and valuable resource of bioactive and complex secondary metabolites, many of which have important clinical applications. With the advances in high throughput genome sequencing methods, various in silico genome mining strategies have been developed and applied to the mapping of the Streptomyces genome. These studies have revealed that Streptomyces possess an even more significant number of uncharacterized silent secondary metabolite biosynthetic gene clusters (smBGCs) than previously estimated. Linking smBGCs to their encoded products has played a critical role in the discovery of novel secondary metabolites, as well as, knowledge-based engineering of smBGCs to produce altered products. In this mini review, we discuss recent progress in Streptomyces genome sequencing and the application of genome mining approaches to identify and characterize smBGCs. Furthermore, we discuss several challenges that need to be overcome to accelerate the genome mining process and ultimately support the discovery of novel bioactive compounds.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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218
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Prudence SMM, Addington E, Castaño-Espriu L, Mark DR, Pintor-Escobar L, Russell AH, McLean TC. Advances in actinomycete research: an ActinoBase review of 2019. MICROBIOLOGY-SGM 2020; 166:683-694. [PMID: 32558638 PMCID: PMC7641383 DOI: 10.1099/mic.0.000944] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.
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Affiliation(s)
- Samuel M M Prudence
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Emily Addington
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Laia Castaño-Espriu
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | | | - Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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219
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Shen L, Liu M, He Y, Al Anbari WH, Li H, Lin S, Chai C, Wang J, Hu Z, Zhang Y. Novel Antimicrobial Compounds as Ophiobolin-Type Sesterterpenes and Pimarane-Type Diterpene From Bipolaris Species TJ403-B1. Front Microbiol 2020; 11:856. [PMID: 32547498 PMCID: PMC7273749 DOI: 10.3389/fmicb.2020.00856] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 01/30/2023] Open
Abstract
Six previously undescribed ophiobolin-type sesterterpenes, namely, bipolatoxins A–F (1–6); and one previously undescribed pimarane-type diterpene, namely, 1β-hydroxy momilactone A (7); together with three known compounds, namely, 25-hydroxyophiobolin I (8), ophiobolin I (9), and ophiobolin A lactone (10); were isolated and identified from the endophytic fungus Bipolaris species TJ403-B1. Their structures with absolute configurations were elucidated on the basis of extensive spectroscopic analyses (including 1D and 2D nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectroscopy data), single-crystal X-ray diffraction analyses, and comparison of experimental circular dichroism data. All compounds (except for 5) were evaluated for antimicrobial potential, which indicated that bipolatoxin D (4) showed significant inhibitory activity against Enterococcus faecalis with a minimum inhibitory concentration (MIC) value of 8 μg/mL, and ophiobolin A lactone (10) showed significant inhibitory activity against Acinetobacter baumannii and E. faecalis with MIC values of 8 and 8 μg/mL, respectively.
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Affiliation(s)
- Ling Shen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengting Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan He
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weaam Hasan Al Anbari
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huaqiang Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuang Lin
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenwei Chai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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220
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Männle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z, Moore BS, Ziemert N, Kaysser L. Comparative Genomics and Metabolomics in the Genus Nocardia. mSystems 2020; 5:e00125-20. [PMID: 32487740 PMCID: PMC7413640 DOI: 10.1128/msystems.00125-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/13/2020] [Indexed: 01/22/2023] Open
Abstract
Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores.IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.
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Affiliation(s)
- Daniel Männle
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA
| | - Shrikant S Mantri
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katharina Steinke
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Zeyin Lu
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Pharmaceutical Biology, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
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221
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Martínez-Núñez MA, Rodríguez-Escamilla Z. Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes. Toxins (Basel) 2020; 12:E349. [PMID: 32466531 PMCID: PMC7354552 DOI: 10.3390/toxins12060349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico
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222
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Saito S, Atsumi K, Zhou T, Fukaya K, Urabe D, Oku N, Karim MRU, Komaki H, Igarashi Y. A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium. Beilstein J Org Chem 2020; 16:1100-1110. [PMID: 32550925 PMCID: PMC7277628 DOI: 10.3762/bjoc.16.97] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Aside from the well-studied conventional actinomycetes such as Streptomyces, the less investigated genera of actinomycetes also represent a promising source of natural products. Genome mining indicated that members of the underexplored genus Pseudosporangium, from which no secondary metabolites have been reported to date, may harbor the biosynthetic machinery for the formation of novel natural products. The strain RD062863, that is available at a public culture collection, was obtained and subjected to metabolite analysis, which resulted in the discovery of a novel cyclopeptide, pseudosporamide (1), along with three new oligomycin-class polyketides, pseudosporamicins A–C (2–4). The unusual structure of compound 1, featured by a biaryl-bond bridging across a tripeptide scaffold, N-acetyl-ʟ-Tyr-ʟ-Pro-ʟ-Trp, was determined by a combination of spectroscopic analyses, chemical derivatization, ECD calculation, and DFT-based theoretical chemical shift calculation, revealing the presence of an (Sa)-axial chirality around the biaryl bond. Compounds 2–4 lacked hydroxylation on the side chain of the spiroacetal rings, which showed clear contrast to other oligomycin congeners and related polyketides with ring-truncation or expansion. The new macrolides 2–4 displayed potent antimicrobial activity against the Gram-positive bacterium Kocuria rhizohpila and the plant pathogenic fungus Glomerella cingulata. All compounds showed moderate cytotoxicity against P388 murine leukemia cells with IC50 values in the micromolar to submicromolar ranges. These results exemplified the validity of phylogeny-focused strain selection combined with biosynthetic gene-directed genome mining for the efficient discovery of new natural products.
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Affiliation(s)
- Shun Saito
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kota Atsumi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Md Rokon Ul Karim
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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223
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Wang J, Zhang R, Chen X, Sun X, Yan Y, Shen X, Yuan Q. Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases. Microb Cell Fact 2020; 19:110. [PMID: 32448179 PMCID: PMC7247197 DOI: 10.1186/s12934-020-01367-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xin Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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Della Sala G, Mangoni A, Costantino V, Teta R. Identification of the Biosynthetic Gene Cluster of Thermoactinoamides and Discovery of New Congeners by Integrated Genome Mining and MS-Based Molecular Networking. Front Chem 2020; 8:397. [PMID: 32528927 PMCID: PMC7253712 DOI: 10.3389/fchem.2020.00397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/15/2020] [Indexed: 11/21/2022] Open
Abstract
The putative non-ribosomal peptide synthetase (NRPS) gene cluster encoding the biosynthesis of the bioactive cyclohexapeptide thermoactinoamide A (1) was identified in Thermoactinomyces vulgaris DSM 43016. Based on an in silico prediction, the biosynthetic operon was shown to contain two trimodular NRPSs, designated as ThdA and ThdB, respectively. Chemical analysis of a bacterial crude extract showed the presence of thermoactinoamide A (1), thereby supporting this biosynthetic hypothesis. Notably, integrating genome mining with a LC-HRMS/MS molecular networking-based investigation of the microbial metabolome, we succeeded in the identification of 10 structural variants (2–11) of thermoactinoamide A (1), five of them being new compounds (thermoactinoamides G-K, 7–11). As only one thermoactinoamide operon was found in T. vulgaris, it can be assumed that all thermoactinoamide congeners are assembled by the same multimodular NRPS system. In light of these findings, we suggest that the thermoactinoamide synthetase is able to create chemical diversity, combining the relaxed substrate selectivity of some adenylation domains with the iterative and/or alternative use of specific modules. In the frame of our screening program to discover antitumor natural products, thermoactinoamide A (1) was shown to exert a moderate growth-inhibitory effect in BxPC-3 cancer cells in the low micromolar range, while being inactive in PANC-1 and 3AB-OS solid tumor models.
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Affiliation(s)
- Gerardo Della Sala
- Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
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225
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Herisse M, Ishida K, Porter JL, Howden B, Hertweck C, Stinear TP, Pidot SJ. Identification and Mobilization of a Cryptic Antibiotic Biosynthesis Gene Locus from a Human-Pathogenic Nocardia Isolate. ACS Chem Biol 2020; 15:1161-1168. [PMID: 31697466 DOI: 10.1021/acschembio.9b00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genus Nocardia contains >50 human pathogenic species that cause a range of illnesses from skin and soft tissue infections to lung and brain infections. However, despite their membership in the most prominent family of secondary metabolite producers (the Actinomycetes), the ability of Nocardia species, especially those that cause human infections, to produce secondary metabolites has not been as well studied. Using genome mining, we have investigated cryptic secondary metabolite biosynthesis gene clusters from Nocardia species and identified a conserved locus within human pathogenic strains of Nocardia brasiliensis and Nocardia vulneris. Direct capture and heterologous expression in a Streptomyces host activated the biosynthetic locus, revealing it to be the source of the brasiliquinones, benz[a]anthraquinone antibiotics whose biosynthetic pathway has remained hidden for over two decades, until now. Our findings highlight these hitherto neglected human pathogenic Nocardia as a source of diverse and important natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ben Howden
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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226
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Xu D, Tian E, Kong F, Hong K. Bioactive Molecules from Mangrove Streptomyces qinglanensis 172205. Mar Drugs 2020; 18:md18050255. [PMID: 32414163 PMCID: PMC7281499 DOI: 10.3390/md18050255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Five new compounds 15R-17,18-dehydroxantholipin (1), (3E,5E,7E)-3-methyldeca-3,5,7-triene-2,9-dione (2) and qinlactone A–C (3–5) were identified from mangrove Streptomyces qinglanensis 172205 with “genetic dereplication,” which deleted the highly expressed secondary metabolite-enterocin biosynthetic gene cluster. The chemical structures were established by spectroscopic methods, and the absolute configurations were determined by electronic circular dichroism (ECD). Compound 1 exhibited strong anti-microbial and antiproliferative bioactivities, while compounds 2–4 showed weak antiproliferative activities.
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Affiliation(s)
- Dongbo Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (D.X.); (E.T.)
| | - Erli Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (D.X.); (E.T.)
| | - Fandong Kong
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultura Sciences, Haikou 571101, China;
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; (D.X.); (E.T.)
- Correspondence: ; Tel.: +86-27-6875-2442
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227
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Perfumo A, Freiherr von Sass GJ, Nordmann EL, Budisa N, Wagner D. Discovery and Characterization of a New Cold-Active Protease From an Extremophilic Bacterium via Comparative Genome Analysis and in vitro Expression. Front Microbiol 2020; 11:881. [PMID: 32528424 PMCID: PMC7247812 DOI: 10.3389/fmicb.2020.00881] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/16/2020] [Indexed: 01/05/2023] Open
Abstract
Following a screening of Antarctic glacier forefield-bacteria for novel cold-active enzymes, a psychrophilic strain Psychrobacter sp. 94-6PB was selected for further characterization of enzymatic activities. The strain produced lipases and proteases in the temperature range of 4-18°C. The coding sequence of an extracellular serine-protease was then identified via comparative analysis across Psychrobacter sp. genomes, PCR-amplified in our strain 94-6PB and expressed in the heterologous host E. coli. The purified enzyme (80 kDa) resulted to be a cold-active alkaline protease, performing best at temperatures of 20-30°C and pH 7-9. It was stable in presence of common inhibitors [β-mercaptoethanol (β-ME), dithiothreitol (DTT), urea, phenylmethylsulfonyl fluoride (PMSF) and ethylenediaminetetraacetic acid (EDTA)] and compatible with detergents and surfactants (Tween 20, Tween 80, hydrogen peroxide and Triton X-100). Because of these properties, the P94-6PB protease may be suitable for use in a new generation of laundry products for cold washing. Furthermore, we assessed the microdiversity of this enzyme in Psychrobacter organisms from different cold habitats and found several gene clusters that correlated with specific ecological niches. We then discussed the role of habitat specialization in shaping the biodiversity of proteins and enzymes and anticipate far-reaching implications for the search of novel variants of biotechnological products.
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Affiliation(s)
- Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Polar Terrestrial Environmental System Division, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Potsdam, Germany
| | | | - Eva-Lena Nordmann
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Institute of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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228
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Blin K, Pascal Andreu V, de Los Santos ELC, Del Carratore F, Lee SY, Medema MH, Weber T. The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 2020; 47:D625-D630. [PMID: 30395294 PMCID: PMC6324005 DOI: 10.1093/nar/gky1060] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/17/2018] [Indexed: 11/29/2022] Open
Abstract
Natural products originating from microorganisms are frequently used in antimicrobial and anticancer drugs, pesticides, herbicides or fungicides. In the last years, the increasing availability of microbial genome data has made it possible to access the wealth of biosynthetic clusters responsible for the production of these compounds by genome mining. antiSMASH is one of the most popular tools in this field. The antiSMASH database provides pre-computed antiSMASH results for many publicly available microbial genomes and allows for advanced cross-genome searches. The current version 2 of the antiSMASH database contains annotations for 6200 full bacterial genomes and 18,576 bacterial draft genomes and is available at https://antismash-db.secondarymetabolites.org/.
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Affiliation(s)
- Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | | | | | - Francesco Del Carratore
- Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sang Yup Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.,Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
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229
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Williams DE, Andersen RJ. Biologically active marine natural products and their molecular targets discovered using a chemical genetics approach. Nat Prod Rep 2020; 37:617-633. [PMID: 31750842 PMCID: PMC7874888 DOI: 10.1039/c9np00054b] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Covering: 2000 to 2019The discovery of new natural products that have some combination of unprecedented chemical structures, biological activities of therapeutic interest for urgent medical needs, and new molecular targets provides the fuel that sustains the vitality of natural products chemistry research. Unfortunately, finding these important new compounds is neither routine or trivial and a major challenge is finding effective discovery paradigms. This review presents examples that illustrate the effectiveness of a chemical genetics approach to marine natural product (MNP) discovery that intertwines compound discovery, molecular target identification, and phenotypic response/biological activity. The examples include MNPs that have complex unprecedented structures, new or understudied molecular targets, and potent biological activities of therapeutic interest. A variety of methods to identify molecular targets are also featured.
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Affiliation(s)
- David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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230
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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231
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Sigrist R, Luhavaya H, McKinnie SMK, Ferreira da Silva A, Jurberg ID, Moore BS, Gonzaga de Oliveira L. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/ trans-AT PKS-NRPS. ACS Chem Biol 2020; 15:1067-1077. [PMID: 32195572 DOI: 10.1021/acschembio.0c00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpiniamide A is a linear polyketide produced by Streptomyces endophytic bacteria. Despite its relatively simple chemical structure suggestive of a linear assembly line biosynthetic construction involving a hybrid polyketide synthase-nonribosomal peptide synthetase enzymatic protein machine, we report an unexpected nonlinear synthesis of this bacterial natural product. Using a combination of genomics, heterologous expression, mutagenesis, isotope-labeling, and chain terminator experiments, we propose that alpiniamide A is assembled in two halves and then ligated into the mature molecule. We show that each polyketide half is constructed using orthogonal biosynthetic strategies, employing either cis- or trans-acyl transferase mechanisms, thus prompting an alternative proposal for the operation of this PKS-NRPS.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amanda Ferreira da Silva
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Igor D. Jurberg
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
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232
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Exploring the Biocatalytic Potential of Fe/α‐Ketoglutarate‐Dependent Halogenases. Chemistry 2020; 26:7336-7345. [DOI: 10.1002/chem.201905752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/18/2022]
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233
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Blin K, Kim HU, Medema MH, Weber T. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Brief Bioinform 2020; 20:1103-1113. [PMID: 29112695 PMCID: PMC6781578 DOI: 10.1093/bib/bbx146] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/10/2017] [Indexed: 01/06/2023] Open
Abstract
Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. However, mining for a variety of BGCs quickly approaches a complexity level where manual analyses are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software. In this review, we discuss the principles underlying the predictions of antiSMASH and other tools and provide practical advice for their application. Furthermore, we discuss important caveats such as rule-based BGC detection, sequence and annotation quality and cluster boundary prediction, which all have to be considered while planning for, performing and analyzing the results of genome mining studies.
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Affiliation(s)
| | | | | | - Tilmann Weber
- Corresponding author: Tilmann Weber, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. Tel.: +45 24 89 61 32; E-mail:
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234
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Genome Mining as New Challenge in Natural Products Discovery. Mar Drugs 2020; 18:md18040199. [PMID: 32283638 PMCID: PMC7230286 DOI: 10.3390/md18040199] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.
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235
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Soleimany AP, Bhatia SN. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Trends Mol Med 2020; 26:450-468. [PMID: 32359477 DOI: 10.1016/j.molmed.2020.01.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
Diagnostics to accurately detect disease and monitor therapeutic response are essential for effective clinical management. Bioengineering, chemical biology, molecular biology, and computer science tools are converging to guide the design of diagnostics that leverage enzymatic activity to measure or produce biomarkers of disease. We review recent advances in the development of these 'activity-based diagnostics' (ABDx) and their application in infectious and noncommunicable diseases. We highlight efforts towards both molecular probes that respond to disease-specific catalytic activity to produce a diagnostic readout, as well as diagnostics that use enzymes as an engineered component of their sense-and-respond cascade. These technologies exemplify how integrating techniques from multiple disciplines with preclinical validation has enabled ABDx that may realize the goals of precision medicine.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Wyss Institute at Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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236
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Travin DY, Bikmetov D, Severinov K. Translation-Targeting RiPPs and Where to Find Them. Front Genet 2020; 11:226. [PMID: 32296456 PMCID: PMC7136475 DOI: 10.3389/fgene.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
Prokaryotic translation is among the major targets of diverse natural products with antibacterial activity including several classes of clinically relevant antibiotics. In this review, we summarize the information about the structure, biosynthesis, and modes of action of translation inhibiting ribosomally synthesized and post-translationally modified peptides (RiPPs). Azol(in)e-containing RiPPs are known to target translation, and several new compounds inhibiting the ribosome have been characterized recently. We performed a systematic search for biosynthetic gene clusters (BGCs) of azol(in)e-containing RiPPs. This search uncovered several groups of clusters that likely direct the synthesis of novel compounds, some of which may be targeting the ribosome.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Bikmetov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, Piscataway, NJ, United States
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237
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Fukuda TTH, Cassilly CD, Gerdt JP, Henke MT, Helfrich EJN, Mevers E. Research Tales from the Clardy Laboratory: Function-Driven Natural Product Discovery. JOURNAL OF NATURAL PRODUCTS 2020; 83:744-755. [PMID: 32105475 DOI: 10.1021/acs.jnatprod.9b01086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past 70 years, the search for small molecules from nature has transformed biomedical research: natural products are the basis for half of all pharmaceuticals; the quest for total synthesis of natural products fueled development of methodologies for organic synthesis; and their biosynthesis presented unprecedented biochemical transformations, expanding our chemo-enzymatic toolkit. Initially, the discovery of small molecules was driven by bioactivity-guided fractionation. However, this approach yielded the frequent rediscovery of already known metabolites. As a result, focus shifted to identifying novel scaffolds through either structure-first methods or genome mining, relegating function as a secondary concern. Over the past two decades, the laboratory of Jon Clardy has taken an alternative route and focused on an ecology-driven, function-first approach in pursuit of uncovering bacterial small molecules with biological activity. In this review, we highlight several examples that showcase this ecology-first approach. Though the highlighted systems are diverse, unifying themes are (1) to understand how microbes interact with their host or environment, (2) to gain insights into the environmental roles of microbial metabolites, and (3) to explore pharmaceutical potential from these ecologically relevant metabolites.
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Affiliation(s)
- Taise T H Fukuda
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Matthew T Henke
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eric J N Helfrich
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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238
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Rudolf JD, Chang CY. Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases. Nat Prod Rep 2020; 37:425-463. [PMID: 31650156 PMCID: PMC7101268 DOI: 10.1039/c9np00051h] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, Republic of China
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239
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May DS, Crnkovic CM, Krunic A, Wilson TA, Fuchs JR, Orjala JE. 15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria. ACS Chem Biol 2020; 15:758-765. [PMID: 32083834 DOI: 10.1021/acschembio.9b00993] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As genome mining becomes a more widely used approach to identify bacterial natural products, the challenge of matching biosynthetic gene clusters to their cognate secondary metabolites has become more apparent. Bioinformatic platforms such as AntiSMASH have made great progress in predicting chemical structures from genetic information, however the predicted structures are often incomplete. This complicates identifying the predicted compounds by mass spectrometry. Secondary metabolites produced by cyanobacteria represent a unique opportunity for bridging this gap. Cultured cyanobacteria incorporate inorganic nitrogen provided in chemically defined media into all nitrogen-containing secondary metabolites. Thus, stable isotope labeling with 15N labeled nitrate and subsequent comparative metabolomics can be used to match biosynthetic gene clusters to their cognate compounds in cell extracts. Analysis of the sequenced genome of Nostoc sp. UIC 10630 identified six biosynthetic gene clusters predicted to encode the production of a secondary metabolite with at least one nitrogen atom. Comparative metabolomic analysis of the 15N labeled and unlabeled cell extracts revealed four nitrogen containing compounds that contained the same number of nitrogen atoms as were predicted in the biosynthetic gene clusters. Two of the four compounds were new secondary metabolites, and their structures were elucidated by NMR, HRESIMS, and MS/MS.
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Affiliation(s)
- Daniel S. May
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Tyler A. Wilson
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jimmy E. Orjala
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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240
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Huang X, Zhang W, Tang S, Wei S, Lu X. Collaborative Biosynthesis of a Class of Bioactive Azaphilones by Two Separate Gene Clusters Containing Four PKS/NRPSs with Transcriptional Crosstalk in Fungi. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
- College of Bioscience and BioengineeringJiangxi Agricultural University No. 1101 Zhimin Road Nanchang 330045 China
| | - Suhui Wei
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
- Marine Biology and Biotechnology LaboratoryQingdao National Laboratory for Marine Science and Technology No. 1 Wenhai Road, Aoshanwei Qingdao 266101 China
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241
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Lee N, Kim W, Hwang S, Lee Y, Cho S, Palsson B, Cho BK. Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters. Sci Data 2020; 7:55. [PMID: 32054853 PMCID: PMC7018776 DOI: 10.1038/s41597-020-0395-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/24/2020] [Indexed: 01/04/2023] Open
Abstract
Streptomyces are Gram-positive bacteria of significant industrial importance due to their ability to produce a wide range of antibiotics and bioactive secondary metabolites. Recent advances in genome mining have revealed that Streptomyces genomes possess a large number of unexplored silent secondary metabolite biosynthetic gene clusters (smBGCs). This indicates that Streptomyces genomes continue to be an invaluable source for new drug discovery. Here, we present high-quality genome sequences of 22 Streptomyces species and eight different Streptomyces venezuelae strains assembled by a hybrid strategy exploiting both long-read and short-read genome sequencing methods. The assembled genomes have more than 97.4% gene space completeness and total lengths ranging from 6.7 to 10.1 Mbp. Their annotation identified 7,000 protein coding genes, 20 rRNAs, and 68 tRNAs on average. In silico prediction of smBGCs identified a total of 922 clusters, including many clusters whose products are unknown. We anticipate that the availability of these genomes will accelerate discovery of novel secondary metabolites from Streptomyces and elucidate complex smBGC regulation.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- Intelligent Synthetic Biology Center, Daejeon, 34141, Republic of Korea.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark.
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242
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Chen R, Yang S, Zhang L, Zhou YJ. Advanced Strategies for Production of Natural Products in Yeast. iScience 2020; 23:100879. [PMID: 32087574 PMCID: PMC7033514 DOI: 10.1016/j.isci.2020.100879] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022] Open
Abstract
Natural products account for more than 50% of all small-molecule pharmaceutical agents currently in clinical use. However, low availability often becomes problematic when a bioactive natural product is promising to become a pharmaceutical or leading compound. Advances in synthetic biology and metabolic engineering provide a feasible solution for sustainable supply of these compounds. In this review, we have summarized current progress in engineering yeast cell factories for production of natural products, including terpenoids, alkaloids, and phenylpropanoids. We then discuss advanced strategies in metabolic engineering at three different dimensions, including point, line, and plane (corresponding to the individual enzymes and cofactors, metabolic pathways, and the global cellular network). In particular, we comprehensively discuss how to engineer cofactor biosynthesis for enhancing the biosynthesis efficiency, other than the enzyme activity. Finally, current challenges and perspective are also discussed for future engineering direction.
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Affiliation(s)
- Ruibing Chen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Shan Yang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China; Biomedical Innovation R&D Center, School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
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243
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Ganley JG, Derbyshire ER. Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire. Molecules 2020; 25:E625. [PMID: 32023950 PMCID: PMC7036892 DOI: 10.3390/molecules25030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of natural products continues to interest chemists and biologists for their utility in medicine as well as facilitating our understanding of signaling, pathogenesis, and evolution. Despite an attenuation in the discovery rate of new molecules, the current genomics and transcriptomics revolution has illuminated the untapped biosynthetic potential of many diverse organisms. Today, natural product discovery can be driven by biosynthetic gene cluster (BGC) analysis, which is capable of predicting enzymes that catalyze novel reactions and organisms that synthesize new chemical structures. This approach has been particularly effective in mining bacterial and fungal genomes where it has facilitated the discovery of new molecules, increased the understanding of metabolite assembly, and in some instances uncovered enzymes with intriguing synthetic utility. While relatively less is known about the biosynthetic potential of non-fungal eukaryotes, there is compelling evidence to suggest many encode biosynthetic enzymes that produce molecules with unique bioactivities. In this review, we highlight how the advances in genomics and transcriptomics have aided natural product discovery in sources from eukaryotic lineages. We summarize work that has successfully connected genes to previously identified molecules and how advancing these techniques can lead to genetics-guided discovery of novel chemical structures and reactions distributed throughout the tree of life. Ultimately, we discuss the advantage of increasing the known biosynthetic space to ease access to complex natural and non-natural small molecules.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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244
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Huang X, Zhang W, Tang S, Wei S, Lu X. Collaborative Biosynthesis of a Class of Bioactive Azaphilones by Two Separate Gene Clusters Containing Four PKS/NRPSs with Transcriptional Crosstalk in Fungi. Angew Chem Int Ed Engl 2020; 59:4349-4353. [DOI: 10.1002/anie.201915514] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
- College of Bioscience and BioengineeringJiangxi Agricultural University No. 1101 Zhimin Road Nanchang 330045 China
| | - Suhui Wei
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic BiologyKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of Sciences No. 189 Songling Road Qingdao 266101 China
- Marine Biology and Biotechnology LaboratoryQingdao National Laboratory for Marine Science and Technology No. 1 Wenhai Road, Aoshanwei Qingdao 266101 China
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245
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Dalvie NC, Leal J, Whittaker CA, Yang Y, Brady JR, Love KR, Love JC. Host-Informed Expression of CRISPR Guide RNA for Genomic Engineering in Komagataella phaffii. ACS Synth Biol 2020; 9:26-35. [PMID: 31825599 PMCID: PMC7814401 DOI: 10.1021/acssynbio.9b00372] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is growing interest in the use of nonmodel microorganisms as hosts for biopharmaceutical manufacturing. These hosts require genomic engineering to meet clinically relevant product qualities and titers, but the adaptation of tools for editing genomes, such as CRISPR-Cas9, has been slow for poorly characterized hosts. Specifically, a lack of biochemical characterization of RNA polymerase III transcription has hindered reliable expression of guide RNAs in new hosts. Here, we present a sequencing-based strategy for the design of host-specific cassettes for modular, reliable, expression of guide RNAs. Using this strategy, we achieved up to 95% gene editing efficiency in the methylotrophic yeast Komagataella phaffii. We applied this approach for the rapid, multiplexed engineering of a complex phenotype, achieving humanized product glycosylation in two sequential steps of engineering. Reliable extension of simple gene editing tools to nonmodel manufacturing hosts will enable rapid engineering of manufacturing strains tuned for specific product profiles and potentially decrease the costs and timelines for process development.
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Affiliation(s)
- Neil C. Dalvie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Justin Leal
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Charles A. Whittaker
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Yuchen Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Joseph R. Brady
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Kerry R. Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - J. Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
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246
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Ishaque NM, Burgsdorf I, Limlingan Malit JJ, Saha S, Teta R, Ewe D, Kannabiran K, Hrouzek P, Steindler L, Costantino V, Saurav K. Isolation, Genomic and Metabolomic Characterization of Streptomyces tendae VITAKN with Quorum Sensing Inhibitory Activity from Southern India. Microorganisms 2020; 8:E121. [PMID: 31963137 PMCID: PMC7023471 DOI: 10.3390/microorganisms8010121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 01/11/2023] Open
Abstract
Streptomyces are among the most promising genera in terms of production ability to biosynthesize a variety of bioactive secondary metabolites with pharmaceutical interest. Coinciding with the increase in genomic sequencing of these bacteria, mining of their genomes for biosynthetic gene clusters (BGCs) has become a routine component of natural product discovery. Herein, we describe the isolation and characterization of a Streptomyces tendae VITAKN with quorum sensing inhibitory (QSI) activity that was isolated from southern coastal part of India. The nearly complete genome consists of 8,621,231bp with a GC content of 72.2%. Sequence similarity networks of the BGCs detected from this strain against the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) database and 3365 BGCs predicted by antiSMASH analysis of publicly available complete Streptomyces genomes were generated through the BiG-SCAPE-CORASON platform to evaluate its biosynthetic novelty. Crude extract analysis using high-performance liquid chromatography connected to high resolution tandem mass spectrometry (HPLC-HRMS/MS) and dereplication through the Global Natural Product Social Molecular Networking (GNPS) online workflow resulted in the identification of cyclic dipeptides (2, 5-diketopiperazines, DKPs) in the extract, which are known to possess QSI activity. Our results highlight the potential of genome mining coupled with LC-HRMS/MS and in silico tools (GNPS) as a valid approach for the discovery of novel QSI lead compounds. This study also provides the biosynthetic diversity of BGCs and an assessment of the predicted chemical space yet to be discovered.
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Affiliation(s)
- Nabila Mohammed Ishaque
- Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India; (N.M.I.); (K.K.)
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 31905, Israel; (I.B.); (L.S.)
| | - Jessie James Limlingan Malit
- Department of Ocean Science, Division of Life Science and Hong Kong, Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Subhasish Saha
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 37981 Třeboň, Czech Republic; (S.S.); (D.E.); (P.H.)
| | - Roberta Teta
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Daniela Ewe
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 37981 Třeboň, Czech Republic; (S.S.); (D.E.); (P.H.)
| | - Krishnan Kannabiran
- Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India; (N.M.I.); (K.K.)
| | - Pavel Hrouzek
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 37981 Třeboň, Czech Republic; (S.S.); (D.E.); (P.H.)
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 31905, Israel; (I.B.); (L.S.)
| | - Valeria Costantino
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Kumar Saurav
- Department of Biomedical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India; (N.M.I.); (K.K.)
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 31905, Israel; (I.B.); (L.S.)
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 37981 Třeboň, Czech Republic; (S.S.); (D.E.); (P.H.)
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy;
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Cortés-Albayay C, Jarmusch SA, Trusch F, Ebel R, Andrews BA, Jaspars M, Asenjo JA. Downsizing Class II Lasso Peptides: Genome Mining-Guided Isolation of Huascopeptin Containing the First Gly1-Asp7 Macrocycle. J Org Chem 2020; 85:1661-1667. [DOI: 10.1021/acs.joc.9b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlos Cortés-Albayay
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Scott A. Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Institute of Medical Sciences, University of Aberdeen, Foresterhill AB25 2ZD, Scotland, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Errol Road, Invergowrie, Dundee DD2 5DA, U.K
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
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Frederick J, Hennessy F, Horn U, de la Torre Cortés P, van den Broek M, Strych U, Willson R, Hefer CA, Daran JMG, Sewell T, Otten LG, Brady D. The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. BMC Genomics 2020; 21:3. [PMID: 31898479 PMCID: PMC6941271 DOI: 10.1186/s12864-019-6405-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.
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Affiliation(s)
- Joni Frederick
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
- Present Address: LadHyx, UMR CNRS 7646, École Polytechnique, 91128 Palaiseau, France
| | - Fritha Hennessy
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
| | - Uli Horn
- Meraka, CSIR, Meiring Naude Road, Brummeria, 0091 South Africa
| | - Pilar de la Torre Cortés
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ulrich Strych
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Present Address: Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX 77030 USA
| | - Richard Willson
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Chemical and Biomolecular Engineering, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
| | - Charles A. Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002 South Africa
- Present Address: AgResearch Limited, Lincoln Research Centre, Private Bag 4749, Christchurch, 8140 New Zealand
| | - Jean-Marc G. Daran
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Trevor Sewell
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
| | - Linda G. Otten
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dean Brady
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO, Wits, 2050 South Africa
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Li M, Hou F, Wu T, Jiang X, Li F, Liu H, Xian M, Zhang H. Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories. Nat Prod Rep 2020; 37:80-99. [DOI: 10.1039/c9np00016j] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review covers the strategies mostly developed in the last three years for microbial production of isoprenoid, classified according to the engineering targets.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Feifei Hou
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Tong Wu
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Lyngby
- Denmark
| | - Fuli Li
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haobao Liu
- Ministry of Agriculture Key Laboratory for Tobacco Biology and Processing
- Tobacco Research Institute
- Chinese Academy of Agricultural Sciences
- Qingdao
- P. R. China
| | - Mo Xian
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
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250
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A GK, K A, M H, K S, G D. Review on plastic wastes in marine environment - Biodegradation and biotechnological solutions. MARINE POLLUTION BULLETIN 2020; 150:110733. [PMID: 31767203 DOI: 10.1016/j.marpolbul.2019.110733] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 05/23/2023]
Abstract
The marine plastic pollution has drastic effect on marine species. The importance in environmental issues increases the demand to develop a significant technology which does not burden the marine environment or marine life forms. To mitigate the foreseen problems of micro and nanoplastic contamination, different biotechnological solutions has to be considered. Microbial communities exposed to plastic contaminated sites can adapt and form dense biofilms on the plastic surface and produce active catalytic enzymes. These enzymes can be able to degrade the synthetic polymers. In view of their high catalytic activity, microbial enzymes can be applicable for the degradation of synthetic polymers. This review highlights the toxicity of micro and nanoplastics on marine organisms, biodegradation of plastics and futuristic research needs to solve the issues of plastic pollution in marine environment.
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Affiliation(s)
- Ganesh Kumar A
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
| | - Anjana K
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Hinduja M
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Sujitha K
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - Dharani G
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
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