1
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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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2
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Genome and secretome analysis of jute endophyte Grammothele lineata strain SDL-CO-2015-1: Insights into its lignocellulolytic structure and secondary metabolite profile. Genomics 2020; 112:2794-2803. [PMID: 32217134 DOI: 10.1016/j.ygeno.2020.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/02/2020] [Accepted: 03/22/2020] [Indexed: 12/30/2022]
Abstract
Grammothele lineata strain SDL-CO-2015-1, jute (Corchorus olitorius) endophyte has been reported to produce anti-cancer drug paclitaxel in culture condition. Here we investigated the genome using different bioinformatic tools to find its association with the production of commercially important compounds including taxol. Carbohydrate-active enzymes, proteases, and secretory proteins were annotated revealing a complex endophytic relationship with its plant host. The presences of a diverse range of CAZymes including numerous lignocellulolytic enzymes support its potentiality in biomass degradation. Genome annotation led to the identification of 28 clusters for secondary metabolite biosynthesis. Several biosynthesis gene clusters were identified for terpene biosynthesis from antiSMASH analysis but none could be specifically pinned to taxol synthesis. This study will direct us to understand the genomic organization of endophytic basidiomycetes with a potential for producing numerous commercially important enzymes and secondary metabolites taking G. lineata as a model.
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3
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Xu D, Nepal KK, Chen J, Harmody D, Zhu H, McCarthy PJ, Wright AE, Wang G. Nocardiopsistins A-C: New angucyclines with anti-MRSA activity isolated from a marine sponge-derived Nocardiopsis sp. HB-J378. Synth Syst Biotechnol 2018; 3:246-251. [PMID: 30417139 PMCID: PMC6223224 DOI: 10.1016/j.synbio.2018.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/21/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022] Open
Abstract
Marine natural products have become an increasingly important source of new drug leads during recent years. In an attempt to identify novel anti-microbial natural products by bioprospecting deep-sea Actinobacteria, three new angucyclines, nocardiopsistins A-C, were isolated from Nocardiopsis sp. strain HB-J378. Notably, the supplementation of the rare earth salt Lanthanum chloride (LaCl3) during fermentation of HB-J378 significantly increased the yield of these angucyclines. The structures of nocardiopsistins A-C were identified by 1D and 2D NMR and HR-MS data. Nocardiopsistins A-C have activity against MRSA (methicillin-resistant Staphylococcus aureus) with MICs of 3.12–12.5 μg/mL; the potency of nocardiopsistin B is similar to that of the positive control, chloramphenicol. Bioinformatic analysis of the draft genome of HB-J378 identified a set of three core genes in a biosynthetic gene cluster that encode a typical aromatic or type II polyketide synthase (PKS) system, including ketoacyl:ACP synthase α-subunit (KSα), β-subunit (KSβ) and acyl carrier protein (ACP). The production of nocardiopsistins A-C was abolished when the three genes were knocked out, indicating their indispensable role in the production of nocardiopsistins.
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Affiliation(s)
- Dongbo Xu
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
| | - Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, United States
| | - Dedra Harmody
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, United States
| | - Peter J McCarthy
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
| | - Amy E Wright
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL, 34946, United States
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4
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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5
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Khater S, Anand S, Mohanty D. In silico methods for linking genes and secondary metabolites: The way forward. Synth Syst Biotechnol 2016; 1:80-88. [PMID: 29062931 PMCID: PMC5640692 DOI: 10.1016/j.synbio.2016.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 11/26/2022] Open
Abstract
In silico methods for linking genomic space to chemical space have played a crucial role in genomics driven discovery of new natural products as well as biosynthesis of altered natural products by engineering of biosynthetic pathways. Here we give an overview of available computational tools and then briefly describe a novel computational framework, namely retro-biosynthetic enumeration of biosynthetic reactions, which can add to the repertoire of computational tools available for connecting natural products to their biosynthetic gene clusters. Most of the currently available bioinformatics tools for analysis of secondary metabolite biosynthetic gene clusters utilize the “Genes to Metabolites” approach. In contrast to the “Genes to Metabolites” approach, the “Metabolites to Genes” or retro-biosynthetic approach would involve enumerating the various biochemical transformations or enzymatic reactions which would generate the given chemical moiety starting from a set of precursor molecules and identifying enzymatic domains which can potentially catalyze the enumerated biochemical transformations. In this article, we first give a brief overview of the presently available in silico tools and approaches for analysis of secondary metabolite biosynthetic pathways. We also discuss our preliminary work on development of algorithms for retro-biosynthetic enumeration of biochemical transformations to formulate a novel computational method for identifying genes associated with biosynthesis of a given polyketide or nonribosomal peptide.
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Affiliation(s)
- Shradha Khater
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swadha Anand
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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6
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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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8
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Bindman NA, Bobeica SC, Liu WR, van der Donk WA. Facile Removal of Leader Peptides from Lanthipeptides by Incorporation of a Hydroxy Acid. J Am Chem Soc 2015; 137:6975-8. [PMID: 26006047 PMCID: PMC4505723 DOI: 10.1021/jacs.5b04681] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products typically involves a precursor peptide which contains a leader peptide that is important for the modification process, and that is removed in the final step by a protease. Genome mining efforts for new RiPPs are often hampered by the lack of a general method to remove the leader peptides. We describe here the incorporation of hydroxy acids into the precursor peptides in E. coli which results in connection of the leader peptide via an ester linkage that is readily cleaved by simple hydrolysis. We demonstrate the method for two lantibiotics, lacticin 481 and nukacin ISK-1.
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Affiliation(s)
- Noah A. Bindman
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign
| | - Silvia C. Bobeica
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign
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9
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Genotype-driven isolation of enterocin with novel bioactivities from mangrove-derived Streptomyces qinglanensis 172205. Appl Microbiol Biotechnol 2015; 99:5825-32. [DOI: 10.1007/s00253-015-6574-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 01/03/2023]
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Mousa WK, Raizada MN. Biodiversity of genes encoding anti-microbial traits within plant associated microbes. FRONTIERS IN PLANT SCIENCE 2015; 6:231. [PMID: 25914708 PMCID: PMC4392301 DOI: 10.3389/fpls.2015.00231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/23/2015] [Indexed: 05/10/2023]
Abstract
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.
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Affiliation(s)
- Walaa K. Mousa
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
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12
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Cox CL, Tietz JI, Sokolowski K, Melby JO, Doroghazi JR, Mitchell DA. Nucleophilic 1,4-additions for natural product discovery. ACS Chem Biol 2014; 9:2014-22. [PMID: 24937678 PMCID: PMC4168802 DOI: 10.1021/cb500324n] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Natural
products remain an important source of drug candidates,
but the difficulties inherent to traditional isolation, coupled with
unacceptably high rates of compound rediscovery, limit the pace of
natural product detection. Here we describe a reactivity-based screening
method to rapidly identify exported bacterial metabolites that contain
dehydrated amino acids (i.e., carbonyl- or imine-activated
alkenes), a common motif in several classes of natural products. Our
strategy entails the use of a commercially available thiol, dithiothreitol,
for the covalent labeling of activated alkenes by nucleophilic 1,4-addition.
Modification is easily discerned by comparing mass spectra of reacted
and unreacted cell surface extracts. When combined with bioinformatic
analysis of putative natural product gene clusters, targeted screening
and isolation can be performed on a prioritized list of strains. Moreover,
known compounds are easily dereplicated, effectively eliminating superfluous
isolation and characterization. As a proof of principle, this labeling
method was used to identify known natural products belonging to the
thiopeptide, lanthipeptide, and linaridin classes. Further, upon screening
a panel of only 23 actinomycetes, we discovered and characterized
a novel thiopeptide antibiotic, cyclothiazomycin C.
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Affiliation(s)
- Courtney L. Cox
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan I. Tietz
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Karol Sokolowski
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joel O. Melby
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James R. Doroghazi
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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13
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Kegler C, Nollmann FI, Ahrendt T, Fleischhacker F, Bode E, Bode HB. Rapid determination of the amino acid configuration of xenotetrapeptide. Chembiochem 2014; 15:826-8. [PMID: 24616055 DOI: 10.1002/cbic.201300602] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/15/2014] [Indexed: 02/01/2023]
Abstract
An E. coli strain with deletions in five transaminases (ΔaspC ΔilvE ΔtyrB ΔavtA ΔybfQ) was constructed to be unable to degrade several amino acids. This strain was used as an expression host for the analysis of the amino acid configuration of nonribosomally synthesized peptides, including the novel peptide "xenotetrapeptide" from Xenorhabdus nematophila, by using a combination of labeling experiments and mass spectrometry. Additionally, the number of D-amino acids in the produced peptide was assigned following simple cultivation of the expression strain in D2 O.
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Affiliation(s)
- Carsten Kegler
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
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Zimmermann M, Hegemann JD, Xie X, Marahiel MA. Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation. Chem Sci 2014. [DOI: 10.1039/c4sc01428f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report four new class II lasso peptides featuring alanine and serine at position 1, a bioinformatically identified leader motif and its mutational analysis revealing significant impact on precursor processing.
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Affiliation(s)
- Marcel Zimmermann
- Department of Chemistry, Biochemistry
- Philipps-University Marburg
- Hans-Meerwein-Strasse 4 and LOEWE-Center for Synthetic Microbiology
- Marburg, Germany
| | - Julian D. Hegemann
- Department of Chemistry, Biochemistry
- Philipps-University Marburg
- Hans-Meerwein-Strasse 4 and LOEWE-Center for Synthetic Microbiology
- Marburg, Germany
| | - Xiulan Xie
- Department of Chemistry, Biochemistry
- Philipps-University Marburg
- Hans-Meerwein-Strasse 4 and LOEWE-Center for Synthetic Microbiology
- Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry, Biochemistry
- Philipps-University Marburg
- Hans-Meerwein-Strasse 4 and LOEWE-Center for Synthetic Microbiology
- Marburg, Germany
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Bachmann BO, Van Lanen SG, Baltz RH. Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 2013; 41:175-84. [PMID: 24342967 DOI: 10.1007/s10295-013-1389-9] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 11/26/2013] [Indexed: 01/01/2023]
Abstract
Microbial genome mining is a rapidly developing approach to discover new and novel secondary metabolites for drug discovery. Many advances have been made in the past decade to facilitate genome mining, and these are reviewed in this Special Issue of the Journal of Industrial Microbiology and Biotechnology. In this Introductory Review, we discuss the concept of genome mining and why it is important for the revitalization of natural product discovery; what microbes show the most promise for focused genome mining; how microbial genomes can be mined; how genome mining can be leveraged with other technologies; how progress on genome mining can be accelerated; and who should fund future progress in this promising field. We direct interested readers to more focused reviews on the individual topics in this Special Issue for more detailed summaries on the current state-of-the-art.
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Affiliation(s)
- Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7300 Stevenson Center, Nashville, TN, 37225, USA,
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