IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase

Palaniappan, Krishnaveni; Chen, I-Min A.; Chu, Ken; Ratner, Anna; Seshadri, Rekha; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mouncey, Nigel J.

doi:10.1093/nar/gkz932

IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase

Journal Article · Tue Oct 29 00:00:00 EDT 2019 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkz932· OSTI ID:1661596

Palaniappan, Krishnaveni ^[1]; Chen, I-Min A. ^[1]; Chu, Ken ^[1]; Ratner, Anna ^[1]; Seshadri, Rekha ^[1]; Kyrpides, Nikos C. ^[1]; Ivanova, Natalia N. ^[1]; Mouncey, Nigel J. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division

Microbial secondary metabolism is a reservoir of bioactive compounds of immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production of these secondary metabolites (SMs) (also called natural products) is often encoded by collocated groups of genes called biosynthetic gene clusters (BGCs). Here, high-throughput genome sequencing of both isolates and metagenomic samples combined with the development of specialized computational workflows is enabling systematic identification of BGCs and the discovery of novel SMs. In order to advance exploration of microbial secondary metabolism and its diversity, we developed the largest publicly available database of predicted BGCs combined with experimentally verified BGCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc-public). Here we describe the first major content update of the IMG-ABC knowledgebase, since its initial release in 2015, refreshing the BGC prediction pipeline with the latest version of antiSMASH (v5) as well as presenting the data in the context of underlying environmental metadata sourced from GOLD (https://gold.jgi.doe.gov/). This update has greatly improved the quality and expanded the types of predicted BGCs compared to the previous version.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1661596

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 48; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (45)

Metabolites from Symbiotic Bacteria Piel, Joern ChemInform, Vol. 35, Issue 46 https://doi.org/10.1002/chin.200446294	journal	November 2004
Natural product discovery: past, present, and future Katz, Leonard; Baltz, Richard H. Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 2-3 https://doi.org/10.1007/s10295-015-1723-5	journal	January 2016
Gifted microbes for genome mining and natural product discovery Baltz, Richard H. Journal of Industrial Microbiology & Biotechnology, Vol. 44, Issue 4-5 https://doi.org/10.1007/s10295-016-1815-x	journal	August 2016
New voyages to explore the natural product galaxy Mouncey, Nigel J.; Otani, Hiroshi; Udwary, Daniel Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 3-4 https://doi.org/10.1007/s10295-018-02122-w	journal	January 2019
Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities Baltz, Richard H. Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 3-4 https://doi.org/10.1007/s10295-018-2115-4	journal	November 2018
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters Cimermancic, Peter; Medema, Marnix H.; Claesen, Jan Cell, Vol. 158, Issue 2 https://doi.org/10.1016/j.cell.2014.06.034	journal	July 2014
A New Golden Age of Natural Products Drug Discovery Shen, Ben Cell, Vol. 163, Issue 6 https://doi.org/10.1016/j.cell.2015.11.031	journal	December 2015
Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases Guo, Chun-Jun; Chang, Fang-Yuan; Wyche, Thomas P. Cell, Vol. 168, Issue 3 https://doi.org/10.1016/j.cell.2016.12.021	journal	January 2017
Metabolic engineering of microbial pathways for advanced biofuels production Zhang, Fuzhong; Rodriguez, Sarah; Keasling, Jay D. Current Opinion in Biotechnology, Vol. 22, Issue 6 https://doi.org/10.1016/j.copbio.2011.04.024	journal	December 2011
Cysteine S -glycosylation, a new post-translational modification found in glycopeptide bacteriocins Stepper, Judith; Shastri, Shilpa; Loo, Trevor S. FEBS Letters, Vol. 585, Issue 4 https://doi.org/10.1016/j.febslet.2011.01.023	journal	January 2011
The glycocins: in a class of their own Norris, Gillian E.; Patchett, Mark L. Current Opinion in Structural Biology, Vol. 40 https://doi.org/10.1016/j.sbi.2016.09.003	journal	October 2016
Natural Products and the Gene Cluster Revolution Jensen, Paul R. Trends in Microbiology, Vol. 24, Issue 12 https://doi.org/10.1016/j.tim.2016.07.006	journal	December 2016
Natural Products as Sources of New Drugs from 1981 to 2014 Newman, David J.; Cragg, Gordon M. Journal of Natural Products, Vol. 79, Issue 3 https://doi.org/10.1021/acs.jnatprod.5b01055	journal	October 2015
Rapid Discovery of Glycocins through Pathway Refactoring in Escherichia coli Ren, Hengqian; Biswas, Subhanip; Ho, Sherri ACS Chemical Biology, Vol. 13, Issue 10 https://doi.org/10.1021/acschembio.8b00599	journal	September 2018
The Glycosyltransferase Involved in Thurandacin Biosynthesis Catalyzes Both O- and S-Glycosylation Wang, Huan; Oman, Trent J.; Zhang, Ran Journal of the American Chemical Society, Vol. 136, Issue 1 https://doi.org/10.1021/ja411159k	journal	December 2013
Specialized microbial metabolites: functions and origins Davies, Julian The Journal of Antibiotics, Vol. 66, Issue 7 https://doi.org/10.1038/ja.2013.61	journal	June 2013
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
A new antibiotic kills pathogens without detectable resistance Ling, Losee L.; Schneider, Tanja; Peoples, Aaron J. Nature, Vol. 517, Issue 7535 https://doi.org/10.1038/nature14098	journal	January 2015
A roadmap for natural product discovery based on large-scale genomics and metabolomics Doroghazi, James R.; Albright, Jessica C.; Goering, Anthony W. Nature Chemical Biology, Vol. 10, Issue 11 https://doi.org/10.1038/nchembio.1659	journal	September 2014
Computational approaches to natural product discovery Medema, Marnix H.; Fischbach, Michael A. Nature Chemical Biology, Vol. 11, Issue 9 https://doi.org/10.1038/nchembio.1884	journal	August 2015
Minimum Information about a Biosynthetic Gene cluster Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin Nature Chemical Biology, Vol. 11, Issue 9 https://doi.org/10.1038/nchembio.1890	journal	August 2015
A new genome-mining tool redefines the lasso peptide biosynthetic landscape Tietz, Jonathan I.; Schwalen, Christopher J.; Patel, Parth S. Nature Chemical Biology, Vol. 13, Issue 5 https://doi.org/10.1038/nchembio.2319	journal	February 2017
Sublancin is not a lantibiotic but an S-linked glycopeptide Oman, Trent J.; Boettcher, John M.; Wang, Huan Nature Chemical Biology, Vol. 7, Issue 2 https://doi.org/10.1038/nchembio.509	journal	January 2011
Heterologous biosynthesis and characterization of a glycocin from a thermophilic bacterium Kaunietis, Arnoldas; Buivydas, Andrius; Čitavičius, Donaldas J. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09065-5	journal	March 2019
Metabolites from symbiotic bacteria Piel, Jörn Nat. Prod. Rep., Vol. 26, Issue 3 https://doi.org/10.1039/B703499G	journal	January 2009
Natural products in soil microbe interactions and evolution Traxler, Matthew F.; Kolter, Roberto Natural Product Reports, Vol. 32, Issue 7 https://doi.org/10.1039/C5NP00013K	journal	January 2015
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites Chavali, Arvind K.; Rhee, Seung Y. Briefings in Bioinformatics, Vol. 19, Issue 5 https://doi.org/10.1093/bib/bbx020	journal	April 2017
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters Blin, Kai; Kim, Hyun Uk; Medema, Marnix H. Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx146	journal	November 2017
An iterative glycosyltransferase EntS catalyzes transfer and extension of O- and S-linked monosaccharide in enterocin 96 Nagar, Rupa; Rao, Alka Glycobiology, Vol. 27, Issue 8 https://doi.org/10.1093/glycob/cwx042	journal	May 2017
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences Medema, Marnix H.; Blin, Kai; Cimermancic, Peter Nucleic Acids Research, Vol. 39, Issue suppl_2 https://doi.org/10.1093/nar/gkr466	journal	June 2011
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers Blin, Kai; Medema, Marnix H.; Kazempour, Daniyal Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt449	journal	May 2013
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters Weber, Tilmann; Blin, Kai; Duddela, Srikanth Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv437	journal	May 2015
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1103	journal	November 2016
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters Blin, Kai; Medema, Marnix H.; Kottmann, Renzo Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw960	journal	October 2016
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification Blin, Kai; Wolf, Thomas; Chevrette, Marc G. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx319	journal	April 2017
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 2018
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline Blin, Kai; Shaw, Simon; Steinke, Katharina Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz310	journal	April 2019
Thermoactinomyces sacchari sp.nov., a Thermophilic Actinomycete Causing Bagassosis Lacey, J. Journal of General Microbiology, Vol. 66, Issue 3 https://doi.org/10.1099/00221287-66-3-327	journal	June 1971
Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria Mendes, R.; Kruijt, M.; de Bruijn, I. Science, Vol. 332, Issue 6033 https://doi.org/10.1126/science.1203980	journal	May 2011
Small molecules from the human microbiota Donia, M. S.; Fischbach, M. A. Science, Vol. 349, Issue 6246 https://doi.org/10.1126/science.1254766	journal	July 2015
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken mBio, Vol. 6, Issue 4 https://doi.org/10.1128/mBio.00932-15	journal	July 2015
Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology Grubbs, Kirk J.; Bleich, Rachel M.; Santa Maria, Kevin C. mSystems, Vol. 2, Issue 6 https://doi.org/10.1128/mSystems.00040-17	journal	November 2017
Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products Gomez-Escribano, Juan; Alt, Silke; Bibb, Mervyn Marine Drugs, Vol. 14, Issue 4 https://doi.org/10.3390/md14040078	journal	April 2016
New Approaches to Detect Biosynthetic Gene Clusters in the Environment Chen, Ray; Wong, Hon; Burns, Brendan Medicines, Vol. 6, Issue 1 https://doi.org/10.3390/medicines6010032	journal	February 2019

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