title: Gifted microbes for genome mining and natural product discovery.
abstract: Actinomycetes are historically important sources for secondary metabolites (SMs) with applications in human medicine, animal health, and plant crop protection. It is now clear that actinomycetes and other microorganisms with large genomes have the capacity to produce many more SMs than was anticipated from standard fermentation studies. Indeed ~90 % of SM gene clusters (SMGCs) predicted from genome sequencing are cryptic under conventional fermentation and analytical analyses. Previous studies have suggested that among the actinomycetes with large genomes, some have the coding capacity to produce many more SMs than others, and that strains with the largest genomes tend to be the most gifted. These contentions have been evaluated more quantitatively by antiSMASH 3.0 analyses of microbial genomes, and the results indicate that many actinomycetes with large genomes are gifted for SM production, encoding 20-50 SMGCs, and devoting 0.8-3.0 Mb of coding capacity to SM production. Several Proteobacteria and Firmacutes with large genomes encode 20-30 SMGCs and devote 0.8-1.3 Mb of DNA to SM production, whereas cultured bacteria and archaea with small genomes devote insignificant coding capacity to SM production. Fully sequenced genomes of uncultured bacteria and archaea have small genomes nearly devoid of SMGCs.
authors: CognoGen Biotechnology Consulting, 7636 Andora Drive, Sarasota, FL, 34238, USA. rbaltz923@gmail.com.
authors: Richard H
authors: RH
authors: Baltz
mesh_terms: D039903:Actinobacteria / Q000235:genetics*; D020561:Alphaproteobacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D041963:Bacteroidetes / Q000235:genetics; D020562:Betaproteobacteria / Q000235:genetics; D001688:Biological Products / Q000032:analysis*; D000458:Cyanobacteria / Q000235:genetics; D020564:Deltaproteobacteria / Q000235:genetics; D020565:Epsilonproteobacteria / Q000235:genetics; D005285:Fermentation; D020563:Gammaproteobacteria / Q000235:genetics; D064349:Genome, Microbial; D005810:Multigene Family; D017855:Transferases (Other Substituted Phosphate Groups) / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D001688:Biological Products; C082662:phosphopantetheinyl transferase; D017855:Transferases (Other Substituted Phosphate Groups)
keywords: Actinomycetes; Burkholderia; Cryptic pathways; Genome mining; Myxobacteria; Natural products; Secondary metabolites; Streptomyces; Uncultured microbes; antiSMASH 3.0