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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #311879
Title: A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

Author
item Labeda, David
item DOROGHAZI, JAMES - University Of Illinois
item JU, KU-SAN - University Of Illinois
item METCALF, WILLIAM - University Of Illinois

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2015
Publication Date: 1/15/2015
Citation: Labeda, D.P., Doroghazi, J.R., Ju, K., Metcalf, W.W. 2015. A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining [abstract].

Interpretive Summary:

Technical Abstract: The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomycetaceae. The partial sequences of 5 house-keeping protein genes (atpD, gyrB, recA, rpoB, and trpB) are being generated for the type strains of all species in the Streptomycetaceae to provide a tool for the study of the systematics of this family as well as a definitive method for the identification of uncharacterized Streptomyces strains using multi-locus sequence analysis (MLSA). The database currently includes more than 731 unique sequence type profiles generated from 878 strains, including 205 strains with genome sequences. It is possible to classify previously unidentified strains as either known or new species with these data. The BIGSdb software provides for searching genome sequences for specific gene loci of interest and a pilot study was done using the phosphoenolpyruvate mutase (pepM) gene from Streptomyces griseus as a new locus for searching. Many of the genomes currently included in the database are known producers of phosphonate-containing natural products. A total of 54 of the 250 genomes in the study were found to contain one of 46 different alleles of the pepM locus, generally clustered within phylogenetic groups defined from MLSA analysis, demonstrating the utility of the sequence database and associated software to discover biosynthetic genes. This was confirmed by configuring the gene tunB (the radical SAM protein) from the tunicamycin biosynthetic pathway as a locus for searching. Alleles of tunB were found in the strains expected that were present in the database (e.g., Streptomyces chartreusis NRRL 12388, Streptomyces clavuligerus ATCC 27064, and Streptomyces lysosuperficus ATCC 31396), but this gene locus was also unexpectedly found in Streptomyces niger NRRL B-3857 and Streptomyces species NRRL F-6144. Studies are in progress to determine if tunicamycin is produced by these strains.