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Title: Whole genome sequence of two Rathayibacter toxicus strains reveals a tunicamycin biosynthetic cluster similar to Streptomyces chartreusis

Author
item Sechler, Aaron
item Tancos, Matthew
item SCHNEIDER, DAVID - University Of Saskatoon
item KING, JONAS - Mississippi State University
item FENNESEY, CHRISTINE - National Cancer Institute (NCI, NIH)
item SCHROEDER, BRENDA - University Of Idaho
item Luster, Douglas - Doug
item Schneider, William
item Rogers, Elizabeth

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2017
Publication Date: 8/10/2017
Citation: Sechler, A.J., Tancos, M.A., Schneider, D.J., King, J.G., Fennesey, C.M., Schroeder, B.K., Luster, D.G., Schneider, W.L., Rogers, E.E. 2017. Whole genome sequence of two Rathayibacter toxicus strains reveals a tunicamycin biosynthetic cluster similar to Streptomyces chartreusis. PLoS One. 12(8):e0183005.

Interpretive Summary: Rathayibacter toxicus is a bacterium that grows in developing grass seeds and can produce a toxin harmful to grazing livestock. So far, R. toxicus has only been found in Australia. The threat it poses to U.S. agriculture is such that the USDA Animal Plant Health Inspection Service (APHIS) has placed R. toxicus on a list of high-consequence agents with the potential to pose a severe threat to public health and safety. It was not known how R. toxicus makes its toxin. Here we report the complete genome sequence of two strains of R. toxicus and the identification of a group of genes that are probably responsible for toxin production. This work is a critical first step toward understanding the control of toxin production and will aid in the development of diagnostic tests to identify R. toxicus.

Technical Abstract: Rathayibacter toxicus is a forage grass associated Gram-positive bacterium of major concern to food safety and agriculture. The species is listed by USDA-APHIS as a plant pathogen select agent due to the fact that it produces a tunicamycin-like toxin that is lethal to livestock. The complete genomes of two strains of R. toxicus, including the type strain FH-79, were sequenced and analyzed in comparison with all available, complete R. toxicus genomes. Genome sizes ranged from 2,343,780 to 2,401,933 nucleotides, with 2078 to 2137 predicted open reading frames; all four strains showed remarkable synteny over nearly the entire genome, with only a small transposed region. A cluster of genes with similarity to the tunicamycin biosynthetic cluster from Streptomyces chartreusis was identified. The tunicamycin gene cluster (TGC) in R. toxicus contained 14 genes in two transcriptional units, with all of the functional elements for tunicamycin biosynthesis present. The TGC had a significantly lower GC content (52%) than the rest of the genome (61.5%), suggesting that the TGC may have originated from a horizontal transfer event. Further analysis indicated numerous other potential horizontal transfer events are present in the genome. In addition to the TGC, genes potentially associated with carotenoid and exopolysaccharide production, bacteriocins and secondary metabolites were identified. A CRISPR array is evident. There were relatively few plant-associated cell-wall hydrolyzing enzymes, but there were numerous secreted serine proteases that share sequence homology to the pathogenicity-associated protein Pat-1 of Clavibacter michiganensis. Overall, the genome provides clear insight into the possible mechanisms for toxin production in R. toxicus, providing a basis for future genetic approaches.