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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #362152

Research Project: Molecular Identification, Characterization, and Biology of Foreign and Emerging Viral and Bacterial Plant Pathogens

Location: Foreign Disease-Weed Science Research

Title: Dual RNA-seq analyses of Rathayibacter toxicus and bacteriophage NCPPB3778 over a time course following infection

item DRURY, AUSTIN - Mississippi State University
item MASTERS, JILLIAN - Mississippi State University
item Sechler, Aaron
item Tancos, Matthew
item Rogers, Elizabeth
item KING, JONAS - Mississippi State University

Submitted to: American Society for Microbiology Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Rathayibacter toxicus (Actinobacteria: Microbacteriaceae) is a Gram-positive bacterium of major concern to agriculture that has to date only been found in Australia. This species is listed by USDA-APHIS as a select agent because it produces a tunicamycin-like corynetoxin that is lethal, and severely harmful at sub-lethal doses, if consumed by a vertebrate. Tunicamycin production is often associated with the presence of an R. toxicus specific bacteriophage NCPPB3778, although toxin production has also been measured in the absence of phage. The complete genomes of two strains of R. toxicus were recently sequenced and a clear tunicamycin biosynthetic cluster similar to Streptomyces was discovered along with several other putative antimicrobial biosynthetic pathways. Here, we used high-resolution dual analysis of virus and host transcriptomes by deep RNA sequencing to investigate the bacterial transcriptome and production of NCPPB3778 transcripts during the course of infection. We also conducted a transcriptome-informed analysis of the phage genome focusing on potential bacterial transcriptional regulators. The bacterial analyses showed around 200 differentially expressed genes from each time point vs. pre-infection controls. Most notably, a set of bacteriocin biosynthesis genes were sharply upregulated at all time points following infection. Tunicamycin biosynthesis cluster genes were significantly upregulated in samples from the last post-infection time point, suggesting phage involvement in toxin production. Our analyses of NCPPB3778 showed that the genome encodes two putative copies of the actinobacterial-specific transcription factor whiB, one of which is highly expressed during infection. Its presence in this phage-host system adds to a growing list of examples of exaptation of whiB by actinobacteriophages in an apparently widespread strategy to modulate host transcriptional machinery upon infection.