Locating and Activating Molecular 'Time Bombs': Induction of Mycolata Prophages.

Zoe A Dyson,Steve Petrovski,Robert J Seviour,Stephen R Doyle,Teagan L Brown,Ben Farrar,Joseph Tucci,Baochuan Lin

doi:10.1371/journal.pone.0159957

Abstract

Little is known about the prevalence, functionality and ecological roles of temperate phages for members of the mycolic acid producing bacteria, the Mycolata. While many lytic phages infective for these organisms have been isolated, and assessed for their suitability for use as biological control agents of activated sludge foaming, no studies have investigated how temperate phages might be induced for this purpose. Bioinformatic analysis using the PHAge Search Tool (PHAST) on Mycolata whole genome sequence data in GenBank for members of the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella revealed 83% contained putative prophage DNA sequences. Subsequent prophage inductions using mitomycin C were conducted on 17 Mycolata strains. This led to the isolation and genome characterization of three novel Caudovirales temperate phages, namely GAL1, GMA1, and TPA4, induced from Gordonia alkanivorans, Gordonia malaquae, and Tsukamurella paurometabola, respectively. All possessed highly distinctive dsDNA genome sequences.

Highlights

The availability of generation DNA sequencing has resulted in a dramatic increase in the number of draft and fully annotated bacterial genomes
Bacterial and plasmid whole genome sequence data were obtained from GenBank by searching for the genera of interest by name (Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella), and those present are described in detail in S1 and S2 Tables
All available whole genome sequence data from Gordonia, Nocardia, Rhodococcus, Tsukamurella, Mycobacterium strains and their corresponding plasmid sequences were downloaded from the GenBank database on 26th February 2014, and 1st July 2014

Summary

Introduction

The availability of generation DNA sequencing has resulted in a dramatic increase in the number of draft and fully annotated bacterial genomes. Complete genome sequences of phages infective for other mycolic acid producing bacteria, the Mycolata, a distinct evolutionary lineage in the Actinobacteria, have been obtained [3,4,5,6,7,8,9]. Their hosts include members of the genera Gordonia, Nocardia, Rhodococcus, and Tsukamurella. Some share both nucleotide and amino acid sequence similarity with each other, and with some mycobacteriophages [4,5,6, 8,9]

Methods

Results

Conclusion