A Global Transcriptional Switch between the Attack and Growth Forms of Bdellovibrio bacteriovorus

Iris Karunker,Mally Dori-Bachash,Rotem Sorek,Edouard Jurkevitch,Or Rotem,Brian Stevenson

doi:10.1371/journal.pone.0061850

Iris Karunker, Mally Dori-Bachash + Show 4 more

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https://doi.org/10.1371/journal.pone.0061850

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Abstract

Bdellovibrio bacteriovorus is an obligate predator of bacteria ubiquitously found in the environment. Its life cycle is composed of two essential phases: a free-living, non-replicative, fast swimming attack phase (AP) wherein the predator searches for prey; and a non-motile, actively dividing growth phase (GP) in which it consumes the prey. The molecular regulatory mechanisms governing the switch between AP and GP are largely unknown. We used RNA-seq to generate a single-base-resolution map of the Bdellovibrio transcriptome in AP and GP, revealing a specific "AP" transcriptional program, which is largely mutually exclusive of the GP program. Based on the expression map, most genes in the Bdellovibrio genome are classified as "AP only" or "GP only". We experimentally generated a genome-wide map of 140 AP promoters, controlling the majority of AP-specific genes. This revealed a common sigma-like DNA binding site highly similar to the E. coli flagellar genes regulator sigma28 (FliA). Further analyses suggest that FliA has evolved to become a global AP regulator in Bdellovibrio. Our results also reveal a non-coding RNA that is massively expressed in AP. This ncRNA contains a c-di-GMP riboswitch. We suggest it functions as an intracellular reservoir for c-di-GMP, playing a role in the rapid switch from AP to GP.

Highlights

Bdellovibrio bacteriovorus is an obligate predator of gram negative bacteria ubiquitously found in bulk soil, in the rhizosphere of plants, and in freshwater bodies such as rivers and water treatment facilities [1]
To attain the transcriptional landscape of B. bacteriovorus under different growth phases, RNA was extracted either from (i) attackphase B. bacteriovorus; (ii) B. bacteriovorus synchronically growing within E. coli 1 hour after infection; and (iii) B. bacteriovorus synchronically growing within E. coli 3 hours after infection
Mapping of reads to the genomes of B. bacteriovorus and E. coli enabled separation between RNA derived from the predator and that derived from the prey; this mapping revealed that 1 hour post infection, 99.6% of the RNA is still that of the prey, whereas 3 hours post infection, RNA of the predator increased 13-folds (Table 1)

Summary

Introduction

Bdellovibrio bacteriovorus is an obligate predator of gram negative bacteria ubiquitously found in bulk soil, in the rhizosphere of plants, and in freshwater bodies such as rivers and water treatment facilities [1]. This organism can prey on a wide range of bacteria, including many pathogens of humans and plants, and has been suggested as an effective "living antibiotics" [2]. The GP cycle of B. bacteriovorus lasts about 4 hours, with the prey being killed within 30 minutes, and bdelloplast exhaustion and division of elongated B. bacteriovorus cells occurring about 3 hours after the initial attachment to the prey [6]. The cycle is completed by a subsequent rupturing of the bdelloplast envelope and a release of daughter AP cells

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