MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli
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ORIGINAL PAPER
MazF activation causes ACA sequence‑independent and selective alterations in RNA levels in Escherichia coli Kentaro Akiyama1 · Kazuki Fujisawa1 · Hiro Kondo1 · Yuya Netsu1 · Koji Nishikawa1 · Yoshio Takata1 · Yuya Nakamura2 · Yuta Kino2 · Shotaro Ayukawa3 · Masayuki Yamamura4 · Nobuhiro Hayashi2 · Yoh‑ichi Tagawa2 · Nobutaka Nakashima3,2,5 Received: 7 June 2019 / Revised: 21 August 2019 / Accepted: 27 August 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019
Abstract Escherichia coli MazF is a toxin protein that cleaves RNA at ACA sequences. Its activation has been thought to cause growth inhibition, primarily through indiscriminate cleavage of RNA. To investigate responses following MazF activation, transcriptomic profiles of mazF-overexpressing and non-overexpressing E. coli K12 cells were compared. Analyses of differentially expressed genes demonstrated that the presence and the number of ACA trimers in RNA was unrelated to cellular RNA levels. Mapping differentially expressed genes onto the chromosome identified two chromosomal segments in which upregulated genes formed clusters, and these segments were absent in the chromosomes of E. coli strains other than K12. These results suggest that MazF regulates selective, rather than indiscriminate, categories of genes, and is involved in the regulation of horizontally acquired genes. We conclude that the primary role of MazF is not only cleaving RNA indiscriminately but also generating a specific cellular state. Keywords Horizontal gene transfer · MazF · Metatranscriptome · RNA-interferase · RNA-seq · Toxin-antitoxin
Introduction Communicated by Erko Stackebrandt. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00203-019-01726-9) contains supplementary material, which is available to authorized users. * Nobutaka Nakashima n‑[email protected] 1
iGEM Team Tokyo_Tech 2016, Tokyo Institute of Technology, 2‑12‑1 Ookayama, Meguro‑ku, Tokyo 152‑8550, Japan
2
School of Life Science and Technology, Tokyo Institute of Technology, 2‑12‑1 Ookayama, Meguro‑ku, Tokyo 152‑8550, Japan
3
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‑17‑2‑1 Tsukisamu‑Higashi 2‑jyo, Toyohira‑ku, Sapporo 062‑8517, Japan
4
School of Computing, Tokyo Institute of Technology, 4259 Nagatsuta‑cho, Midori‑ku, Yokohama 226‑8503, Japan
5
Computational Bio Big Data Open Innovation Laboratory (CBBD‑OIL), AIST, 2‑17‑2‑1 Tsukisamu‑Higashi, Toyohira‑ku, Sapporo 062‑8517, Japan
Bacterial chromosomes encode various toxin–antitoxin (TA) systems. For example, the chromosome of the Escherichia coli MG1655 strain, a derivative of the K12 linage, encodes at least 37 TA systems (Yamaguchi and Inouye 2011; Wang et al. 2012). The function of a toxin-encoding gene is repressed by the action of a cognate antitoxin gene in vegetatively growing cells but is de-repressed (activated) under certain conditions to cause complete cell death, reversible growth arre
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