Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element

• Published in: Scientific reports Vol. 8; no. 1; pp. 5550 - 11
• Main Authors: Miyazaki, Ryo, Yano, Hirokazu, Sentchilo, Vladimir, van der Meer, Jan Roelof
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.04.2018; Nature Publishing Group
• Subjects: 14/63; 38; 38/44; 38/91; 631/326/171; 631/326/325/2482; 631/326/41/1969; Amino acids; Cell cycle; Chromosomes; Gene expression; Genomes; Humanities and Social Sciences; Metabolism; multidisciplinary; Physiology; Pseudomonas putida; Reproductive fitness; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Stationary phase
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-23858-6

Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICE clc , a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICE clc -located genes. We found that the presence of ICE clc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICE clc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICE clc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICE clc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida .