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Front. Microbiol. | doi: 10.3389/fmicb.2018.02877

Dual RNA-Seq uncovers metabolic amino acids dependency of the intracellular bacterium Piscirickettsia salmonis infecting Atlantic salmon

 Diego Valenzuela-Miranda1 and Cristian Gallardo-Escárate1*
  • 1Centro Interdisciplinario para la Investigación Acuícola, Chile

High-throughput sequencing technologies have offered the possibility to understand the complexity of the transcriptomic responses of an organism during a wide variety of biological scenarios, such as the case of pathogenic infections. Recently, the simultaneous sequencing of both pathogen and host transcriptomes (Dual RNA-seq) during the infection has become a promising approach to uncover the complexity of the host-pathogen interactions. In this study, through a double rRNA depletion and RNA sequencing protocols, we simultaneously analyzed the transcriptome of the intracellular bacterium Piscirickettsia salmonis and its host the Atlantic salmon (Salmo salar) during the course of the infection. Beyond canonical host immune-related response and pathogen virulent factors, both bacteria and host displayed a large number of genes associated with metabolism and particularly related with the amino acid metabolism. Notably, genome-wide comparison among P. salmonis genomes and different fish pathogens genomes revealed a lack of the biosynthetic pathway for several amino acids such as valine, leucine and isoleucine. To support this finding, in vitro experiments evidenced that when these amino acids are restricted the bacterial growth dynamics is significantly affected. However, this condition is phenotypically reversed when the amino acids are supplemented in the bacterial growth medium. Based on our results, a metabolic dependency of P. salmonis on S. salar amino acids is suggested, which could imply novel mechanisms of pathogenesis based on the capacity to uptake nutrients from the host. Overall, dual transcriptome sequencing leads to the understanding of host-pathogen interactions from a different perspective, beyond biological processes related to immunity.

Keywords: Dual RNA-Seq, Piscirickettsia salmonis, Atlantic salmon, nutritional immunity, metabolic dependencies, Amino acid

Received: 07 Aug 2018; Accepted: 09 Nov 2018.

Edited by:

Suhelen Egan, University of New South Wales, Australia

Reviewed by:

Chang Chen, University of Illinois at Chicago, United States
Weiming Sun, Yantai University, China
Khalil Eslamloo, Memorial University of Newfoundland, Canada  

Copyright: © 2018 Valenzuela-Miranda and Gallardo-Escárate. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Cristian Gallardo-Escárate, Centro Interdisciplinario para la Investigación Acuícola, Concepción, Chile,