Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information

Christophe Gitton,Muriel Cocaign-Bousquet,Clémentine Dressaire,Pascal Loubière,Véronique Monnet,Emma Redon

doi:10.1186/1475-2859-10-s1-s18

Abstract

BackgroundAmino acid assimilation is crucial for bacteria and this is particularly true for Lactic Acid Bacteria (LAB) that are generally auxotroph for amino acids. The global response of the LAB model Lactococcus lactis ssp. lactis was characterized during progressive isoleucine starvation in batch culture using a chemically defined medium in which isoleucine concentration was fixed so as to become the sole limiting nutriment. Dynamic analyses were performed using transcriptomic and proteomic approaches and the results were analysed conjointly with fermentation kinetic data.ResultsThe response was first deduced from transcriptomic analysis and corroborated by proteomic results. It occurred progressively and could be divided into three major mechanisms: (i) a global down-regulation of processes linked to bacterial growth and catabolism (transcription, translation, carbon metabolism and transport, pyrimidine and fatty acid metabolism), (ii) a specific positive response related to the limiting nutrient (activation of pathways of carbon or nitrogen metabolism and leading to isoleucine supply) and (iii) an unexpected oxidative stress response (positive regulation of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms during this adaptation was analysed on the basis of transcriptomic data comparisons. The global regulator CodY seemed specifically dedicated to the regulation of isoleucine supply. Other regulations were massively related to growth rate and stringent response.ConclusionThis integrative biology approach provided an overview of the metabolic pathways involved during isoleucine starvation and their regulations. It has extended significantly the physiological understanding of the metabolism of L. lactis ssp. lactis. The approach can be generalised to other conditions and will contribute significantly to the identification of the biological processes involved in complex regulatory networks of micro-organisms.

Highlights

Amino acid assimilation is crucial for bacteria and this is true for Lactic Acid Bacteria (LAB) that are generally auxotroph for amino acids
The dynamic adaptation of L. lactis IL1403 to amino acid starvation was studied in batch culture
A sound description of the response to isoleucine starvation was obtained through a fermentation study coupled with proteomic and transcriptomic analyses in the bacterium model L. lactis IL1403

Summary

Introduction

Amino acid assimilation is crucial for bacteria and this is true for Lactic Acid Bacteria (LAB) that are generally auxotroph for amino acids. The general mechanism of the stringent response, which is mediated by the RelA protein and (p)ppGpp alarmone [13,14,15,16], was seen to be involved Other regulators such as stressrelated alternative sigma factor(s), the carbon catabolite repressor or even other unidentified regulators were assumed to interfere. The well known nitrogen metabolism regulator CodY [18], whose activity was shown to be mediated by the branched chain amino acids (BCAA) pool [18,19], is expected to be involved Since such starvation is always accompanied by modified growth rates, it might be assumed that other general mechanisms associated to growth rate regulation [17,20], would be involved

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