Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Abstract

BackgroundThe maintenance of internal pH in bacterial cells is challenged by natural stress conditions, during host infection or in biotechnological production processes. Comprehensive transcriptomic and proteomic analyses has been conducted in several bacterial model systems, yet questions remain as to the mechanisms of pH homeostasis.ResultsHere we present the comprehensive analysis of pH homeostasis in C. glutamicum, a bacterium of industrial importance. At pH values between 6 and 9 effective maintenance of the internal pH at 7.5 ± 0.5 pH units was found. By DNA microarray analyses differential mRNA patterns were identified. The expression profiles were validated and extended by 1D-LC-ESI-MS/MS based quantification of soluble and membrane proteins. Regulators involved were identified and thereby participation of numerous signaling modules in pH response was found. The functional analysis revealed for the first time the occurrence of oxidative stress in C. glutamicum cells at neutral and low pH conditions accompanied by activation of the iron starvation response. Intracellular metabolite pool analysis unraveled inhibition of the TCA and other pathways at low pH. Methionine and cysteine synthesis were found to be activated via the McbR regulator, cysteine accumulation was observed and addition of cysteine was shown to be toxic under acidic conditions.ConclusionsNovel limitations for C. glutamicum at non-optimal pH values were identified by a comprehensive analysis on the level of the transcriptome, proteome, and metabolome indicating a functional link between pH acclimatization, oxidative stress, iron homeostasis, and metabolic alterations. The results offer new insights into bacterial stress physiology and new starting points for bacterial strain design or pathogen defense.

Mycothiol protects <i>Corynebacterium glutamicum</i> against acid stress via maintaining intracellular pH homeostasis, scavenging ROS, and <i>S</i>-mycothiolating MetE

“…Further studies on acid stress response in C. glutamicum, based on transcriptome, proteome, and metabolome, unraveled a functional link between pH acclimatization, oxidative stress, iron homeostasis, and metabolic alterations (Follmann et al, 2009). The occurrence of oxidative stress under acid stress was also observed in Bacillus cereus, accompanied by the formation of reactive oxygen species (ROS), and the activation of oxidative stress associated genes such as thioredoxins, catalases and superoxide dismutase (Mols and Abee, 2011b;Mols et al, 2010).…”

“…Acid stress is one of the common conditions bacteria are exposed to in nature, which generally affects the solubility of nutrients and trace elements, and the physiology of the cell (Follmann et al, 2009). To survive acid stress, bacteria adopt a variety of acid-resistant mechanisms, including the restriction of proton entry, the expelling of intracellular protons, the production of macromolecular protection proteins and chaperones, and the neutralization of the cytoplasm (Baker-Austin and Dopson, 2007;Foster, 2004;Krulwich et al, 2011).…”

“…Corynebacterium glutamicum, a fast growing soil bacterium widely used for the industrial production of amino acids and nucleotides, serves also as a laboratory model for the investigation of its pathogenic relatives C. diphtheriae, C. jeikeium or mycobacteria (Follmann et al, 2009), and for the disclosing of catabolism mechanisms of aromatic compounds in high GC content Gram-positive bacteria (Shen et al, 2012). C. glutamicum is an acid sensitive bacterium as the minimal pH it tolerated was found to be 5.5 (Jakob et al, 2007).…”

“…Interestingly, the atp gene cluster encoding the F 1 F 0 -ATPase, whose roles in proton pumping under acid stress are well documented, was found to be down-regulated under acidic conditions (BarriusoIglesias et al, 2008;Zhang et al, 2007). Besides, the genes encoding glutamate decarboxylase, arginine decarboxylase and arginine deiminase, which represent another widely-distributed acid resistance mechanism resulting in the alkalization of the cytoplasm, are missing in C. glutamicum (Follmann et al, 2009). Therefore, there are some novel acid adaptation mechanisms in the acid sensitive C. glutamicum that are worthy of investigation.…”

“…The occurrence of oxidative stress under acid stress was also observed in Bacillus cereus, accompanied by the formation of reactive oxygen species (ROS), and the activation of oxidative stress associated genes such as thioredoxins, catalases and superoxide dismutase (Mols and Abee, 2011b;Mols et al, 2010). However, although elimination of acid induced H 2 O 2 by the addition of external catalase facilitates the growth of C. glutamicum at a neutral pH, the addition of catalase had no significant beneficial effect on growth under acidic pH conditions (Follmann et al, 2009). This observation raises the question as whether, and how, other non-enzymatic antioxidants, such as mycothiol, function in the adaptation of C. glutamicum to acidic pH conditions.…”