title: Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  Novel 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.
authors.affiliation: University of Cologne, Institute of Biochemistry, Zuelpicher Str, 47, 50674 Cologne, Germany. martin.follmann@uni-koeln.de
authors.forename: Martin
authors.initials: M
authors.lastname: Follmann
authors.forename: Ines
authors.initials: I
authors.lastname: Ochrombel
authors.forename: Reinhard
authors.initials: R
authors.lastname: Krämer
authors.forename: Christian
authors.initials: C
authors.lastname: Trötschel
authors.forename: Ansgar
authors.initials: A
authors.lastname: Poetsch
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.forename: Andrea
authors.initials: A
authors.lastname: Hüser
authors.forename: Marcus
authors.initials: M
authors.lastname: Persicke
authors.forename: Dominic
authors.initials: D
authors.lastname: Seiferling
authors.forename: Jörn
authors.initials: J
authors.lastname: Kalinowski
authors.forename: Kay
authors.initials: K
authors.lastname: Marin
mesh_terms: D000064:Acclimatization; D048230:Corynebacterium glutamicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D006706:Homeostasis / Q000235:genetics*; D006861:Hydrogen Peroxide / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007501:Iron / Q000378:metabolism*; D055442:Metabolome; D008715:Methionine / Q000096:biosynthesis*; D020411:Oligonucleotide Array Sequence Analysis; D018384:Oxidative Stress / Q000235:genetics*; D020543:Proteome / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics
chemical_list: D020543:Proteome; D012329:RNA, Bacterial; D008715:Methionine; D006861:Hydrogen Peroxide; D007501:Iron