pH-Dependent Catabolic Protein Expression during Anaerobic Growth of Escherichia coli K-12

Abstract

During aerobic growth of Escherichia coli, expression of catabolic enzymes and envelope and periplasmic proteins is regulated by pH. Additional modes of pH regulation were revealed under anaerobiosis. E. coli K-12 strain W3110 was cultured anaerobically in broth medium buffered at pH 5.5 or 8.5 for protein identification on proteomic two-dimensional gels. A total of 32 proteins from anaerobic cultures show pH-dependent expression, and only four of these proteins (DsbA, TnaA, GatY, and HdeA) showed pH regulation in aerated cultures. The levels of 19 proteins were elevated at the high pH; these proteins included metabolic enzymes (DhaKLM, GapA, TnaA, HisC, and HisD), periplasmic proteins (ProX, OppA, DegQ, MalB, and MglB), and stress proteins (DsbA, Tig, and UspA). High-pH induction of the glycolytic enzymes DhaKLM and GapA suggested that there was increased fermentation to acids, which helped neutralize alkalinity. Reporter lac fusion constructs showed base induction of sdaA encoding serine deaminase under anaerobiosis; in addition, the glutamate decarboxylase genes gadA and gadB were induced at the high pH anaerobically but not with aeration. This result is consistent with the hypothesis that there is a connection between the gad system and GabT metabolism of 4-aminobutanoate. On the other hand, 13 other proteins were induced by acid; these proteins included metabolic enzymes (GatY and AckA), periplasmic proteins (TolC, HdeA, and OmpA), and redox enzymes (GuaB, HmpA, and Lpd). The acid induction of NikA (nickel transporter) is of interest because E. coli requires nickel for anaerobic fermentation. The position of the NikA spot coincided with the position of a small unidentified spot whose induction in aerobic cultures was reported previously; thus, NikA appeared to be induced slightly by acid during aeration but showed stronger induction under anaerobic conditions. Overall, anaerobic growth revealed several more pH-regulated proteins; in particular, anaerobiosis enabled induction of several additional catabolic enzymes and sugar transporters at the high pH, at which production of fermentation acids may be advantageous for the cell.pH response is important for growth and survival of Escherichia coli in an environment such as the human gastrointestinal tract, in which the pH fluctuates over the range from pH 6 to 8 (14, 18). The role of pH in gene expression in E. coli and related enteric bacteria has been studied extensively, but it has been studied largely under aerobic conditions (7,11,59,64,66; for reviews see references 15 and 54). Relatively few studies have addressed the relationship between pH and anaerobiosis, the predominant condition of enteric growth (2); the beststudied cases include anaerobic acid induction of amino acid decarboxylases (1, 6, 61) and a limited two-dimensional (2-D) gel study of protein profiles (7). However, enteric bacteria behave very differently under anaerobic and aerobic conditions; for example, in microarrays more than one-third of the genes expressed during aerobic growth are ...

STOP1 Regulates Multiple Genes That Protect Arabidopsis from Proton and Aluminum Toxicities

“…In addition, an integrated analysis of metabolites and transcripts revealed that metabolic pathways that have been assumed to regulate cytosolic pH of the plant (biochemical pH stat [Sakano, 1998] and g-aminobutyric acid [GABA] shunt [Bouche and Fromm, 2004] pathways) were also down-regulated in the mutant. Interestingly, both ion homeostasis and pH-regulating metabolism are critical for low pH resistance in other organisms, such as Escherichia coli (Yohannes et al, 2004) and fish (Hirata et al, 2003) and possibly in higher plants (Yan et al, 1992). These results indicated that STOP1 regulates multiple tolerant mechanisms to major stress factors of acid soil and that some of the H 1 -resistant systems down-regulated in the stop1 mutant are similar to those of other organisms.…”

“…Interestingly, orthologs of these genes have been identified as critical for adaptation to acidic environments in other organisms (Castanie-Cornet et al, 1999). For E. coli, GAD is essential for surviving in low-pH medium (Yohannes et al, 2004). These genes, which are down-regulated in the stop1 mutant, could be involved in low-pH-tolerant mechanisms in Arabidopsis.…”

Computational identification of significantly regulated metabolic reactions by integration of data on enzyme activity and gene expression

“…Among the reactions that were significantly regulated by the control of enzyme activity, we identified reactions in which our results agreed with the previous case studies (6,(19)(20)(21)(22)(23)(24)(25) by looking for perturbations that had high significance scores. Following anaerobic perturbation, we identified significant reactions that are related to the central metabolism.…”

Role of Indole Production on Virulence of Vibrio cholerae Using Galleria mellonella Larvae Model

“…This might be due to the test bacterium was a clinical isolate and preferred the conditions close to that of the human intestine (neutral pH). In E. coli, it has been found that alkalinity could induce the expression of tnaA gene leading to high tryptophanase activity and active indole production [13,28,29]. In this study, we found that at pH 7, all clinical isolates of V. cholerae and environmental isolates produced similar amounts of indole, although indole production in one environmental isolate was significantly different ( Table 1).…”