Escherichia coli grows over a wide range of pHs (pH 4.4 to 9.2), and its own metabolism shifts the external pH toward either extreme, depending on available nutrients and electron acceptors. Responses to pH values across the growth range were examined through two-dimensional electrophoresis (2-D gels) of the proteome and through lac gene fusions. Strain W3110 was grown to early log phase in complex broth buffered at pH 4.9, 6.0, 8.0, or 9.1. 2-D gel analysis revealed the pH dependence of 19 proteins not previously known to be pH dependent. At low pH, several acetate-induced proteins were elevated (LuxS, Tpx, and YfiD), whereas acetaterepressed proteins were lowered (Pta, TnaA, DksA, AroK, and MalE). These responses could be mediated by the reuptake of acetate driven by changes in pH. The amplified proton gradient could also be responsible for the acid induction of the tricarboxylic acid (TCA) enzymes SucB and SucC. In addition to the autoinducer LuxS, low pH induced another potential autoinducer component, the LuxH homolog RibB. pH modulated the expression of several periplasmic and outer membrane proteins: acid induced YcdO and YdiY; base induced OmpA, MalE, and YceI; and either acid or base induced OmpX relative to pH 7. Two pH-dependent periplasmic proteins were redox modulators: Tpx (acid-induced) and DsbA (base-induced). The locus alx, induced in extreme base, was identified as ygjT, whose product is a putative membrane-bound redox modulator. The cytoplasmic superoxide stress protein SodB was induced by acid, possibly in response to increased iron solubility. High pH induced amino acid metabolic enzymes (TnaA and CysK) as well as lac fusions to the genes encoding AstD and GabT. These enzymes participate in arginine and glutamate catabolic pathways that channel carbon into acids instead of producing alkaline amines. Overall, these data are consistent with a model in which E. coli modulates multiple transporters and pathways of amino acid consumption so as to minimize the shift of its external pH toward either acidic or alkaline extreme.

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 ...

Cellulose fibrils play a role in attachment of Agrobacterium tumefaciens to its plant host. While the genes for cellulose biosynthesis in the bacterium have been identified, little is known concerning the regulation of the process. The signal molecule cyclic di-GMP (c-di-GMP) has been linked to the regulation of exopolysaccharide biosynthesis in many bacterial species, including A. tumefaciens. In this study, we identified two putative diguanylate cyclase genes, celR (atu1297) and atu1060, that influence production of cellulose in A. tumefaciens. Overexpression of either gene resulted in increased cellulose production, while deletion of celR, but not atu1060, resulted in decreased cellulose biosynthesis. celR overexpression also affected other phenotypes, including biofilm formation, formation of a polar adhesion structure, plant surface attachment, and virulence, suggesting that the gene plays a role in regulating these processes. Analysis of celR and ⌬cel mutants allowed differentiation between phenotypes associated with cellulose production, such as biofilm formation, and phenotypes probably resulting from c-di-GMP signaling, which include polar adhesion, attachment to plant tissue, and virulence. Phylogenetic comparisons suggest that species containing both celR and celA, which encodes the catalytic subunit of cellulose synthase, adapted the CelR protein to regulate cellulose production while those that lack celA use CelR, called PleD, to regulate specific processes associated with polar localization and cell division.

Protein spectra from 4n and 6n species of Triticum were obtained by electrophoresis of seed extracts on polyacrylamide gels. Homologies among the species with regard to protein bands were tested by comparing each species with the standard T. dicoccum in a protein mixture spectrum. By reference to two pairs of homologous bands, each spectrum was then adjusted to the migration velocity of the standard by photographic enlargement. The homologies were found to be consistent with evidence from conventional methods regarding genome relationships among the Triticum polyploids. T. dicoccoides and other known AABB tetraploids showed nine fast‐moving albumin homologues, while T. timopheevi and other known AAGG tetraploids showed seven. The two genomic groups had five albumin bands in common. The hexaploid (AABBDD) subspecies showed 12 albumin homologues, 9 of which were also homologous with the 9 of the AABB tetraploids and 3 of which were attributed to the D‐genome donor. Differences among species within each of the tetraploid genomic groups and among the hexaploid subspecies were largely confined to the slow‐moving bands of the gliadin series.

As Kihara had only 1 to 3 accessions of each diploid analyzer species in his germplasm collection, we conclude the genome formulae for Aegilops and Triticum published by him between 1920 and 1960 were largely based on the typological concept applied to cytogenetic research. The same restriction applies to his concept of “modified genomes” in the tetraploid Aegilops species, which therefore may not actually be modified. Genome analysis by itself is not a very fine‐tuned experimental technique. A biological species concept based on several different biosystematic studies in Aegilops and Triticum is preferable to a species concept based only on genome analysis in meiocytes of F1 hybrids. Biosystematic studies recognize Aegilopa sharonensis, Ae. peregrinu, and Triticum urartu as valid species distinct from other species. Our attempts tc resynthesize tetraploid wheats using Ae. spelfoides and Ae. searsii as female parents and T. monococcum and T. urartu as male parents met with little success. There may be an embryo lethality mechanism operating in these F1 hybrid combinations. Sterile hybrid plants were obtained with Ae. longissima, Ae. shuronensis, and Ae. bicornis as female parents in crosses with the two Triticum species as males. Amphidiploid seed was obtained with the use of colchicine.