NORMAL GENOMIC

• Nagata K et al.
• Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein withan exposed histidine triad from Thermus thermophilus HB8 at 2.0 A.
• Proteins. 2008; 70: 1103-7

• Kannan G, Wilks JC, Fitzgerald DM, Jones BD, Bondurant SS, Slonczewski JL
• Rapid acid treatment of Escherichia coli: transcriptomic response andrecovery.
• BMC Microbiol. 2008; 8: 37-37
• Display abstract

• BACKGROUND: Many E. coli genes show pH-dependent expression duringlogarithmic growth in acid (pH 5-6) or in base (pH 8-9). The effect ofrapid pH change, however, has rarely been tested. Rapid acid treatmentcould distinguish between genes responding to external pH, and genesresponding to cytoplasmic acidification, which occurs transientlyfollowing rapid external acidification. It could reveal previously unknownacid-stress genes whose effects are transient, as well as show whichacid-stress genes have a delayed response. RESULTS: Microarrayhybridization was employed to observe the global gene expression of E.coli K-12 W3110 following rapid acidification of the external medium, frompH 7.6 to pH 5.5. Fluorimetric observation of pH-dependent tetR-YFP showedthat rapid external acidification led to a half-unit drop in cytoplasmicpH (from pH 7.6 to pH 6.4) which began to recover within 20 s. Followingacid treatment, 630 genes were up-regulated and 586 genes weredown-regulated. Up-regulated genes included amino-acid decarboxylases(cadA, adiY, gadA), succinate dehydrogenase (sdhABCD), biofilm-associatedgenes (bdm, gatAB, and ymgABC), and the Gad, Fur and Rcs regulons. Geneswith response patterns consistent with cytoplasmic acid stress wererevealed by addition of benzoate, a membrane-permeant acid thatpermanently depresses cytoplasmic pH without affecting external pH.Several genes (yagU, ygiN, yjeI, and yneI) were up-regulated specificallyby external acidification, while other genes (fimB, ygaC, yhcN, yhjX,ymgABC, yodA) presented a benzoate response consistent with cytoplasmic pHstress. Other genes (the nuo operon for NADH dehydrogenase I, and theHslUV protease) showed delayed up-regulation by acid, with expressionrising by 10 min following the acid shift. CONCLUSION: Transcriptomicprofiling of E. coli K-12 distinguished three different classes of changein gene expression following rapid acid treatment: up-regulation with orwithout recovery, and delayed response to acid. For eight genes showingacid response and recovery (fimB, ygaC, yhcN, yhjX, ymgABC, yodA),responses to the permeant acid benzoate revealed expression patternsconsistent with sensing of cytoplasmic pH. The delayed acid response ofnuo genes shows that NADH dehydrogenase I is probably induced as asecondary result of acid-associated metabolism, not as a direct responseto cytoplasmic acidification.

• Okazaki N et al.
• Structure of a UPF0150-family protein from Thermus thermophilus HB8.
• Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007; 63: 173-7
• Display abstract

• TTHA0281 is a hypothetical protein from Thermus thermophilus HB8 thatbelongs to an uncharacterized protein family, UPF0150, in the Pfamdatabase and to COG1598 in the National Center for BiotechnologyInformation Database of Clusters of Orthologous Groups. The X-ray crystalstructure of the protein was determined by a multiple-wavelength anomalousdispersion technique and was refined at 1.9 A resolution to a final Rfactor of 18.5%. The TTHA0281 monomer adopts an alpha-beta-beta-beta-alphafold and forms a homotetramer. Based on the properties and functions ofstructural homologues of the TTHA0281 monomer, the TTHA0281 protein isspeculated to be involved in RNA metabolism, including RNA binding andcleavage.

• Ebihara A, Yao M, Masui R, Tanaka I, Yokoyama S, Kuramitsu S
• Crystal structure of hypothetical protein TTHB192 from Thermusthermophilus HB8 reveals a new protein family with an RNA recognitionmotif-like domain.
• Protein Sci. 2006; 15: 1494-9
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• We have determined the crystal structure of hypothetical protein TTHB192from Thermus thermophilus HB8 at 1.9 A resolution. This protein is amember of the Escherichia coli ygcH sequence family, which containsapproximately 15 sequence homologs of bacterial origin. These homologshave a high isoelectric point. The crystal structure reveals that TTHB192consists of two independently folded domains, and that each domainexhibits a ferredoxin-like fold with a four-stranded antiparallelbeta-sheet packed on one side by alpha-helices. These two tandem domainsface each other to generate a beta-sheet platform. TTHB192 displaysoverall structural similarity to Sex-lethal protein and poly(A)-bindingprotein fragments. These proteins have RNA binding activity which issupported by a beta-sheet platform formed by two tandem repeats of an RNArecognition motif domain with signature sequence motifs on the beta-sheetsurface. Although TTHB192 does not have the same signature sequence motifas the RNA recognition motif domain, the presence of an evolutionarilyconserved basic patch on the beta-sheet platform could be functionallyrelevant for nucleic acid-binding. This report shows that TTHB192 and itssequence homologs adopt an RNA recognition motif-like domain and providesthe first testable functional hypothesis for this protein family.

• Hayes ET et al.
• Oxygen limitation modulates pH regulation of catabolism and hydrogenases,multidrug transporters, and envelope composition in Escherichia coli K-12.
• BMC Microbiol. 2006; 6: 89-89
• Display abstract

• BACKGROUND: In Escherichia coli, pH regulates genes for amino-acid andsugar catabolism, electron transport, oxidative stress, periplasmic andenvelope proteins. Many pH-dependent genes are co-regulated byanaerobiosis, but the overall intersection of pH stress and oxygenlimitation has not been investigated. RESULTS: The pH dependence of geneexpression was analyzed in oxygen-limited cultures of E. coli K-12 strainW3110. E. coli K-12 strain W3110 was cultured in closed tubes containingLBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix arrayhybridization revealed pH-dependent expression of 1,384 genes and 610intergenic regions. A core group of 251 genes showed pH responses similarto those in a previous study of cultures grown with aeration. The highlyacid-induced gene yagU was shown to be required for extreme-acidresistance (survival at pH 2). Acid also up-regulated fimbriae (fimAC),periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa),and the "constitutive" Na+/H+ antiporter (nhaB). Base up-regulated coregenes for maltodextrin transport (lamB, mal), ATP synthase (atp), and DNArepair (recA, mutL). Other genes showed opposite pH responses with orwithout aeration, for example ETS components (cyo,nuo, sdh) andhydrogenases (hya, hyb, hyc, hyf, hyp). A hypF strain lacking allhydrogenase activity showed loss of extreme-acid resistance. Under oxygenlimitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps).Acid up-regulated the catabolism of sugar derivatives whose fermentationminimized acid production (gnd, gnt, srl), and also a cluster of 13 genesin the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL), butdown-regulated penicillin-binding proteins (dacACD, mreBC). Intergenicregions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB,gadY, rybC). CONCLUSION: pH regulates a core set of genes independently ofoxygen, including yagU, fimbriae, periplasmic chaperones, and nhaB. Underoxygen limitation, however, pH regulation is reversed for genes encodingelectron transport components and hydrogenases. Extreme-acid resistancerequires yagU and hydrogenase production. Ribosome synthesis isdown-regulated at low pH under oxygen limitation, possibly due to therestricted energy yield of catabolism. Under oxygen limitation, pHregulates metabolism and transport so as to maximize alternative catabolicoptions while minimizing acidification or alkalinization of the cytoplasm.

• Iwasaki W, Miyatake H, Miki K
• Crystal structure of the small form of glucose-inhibited division proteinA from Thermus thermophilus HB8.
• Proteins. 2005; 61: 1121-6

• Neugebauer H, Herrmann C, Kammer W, Schwarz G, Nordheim A, Braun V
• ExbBD-dependent transport of maltodextrins through the novel MalA proteinacross the outer membrane of Caulobacter crescentus.
• J Bacteriol. 2005; 187: 8300-11
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• Analysis of the genome sequence of Caulobacter crescentus predicts 67TonB-dependent outer membrane proteins. To demonstrate that among them areproteins that transport nutrients other than chelated Fe(3+) and vitaminB(12)-the substrates hitherto known to be transported by TonB-dependenttransporters-the outer membrane protein profile of cells grown ondifferent substrates was determined by two-dimensional electrophoresis.Maltose induced the synthesis of a hitherto unknown 99.5-kDa protein,designated here as MalA, encoded by the cc2287 genomic locus. MalAmediated growth on maltodextrins and transported [(14)C]maltodextrins from[(14)C]maltose to [(14)C]maltopentaose. [(14)C]maltose transport showedbiphasic kinetics, with a fast initial rate and a slower second rate. Theinitial transport had a K(d) of 0.2 microM, while the second transport hada K(d) of 5 microM. It is proposed that the fast rate reflects binding toMalA and the second rate reflects transport into the cells. Energydepletion of cells by 100 microM carbonyl cyanide 3-chlorophenylhydrazoneabolished maltose binding and transport. Deletion of the malA genediminished maltose transport to 1% of the wild-type malA strain andimpaired transport of the larger maltodextrins. The malA mutant was unableto grow on maltodextrins larger than maltotetraose. Deletion of two C.crescentus genes homologous to the exbB exbD genes of Escherichia coliabolished [(14)C]maltodextrin binding and transport and growth onmaltodextrins larger than maltotetraose. These mutants also showedimpaired growth on Fe(3+)-rhodotorulate as the sole iron source, whichprovided evidence of energy-coupled transport. Unexpectedly, a deletionmutant of a tonB homolog transported maltose at the wild-type rate andgrew on all maltodextrins tested. Since Fe(3+)-rhodotorulate served as aniron source for the tonB mutant, an additional gene encoding a proteinwith a TonB function is postulated. Permeation of maltose and maltotriosethrough the outer membrane of the C. crescentus malA mutant was slowerthan permeation through the outer membrane of an E. coli lamB mutant,which suggests a low porin activity in C. crescentus. The pores of the C.crescentus porins are slightly larger than those of E. coli K-12, sincemaltotetraose supported growth of the C. crescentus malA mutant but failedto support growth of the E. coli lamB mutant. The data are consistent withthe proposal that binding of maltodextrins to MalA requires energy andMalA actively transports maltodextrins with K(d) values 1,000-fold smallerthan those for the LamB porin and 100-fold larger than those for thevitamin B(12) and ferric siderophore outer membrane transporters. MalA isthe first example of an outer membrane protein for which anExbB/ExbD-dependent transport of a nutrient other than iron and vitaminB(12) has been demonstrated.

• Kukimoto-Niino M et al.
• Crystal structure of a predicted phosphoribosyltransferase (TT1426) fromThermus thermophilus HB8 at 2.01 A resolution.
• Protein Sci. 2005; 14: 823-7
• Display abstract

• TT1426, from Thermus thermophilus HB8, is a conserved hypothetical proteinwith a predicted phosphoribosyltransferase (PRTase) domain, as revealed bya Pfam database search. The 2.01 A crystal structure of TT1426 has beendetermined by the multiwavelength anomalous dispersion (MAD) method.TT1426 comprises a core domain consisting of a central five-stranded betasheet surrounded by four alpha-helices, and a subdomain in the C terminus.The core domain structure resembles those of the type I PRTase familyproteins, although a significant structural difference exists in aninserted 43-residue region. The C-terminal subdomain corresponds to the"hood," which contains a substrate-binding site in the type I PRTases. Thehood structure of TT1426 differs from those of the other type I PRTases,suggesting the possibility that TT1426 binds an unknown substrate. Thestructure-based sequence alignment provides clues about the amino acidresidues involved in catalysis and substrate binding.

• Yohannes E, Thurber AE, Wilks JC, Tate DP, Slonczewski JL
• Polyamine stress at high pH in Escherichia coli K-12.
• BMC Microbiol. 2005; 5: 59-59
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• BACKGROUND: Polyamines such as spermine and spermidine are required forgrowth of Escherichia coli; they interact with nucleic acids, and theybind to ribosomes. Polyamines block porins and decrease membranepermeability, activities that may protect cells in acid. At highconcentrations, however, polyamines impair growth. They impair growth moreseverely at high pH, probably due to their increased uptake asmembrane-permeant weak bases. The role of pH is critical in understandingpolyamine stress. RESULTS: The effect of polyamines was tested on survivalof Escherichia coli K-12 W3110 in extreme acid or base (pH conditionsoutside the growth range). At pH 2, 10 mM spermine increased survival by2-fold, and putrescine increased survival by 30%. At pH 9.8, however, E.coli survival was decreased 100-fold by 10 mM spermine, putrescine,cadaverine, or spermidine. At pH 8.5, spermine decreased the growth ratesubstantially, whereas little effect was seen at pH 5.5. Spermidinerequired ten-fold higher concentrations to impair growth. On proteomic 2-Dgels, spermine and spermidine caused differential expression of 31different proteins. During log-phase growth at pH 7.0, 1 mM spermineinduced eight proteins, including PykF, GlpK, SerS, DeaD, OmpC and OmpF.Proteins repressed included acetate-inducible enzymes (YfiD, Pta, Lpd) aswell as RapA (HepA), and FabB. At pH 8.5, spermine induced additionalproteins: TnaA, OmpA, YrdA and NanA (YhcJ) and also repressed 17 proteins.Four of the proteins that spermine induced (GlpK, OmpA, OmpF, TnaA) andfive that were repressed (Lpd, Pta, SucB, TpiA, YfiD) show similarinduction or repression, respectively, in base compared to acid. Most ofthese base stress proteins were also regulated by spermidine, but only atten-fold higher concentration (10 mM) at high pH (pH 8.5). CONCLUSION:Polyamines increase survival in extreme acid, but decrease E. colisurvival in extreme base. Growth inhibition by spermine and spermidinerequires neutral or higher pH. At or above pH 7, spermine and spermidineregulate specific proteins, many of which are known to be regulated bybase stress. High pH amplifies polyamine stress; and naturally occurringpolyamines may play an important role in base stress.

• Ebihara A et al.
• Structure-based functional identification of a novel heme-binding proteinfrom Thermus thermophilus HB8.
• J Struct Funct Genomics. 2005; 6: 21-32
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• The TT1485 gene from Thermus thermophilus HB8 encodes a hypotheticalprotein of unknown function with about 20 sequence homologs of bacterialor archaeal origin. Together they form a family of uncharacterizedproteins, the cluster of orthologous group COG3253. Using a combination ofamino acid sequence analysis, three-dimensional structural studies andbiochemical assays, we identified TT1485 as a novel heme-binding protein.The crystal structure reveals that this protein is a pentamer and eachmonomer exhibits a beta-barrel fold. TT1485 is structurally similar tomuconolactone isomerase, but this provided no functional clues. Amino acidsequence analysis revealed remote homology to a heme enzyme, chloritedismutase. Strikingly, amino acid residues that are highly conserved inthe homologous hypothetical proteins and chlorite dismutase cluster arounda deep cavity on the surface of each monomer. Molecular modeling showsthat the cavity can accommodate a heme group with a strictly conserved Hisas a heme ligand. TT1485 reconstituted with iron protoporphyrin IXchloride gave a low chlorite dismutase activity, indicating that TT1485catalyzes a reaction other than chlorite degradation. The presence of apossible Fe-His-Asp triad in the heme proximal site suggests that TT1485functions as a novel heme peroxidase to detoxify hydrogen peroxide withinthe cell.

• Maurer LM, Yohannes E, Bondurant SS, Radmacher M, Slonczewski JL
• pH regulates genes for flagellar motility, catabolism, and oxidativestress in Escherichia coli K-12.
• J Bacteriol. 2005; 187: 304-19
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• Gene expression profiles of Escherichia coli K-12 W3110 were compared as afunction of steady-state external pH. Cultures were grown to an opticaldensity at 600 nm of 0.3 in potassium-modified Luria-Bertani mediumbuffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions,cDNA from RNA of five independent cultures was hybridized to Affymetrix E.coli arrays. Analysis of variance with an alpha level of 0.001 resulted in98% power to detect genes showing a twofold difference in expression.Normalized expression indices were calculated for each gene and intergenicregion (IG). Differential expression among the three pH classes wasobserved for 763 genes and 353 IGs. Hierarchical clustering yielded sixwell-defined clusters of pH profiles, designated Acid High (highestexpression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High(highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest atpH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higherat both pH extremes). Flagellar and chemotaxis genes were repressed at pH8.7 (Base Low cluster), where the cell's transmembrane proton potential isdiminished by the maintenance of an inverted pH gradient. High pH alsorepressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases Iand II. By contrast, the proton-importing ATP synthase F1Fo and themicroaerophilic cytochrome d (cyd), which minimizes proton export, wereinduced at pH 8.7. These observations are consistent with a model in whichhigh pH represses synthesis of flagella, which expend proton motive force,while stepping up electron transport and ATPase components that keepprotons inside the cell. Acid-induced genes, on the other hand, werecoinduced by conditions associated with increased metabolic rate, such asoxidative stress. All six pH-dependent clusters included envelope andperiplasmic proteins, which directly experience external pH. Overall, thisstudy showed that (i) low pH accelerates acid consumption and protonexport, while coinducing oxidative stress and heat shock regulons; (ii)high pH accelerates proton import, while repressing the energy-expensiveflagellar and chemotaxis regulons; and (iii) pH differentially regulates alarge number of periplasmic and envelope proteins.

• Kishishita S et al.
• Crystal structure of a conserved hypothetical protein TT1751 from Thermusthermophilus HB8.
• Proteins. 2004; 57: 883-7

• Wang H et al.
• Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8.
• Protein Sci. 2004; 13: 2806-10
• Display abstract

• Ribosomal protein L27 is located near the peptidyltransferase center atthe interface of ribosomal subunits, and is important for ribosomalassembly and function. We report the crystal structure of ribosomalprotein L27 from Thermus thermophilus HB8, which was determined by themultiwavelength anomalous dispersion method and refined to an R-factor of19.7% (R(free) = 23.6%) at 2.8 A resolution. The overall fold is an allbeta-sheet hybrid. It consists of two sets of four-stranded beta-sheetsformed around a well-defined hydrophobic core, with a highly positivecharge on the protein surface. The structure of ribosomal protein L27 fromT. thermophilus HB8 in the RNA-free form is investigated, and itsfunctional roles in the ribosomal subunit are discussed.

• Kukimoto-Niino M et al.
• Crystal structure of the GTP-binding protein Obg from Thermus thermophilusHB8.
• J Mol Biol. 2004; 337: 761-70
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• Obg comprises a unique family of high-molecular mass GTPases conservedfrom bacteria to eukaryotes. Bacterial Obg is essential for cellulargrowth, sporulation, and differentiation. Here, we report the crystalstructure of the full-length form of Obg from Thermus thermophilus HB8 at2.07 A resolution, in the nucleotide-free state. It reveals a three-domainarrangement, composed of the N-terminal domain, the guaninenucleotide-binding domain (G domain), and the C-terminal domain. TheN-terminal and G domains have the Obg fold and the Ras-like fold,respectively. These global folds are similar to those of the recentlypublished structure of the C-terminal domain-truncated form of Obg fromBacillus subtilis. On the other hand, the C-terminal domain of Obg wasfound to have a novel fold (the OCT fold). A comparison of theT.thermophilus and B.subtilis nucleotide-free Obg structures revealedsignificant conformational changes in the switch-I and switch-II regionsof the G domain. Notably, the N-terminal domain is rotated drastically, byalmost 180 degrees, around the G domain axis. In the T.thermophilus Obgcrystal, the nucleotide-binding site of the G domain interacts with theC-terminal domain of the adjacent molecule. These data suggest a possibledomain rearrangement of Obg, and a potential role of the C-terminal domainin the regulation of the nucleotide-binding state.

• Yohannes E, Barnhart DM, Slonczewski JL
• pH-dependent catabolic protein expression during anaerobic growth ofEscherichia coli K-12.
• J Bacteriol. 2004; 186: 192-9
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• During aerobic growth of Escherichia coli, expression of catabolic enzymesand envelope and periplasmic proteins is regulated by pH. Additional modesof pH regulation were revealed under anaerobiosis. E. coli K-12 strainW3110 was cultured anaerobically in broth medium buffered at pH 5.5 or 8.5for protein identification on proteomic two-dimensional gels. A total of32 proteins from anaerobic cultures show pH-dependent expression, and onlyfour of these proteins (DsbA, TnaA, GatY, and HdeA) showed pH regulationin aerated cultures. The levels of 19 proteins were elevated at the highpH; these proteins included metabolic enzymes (DhaKLM, GapA, TnaA, HisC,and HisD), periplasmic proteins (ProX, OppA, DegQ, MalB, and MglB), andstress proteins (DsbA, Tig, and UspA). High-pH induction of the glycolyticenzymes DhaKLM and GapA suggested that there was increased fermentation toacids, which helped neutralize alkalinity. Reporter lac fusion constructsshowed base induction of sdaA encoding serine deaminase underanaerobiosis; in addition, the glutamate decarboxylase genes gadA and gadBwere induced at the high pH anaerobically but not with aeration. Thisresult is consistent with the hypothesis that there is a connectionbetween the gad system and GabT metabolism of 4-aminobutanoate. On theother hand, 13 other proteins were induced by acid; these proteinsincluded metabolic enzymes (GatY and AckA), periplasmic proteins (TolC,HdeA, and OmpA), and redox enzymes (GuaB, HmpA, and Lpd). The acidinduction of NikA (nickel transporter) is of interest because E. colirequires nickel for anaerobic fermentation. The position of the NikA spotcoincided with the position of a small unidentified spot whose inductionin aerobic cultures was reported previously; thus, NikA appeared to beinduced slightly by acid during aeration but showed stronger inductionunder anaerobic conditions. Overall, anaerobic growth revealed severalmore pH-regulated proteins; in particular, anaerobiosis enabled inductionof several additional catabolic enzymes and sugar transporters at the highpH, at which production of fermentation acids may be advantageous for thecell.

• Handa N et al.
• Crystal structure of the conserved protein TT1542 from Thermusthermophilus HB8.
• Protein Sci. 2003; 12: 1621-32
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• The TT1542 protein from Thermus thermophilus HB8 is annotated as aconserved hypothetical protein, and belongs to the DUF158 family in thePfam database. A BLAST search revealed that homologs of TT1542 are presentin a wide range of organisms. The TT1542 homologs in eukaryotes, PIG-L inmammals, and GPI12 in yeast and protozoa, haveN-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) de-N-acetylaseactivity. Although most of the homologs in prokaryotes are hypotheticaland have no known function, Rv1082 and Rv1170 from Mycobacteriumtuberculosis are enzymes involved in the mycothiol detoxification pathway.Here we report the crystal structure of the TT1542 protein at 2.0 Aresolution, which represents the first structure for this superfamily ofproteins. The structure of the TT1542 monomer consists of a twistedbeta-sheet composed of six parallel beta-strands and one antiparallelbeta-strand (with the strand order 3-2-1-4-5-7-6) sandwiched between sixalpha-helices. The N-terminal five beta-strands and four alpha-helicesform an incomplete Rossmann fold-like structure. The structure shares somesimilarity to the sugar-processing enzymes with Rossmann fold-likedomains, especially those of the GPGTF (glycogen phosphorylase/glycosyltransferase) superfamily, and also to the NAD(P)-binding Rossmann folddomains. TT1542 is a homohexamer in the crystal and in solution, the sixmonomers forming a cylindrical structure. Putative active sites aresuggested by the structure and conserved amino acid residues.

• Kirkpatrick C, Maurer LM, Oyelakin NE, Yoncheva YN, Maurer R, Slonczewski JL
• Acetate and formate stress: opposite responses in the proteome ofEscherichia coli.
• J Bacteriol. 2001; 183: 6466-77
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• Acetate and formate are major fermentation products of Escherichia coli.Below pH 7, the balance shifts to lactate; an oversupply of acetate orformate retards growth. E. coli W3110 was grown with aeration inpotassium-modified Luria broth buffered at pH 6.7 in the presence orabsence of added acetate or formate, and the protein profiles werecompared by two-dimensional sodium dodecyl sulfate-polyacrylamide gelelectrophoresis. Acetate increased the steady-state expression levels of37 proteins, including periplasmic transporters for amino acids andpeptides (ArtI, FliY, OppA, and ProX), metabolic enzymes (YfiD and GatY),the RpoS growth phase regulon, and the autoinducer synthesis protein LuxS.Acetate repressed 17 proteins, among them phosphotransferase (Pta). AnackA-pta deletion, which nearly eliminates interconversion between acetateand acetyl-coenzyme A (acetyl-CoA), led to elevated basal levels of 16 ofthe acetate-inducible proteins, including the RpoS regulon. Consistentwith RpoS activation, the ackA-pta strain also showed constitutiveextreme-acid resistance. Formate, however, repressed 10 of theacetate-inducible proteins, including the RpoS regulon. Ten of theproteins with elevated basal levels in the ackA-pta strain were repressedby growth of the mutant with formate; thus, the formate response tookprecedence over the loss of the ackA-pta pathway. The similar effects ofexogenous acetate and the ackA-pta deletion, and the opposite effect offormate, could have several causes; one possibility is that the excessbuildup of acetyl-CoA upregulates stress proteins but excess formatedepletes acetyl-CoA and downregulates these proteins.

• Castanie-Cornet MP, Penfound TA, Smith D, Elliott JF, Foster JW
• Control of acid resistance in Escherichia coli.
• J Bacteriol. 1999; 181: 3525-35
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• Acid resistance (AR) in Escherichia coli is defined as the ability towithstand an acid challenge of pH 2.5 or less and is a trait generallyrestricted to stationary-phase cells. Earlier reports described three ARsystems in E. coli. In the present study, the genetics and control ofthese three systems have been more clearly defined. Expression of thefirst AR system (designated the oxidative or glucose-repressed AR system)was previously shown to require the alternative sigma factor RpoS.Consistent with glucose repression, this system also proved to bedependent in many situations on the cyclic AMP receptor protein. Thesecond AR system required the addition of arginine during pH 2.5 acidchallenge, the structural gene for arginine decarboxylase (adiA), and theregulator cysB, confirming earlier reports. The third AR system requiredglutamate for protection at pH 2.5, one of two genes encoding glutamatedecarboxylase (gadA or gadB), and the gene encoding the putativeglutamate:gamma-aminobutyric acid antiporter (gadC). Only one of the twoglutamate decarboxylases was needed for protection at pH 2.5. However,survival at pH 2 required both glutamate decarboxylase isozymes.Stationary phase and acid pH regulation of the gad genes proved separable.Stationary-phase induction of gadA and gadB required the alternative sigmafactor sigmaS encoded by rpoS. However, acid induction of these enzymes,which was demonstrated to occur in exponential- and stationary-phasecells, proved to be sigmaS independent. Neither gad gene required thepresence of volatile fatty acids for induction. The data also indicatethat AR via the amino acid decarboxylase systems requires more than aninducible decarboxylase and antiporter. Another surprising finding wasthat the sigmaS-dependent oxidative system, originally thought to be acidinduced, actually proved to be induced following entry into stationaryphase regardless of the pH. However, an inhibitor produced at pH 8 somehowinterferes with the activity of this system, giving the illusion of acidinduction. The results also revealed that the AR system affording the mosteffective protection at pH 2 in complex medium (either Luria-Bertani brothor brain heart infusion broth plus 0.4% glucose) is theglutamate-dependent GAD system. Thus, E. coli possesses three overlappingacid survival systems whose various levels of control and differingrequirements for activity ensure that at least one system will beavailable to protect the stationary-phase cell under naturally occurringacidic environments.

• Blankenhorn D, Phillips J, Slonczewski JL
• Acid- and base-induced proteins during aerobic and anaerobic growth ofEscherichia coli revealed by two-dimensional gel electrophoresis.
• J Bacteriol. 1999; 181: 2209-16
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• Proteins induced by acid or base, during long-term aerobic or anaerobicgrowth in complex medium, were identified in Escherichia coli.Two-dimensional gel electrophoresis revealed pH-dependent induction of 18proteins, nine of which were identified by N-terminal sequencing. At pH 9,tryptophan deaminase (TnaA) was induced to a high level, becoming one ofthe most abundant proteins observed. TnaA may reverse alkalinization bymetabolizing amino acids to produce acidic products. Also induced at highpH, but only in anaerobiosis, was glutamate decarboxylase (GadA). The gadsystem (GadA/GadBC) neutralizes acidity and enhances survival in extremeacid; its induction during anaerobic growth may help protectalkaline-grown cells from the acidification resulting from anaerobicfermentation. To investigate possible responses to internal acidification,cultures were grown in propionate, a membrane-permeant weak acid whichacidifies the cytoplasm. YfiD, a homologue of pyruvate formate lyase, wasinduced to high levels at pH 4.4 and induced twofold more by propionate atpH 6; both of these conditions cause internal acidification. At neutral oralkaline pH, YfiD was virtually absent. YfiD is therefore a strongcandidate for response to internal acidification. Acid or propionate alsoincreased the expression of alkyl hydroperoxide reductase (AhpC) but onlyduring aerobic growth. At neutral or high pH, AhpC showed no significantdifference between aerobic and anaerobic growth. The increase of AhpC inacid may help protect the cell from the greater concentrations ofoxidizing intermediates at low pH. Isocitrate lyase (AceA) was induced byoxygen across the pH range but showed substantially greater induction inacid or in base than at pH 7. Additional responses observed included theinduction of MalE at high pH and induction of several enzymes of sugarmetabolism at low pH: the phosphotransferase system components ManX andPtsH and the galactitol fermentation enzyme GatY. Overall, our resultsindicate complex relationships between pH and oxygen and a novel permeantacid-inducible gene, YfiD.

• White S, Tuttle FE, Blankenhorn D, Dosch DC, Slonczewski JL
• pH dependence and gene structure of inaA in Escherichia coli.
• J Bacteriol. 1992; 174: 1537-43
• Display abstract

• The weak-acid-inducible locus inaA in Escherichia coli was mapped to 48.6min by P1 cotransduction of inaA Mud lac fusions and linked Tn10insertions. The inaA1::lac fusion tested negative for phenotypescharacteristic of mutations in the nearby locus ubiG. Sequence analysis ofa fragment amplified by polymerase chain reaction located the inaA1::lacfusion joint within an open reading frame 311 nucleotides downstream ofnrdB, transcribed in the opposite direction, encoding a 168-amino-acidpolypeptide. Constitutive mutant strains identified on lactose MacConkeyrevealed a novel regulatory locus unlinked to inaA, which mapped at 34 min(designated inaR). Expression of inaA1::lac increased slightly withexternal acidification; the presence of benzoate, a membrane-permeant weakacid, greatly increased the acid effect. The expression at variouscombinations of benzoate and external pH correlated with the decrease inintracellular pH. The uncouplers salicylate and dinitrophenol also causedacid-dependent induction of inaA, but substantial induction was seen atexternal pH values higher than the internal pH; this effect cannot becaused by internal acidification. Nondissociating analogs of benzoate andsalicylate, benzyl alcohol and salicyl alcohol, did not induce inaA.Expression of inaA was inversely related to growth temperature over therange of 30 to 45 degrees C. The inaA1::lac fusion was transferred to astrain defective for K+ uptake (kdpABC trkA trkD) in which pH homeostasiswas shown to depend on the external K+ concentration. In this construct,inaA1::lac retained pH-dependent induction by benzoate but was not inducedat low K+ concentrations. Induction of inaA appears to involve severalfactors in addition to internal pH. inaR may be related to the nearbylocus marA/soxQ, which is inducible by acidic benzyl derivatives.