TABLE 2.

Differentially expressed transcripts between cultures grown aerobically without nitrate and cultures grown aerobically with nitratea

TranscriptGene nameFold changebGrowth phasecProtein descriptiond
PA0045−3.5ESHypothetical protein
PA0046−3.4/−5.4BHypothetical protein
PA0047−3.1/−3.8BHypothetical protein
PA0129 gabP 4.3MLGamma-aminobutyrate permease
PA01304.2MLProbable aldehyde dehydrogenase
PA01313.9MLHypothetical protein
PA01323.5MLBeta-alanine-pyruvate transaminase
PA0160−3.8MLHypothetical protein
PA0164−4.8MLProbable gamma-glutamyltranspeptidase
PA01743.2MLConserved hypothetical protein
PA01754.8MLProbable chemotaxis protein methyltransferase
PA01763.7MLProbable chemotaxis transducer
PA01773.8MLProbable purine-binding chemotaxis protein
PA01783MLProbable two-component sensor
PA01793.5MLProbable two-component response regulator
PA02008.7ESHypothetical protein
PA0386−3.2ESProbable oxidase
PA0447 gcdH 3.4ESGlutaryl-CoA dehydrogenase
PA04594MLProbable ClpA/B protease ATP-binding subunit
PA04943.2MLProbable acyl-CoA carboxylase subunit
PA0509 nirN 11.8ESProbable c-type cytochrome
PA051017.5ESProbable uroporphyrin-III C-methyltransferase
PA051213.9ESConserved hypothetical protein
PA051316ESProbable transcriptional regulator
PA0514 nirL 16.1ESHeme d1 biosynthesis protein NirL
PA0516 nirF 16.3ESHeme d1 biosynthesis protein NirF
PA0518 nirM 4.9ESCytochrome c551 precursor
PA0519 nirS 9.3ESNitrite reductase precursor
PA052123.6ESProbable cytochrome c oxidase subunit
PA05268.1ESHypothetical protein
PA05864.1MLConserved hypothetical protein
PA05874.5MLConserved hypothetical protein
PA06143.3MLHypothetical protein
PA06233.5MLProbable bacteriophage protein
PA06244.1MLHypothetical protein
PA06274.6MLConserved hypothetical protein
PA06284.5MLConserved hypothetical protein
PA06324.3MLHypothetical protein
PA06334MLHypothetical protein
PA06393.8MLConserved hypothetical protein
PA07423.6MLHypothetical protein
PA07433.3MLProbable 3-hydroxyisobutyrate dehydrogenase
PA07443.7MLProbable enoyl-CoA hydratase/isomerase
PA07465.5MLProbable acyl-CoA dehydrogenase
PA07475.5MLProbable aldehyde dehydrogenase
PA0782 putA −5.1ESProline dehydrogenase PutA
PA0792 prpD 3.9MLPropionate catabolic protein PrpD
PA07934MLHypothetical protein
PA0795 prpC 4.3MLCitrate synthase 2
PA0887 acsA 3.8MLAcetyl-CoA synthetase
PA0889 aotQ −3.2ESArginine/ornithine transport protein AotQ
PA09103.4MLHypothetical protein
PA09857.6MLProbable colicin-like toxin
PA1070 braG 4.1MLBranched-chain amino acid transport protein BraG
PA1071 braF 3.7MLBranched-chain amino acid transport protein BraF
PA1072 braE 3.4MLBranched-chain amino acid transport protein BraE
PA1073 braD 3MLBranched-chain amino acid transport protein BraD
PA1173 napB 6MLCytochrome c-type protein NapB precursor
PA1174 napA 3.8MLPeriplasmic nitrate reductase protein NapA
PA1175 napD 3.3MLNapD protein of periplasmic nitrate reductase
PA1249 aprA 6.7MLAlkaline metalloproteinase precursor
PA12826.3ESProbable MFS transporter
PA1317 cyoA −3.7MLCytochrome o ubiquinol oxidase subunit II
PA1318 cyoB −3.1MLCytochrome o ubiquinol oxidase subunit I
PA1319 cyoC −3MLCytochrome o ubiquinol oxidase subunit III
PA1320 cyoD −4.8MLCytochrome o ubiquinol oxidase subunit IV
PA1337 ansB 4.8MLGlutaminase-asparaginase
PA1338 ggt 3.4MLGamma-glutamyltranspeptidase precursor
PA14187.5MLProbable sodium-solute symport protein
PA141910.9MLProbable transporter
PA14206MLHypothetical protein
PA1421 gbuA 5.6MLGuanidinobutyrase
PA1428−7.4ESConserved hypothetical protein
PA1559−3.6MLHypothetical protein
PA1566−5.9ESConserved hypothetical protein
PA1596 htpG −3.2MLHeat shock protein HtpG
PA1657−5ESConserved hypothetical protein
PA1660−4.8ESHypothetical protein
PA1661−3.4ESHypothetical protein
PA1662−3.3ESProbable ClpA/B-type protease
PA1663−3.3ESProbable transcriptional regulator
PA1664−4ESHypothetical protein
PA1665−4.4ESHypothetical protein
PA1666−3ESHypothetical protein
PA1667−4.8ESHypothetical protein
PA1668−3.2ESHypothetical protein
PA1669−4.7ESHypothetical protein
PA17613.2MLHypothetical protein
PA17623.7MLHypothetical protein
PA1790−4.8ESHypothetical protein
PA18474.3ESConserved hypothetical protein
PA185512.7MLHypothetical protein
PA185629/4.1BProbable cytochrome oxidase subunit
PA18833ESProbable NADH-ubiquinone/plastoquinone oxidoreductase
PA18883.9MLHypothetical protein
PA1902 phzD2 −13.5ESPhenazine biosynthesis protein PhzD
PA1903 phzE2 −12.3ESPhenazine biosynthesis protein PhzE
PA1904 phzF2 −12.9ESProbable phenazine biosynthesis protein
PA1971 braZ −3.3ESBranched chain amino acid transporter BraZ
PA1985 pqqA 3.6MLPyrroloquinoline quinone biosynthesis protein A
PA1986 pqqB 3MLPyrroloquinoline quinone biosynthesis protein B
PA1987 pqqC 4MLPyrroloquinoline quinone biosynthesis protein C
PA1988 pqqD 5MLPyrroloquinoline quinone biosynthesis protein D
PA1989 pqqE 3.3MLPyrroloquinoline quinone biosynthesis protein E
PA19905.6MLProbable peptidase
PA19998.2MLProbable CoA transferase, subunit A
PA2003 bdhA 3.1ML3-Hydroxybutyrate dehydrogenase
PA20119.1MLHydroxymethylglutaryl-CoA lyase
PA20129.1MLProbable acyl-CoA carboxylase alpha chain
PA20135.2MLProbable enoyl-CoA hydratase/isomerase
PA20144.4MLProbable acyl-CoA carboxyltransferase beta chain
PA20243.7MLProbable ring-cleaving dioxygenase
PA2052 cynS 3.2MLCyanate lyase
PA2066−4.4ESHypothetical protein
PA2067−3.9ESProbable hydrolase
PA2068−7.5ESProbable MFS transporter
PA2069−7.7ESProbable carbamoyl transferase
PA21107.9ESHypothetical protein
PA21124.1MLConserved hypothetical protein
PA21143.1ESProbable MFS transporter
PA2194 hcnB −3.3ESHydrogen cyanide synthase HcnB
PA2250 lpdV 3.7ESLipoamide dehydrogenase-Val
PA2266−3ESProbable cytochrome c precursor
PA2300 chiC −6.1ESChitinase
PA2306−3.1ESConserved hypothetical protein
PA2327−4ESProbable permease of ABC transporter
PA2329−4.1MLProbable ATP-binding component of ABC transporter
PA2330−5.2/−3.6BHypothetical protein
PA2331−6.7/−3.2BHypothetical protein
PA2358−3.7MLHypothetical protein
PA23704.8MLHypothetical protein
PA2404−3.5ESHypothetical protein
PA2405−6.2/−5BHypothetical protein
PA2406−3ESHypothetical protein
PA2408−3.2MLProbable ATP-binding component of ABC transporter
PA2442 gcvT2 3.2ESGlycine cleavage system protein T2
PA2443 sdaA 6ML l-Serine dehydratase
PA2444 glyA2 6.8MLSerine hydroxymethyltransferase
PA2445 gcvP2 3.1MLGlycine cleavage system protein P2
PA2446 gcvH2 3.1MLGlycine cleavage system protein H2
PA2460−3.3ESHypothetical protein
PA24833ESConserved hypothetical protein
PA25528.9MLProbable acyl-CoA dehydrogenase
PA255310.9MLProbable acyl-CoA thiolase
PA25546.7MLProbable short-chain dehydrogenase
PA25553.9MLProbable AMP-binding enzyme
PA2570 palL −5.1ESPA-I galactophilic lectin
PA25733.1MLProbable chemotaxis transducer
PA2593−5.2ESHypothetical protein
PA2629 purB −3.6ESAdenylosuccinate lyase
PA266341.4ESHypothetical protein
PA26913ESConserved hypothetical protein
PA2763−6.5ESHypothetical protein
PA2798−3.2ESProbable two-component response regulator
PA2968 fabD −3.2ESMalonyl-CoA-(acyl carrier protein) transacylase
PA2969 plsX −3.3ESFatty acid biosynthesis protein PlsX
PA3019−3.2ESProbable ATP-binding component of ABC transporter
PA31883.4MLProbable permease of ABC sugar transporter
PA3221 csaA 8.1ESCsaA protein
PA32227ESHypothetical protein
PA32323.2MLProbable nuclease
PA32345MLProbable sodium-solute symporter
PA32353.5MLConserved hypothetical protein
PA3294−4ESHypothetical protein
PA3327−3.9ESProbable nonribosomal peptide synthetase
PA3328−7.9ESProbable FAD-dependent monooxygenase
PA3329−9.6ESHypothetical protein
PA3330−10.9ESProbable short-chain dehydrogenase
PA3331−8.4ESCytochrome P450
PA3333 fabH2 −9.1ES3-Oxoacyl (acyl carrier protein) synthase III
PA3334−8.4ESProbable acyl carrier protein
PA3335−11.5ESHypothetical protein
PA3336−12.5ESProbable MFS transporter
PA3391 nosR 35.5ESRegulatory protein NosR
PA3393 nosD 31.3ESNosD protein
PA3394 nosF 33.4ESNosF protein
PA3395 nosY 36ESNosY protein
PA3396 nosL 21.6ESNosL protein
PA34163.9MLProbable pyruvate dehydrogenase E1 component, beta chain
PA3418 ldh 3.3MLLeucine dehydrogenase
PA3430−3MLProbable aldolase
PA3431−8.8MLConserved hypothetical protein
PA3432−10.1MLHypothetical protein
PA3478 rhlB −6.5ESRhamnosyltransferase chain B
PA3479 rhlA −6.5ESRhamnosyltransferase chain A
PA3486−12ESConserved hypothetical protein
PA3487 pldA −3.2ESPhospholipase D
PA35304.1ESConserved hypothetical protein
PA35526.5ESConserved hypothetical protein
PA3569 mmsB 3.9ML3-Hydroxyisobutyrate dehydrogenase
PA3570 mmsA 4.8MLMethylmalonate-semialdehyde dehydrogenase
PA3605−5.3ESHypothetical protein
PA3655 tsf −3.1MLElongation factor Ts
PA3700 lysS −3.6ESLysyl-tRNA synthetase
PA37234.2MLProbable FMN oxidoreductase
PA3741−4.7ESHypothetical protein
PA3742 rplS −3.7ML50S ribosomal protein L19
PA3811 hscB 3.2ESHeat shock protein HscB
PA3813 iscU 3.6ESProbable iron-binding protein IscU
PA3872 narI 37ESRespiratory nitrate reductase gamma chain
PA3876 narK2 3.4MLNitrite extrusion protein 2
PA38807.6ESConserved hypothetical protein
PA38813.1ESHypothetical protein
PA3901 fecA −5.7MLFe(III) dicitrate transport protein FecA
PA3905−4.1ESHypothetical protein
PA3907−3.8ESHypothetical protein
PA39123.3MLConserved hypothetical protein
PA39133.6/14.8BProbable protease
PA3914 moeAI 7.3/−62.7BMolybdenum cofactor biosynthetic protein A1
PA3915 moaBI 6.3/−15.6BMolybdopterin biosynthetic protein B1
PA3916 moaE 5.8ESMolybdopterin-converting factor, large subunit
PA3917 moaD 6.7ESMolybdopterin-converting factor, small subunit
PA3918 moaC 6.3ESMolybdopterin biosynthetic protein C
PA3979−3.1ESHypothetical protein
PA4055 ribC −4.1ESRiboflavin synthase alpha chain
PA40634.1ESHypothetical protein
PA4142−4.1ESProbable secretion protein
PA41705.8ESHypothetical protein
PA4210 phzAI −11.9ESProbable phenazine biosynthesis protein
PA4211 phzBI −14.8ESProbable phenazine biosynthesis protein
PA4217 phzS −13.1ESFlavin-containing monooxygenase
PA4235 bfrA 3.4ESBacterioferritin
PA4292−4.5ESProbable phosphate transporter
PA4432 rpsI −4ES30S ribosomal protein S9
PA4479 mreD −3.1ESRod shape-determining protein MreD
PA44973.8MLProbable binding protein component of ABC transporter
PA4512 lpxO1 −3.1ESLipopolysaccharide biosynthetic protein
PA46104.2ESHypothetical protein
PA4620−3ESHypothetical protein
PA4665 prfA −3.5ESPeptide chain release factor 1
PA4670 prs −3.9ESRibose-phosphate pyrophosphokinase
PA4672−5ESPeptidyl-tRNA hydrolase
PA4743 rbfA −3.2ESRibosome-binding factor A
PA4762 grpE −3.1MLHeat shock protein GrpE
PA4853 fis −3.4ESDNA-binding protein Fis
PA4916−9.8MLHypothetical protein
PA4917−6.7MLHypothetical protein
PA4918−7.2MLHypothetical protein
PA4919 pncB1 −6.2MLNicotinate phosphoribosyltransferase
PA4920 nadE −4.4MLNH3-dependent NAD synthetase
PA4921−3.9MLHypothetical protein
PA50234.3ESConserved hypothetical protein
PA5048−4.2ESProbable nuclease
PA5117 typA −5ESRegulatory protein TypA
PA5118 thiI −3.5ESThiazole biosynthesis protein Thil
PA5139−5ESHypothetical protein
PA51673ESProbable C4-dicarboxylate-binding protein
PA51684.3ESProbable dicarboxylate transporter
PA51693.6ESProbable C4-dicarboxylate transporter
PA52753.8ESConserved hypothetical protein
PA5296 rep −3.1ESATP-dependent DNA helicase Rep
PA5304 dadA −4.3ES d-Amino acid dehydrogenase, small subunit
PA5372 betA 4.2MLCholine dehydrogenase
PA5415 glyAI 4.3MLSerine hydroxymethyltransferase
PA5436−3.4ESProbable biotin carboxylase subunit of a transcarboxylase
PA5446−7.2MLHypothetical protein
PA5448 wbpY 3.2MLGlycosyltransferase WbpY
PA5460−3.2MLHypothetical protein
PA54963.1ESHypothetical protein
PA5553 atpC −3MLATP synthase epsilon chain
PA5554 atpD −3.1MLATP synthase beta chain
PA5556 atpA −3.4MLATP synthase alpha chain
PA5557 atpH −3MLATP synthase delta chain
ig3266712.9/3.5BIntergenic region between PA0458 and PA0459, 326671-327284, plus strand
ig43263943.2ESIntergenic region between PA3969 and PA3970, 4326394-4327696, plus strand
ig4713098−5.3ESIntergenic region between PA4280 and PA4281, 4713098-4713795, plus strand
  • a Only transcripts identified as nitrate regulated that demonstrated a change of equal to or greater than threefold are reported. A list of all transcripts identified as being nitrate regulated exhibiting a statistically significant change (P ≤ 0.05) is available online ( http://www.urmc.rochester.edu/smd/mbi/bhi/ ). Genes are identified by transcript number, gene name, and protein description (http://www.pseudomonas.com ).

  • b The change (n-fold) was calculated by comparing PAO1 grown aerobically lacking nitrate (baseline) to PAO1 grown aerobically with nitrate (experimental). A positive change represents induction caused by the presence of nitrate, and a negative change represents repression caused by the presence of nitrate. When two values are given, the first is for the ML phase and the second is for the ES phase.

  • c Growth stage(s) during which statistically significantly differential transcript expression was observed. ML, midexponential phase; ES, early stationary phase; B, both midexponential and early stationary phases.

  • d Protein descriptions are from the Pseudomonas Genome Project website (www.pseudomonas.com ). CoA, coenzyme A; FAD, flavin adenine dinucleotide; MSF, major facilitator superfamily; ABC, ATP-binding cassette; FMN, flavin mononucleotide.