Differentially expressed transcripts between cultures grown aerobically with nitrate and cultures grown anaerobically with nitratea

TranscriptGeneFold changebGrowth phasecProtein descriptiond
PA0024 hemF 4.5ESCoproporphyrinogen III oxidase, aerobic
PA0025 aroE 3.5ESShikimate dehydrogenase
PA0049−5.1ESHypothetical protein
PA01494.1MLProbable sigma-70 factor, ECF subfamily
PA0179−4.3MLProbable two-component response regulator
PA0200−5.5MLHypothetical protein
PA0430 metF 3.4ES5,10-Methylenetetrahydrofolate reductase
PA04336.5MLHypothetical protein
PA0447 gcdH −5.2ESGlutaryl-CoA dehydrogenase
PA04719.7MLProbable transmembrane sensor
PA04724.1MLProbable sigma-70 factor, ECF subfamily
PA0586−4.6MLHypothetical protein
PA0587−4.9MLHypothetical protein
PA0747−3.8MLProbable aldehyde dehydrogenase
PA0792 prpD −3.1MLPropionate catabolic protein PrpD
PA08025.3MLHypothetical protein
PA0836−3.1MLProbable acetate kinase
PA0918−3.6MLCytochrome b561
PA09303.9MLTwo-component sensor
PA0997 pqsB −4.3/−18BBeta keto acyl-acyl carrier protein synthase
PA0998 pqsC −11.1/−43.7BBeta keto acyl-acyl carrier protein synthase
PA0999 pqsD −21ES3-Oxoacyl (acyl carrier protein) synthase III
PA1000 pqsE −10.8MLQuinolone signal reponse signal
PA1002 phnB −9.6ESAnthranilate synthase component II
PA10453MLHypothetical protein
PA1052−3.5MLHypothetical protein
PA1076−3.8MLHypothetical protein
PA1140−3.2MLHypothetical protein
PA1173 napB −4.1MLCytochrome c-type protein NapB precursor
PA1174 napA −3.2MLPeriplasmic nitrate reductase protein NapA
PA1175 napD −3.8MLNapD protein of periplasmic nitrate reductase
PA1176 napF −3.8MLFerredoxin protein NapF
PA1179 phoP −3.4ESTwo-component response regulator PhoP
PA1180 phoQ −4.8ESTwo-component sensor PhoQ
PA1195−6.1MLHypothetical protein
PA1282−6.1ESProbable MFS transporter
PA1323−3.8MLHypothetical protein
PA1324−3MLHypothetical protein
PA13313.3MLHypothetical protein
PA1418−8.4MLProbable sodium-solute symport protein
PA1419−14.2MLProbable transporter
PA1420−15.5MLHypothetical protein
PA1421 gbuA −15MLGuanidinobutyrase
PA1429−3MLProbable cation-transporting P-type ATPase
PA1516−3.3MLHypothetical protein
PA1517−4.3MLHypothetical protein
PA1518−4.1MLHypothetical protein
PA1523 xdhB −4.4MLXanthine dehydrogenase
PA1546 hemN −4MLOxygen-independent coproporphyrinogen III oxidase
PA1556−3.2MLProbable cytochrome c oxidase subunit
PA1561 aer −4.5MLAerotaxis receptor Aer
PA1673−5.3MLHypothetical protein
PA1789−3.9MLHypothetical protein
PA1806 fabI −3.3MLNADH-dependent enoyl-ACP reductase
PA1882−3ESProbable transporter
PA1883−3ESProbable NADH-ubiquinone plastoquinone oxidoreductase
PA1939−3.7ESHypothetical protein
PA2012−6.5MLProbable acyl-CoA carboxylase alpha chain
PA2013−4.8MLProbable enoyl-CoA hydratase isomerase
PA2014−4.9MLProbable acyl-CoA carboxyltransferase beta chain
PA2015−6.8MLProbable acyl-CoA dehydrogenase
PA2016−9.4MLProbable transcriptional regulator
PA2024−4.7MLProbable ring-cleaving dioxygenase
PA2026−3.2ESHypothetical protein
PA2073−6.6MLProbable transporter (membrane subunit)
PA2110−7.4ESHypothetical protein
PA2112−4MLHypothetical protein
PA2113−3.5/−3.9BProbable porin
PA2114−4.5/−4.4BProbable MFS transporter
PA2119−5.7MLAlcohol dehydrogenase (Zn dependent)
PA2128 cupA1 4.2ESFimbrial subunit CupA1
PA2129 cupA2 9.5MLChaperone CupA2
PA2130 cupA3 3.6MLUsher protein CupA3
PA2193 hcnA −3.1ESHydrogen cyanide synthase HcnA
PA2259 ptxS −4.8MLTranscriptional regulator PtxS
PA2261−9.4MLProbable 2-ketogluconate kinase
PA2264−3.2MLConserved hypothetical protein
PA2265−3.4MLGluconate dehydrogenase
PA2302−3.8ESProbable nonribosomal peptide synthetase
PA2303−3.2ESHypothetical protein
PA2366−3.9ESHypothetical protein
PA2423−3.3ESHypothetical protein
PA24788.4MLProbable thiol-disulfide interchange protein
PA2552−5.1MLProbable acyl-CoA dehydrogenase
PA2553−7.6MLProbable acyl-CoA thiolase
PA2554−7.1MLProbable short-chain dehydrogenase
PA2555−7.9MLProbable AMP-binding enzyme
PA2557−4.3MLProbable AMP-binding enzyme
PA2572−3MLProbable two-component response regulator
PA2573−3.6MLProbable chemotaxis transducer
PA2753−9MLHypothetical protein
PA2754−5MLHypothetical protein
PA2759−3.1MLHypothetical protein
PA2780−3.5MLHypothetical protein
PA2790−3.3MLHypothetical protein
PA3181−3.2ML2-Keto-3-deoxy-6-phosphogluconate aldolase
PA3329−7.2ESHypothetical protein
PA3330−4.7ESProbable short chain dehydrogenase
PA3333 fabH2 −3.8ES3-Oxoacyl (acyl carrier protein) synthase III
PA3334−3.6ESProbable acyl carrier protein
PA3337 rfaD −12.2MLADP-l-glycero-d-manno-heptose 6-epimerase
PA3418 idh −4.2MLLeucine dehydrogenase
PA3425−3.2ESHypothetical protein
PA3458−6.3MLProbable transcriptional regulator
PA3465−5.4MLHypothetical protein
PA3520−3.9/−11.2BHypothetical protein
PA3531 bfrB −8MLBacterioferritin
PA3552−11.5ESHypothetical protein
PA3553−14.8ESProbable glycosyl transferase
PA3688−3MLHypothetical protein
PA3724 lasB −5.7ESElastase LasB
PA3790 oprC 10.2MLOuter membrane protein OprC
PA38663ESPyocin protein
PA3876 narK2 −5.9MLNitrite extrusion protein 2
PA3877 narK1 −7.3MLNitrite extrusion protein 1
PA3914 moeA1 −8.8ESMolybdenum cofactor biosynthetic protein A1
PA3915 moaB1 −3.9/−7.8BMolybdopterin biosynthetic protein B1
PA3916 moaE −3.4/−5.3BMolybdopterin converting factor, large subunit
PA3917 moaD −5.7ESMolybdopterin converting factor, small subunit
PA3918 moaC −3.4/−6BMolybdopterin biosynthetic protein C
PA3919−4.8MLHypothetical protein
PA4063−3ESHypothetical protein
PA4064−3.1ESProbable ATP-binding component of ABC transporter
PA4070−5.2MLProbable transcriptional regulator
PA4129−4.9ESHypothetical protein
PA4134−6.7ESHypothetical protein
PA4211 phzBI −3.5ESProbable phenazine biosynthesis protein
PA4309 pctA −4.3MLChemotactic transducer PctA
PA43543.1ESHypothetical protein
PA43718.8MLHypothetical protein
PA4504−3.5MLProbable permease of ABC transporter
PA4571−6.4MLProbable cytochrome c
PA4577−6MLHypothetical protein
PA4602 glyA3 3ESSerine hydroxymethyltransferase
PA4619−3.1MLProbable c-type cytochrome
PA4739−3.8ESHypothetical protein
PA48523.1MLHypothetical protein
PA4878−4.3ESProbable transcriptional regulator
PA5027−5MLHypothetical protein
PA5170 arcD −17.1MLArginine-ornithine antiporter
PA5171 arcA −6.6MLArginine deiminase
PA5172 arcB −5.7MLOrnithine carbamoyltransferase, catabolic
PA5208−3.2MLConserved hypothetical protein
PA52163.8MLProbable permease of ABC iron transporter
PA52175.2MLProbable binding protein component of ABC iron transporter
PA54963.2ESHypothetical protein
PA54973.5ESHypothetical protein
PA55043.1MLProbable permease of ABC transporter
PA5506−3.9MLHypothetical protein
PA5507−4.1MLHypothetical protein
PA5508−3MLProbable glutamine synthetase
PA5510−3.4MLProbable transporter
PA5570 rpmH 3.3ML50S ribosomal protein L34
  • a Only transcripts identified as anaerobically regulated that demonstrated a change of equal to or greater than threefold are reported. A list of all transcripts identified as being anaerobically regulated exhibiting a statistically significant change (P ≤ 0.05) is available online ( ). Genes are identified by transcript number, gene name, and protein description ( ).

  • b The change (n-fold) was calculated by comparing PAO1 grown aerobically with nitrate present (baseline) to PAO1 grown anaerobically with nitrate present (experimental). A positive change represents an induction caused by the lack of oxygen, and a negative change represents repression caused by the lack of oxygen. 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 ( ECF, extracytoplasmic function; CoA, coenzyme A; MSF, major facilitator superfamily; ABC, ATP-binding cassette.