TABLE 1.

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 ( 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 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 (www.pseudomonas.com). ECF, extracytoplasmic function; CoA, coenzyme A; MSF, major facilitator superfamily; ABC, ATP-binding cassette.