TABLE 2.
Differentially expressed transcripts between cultures grown aerobically without nitrate and cultures grown aerobically with nitratea
| Transcript | Gene name | Fold changeb | Growth phasec | Protein descriptiond |
|---|---|---|---|---|
| PA0045 | −3.5 | ES | Hypothetical protein | |
| PA0046 | −3.4/−5.4 | B | Hypothetical protein | |
| PA0047 | −3.1/−3.8 | B | Hypothetical protein | |
| PA0129 | gabP | 4.3 | ML | Gamma-aminobutyrate permease |
| PA0130 | 4.2 | ML | Probable aldehyde dehydrogenase | |
| PA0131 | 3.9 | ML | Hypothetical protein | |
| PA0132 | 3.5 | ML | Beta-alanine-pyruvate transaminase | |
| PA0160 | −3.8 | ML | Hypothetical protein | |
| PA0164 | −4.8 | ML | Probable gamma-glutamyltranspeptidase | |
| PA0174 | 3.2 | ML | Conserved hypothetical protein | |
| PA0175 | 4.8 | ML | Probable chemotaxis protein methyltransferase | |
| PA0176 | 3.7 | ML | Probable chemotaxis transducer | |
| PA0177 | 3.8 | ML | Probable purine-binding chemotaxis protein | |
| PA0178 | 3 | ML | Probable two-component sensor | |
| PA0179 | 3.5 | ML | Probable two-component response regulator | |
| PA0200 | 8.7 | ES | Hypothetical protein | |
| PA0386 | −3.2 | ES | Probable oxidase | |
| PA0447 | gcdH | 3.4 | ES | Glutaryl-CoA dehydrogenase |
| PA0459 | 4 | ML | Probable ClpA/B protease ATP-binding subunit | |
| PA0494 | 3.2 | ML | Probable acyl-CoA carboxylase subunit | |
| PA0509 | nirN | 11.8 | ES | Probable c-type cytochrome |
| PA0510 | 17.5 | ES | Probable uroporphyrin-III C-methyltransferase | |
| PA0512 | 13.9 | ES | Conserved hypothetical protein | |
| PA0513 | 16 | ES | Probable transcriptional regulator | |
| PA0514 | nirL | 16.1 | ES | Heme d1 biosynthesis protein NirL |
| PA0516 | nirF | 16.3 | ES | Heme d1 biosynthesis protein NirF |
| PA0518 | nirM | 4.9 | ES | Cytochrome c551 precursor |
| PA0519 | nirS | 9.3 | ES | Nitrite reductase precursor |
| PA0521 | 23.6 | ES | Probable cytochrome c oxidase subunit | |
| PA0526 | 8.1 | ES | Hypothetical protein | |
| PA0586 | 4.1 | ML | Conserved hypothetical protein | |
| PA0587 | 4.5 | ML | Conserved hypothetical protein | |
| PA0614 | 3.3 | ML | Hypothetical protein | |
| PA0623 | 3.5 | ML | Probable bacteriophage protein | |
| PA0624 | 4.1 | ML | Hypothetical protein | |
| PA0627 | 4.6 | ML | Conserved hypothetical protein | |
| PA0628 | 4.5 | ML | Conserved hypothetical protein | |
| PA0632 | 4.3 | ML | Hypothetical protein | |
| PA0633 | 4 | ML | Hypothetical protein | |
| PA0639 | 3.8 | ML | Conserved hypothetical protein | |
| PA0742 | 3.6 | ML | Hypothetical protein | |
| PA0743 | 3.3 | ML | Probable 3-hydroxyisobutyrate dehydrogenase | |
| PA0744 | 3.7 | ML | Probable enoyl-CoA hydratase/isomerase | |
| PA0746 | 5.5 | ML | Probable acyl-CoA dehydrogenase | |
| PA0747 | 5.5 | ML | Probable aldehyde dehydrogenase | |
| PA0782 | putA | −5.1 | ES | Proline dehydrogenase PutA |
| PA0792 | prpD | 3.9 | ML | Propionate catabolic protein PrpD |
| PA0793 | 4 | ML | Hypothetical protein | |
| PA0795 | prpC | 4.3 | ML | Citrate synthase 2 |
| PA0887 | acsA | 3.8 | ML | Acetyl-CoA synthetase |
| PA0889 | aotQ | −3.2 | ES | Arginine/ornithine transport protein AotQ |
| PA0910 | 3.4 | ML | Hypothetical protein | |
| PA0985 | 7.6 | ML | Probable colicin-like toxin | |
| PA1070 | braG | 4.1 | ML | Branched-chain amino acid transport protein BraG |
| PA1071 | braF | 3.7 | ML | Branched-chain amino acid transport protein BraF |
| PA1072 | braE | 3.4 | ML | Branched-chain amino acid transport protein BraE |
| PA1073 | braD | 3 | ML | Branched-chain amino acid transport protein BraD |
| PA1173 | napB | 6 | ML | Cytochrome c-type protein NapB precursor |
| PA1174 | napA | 3.8 | ML | Periplasmic nitrate reductase protein NapA |
| PA1175 | napD | 3.3 | ML | NapD protein of periplasmic nitrate reductase |
| PA1249 | aprA | 6.7 | ML | Alkaline metalloproteinase precursor |
| PA1282 | 6.3 | ES | Probable MFS transporter | |
| PA1317 | cyoA | −3.7 | ML | Cytochrome o ubiquinol oxidase subunit II |
| PA1318 | cyoB | −3.1 | ML | Cytochrome o ubiquinol oxidase subunit I |
| PA1319 | cyoC | −3 | ML | Cytochrome o ubiquinol oxidase subunit III |
| PA1320 | cyoD | −4.8 | ML | Cytochrome o ubiquinol oxidase subunit IV |
| PA1337 | ansB | 4.8 | ML | Glutaminase-asparaginase |
| PA1338 | ggt | 3.4 | ML | Gamma-glutamyltranspeptidase precursor |
| PA1418 | 7.5 | ML | Probable sodium-solute symport protein | |
| PA1419 | 10.9 | ML | Probable transporter | |
| PA1420 | 6 | ML | Hypothetical protein | |
| PA1421 | gbuA | 5.6 | ML | Guanidinobutyrase |
| PA1428 | −7.4 | ES | Conserved hypothetical protein | |
| PA1559 | −3.6 | ML | Hypothetical protein | |
| PA1566 | −5.9 | ES | Conserved hypothetical protein | |
| PA1596 | htpG | −3.2 | ML | Heat shock protein HtpG |
| PA1657 | −5 | ES | Conserved hypothetical protein | |
| PA1660 | −4.8 | ES | Hypothetical protein | |
| PA1661 | −3.4 | ES | Hypothetical protein | |
| PA1662 | −3.3 | ES | Probable ClpA/B-type protease | |
| PA1663 | −3.3 | ES | Probable transcriptional regulator | |
| PA1664 | −4 | ES | Hypothetical protein | |
| PA1665 | −4.4 | ES | Hypothetical protein | |
| PA1666 | −3 | ES | Hypothetical protein | |
| PA1667 | −4.8 | ES | Hypothetical protein | |
| PA1668 | −3.2 | ES | Hypothetical protein | |
| PA1669 | −4.7 | ES | Hypothetical protein | |
| PA1761 | 3.2 | ML | Hypothetical protein | |
| PA1762 | 3.7 | ML | Hypothetical protein | |
| PA1790 | −4.8 | ES | Hypothetical protein | |
| PA1847 | 4.3 | ES | Conserved hypothetical protein | |
| PA1855 | 12.7 | ML | Hypothetical protein | |
| PA1856 | 29/4.1 | B | Probable cytochrome oxidase subunit | |
| PA1883 | 3 | ES | Probable NADH-ubiquinone/plastoquinone oxidoreductase | |
| PA1888 | 3.9 | ML | Hypothetical protein | |
| PA1902 | phzD2 | −13.5 | ES | Phenazine biosynthesis protein PhzD |
| PA1903 | phzE2 | −12.3 | ES | Phenazine biosynthesis protein PhzE |
| PA1904 | phzF2 | −12.9 | ES | Probable phenazine biosynthesis protein |
| PA1971 | braZ | −3.3 | ES | Branched chain amino acid transporter BraZ |
| PA1985 | pqqA | 3.6 | ML | Pyrroloquinoline quinone biosynthesis protein A |
| PA1986 | pqqB | 3 | ML | Pyrroloquinoline quinone biosynthesis protein B |
| PA1987 | pqqC | 4 | ML | Pyrroloquinoline quinone biosynthesis protein C |
| PA1988 | pqqD | 5 | ML | Pyrroloquinoline quinone biosynthesis protein D |
| PA1989 | pqqE | 3.3 | ML | Pyrroloquinoline quinone biosynthesis protein E |
| PA1990 | 5.6 | ML | Probable peptidase | |
| PA1999 | 8.2 | ML | Probable CoA transferase, subunit A | |
| PA2003 | bdhA | 3.1 | ML | 3-Hydroxybutyrate dehydrogenase |
| PA2011 | 9.1 | ML | Hydroxymethylglutaryl-CoA lyase | |
| PA2012 | 9.1 | ML | Probable acyl-CoA carboxylase alpha chain | |
| PA2013 | 5.2 | ML | Probable enoyl-CoA hydratase/isomerase | |
| PA2014 | 4.4 | ML | Probable acyl-CoA carboxyltransferase beta chain | |
| PA2024 | 3.7 | ML | Probable ring-cleaving dioxygenase | |
| PA2052 | cynS | 3.2 | ML | Cyanate lyase |
| PA2066 | −4.4 | ES | Hypothetical protein | |
| PA2067 | −3.9 | ES | Probable hydrolase | |
| PA2068 | −7.5 | ES | Probable MFS transporter | |
| PA2069 | −7.7 | ES | Probable carbamoyl transferase | |
| PA2110 | 7.9 | ES | Hypothetical protein | |
| PA2112 | 4.1 | ML | Conserved hypothetical protein | |
| PA2114 | 3.1 | ES | Probable MFS transporter | |
| PA2194 | hcnB | −3.3 | ES | Hydrogen cyanide synthase HcnB |
| PA2250 | lpdV | 3.7 | ES | Lipoamide dehydrogenase-Val |
| PA2266 | −3 | ES | Probable cytochrome c precursor | |
| PA2300 | chiC | −6.1 | ES | Chitinase |
| PA2306 | −3.1 | ES | Conserved hypothetical protein | |
| PA2327 | −4 | ES | Probable permease of ABC transporter | |
| PA2329 | −4.1 | ML | Probable ATP-binding component of ABC transporter | |
| PA2330 | −5.2/−3.6 | B | Hypothetical protein | |
| PA2331 | −6.7/−3.2 | B | Hypothetical protein | |
| PA2358 | −3.7 | ML | Hypothetical protein | |
| PA2370 | 4.8 | ML | Hypothetical protein | |
| PA2404 | −3.5 | ES | Hypothetical protein | |
| PA2405 | −6.2/−5 | B | Hypothetical protein | |
| PA2406 | −3 | ES | Hypothetical protein | |
| PA2408 | −3.2 | ML | Probable ATP-binding component of ABC transporter | |
| PA2442 | gcvT2 | 3.2 | ES | Glycine cleavage system protein T2 |
| PA2443 | sdaA | 6 | ML | l-Serine dehydratase |
| PA2444 | glyA2 | 6.8 | ML | Serine hydroxymethyltransferase |
| PA2445 | gcvP2 | 3.1 | ML | Glycine cleavage system protein P2 |
| PA2446 | gcvH2 | 3.1 | ML | Glycine cleavage system protein H2 |
| PA2460 | −3.3 | ES | Hypothetical protein | |
| PA2483 | 3 | ES | Conserved hypothetical protein | |
| PA2552 | 8.9 | ML | Probable acyl-CoA dehydrogenase | |
| PA2553 | 10.9 | ML | Probable acyl-CoA thiolase | |
| PA2554 | 6.7 | ML | Probable short-chain dehydrogenase | |
| PA2555 | 3.9 | ML | Probable AMP-binding enzyme | |
| PA2570 | palL | −5.1 | ES | PA-I galactophilic lectin |
| PA2573 | 3.1 | ML | Probable chemotaxis transducer | |
| PA2593 | −5.2 | ES | Hypothetical protein | |
| PA2629 | purB | −3.6 | ES | Adenylosuccinate lyase |
| PA2663 | 41.4 | ES | Hypothetical protein | |
| PA2691 | 3 | ES | Conserved hypothetical protein | |
| PA2763 | −6.5 | ES | Hypothetical protein | |
| PA2798 | −3.2 | ES | Probable two-component response regulator | |
| PA2968 | fabD | −3.2 | ES | Malonyl-CoA-(acyl carrier protein) transacylase |
| PA2969 | plsX | −3.3 | ES | Fatty acid biosynthesis protein PlsX |
| PA3019 | −3.2 | ES | Probable ATP-binding component of ABC transporter | |
| PA3188 | 3.4 | ML | Probable permease of ABC sugar transporter | |
| PA3221 | csaA | 8.1 | ES | CsaA protein |
| PA3222 | 7 | ES | Hypothetical protein | |
| PA3232 | 3.2 | ML | Probable nuclease | |
| PA3234 | 5 | ML | Probable sodium-solute symporter | |
| PA3235 | 3.5 | ML | Conserved hypothetical protein | |
| PA3294 | −4 | ES | Hypothetical protein | |
| PA3327 | −3.9 | ES | Probable nonribosomal peptide synthetase | |
| PA3328 | −7.9 | ES | Probable FAD-dependent monooxygenase | |
| PA3329 | −9.6 | ES | Hypothetical protein | |
| PA3330 | −10.9 | ES | Probable short-chain dehydrogenase | |
| PA3331 | −8.4 | ES | Cytochrome P450 | |
| PA3333 | fabH2 | −9.1 | ES | 3-Oxoacyl (acyl carrier protein) synthase III |
| PA3334 | −8.4 | ES | Probable acyl carrier protein | |
| PA3335 | −11.5 | ES | Hypothetical protein | |
| PA3336 | −12.5 | ES | Probable MFS transporter | |
| PA3391 | nosR | 35.5 | ES | Regulatory protein NosR |
| PA3393 | nosD | 31.3 | ES | NosD protein |
| PA3394 | nosF | 33.4 | ES | NosF protein |
| PA3395 | nosY | 36 | ES | NosY protein |
| PA3396 | nosL | 21.6 | ES | NosL protein |
| PA3416 | 3.9 | ML | Probable pyruvate dehydrogenase E1 component, beta chain | |
| PA3418 | ldh | 3.3 | ML | Leucine dehydrogenase |
| PA3430 | −3 | ML | Probable aldolase | |
| PA3431 | −8.8 | ML | Conserved hypothetical protein | |
| PA3432 | −10.1 | ML | Hypothetical protein | |
| PA3478 | rhlB | −6.5 | ES | Rhamnosyltransferase chain B |
| PA3479 | rhlA | −6.5 | ES | Rhamnosyltransferase chain A |
| PA3486 | −12 | ES | Conserved hypothetical protein | |
| PA3487 | pldA | −3.2 | ES | Phospholipase D |
| PA3530 | 4.1 | ES | Conserved hypothetical protein | |
| PA3552 | 6.5 | ES | Conserved hypothetical protein | |
| PA3569 | mmsB | 3.9 | ML | 3-Hydroxyisobutyrate dehydrogenase |
| PA3570 | mmsA | 4.8 | ML | Methylmalonate-semialdehyde dehydrogenase |
| PA3605 | −5.3 | ES | Hypothetical protein | |
| PA3655 | tsf | −3.1 | ML | Elongation factor Ts |
| PA3700 | lysS | −3.6 | ES | Lysyl-tRNA synthetase |
| PA3723 | 4.2 | ML | Probable FMN oxidoreductase | |
| PA3741 | −4.7 | ES | Hypothetical protein | |
| PA3742 | rplS | −3.7 | ML | 50S ribosomal protein L19 |
| PA3811 | hscB | 3.2 | ES | Heat shock protein HscB |
| PA3813 | iscU | 3.6 | ES | Probable iron-binding protein IscU |
| PA3872 | narI | 37 | ES | Respiratory nitrate reductase gamma chain |
| PA3876 | narK2 | 3.4 | ML | Nitrite extrusion protein 2 |
| PA3880 | 7.6 | ES | Conserved hypothetical protein | |
| PA3881 | 3.1 | ES | Hypothetical protein | |
| PA3901 | fecA | −5.7 | ML | Fe(III) dicitrate transport protein FecA |
| PA3905 | −4.1 | ES | Hypothetical protein | |
| PA3907 | −3.8 | ES | Hypothetical protein | |
| PA3912 | 3.3 | ML | Conserved hypothetical protein | |
| PA3913 | 3.6/14.8 | B | Probable protease | |
| PA3914 | moeAI | 7.3/−62.7 | B | Molybdenum cofactor biosynthetic protein A1 |
| PA3915 | moaBI | 6.3/−15.6 | B | Molybdopterin biosynthetic protein B1 |
| PA3916 | moaE | 5.8 | ES | Molybdopterin-converting factor, large subunit |
| PA3917 | moaD | 6.7 | ES | Molybdopterin-converting factor, small subunit |
| PA3918 | moaC | 6.3 | ES | Molybdopterin biosynthetic protein C |
| PA3979 | −3.1 | ES | Hypothetical protein | |
| PA4055 | ribC | −4.1 | ES | Riboflavin synthase alpha chain |
| PA4063 | 4.1 | ES | Hypothetical protein | |
| PA4142 | −4.1 | ES | Probable secretion protein | |
| PA4170 | 5.8 | ES | Hypothetical protein | |
| PA4210 | phzAI | −11.9 | ES | Probable phenazine biosynthesis protein |
| PA4211 | phzBI | −14.8 | ES | Probable phenazine biosynthesis protein |
| PA4217 | phzS | −13.1 | ES | Flavin-containing monooxygenase |
| PA4235 | bfrA | 3.4 | ES | Bacterioferritin |
| PA4292 | −4.5 | ES | Probable phosphate transporter | |
| PA4432 | rpsI | −4 | ES | 30S ribosomal protein S9 |
| PA4479 | mreD | −3.1 | ES | Rod shape-determining protein MreD |
| PA4497 | 3.8 | ML | Probable binding protein component of ABC transporter | |
| PA4512 | lpxO1 | −3.1 | ES | Lipopolysaccharide biosynthetic protein |
| PA4610 | 4.2 | ES | Hypothetical protein | |
| PA4620 | −3 | ES | Hypothetical protein | |
| PA4665 | prfA | −3.5 | ES | Peptide chain release factor 1 |
| PA4670 | prs | −3.9 | ES | Ribose-phosphate pyrophosphokinase |
| PA4672 | −5 | ES | Peptidyl-tRNA hydrolase | |
| PA4743 | rbfA | −3.2 | ES | Ribosome-binding factor A |
| PA4762 | grpE | −3.1 | ML | Heat shock protein GrpE |
| PA4853 | fis | −3.4 | ES | DNA-binding protein Fis |
| PA4916 | −9.8 | ML | Hypothetical protein | |
| PA4917 | −6.7 | ML | Hypothetical protein | |
| PA4918 | −7.2 | ML | Hypothetical protein | |
| PA4919 | pncB1 | −6.2 | ML | Nicotinate phosphoribosyltransferase |
| PA4920 | nadE | −4.4 | ML | NH3-dependent NAD synthetase |
| PA4921 | −3.9 | ML | Hypothetical protein | |
| PA5023 | 4.3 | ES | Conserved hypothetical protein | |
| PA5048 | −4.2 | ES | Probable nuclease | |
| PA5117 | typA | −5 | ES | Regulatory protein TypA |
| PA5118 | thiI | −3.5 | ES | Thiazole biosynthesis protein Thil |
| PA5139 | −5 | ES | Hypothetical protein | |
| PA5167 | 3 | ES | Probable C4-dicarboxylate-binding protein | |
| PA5168 | 4.3 | ES | Probable dicarboxylate transporter | |
| PA5169 | 3.6 | ES | Probable C4-dicarboxylate transporter | |
| PA5275 | 3.8 | ES | Conserved hypothetical protein | |
| PA5296 | rep | −3.1 | ES | ATP-dependent DNA helicase Rep |
| PA5304 | dadA | −4.3 | ES | d-Amino acid dehydrogenase, small subunit |
| PA5372 | betA | 4.2 | ML | Choline dehydrogenase |
| PA5415 | glyAI | 4.3 | ML | Serine hydroxymethyltransferase |
| PA5436 | −3.4 | ES | Probable biotin carboxylase subunit of a transcarboxylase | |
| PA5446 | −7.2 | ML | Hypothetical protein | |
| PA5448 | wbpY | 3.2 | ML | Glycosyltransferase WbpY |
| PA5460 | −3.2 | ML | Hypothetical protein | |
| PA5496 | 3.1 | ES | Hypothetical protein | |
| PA5553 | atpC | −3 | ML | ATP synthase epsilon chain |
| PA5554 | atpD | −3.1 | ML | ATP synthase beta chain |
| PA5556 | atpA | −3.4 | ML | ATP synthase alpha chain |
| PA5557 | atpH | −3 | ML | ATP synthase delta chain |
| ig326671 | 2.9/3.5 | B | Intergenic region between PA0458 and PA0459, 326671-327284, plus strand | |
| ig4326394 | 3.2 | ES | Intergenic region between PA3969 and PA3970, 4326394-4327696, plus strand | |
| ig4713098 | −5.3 | ES | Intergenic 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.