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Table 2 PhaR-repressed genes associated with a PhaR-binding consensus sequence

From: Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation

Gene or orf PhaR binding site USDA110 RPKM ΔphaR RPKM Fold changea Description
cyoA (blr0149) TGCGGCGCAGCA 22.29 77.7 3.49 cytochrome O ubiquinol oxidase subunit II
phaZ3 (blr0899) TGCAGTGCAGCA 32.68 89.48 2.74 poly(3-hydroxyalkanoate) depolymerase
phaZ1 (blr0908) CGCATCGCAGCA 129.32 542.25 4.19 poly(3-hydroxybutyrate) depolymerase
rhlE (bll1447) TGCAGTGCAGAA 152.94 551.69 3.61 dead-box ATP-dependent RNA helicas
blr2242 TGCGCCGCAGCA 66.21 190.65 2.88 unknown protein
bll2363 TGCGCCGCACAA 374.44 1256.32 3.36 unknown protein
blr2367 TGCACCGCAGCA 55.14 347.34 6.30 acetyltransferase
bll2471 TGGATCGCACCA 86.78 512.16 5.90 hypothetical protein (Hemerythrin HHE cation binding region)
bll2537 CGCGTCGCAGCA 39.54 83.05 2.10 hypothetical protein
phaP5 (blr2887) TGCATCGCACAA 122.86 15,882.63 129.27 phasin
ppc (blr2955) TGCGCTGCGGCA 46.27 93.71 2.03 PEP carboxylase
bll3794 TGCATTGCAGCG 104.59 404.72 3.87 hypothetical protein
blr4162 TGCATCGCACCA 79.46 931 11.72 hypothetical protein (cellulose synthase catalytic subunit protein)
bsr4236 TGCATTGCAACA 38.73 435.02 11.23 unknown protein
nifR (blr4486) TGCAGTGCAGCA 112.16 225.25 2.01 nitrogen regulation protein
metN (blr4501) TGCACCGCAACA 14.42 29.08 2.02 probable ABC transporter ATP-binding protein
bsr4726 TGCGGTGCACAC 157.38 1402.14 8.91 hypothetical protein
bll4785 CGCGCCGCACAA 90.88 279.72 3.08 transcriptional regulatory protein Fis family
phaP1 (bll5155) TGCAACGCACAA 215.67 10,738.12 49.79 phasin
bsr5273 TGCGGTGCATCA 45.13 222.49 4.93 hypothetical protein
bll5524 AGCAGTGCAGCA 106.54 220.06 2.07 hypothetical protein
blr5525 AGCAGTGCAGCA 23.4 46.85 2.00 hypothetical protein
blr5594 TGCGGCGCACAA 26.16 71.75 2.74 MFS permease
bll6290 TGCGGCGGACCA 146.99 458.11 3.12 two-component response regulator
blr6718 TGCCATGCAGCA 42.45 111.4 2.62 hypothetical protein
nirK (blr7089) TGCGCTGCAACA 13.49 41.36 3.07 respiratory nitrite reductase
phaP4 (bll7395) TGCGCTGCACAA 489.78 2956.78 6.04 phasin
blr7872 TGCGCTGCAACA 6.30 20.63 3.27 HlyD family secretion protein
  1. aFold change: ΔphaR RPKM/USDA110 RPKM