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Table 3 PhaR-activated genes associated with a PhaR-binding consensus sequence

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

Genes or orf PhaR binding site USDA110 RPKM ΔphaR RPKM Fold changea Description
phbB2 (bll0225) TGCGCTGCACAC 154.34 74.52 2.07 acetoacetyl CoA reductase
ragA (bll0304) TGCGACGCCGCA 8.95 2.29 3.91 two-component response regulator
blr0305 TGCGACGCCGCA 45.61 16.48 2.77 unknown protein
bll0805 CGCAACGCACAA 185.17 76.29 2.43 hypothetical protein
blr0806 CGCAACGCACAA 52.09 23.58 2.21 hypothetical protein
bll1416 TGCGCGGCAGCA 52.49 20.56 2.55 unknown protein
blr2204 TGCAGTCCAGAA 19.07 9.05 2.11 transcriptional regulatory protein AraC family
bll2446 TTCGCCGCAGAA 275.72 129.25 2.13 hypothetical protein
bsr2601 TGCACCGCAGCC 32.44 15.65 2.07 unknown protein
blr2810 TGCATTGCGCAA 15.88 7.35 2.16 aldo/keto reductase
bll2914 TGCGCTGGAGAA 25.07 9.61 2.61 probable amidase
bll3387 TGCGCCGCAACA 278.27 54.25 5.13 unknown protein
blr3795 TGCATTGCAGCG 40.09 19.03 2.11 ABC transporter HlyB/MsbA family
blr3904 TGCAGTGCTGCA 312.33 109.92 2.84 probable iron transport protein
blr4188 CGCAGTGCAGCA 28.85 12.98 2.22 hypothetical protein
bll4430 TGCAGCGCAGCA 104.34 38.21 2.73 hypothetical protein
bsr4431 TGCAGCGCAGCA 216.36 77.85 2.78 hypothetical protein
pdhA (bll4783) TGCAGTGCGGCA 249.67 111.10 2.25 pyruvate dehydrogenase alpha subunit
bll4833 TGCGGCGCACCA 530.73 140.09 3.79 unknown protein
bsr4834 TGCGGCGCACCA 168.95 52.96 3.19 unknown protein
blr4841 TGCCGCGCACAA 30.64 14.59 2.10 unknown protein
bll4952 TGCATCGCACAA 27.07 7.50 3.61 NfeD protein homolog
bll5160 TGCGGCGCACAA 106.54 46.40 2.30 conserved hypothetical protein; putative alpha/beta-Hydrolases
bsl5321 CGCGGCGCAGCA 415.34 205.51 2.02 unknown protein
bll5335 TGCGCCGGACAA 35.29 16.85 2.09 putative thiolase
blr5540 TGCGGTGCCCAA 231.26 58.07 3.98 hypothetical protein
bsl5717 TGCGGCGCCCAA 109.78 34.94 3.14 hypothetical protein
bll5961 TGCGGTGCAACA 12.66 4.23 2.99 transcriptional regulatory protein Crp family
blr5962 TGCGGTGCAACA 40.98 7.40 5.54 ABC transporter ATP-binding protein
bll6121 TGCAGCGCACAA 21.88 9.39 2.33 probable sulfite oxidase
bll6206 CGCGCCGCACAA 74.19 35.28 2.10 hypothetical protein
exaA (blr6207) CGCGCCGCACAA 93.32 23.85 3.91 probable quinoprotein ethanol dehydrogenase precursor
blr6443 TGCAATGCAACA 13.79 2.83 4.87 ABC transporter permease protein
blr6465 CGCGATGCACAA 39.03 14.29 2.73 putative steroid monooxygenase
bll6733 TGCGACGAAGCA 45.09 21.88 2.06 putative amidase
pqqA (bsr6735) TGCAGTGCAACA 156.84 40.03 3.92 putative pyrroloquinoline quinone synthesis protein A
blr6837 CGCAGTGCAGCA 34.10 7.30 4.67 hypothetical protein
blr6886 CGCATTGCACAA 57.55 25.47 2.26 transcriptional regulatory protein MarR family
bll7487 TGCGGAGCACAA 456.33 176.20 2.59 unknown protein
bll7511 TGCAACGCAGAT 167.13 62.44 2.68 unknown protein
bll7663 TGCACCGCAGCA 57.90 24.14 2.40 unknown protein
pckA (bll8141) TGCGACGCACAA 386.03 107.43 3.59 phosphoenolpyruvate carboxykinase
  1. aFold change: USDA110 RPKM/ΔphaR RPKM