TABLE 1 

CceR binding sites across the R. sphaeroides genome identified by ChIP-seq

No.Gene IDAnnotationaChrIDChIP FCbMotif startPredicted sequencecRegd
1RSP_0037flgMchr12.41742534GAGGTTCGGCCTAACATGC
2RSP_0974-9Succinate dehydrogenase complex (sdh)chr11.72734837CATGATTGCGCAAACATGT+
3RSP_1039-35F0F1 ATP synthase (atpIBEXF)chr15.32801009GATGTTCGTGGTGCATTCG+
4RSP_1663cceRchr118.7255473GCCGTTATCGCTAACATGGND
5RSP_1680Phosphoenolpyruvate carboxykinase (pckA)chr15.4272325GACGTTAGCGCAACCAGCG+
6RSP_2296-2300F0F1 ATP synthase (atpHAGDC)chr17.3918845GATGTTAGCGGCACCATCG+
7RSP_2410RNA polymerase factor sigma-32 (rpoH1)chr181039219GACGTCAGCGCTACCATGG
8RSP_2425Putative CarD-like transcriptional regulatorchr12.41056109GATTTTCTAGCGACCATTC
9RSP_2646-5edd, edachr16.71289714TTTGTTAGCGCTAACTAGC
10RSP_2734-6zwf, pgl, pgichr116.91383134GCCGTTAGCGCTAACAGGC
11RSP_3896repCplasmidA7.689831GCAGTTTCTGCGAACAAGG
12RSP_3926UDP-glucuronate 5′-epimeraseplasmidA2.5100456CATGATAGCGCAAACATCG
13RSP_4045Fructose-bisphosphate aldolase (fbaB)chr12.31127172GTTGTTCGCGCTAACTTGG+
14RSP_6037Hypothetical proteinchr17.1692742GCTGTTAGGGCAAACATGGNA
15RSP_6082Hypothetical proteinchr18.61642463GTTGTTAGCGCCAACATTCNA
16RSP_7376Hypothetical proteinplasmidC2.952671GATGTTCCGCCTAACAGCGNA
17chr22.6704863GAGGTCCGTGGCAACATGGNA
18plasmidD3.930048TACGTTTAGCCTAACAGCGNA
19plasmidC2.754188GTTGTTAGCCCTGAGATCCNA
  • a Binding sites not found ≤500 bp upstream of the start codon of an annotated gene were not assigned to any operon. Operons designated based on predicted operon structures (65).

  • b ChIP FC, ChIP-seq fold change (the fold enrichment of the CceR binding at target promoters relative to the mock anti-Myc ChIP control).

  • c Bold letters indicate the most conserved bases in the proposed CceR binding site.

  • d Regulatory role of CceR on target operon based on gene expression analysis. +, activation; –, repression; ND, not determined (this applies only to cceR, as the comparison between WT and the ΔCceR strain does not allow assessment of differential expression of the deleted cceR gene); NA, not applicable (these genes are not represented on the R. sphaeroides Affymetrix gene chip, and thus their expression levels could not be determined). No entry indicates that the genes were not observed to be differentially expressed under the conditions tested.