RegulonDB RegulonDB 11.2: Operon Form
   

yihV-csqR operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yihV-csqR
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: yihV-csqR
Gene(s): yihV, csqR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Expression of yihV is increased during growth on lactose Kaznadzey A,2018 Both YihW and CRP function as repressors for yihV during growth in glucose Kaznadzey A,2018
CsqR represses the expression of the yihV gene during the exponential growth phase Shimada T,2019 In the presence of the effectors sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQG), CsqR is inactivated, which derepresses the expression of the yihV gene Shimada T,2019
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yihVp1
+1: 4073712
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: tttatcgtcaaaaaattgacagccgtcactttttaaacaattggtgaaattaaaatgaacGcatcccaaaatgtttaagga
                              -35                  -10      +1                   
Note(s): yhiVp is activated during growth on lactose Kaznadzey A,2018
The sequence for the yihVp promoter was not shown. Only the position with respect to its ATG is mentioned in the article Kaznadzey A,2018 Two transcriptional start sites (TSS) are mentioned at -25 and -27 from ATG of the yhiV gene Kaznadzey A,2018
Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.01. P-value: 5.545e-5
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
[EXP-IPI]
Reference(s): [1] Dornenburg JE., et al., 2010
[2] Huerta AM., et al., 2003
[3] Kaznadzey A., et al., 2018
TF binding sites (TFBSs)
[CsqR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CsqR repressor yihVp1 4073662 4073687 -38.0 tttatcgtcaAAAAATTGACAGCCGTCACTTTTTAAacaattggtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4]


Transcription unit          
Name: yihW
Gene(s): csqR   Genome Browser M3D Gene expression COLOMBOS
Note(s): CRP activates yihW under lactose growth conditions and represses it under glucose growth conditions Kaznadzey A,2018
CsqR represses its own expression during the exponential growth phase Shimada T,2019 In the presence of the effectors sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQG), CsqR is inactivated, which derepresses the expression of the csqR gene; however, for activation of the csqR gene, an as-yet-unidentified regulator is apparently needed Shimada T,2019
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [3] Kaznadzey A., et al., 2018
Promoter
Name: csqRp
+1: 4074641
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: agccgggatccctgactgtgatcaaacccgatcttttttgtcactttttgtataaaatgcCagggtgatggtttttcgagg
Note(s): Two transcriptional start sites (TSS) are mentioned at -27 and -28 from ATG of the yhiW gene Kaznadzey A,2018
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
[EXP-IPI]
Reference(s): [1] Dornenburg JE., et al., 2010
[3] Kaznadzey A., et al., 2018
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator csqRp 4074594 4074617 -36.0 cgggatccctGACTGTGATCAAACCCGATCTTTTttgtcacttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-PATTERN-DISCOVERY], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP repressor csqRp 4074594 4074617 -36.0 cgggatccctGACTGTGATCAAACCCGATCTTTTttgtcacttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-PATTERN-DISCOVERY], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[CsqR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CsqR repressor csqRp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-IPI] Inferred from physical interaction

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-PATTERN-DISCOVERY] Manually curated inference based on sequence pattern discovery


Reference(s)    

 [1] Dornenburg JE., Devita AM., Palumbo MJ., Wade JT., 2010, Widespread antisense transcription in Escherichia coli., MBio 1(1)

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Kaznadzey A., Shelyakin P., Belousova E., Eremina A., Shvyreva U., Bykova D., Emelianenko V., Korosteleva A., Tutukina M., Gelfand MS., 2018, The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation., Sci Rep 8(1):3177

 [4] Shimada T., Yamamoto K., Nakano M., Watanabe H., Schleheck D., Ishihama A., 2019, Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12., Microbiology 165(1):78-89

RegulonDB