RegulonDB RegulonDB 11.1: Operon Form
   

srlAEBD-gutM-srlR-gutQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: srlAEBD-gutM-srlR-gutQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: srlAEBD-gutM-srlR-gutQ
Synonym(s): OP00177, gutABDMR, srlABDMR
Gene(s): srlA, srlE, srlB, srlD, gutM, srlR, gutQ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] McEntee K. 1977
[2] Yamada M., et al., 1988
[3] Yamada M., et al., 1987
Promoter
Name: srlAp
+1: 2825791
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: atctttcattttgcgatcaaaataacacttttaaatctttcaatctgattagattaggttGccgtttggtaataaaacaat
                             -35                  -10       +1                   
Note(s): Based on the one-round PCR product method, a novel site-directed mutagenesis method, it was determined that an srlA-driven expression system is a tool applicable for strong expression of foreign genes under cultivation conditions in LB medium without induction Nakamura M, Aihara J, Hoshida H, Akada R,2018 In addition, it was determined that the sequence adjacent to the start codon of the srlA gene is essential for high expression and that its promoter region is 100 bp. srlAp is a constitutive promoter in LB medium, and it is a sorbitol-enhanceable and glucose-, fructose-, galactose-, mannose-, xylose-, and arabinose- repressible promoter Nakamura M, Aihara J, Hoshida H, Akada R,2018
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[2] Yamada M., et al., 1988
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
remote CRP-cyclic-AMP activator srlAp 2825438 2825459 -342.0 atctgcatcaCATTGTGCTGCGGCTCAAGCAGgaagccgcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [5]
proximal CRP-cyclic-AMP activator srlAp 2825739 2825760 -41.5 ttatctttcaTTTTGCGATCAAAATAACACTTttaaatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [5]
[GutM,+] 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 GutM activator srlAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
[H-NS,+] 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 H-NS activator srlAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[SrlR,-] 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 SrlR repressor srlAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]


Transcription unit       
Name: srlR
Synonym(s): gutR
Gene(s): srlR   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [2] Yamada M., et al., 1988
Promoter
Name: srlRp
+1: 2828860
Distance from start of the gene: 187
Sequence: cgatcagcagcgcatcgtcgacaccttgtttatgaaaggactgaccgtcttcgcccgaccGcaaaaaattcccgcaattac
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Yamada M., et al., 1988


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IMP] Inferred from mutant phenotype


Reference(s)    

 [1] McEntee K., 1977, Genetic analysis of the Escherichia coli K-12 srl region., J Bacteriol 132(3):904-11

 [2] Yamada M., Saier MH., 1988, Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli., J Mol Biol 203(3):569-83

 [3] Yamada M., Saier MH., 1987, Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon., J Biol Chem 262(12):5455-63

 [4] 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

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [6] White-Ziegler CA., Malhowski AJ., Young S., 2007, Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12., J Bacteriol 189(15):5429-40

 [7] Beisel CL., Storz G., 2011, The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli., Mol Cell 41(3):286-97

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