RegulonDB RegulonDB 11.1: Operon Form
   

motRAB-cheAW operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: motRAB-cheAW
Gene(s): cheW, cheA, motB, motA, motR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The CpxR-dependent expression of the motAB-cheAW operon is diminished under the stress condition caused by the introduction of the R1-16 plasmid, which encodes the type IV secretion system (T4S machinery) in the cell Zahrl D,2006
The mRNA produced by the motAB-cheAW operon has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid downregulated the expression of motAB as well as other flagellar genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
The motA gene is downregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Reference(s): [1] Mirel DB., et al., 1992
[2] Silverman M., et al., 1977
Promoter
Name: motRp
+1: 1977302
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 0
Sequence: accgccatcccgggcagtaaaaagacgtaaactttcccagaatcctgccgatattatcccAcaactgctggatgaacagag
                                -35                   -10   +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28 (σF) promoters TAAAGTTT in the -35 box and GCCGATAA in the -10 box Park K,2001. Ko M,2000. Ide N,1999. Therefore, we assigned a putative transcription start site for this promoter based on the observation that the majority of the σ28 promoters, determined experimentally, present an important -10 motif (5'-CGA-3') at the positions -12 to -10 and a distance of 6 nucleotides between the transcription start site and the -10 box Yu HH, Di Russo EG, Rounds MA, Tan M,2006. Yu HH,2006. Park K,2001
The motAp promoter is an intragenic promoter controlled by FliA, which is inside the flhC gene. The FliA promoter within the flhC gene constrains evolution of the FlhC amino acid sequence. Fitzgerald DM, Smith C, Lapierre P, Wade JT,2018 Although FlhC has two amino acids (Ala177 and Asp178) overlapping the -10 region, which are highly conserved among γ-proteobacteria, Asp178 is not required for FlhC function Fitzgerald DM, Smith C, Lapierre P, Wade JT,2018 The Ala-Asp motif is conserved due to selective pressure on the motA promoter, rather than on the amino acids themselves Fitzgerald DM, Smith C, Lapierre P, Wade JT,2018
motAp, the promoter within the flhC gene, is the most highly conserved of all FliA promoters Fitzgerald DM, Smith C, Lapierre P, Wade JT,2018
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
Reference(s): [3] Huerta AM., et al., 2003
[4] Ide N., et al., 1999
[5] Ko M., et al., 2000
[6] Park K., et al., 2001
Terminator(s)
Type: rho-independent
Sequence: acccgccgcgAAATTGAAATAAAAAACCCGATGCGCAGATCATCGGGTTCATTTCAATTGAGGAAatcgggagaa
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CpxR,-] 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 CpxR-phosphorylated repressor motRp 1977338 1977339 -37.0 gcagtaaaaaGacgtaaactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9], [10]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.7 1977207 1977240 gcaacattccAGCAGCGGTAACGACGTACCGCTGCTTTTTTTTgccccaatcg
  anti-terminator -5.6 1977232 1977274 gagagtacagGCTGTTTAACTGATACGGTGAGGCGCAACATTCCAGCAGCGGtaacgacgta
  anti-anti-terminator -10.6 1977252 1977305 ccgatattatCCCACAACTGCTGGATGAACAGAGAGTACAGGCTGTTTAACTGATACGGTGAGgcgcaacatt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

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


Reference(s)    

 [1] Mirel DB., Lustre VM., Chamberlin MJ., 1992, An operon of Bacillus subtilis motility genes transcribed by the sigma D form of RNA polymerase., J Bacteriol 174(13):4197-204

 [2] Silverman M., Simon M., 1977, Identification of polypeptides necessary for chemotaxis in Escherichia coli., J Bacteriol 130(3):1317-25

 [3] 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

 [4] Ide N., Ikebe T., Kutsukake K., 1999, Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella., Genes Genet Syst 74(3):113-6

 [5] Ko M., Park C., 2000, Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli., J Mol Biol 303(3):371-82

 [6] Park K., Choi S., Ko M., Park C., 2001, Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus., FEMS Microbiol Lett 202(2):243-50

 [7] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [8] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [9] De Wulf P., Kwon O., Lin EC., 1999, The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons., J Bacteriol 181(21):6772-8

 [10] De Wulf P., McGuire AM., Liu X., Lin EC., 2002, Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli., J Biol Chem 277(29):26652-61

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