RegulonDB RegulonDB 11.2: Operon Form
   

bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: bamA-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE
Synonym(s): ecfK-skp-lpxD-fabZ-lpxAB-rnhB-dnaE, yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE
Gene(s): bamA, skp, lpxD, fabZ, lpxA, lpxB, rnhB, dnaE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: bamAp2
+1: 197026
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 902
Sequence: gcggaagcacaaattgcaccaggtacggaactaaaagccgtagatggtatcgaaacgcctGattgggatgccgtgcgtttg
                            -35                   -10       +1                   
Note(s): This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[1] Rhodius VA., et al., 2005
[3] Salgado H, et al., 2012


Transcription unit       
Name: bamA
Synonym(s): ecfK, yaeT
Gene(s): bamA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for bamA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Promoter
Name: bamAp1
+1: 197821
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 107
Sequence: ctgctgttccttgcgatcgaaaagatcaagggcggaccggtatccgagcgggttcaagacTtttgttatcgcattggctcg
                              -35                    -10    +1                   
Note(s): It was suggested, from high-throughput screening of maps of transcriptional start sites (TSSs), that the TSS (197821) assigned for this promoter is an RNA processing site Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Dartigalongue C., et al., 2001
[2] Huerta AM., et al., 2003


Transcription unit          
Name: hlpA-lpxD-fabZ-lpxA
Gene(s): skp, lpxD, fabZ, lpxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [4] Dartigalongue C., et al., 2001
Promoter
Name: hlpAp
+1: 200455
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 27
Sequence: cgatgactttaggcgatcaatataagatcgccgggccacgcaaagaactgcaccctccggTgcaaatgggatggtaaggag
                          -35                   -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Dartigalongue C., et al., 2001
[2] Huerta AM., et al., 2003
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
remote CpxR-phosphorylated activator hlpAp 200353 200354 -101.0 tcggtaaaacCtggtaagtgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
[GadE,+] 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 GadE activator hlpAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]


Transcription unit       
Name: lpxD
Gene(s): lpxD   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: lpxDp
+1: 200960
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 11
Sequence: acgccgttgcttacaacagcagcgatgtaaaagacatcactgccgacgtactgaaacaggTtaaataagtaatgccttcaa
                             -35                  -10       +1                   
Note(s): It was suggested, from high-throughput screening of maps of transcriptional start sites (TSSs), that the TSS (200960) assigned for this promoter is an RNA processing site and a new TSS was mapped (200962) for this promoter Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Dartigalongue C., et al., 2001
[2] Huerta AM., et al., 2003


Transcription unit       
Name: fabZ
Gene(s): fabZ   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [6] Coleman J., et al., 1988
[7] Crowell DN., et al., 1986
[8] Crowell DN., et al., 1987
[9] Tomasiewicz HG., et al., 1987


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [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


Reference(s)    

 [1] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [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] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

 [5] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [6] Coleman J., Raetz CR., 1988, First committed step of lipid A biosynthesis in Escherichia coli: sequence of the lpxA gene., J Bacteriol 170(3):1268-74

 [7] Crowell DN., Anderson MS., Raetz CR., 1986, Molecular cloning of the genes for lipid A disaccharide synthase and UDP-N-acetylglucosamine acyltransferase in Escherichia coli., J Bacteriol 168(1):152-9

 [8] Crowell DN., Reznikoff WS., Raetz CR., 1987, Nucleotide sequence of the Escherichia coli gene for lipid A disaccharide synthase., J Bacteriol 169(12):5727-34

 [9] Tomasiewicz HG., McHenry CS., 1987, Sequence analysis of the Escherichia coli dnaE gene., J Bacteriol 169(12):5735-44

 [10] Grabowicz M., Koren D., Silhavy TJ., 2016, The CpxQ sRNA Negatively Regulates Skp To Prevent Mistargeting of β-Barrel Outer Membrane Proteins into the Cytoplasmic Membrane., MBio 7(2):e00312-16

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