RegulonDB RegulonDB 10.8: 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: [ITC] 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: [AIPP]
[CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Rhodius VA., et al., 2005
[2] 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 31964733.
Promoter
Name: bamAp
+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: [HIPP]
[TIM]
Reference(s): [3] Dartigalongue C., et al., 2001


Transcription unit          
Name: hlpA-lpxD-fabZ-lpxA
Gene(s): skp, lpxD, fabZ, lpxA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [3] 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: [HIPP]
[TIM]
Reference(s): [3] Dartigalongue C., et al., 2001
TF binding sites (TFBSs)
[CpxR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CpxR-Phosphorylated activator hlpAp 200347 200361 -101.0 tttaacatcgGTAAAACCTGGTAAGtgttctccac nd [APIORCISFBSCS], [CV(GEA)], [GEA] [3]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE activator hlpAp nd nd nd nd nd [GEA] [4]


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: [HIPP]
[TIM]
Reference(s): [3] Dartigalongue C., et al., 2001


Transcription unit       
Name: fabZ
Gene(s): fabZ   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [5] Coleman J., et al., 1988
[6] Crowell DN., et al., 1986
[7] Crowell DN., et al., 1987
[8] Tomasiewicz HG., et al., 1987


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  cpxQ     repressor      
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [AIPP] Automated inference of promoter position

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

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

 [TIM] Transcription initiation mapping

 [HIPP] Human inference of promoter position

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA)] cross validation(GEA)

 [GEA] 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] 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.

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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

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

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