RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

lptD-surA-pdxA-rsmA-apaGH operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	lptD-surA-pdxA-rsmA-apaGH
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	apaGH
Gene(s):	apaH, apaG Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Blanchin-Roland S., et al., 1986
Promoter
Name:	apaGp
+1:	52034
Distance from start of the gene:	428
Sequence:	aacctgccttataacatctccacgccgttgatgttccatctgtttagctatactgatgccAttgccgacatgcactttatg
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IMP] [RS-EPT-CBR]
Reference(s):	[1] Blanchin-Roland S., et al., 1986 [2] Salgado H, et al., 2012

Transcription unit

Name:	rsmA-apaGH
Synonym(s):	ksgA-apaGH, rsmA-apaG-apaH
Gene(s):	apaH, apaG, rsmA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[3] Roa BB., et al., 1989
Promoter
Name:	rsmAp
+1:	52588
Distance from start of the gene:	158
Sequence:	aacgccgacgccgtgctggcgatgtaccacgatcagggtcttcccgtgctaaaataccagGgcttcgggcgcggtgtgaac
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[3] Roa BB., et al., 1989

Transcription unit

Name:	imp
Gene(s):	lptD Genome Browser M3D Gene expression COLOMBOS
Promoter
Name:	impp1
+1:	57156
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	47
Sequence:	gacgctattcggacaggattaacactagcgtagagatgacgagtacgttagtctctgaccGtttgtcacgcgcaacgttac -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[4] Huerta AM., et al., 2003 [5] Ohtsu I., et al., 2004 [2] Salgado H, et al., 2012

Transcription unit

Name:	imp
Gene(s):	lptD Genome Browser M3D Gene expression COLOMBOS
Promoter
Name:	impp2
+1:	57241
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	132
Sequence:	cgttttccggctgcggtcaattgtgggacatcgcctataatttgcattatcatacctgtcAttcaatgccgtgcctaacac -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[4] Huerta AM., et al., 2003 [5] Ohtsu I., et al., 2004 [2] Salgado H, et al., 2012

Transcription unit

Name:	imp-surA-pdxA
Gene(s):	pdxA, surA, lptD Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[6] Dartigalongue C., et al., 2001
Promoter
Name:	impp3
+1:	57336
Sigma Factor:	Sigma24 Sigmulon
Distance from start of the gene:	227
Sequence:	ggccacgccaatgatttttccccaatactgcatatattccccaaatcgacacacggatatCagggctatctcccacaatat -35 -10+1
Note(s):	This promoter was identified by Dartigalongue et al. Dartigalongue C,2001, but Ohtsu et al. Ohtsu I,2004 could not detect it, noting that the contribution of this promoter to imp gene expression was very small, if any.
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Dartigalongue C., et al., 2001 [4] Huerta AM., et al., 2003

Transcription unit

Name:	surA-pdxA-rsmA-apaGH
Synonym(s):	surA-pdxA-ksgA-apaGH
Gene(s):	apaH, apaG, rsmA, pdxA, surA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s):	[3] Roa BB., et al., 1989 [7] Tormo A., et al., 1990
Promoter
Name:	surAp
+1:	Unknown
Sigma Factor:	Sigma24 Sigmulon
Evidence:	[AS-NAS] [EXP-TAS]
Reference(s):	[8] Pease AJ., et al., 2002 [3] Roa BB., et al., 1989 [7] Tormo A., et al., 1990

Transcription unit

Name:	pdxA-rsmA-apaGH
Synonym(s):	pdxA-ksgA-apaG-apaH
Gene(s):	apaH, apaG, rsmA, pdxA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[8] Pease AJ., et al., 2002
Promoter
Name:	pdxAp
+1:	Unknown
Evidence:	[AS-NAS] [EXP-TAS]
Reference(s):	[8] Pease AJ., et al., 2002 [3] Roa BB., et al., 1989

TF binding sites (TFBSs)

[Fis,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	Fis	activator	pdxAp	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[8]

Transcription unit

Name:	pdxA-rsmA
Synonym(s):	pdxA-ksgA
Gene(s):	rsmA, pdxA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[8] Pease AJ., et al., 2002
Promoter
Name:	pdxAp
+1:	Unknown
Evidence:	[AS-NAS] [EXP-TAS]
Reference(s):	[8] Pease AJ., et al., 2002 [3] Roa BB., et al., 1989

TF binding sites (TFBSs)

[Fis,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	Fis	activator	pdxAp	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[8]

Evidence
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[EXP-IMP] Inferred from mutant phenotype
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[AS-NAS] Non-traceable author statement
[EXP-TAS] Traceable author statement to experimental support
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

Reference(s)
[1] Blanchin-Roland S., Blanquet S., Schmitter JM., Fayat G., 1986, The gene for Escherichia coli diadenosine tetraphosphatase is located immediately clockwise to folA and forms an operon with ksgA., Mol Gen Genet 205(3):515-22
[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] Roa BB., Connolly DM., Winkler ME., 1989, Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12., J Bacteriol 171(9):4767-77
[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] Ohtsu I., Kakuda N., Tsukagoshi N., Dokyu N., Takagi H., Wachi M., Aono R., 2004, Transcriptional Analysis of the ostA/imp Gene Involved in Organic Solvent Sensitivity in Escherichia coli., Biosci Biotechnol Biochem 68(2):458-61
[6] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75
[7] Tormo A., Almiron M., Kolter R., 1990, surA, an Escherichia coli gene essential for survival in stationary phase., J Bacteriol 172(8):4339-47
[8] Pease AJ., Roa BR., Luo W., Winkler ME., 2002, Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12., J Bacteriol 184(5):1359-69

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