RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

nnr-tsaE-amiB-mutL-miaA-hfq-hflXKC operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	nnr-tsaE-amiB-mutL-miaA-hfq-hflXKC
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	yjeFE-amiB-mutL-miaA-hfq-hflXKC
Synonym(s):	ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC
Gene(s):	nnr, tsaE, amiB, mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[1] Kitagawa R., et al., 1996 [2] Tsui HC., et al., 1996 [3] Tsui HC., et al., 1994 [4] Tsui HC., et al., 1994
Promoter
Name:	yjeFp1
+1:	4393677
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	389
Sequence:	tttcagctaacgggcgctcgagaataggcgcagaatcgacaaacggtctaaaattcagcgAaacacaatgttgctgaatca -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Huerta AM., et al., 2003 [1] Kitagawa R., et al., 1996 [6] Maciag A., et al., 2011

Transcription unit

Name:	yjeFE-amiB-mutL-miaA-hfq-hflXKC
Synonym(s):	ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC
Gene(s):	nnr, tsaE, amiB, mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[1] Kitagawa R., et al., 1996
Promoter
Name:	yjeFp2
+1:	4393937
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	129
Sequence:	cgagcgcgcagcataccgtgacgtgccatccagtccatttcgccgtggtattgtttgtccAgccatgcttgcagtttgggc -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[5] Huerta AM., et al., 2003 [1] Kitagawa R., et al., 1996 [6] Maciag A., et al., 2011 [7] Salgado H, et al., 2012

Transcription unit

Name:	yjeFE-amiB-mutL-miaA-hfq-hflXKC
Synonym(s):	ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC
Gene(s):	nnr, tsaE, amiB, mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[1] Kitagawa R., et al., 1996
Promoter
Name:	yjeFp3
+1:	4394035
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	31
Sequence:	ggtatcggtaatacctacctgctgaaagcccagttccagcccccactgtttaattttttgCgctaactgattgagatcgag -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[5] Huerta AM., et al., 2003 [1] Kitagawa R., et al., 1996 [6] Maciag A., et al., 2011

Transcription unit

Name:	mutL-miaA-hfq-hflXKC
Gene(s):	mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Promoter
Name:	mutLp2
+1:	4397046
Sigma Factor:	Sigma32 Sigmulon
Distance from start of the gene:	366
Sequence:	ctgctgggtggggcgggtgatgtgctggcgaacagtcagtctgacccctatttaagccagGcggtgctggatttacagttc -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP]
Reference(s):	[5] Huerta AM., et al., 2003 [2] Tsui HC., et al., 1996

Transcription unit

Name:	mutL-miaA-hfq-hflXKC
Gene(s):	mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Promoter
Name:	mutLp1
+1:	4397100
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	312
Sequence:	agccaggcggtgctggatttacagttcggtcattcccagcgggtagggtatgatgtagcgAccagtatgatcagtcagttg -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[5] Huerta AM., et al., 2003 [7] Salgado H, et al., 2012 [2] Tsui HC., et al., 1996

Transcription unit

Name:	miaA-hfq-hflXKC
Gene(s):	miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[8] Nonaka G., et al., 2006
Promoter
Name:	miaAp2
+1:	4398982
Sigma Factor:	Sigma32 Sigmulon
Distance from start of the gene:	270
Sequence:	agtctgccctggcggaattgggtattgatttccagtcagatgcacagcatgtgaccatcaGggcagtgcctttacccttac -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP]
Reference(s):	[5] Huerta AM., et al., 2003 [2] Tsui HC., et al., 1996

Transcription unit

Name:	miaA-hfq-hflXKC
Gene(s):	miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[8] Nonaka G., et al., 2006
Promoter
Name:	miaAp1
+1:	4399052
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	200
Sequence:	tttacccttacgccaacaaaatttacaaatcttgattcctgaactgataggctacctggcGaagcagtccgtattcgaacc -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [RS-EPT-CBR]
Reference(s):	[5] Huerta AM., et al., 2003 [7] Salgado H, et al., 2012 [2] Tsui HC., et al., 1996

Transcription unit

Name:	hfq-hflXKC
Gene(s):	hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[8] Nonaka G., et al., 2006
Promoter
Name:	hfqp2
+1:	4399801
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	487
Sequence:	gatccacaaaggctttcccgggcactggaagtttttttcatttcgggtaaaactttaacgGaactgacgcaaacgtcagga -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP]
Reference(s):	[5] Huerta AM., et al., 2003 [2] Tsui HC., et al., 1996 [9] Zaslaver A., et al., 2006

Transcription unit

Name:	hfq-hflXKC
Gene(s):	hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[8] Nonaka G., et al., 2006
Promoter
Name:	hfqp3
+1:	4400220
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	68
Sequence:	gcgtgacgaagtattacaggttgttggtgctatcgcaggctgaatgtgtacaattgagacGtatcgtgcgcaattttttca -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[5] Huerta AM., et al., 2003 [7] Salgado H, et al., 2012 [2] Tsui HC., et al., 1996 [9] Zaslaver A., et al., 2006

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)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	CRP-cyclic-AMP	repressor	hfqp3	4400113	4400135	-96.5	ctggctgcgtGGTTGGGAAGGGGTTCACTGGCTtgacagtgaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[10]

Transcription unit

Name:	tsaE-amiB-mutL-miaA-hfq-hflXKC
Synonym(s):	yjeE-amiB-mutL-miaA-hfq-hflXKC
Gene(s):	tsaE, amiB, mutL, miaA, hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Promoter
Name:	tsaEp
+1:	Unknown
Note(s):	Promoter activity for the yjeE gene was described by Mangat and Brown (2008) Mangat CS,2008and was based on gene expression analysis. The transcriptional start site for the yjeE gene has not been determined experimentally.
Evidence:	[EXP-IEP]
Reference(s):	[11] Mangat CS., et al., 2008

Transcription unit

Name:	hfq-hflXKC
Gene(s):	hfq, hflX, hflK, hflC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[8] Nonaka G., et al., 2006
Promoter
Name:	hfqp1
+1:	Unknown
Sigma Factor:	Sigma32 Sigmulon
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP]
Reference(s):	[2] Tsui HC., et al., 1996

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF] Inferred by a human based on computational evidence
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping
[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-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IDA] Inferred from direct assay
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

Reference(s)
[1] Kitagawa R., Mitsuki H., Okazaki T., Ogawa T., 1996, A novel DnaA protein-binding site at 94.7 min on the Escherichia coli chromosome., Mol Microbiol 19(5):1137-47
[2] Tsui HC., Feng G., Winkler ME., 1996, Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock., J Bacteriol 178(19):5719-31
[3] Tsui HC., Leung HC., Winkler ME., 1994, Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12., Mol Microbiol 13(1):35-49
[4] Tsui HC., Winkler ME., 1994, Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation., Biochimie 76(12):1168-77
[5] 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
[6] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55
[7] 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.
[8] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89
[9] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8
[10] Lin HH., Hsu CC., Yang CD., Ju YW., Chen YP., Tseng CP., 2011, Negative Effect of Glucose on ompA mRNA Stability: a Potential Role of Cyclic AMP in the Repression of hfq in Escherichia coli., J Bacteriol 193(20):5833-40
[11] Mangat CS., Brown ED., 2008, Known bioactive small molecules probe the function of a widely conserved but enigmatic bacterial ATPase, YjeE., Chem Biol 15(12):1287-95

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