RegulonDB

gcl-hyi-glxR-ybbW-allB-ybbY-glxK operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	gcl-hyi-glxR-ybbW-allB-ybbY-glxK
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	gcl-hyi-glxR-ybbVW-allB-ybbY-glxK
Gene(s):	gcl, hyi, glxR, ybbW, allB, ybbY, glxK Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[1] Cusa E., et al., 1999
Promoter
Name:	gclp
+1:	533907
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	9
Sequence:	gcggagcgggtttttttgacaaaatttgaaagttggaaaaattttccaataaatagaggtAggaataaaatggcaaaaatg -35 -10 +1
Note(s):	The gclp promoter is activated in the presence of glyoxylate and repressed in the presence of allantoin Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A,2010 Single-cell assays show that this promoter is heterogeneously activated by glyoxylate in the cells within the same culture. In some cells the promoter is activated to a greater extent than in others; in approximately 30% of the cells in a given culture the promoter is not activated Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A,2010
Evidence:	[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s):	[2] Huerta AM., et al., 2003

TF binding sites (TFBSs)

[AllR,-] 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)
proximal	AllR-allantoin	repressor	gclp	533879	533895	-20.0	aatttgaaagTTGGAAAAATTTTCCAAtaaatagagg	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[3], [4]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
AllR-allantoin	repressor	gclp	533879	533895	-20.0	aatttgaaagTTGGAAAAATTTTCCAAtaaatagagg	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[3], [4]

Transcription unit

Name:	allB
Gene(s):	allB Genome Browser M3D Gene expression COLOMBOS
Note(s):	The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020.
Evidence:	[EXP-IEP] Inferred from expression pattern
Reference(s):	[5] Li Z., et al., 2019
Promoter
Name:	allBp3
+1:	538944
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	203
Sequence:	tacgataacggttttaacctcactgcgttttcagtaactctggtggccgttattttatctCttggcggtaagtttattcac -35 -10 +1
Evidence:	[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP-RNA-SEQ]
Reference(s):	[5] Li Z., et al., 2019

Transcription unit

Name:	allB
Gene(s):	allB Genome Browser M3D Gene expression COLOMBOS
Note(s):	The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020.
Evidence:	[EXP-IEP] Inferred from expression pattern
Reference(s):	[5] Li Z., et al., 2019
Promoter
Name:	allBp2
+1:	538986
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	161
Sequence:	gtggccgttattttatctcttggcggtaagtttattcactttatggaaccgttatcgcgtGtttcatggtttgtcggcgtc -10 +1
Evidence:	[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP-RNA-SEQ]
Reference(s):	[5] Li Z., et al., 2019

Transcription unit

Name:	allB
Gene(s):	allB Genome Browser M3D Gene expression COLOMBOS
Note(s):	The transcription of the allB gene is induced during the first 24 h after the induction of nitrogen starvation Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020.
Evidence:	[EXP-IEP] Inferred from expression pattern
Reference(s):	[5] Li Z., et al., 2019
Promoter
Name:	allBp1
+1:	539041
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	106
Sequence:	cgcgtgtttcatggtttgtcggcgtcatcgtcgcctttgcggcctacgccttattaaagaAacgtacaacagcagaaaaaa -10 +1
Evidence:	[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP-RNA-SEQ]
Reference(s):	[5] Li Z., et al., 2019

Transcription unit

Name:	ybbY-glxK
Gene(s):	ybbY, glxK Genome Browser M3D Gene expression COLOMBOS
Evidence:	[IC] Inferred by curator
Promoter
Name:	ybbYp
+1:	540359
Distance from start of the gene:	206
Sequence:	gatgccgacttcgtcttcattcagccgaatagcagctatgttcttaccaatgacgatctgGaatatcgccacaaagtcagc
Evidence:	[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s):	[6] Mendoza-Vargas A., et al., 2009

Transcription unit

Name:	glxK
Gene(s):	glxK Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[7] Zaslaver A., et al., 2006
Promoter
Name:	glxKp
+1:	Unknown
Evidence:	[EXP-IEP]
Reference(s):	[7] Zaslaver A., et al., 2006

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	forward

Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
terminator	-13.1	533839	533864	ctgtcgcatcCCGCTCTGCGGAGCGGGTTTTTTTGacaaaatttg
terminator	-7.5	536539	536566	ggcaggggatCGTGTTGTCTGAATTCAGGAAAAGCGAaatttaaaag
anti-terminator	-10.2	533800	533848	atcagcacggCGTTGGGACTGAAAGCACATCCATAATGTCTGTCGCATCCCGCTCTGCggagcgggtt

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-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IMP-SITE-MUTATION] Site mutation
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[EXP-IEP-RNA-SEQ] RNA-seq evidence
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping
[EXP-IEP] Inferred from expression pattern

Reference(s)
[1] Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J., 1999, Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli., J Bacteriol 181(24):7479-84
[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] Hasegawa A., Ogasawara H., Kori A., Teramoto J., Ishihama A., 2008, The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines., Microbiology 154(Pt 11):3366-78
[4] Rintoul MR., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J., 2002, Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS., J Mol Biol 324(4):599-610
[5] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376
[6] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526
[7] 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

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