RegulonDB

RegulonDB RegulonDB 10.10: Operon Form

thrLABC operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	thrLABC
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	thrLABC
Synonym(s):	OP00248, thr, thrABC
Gene(s):	thrL, thrA, thrB, thrC Genome Browser M3D Gene expression COLOMBOS
Note(s):	The thrLABC operon codes for four enzymes involved in threonine and homoserine biosynthesis. thrLABC is regulated in response to the abundance of both isoleucine and threonine FREUNDLICH M,1963. Part of this regulation presumably occurs via attenuation, as thrLABC contains a leader sequence rich in threonine and isoleucine codons followed immediately by a functional transcriptional terminator that acts to prevent transcription of the enzyme-coding genes in the operon Lynn SP,1982. Gardner JF.,1979. Lynn SP, Bauer CE, Chapman K, Gardner JF,1985. Yang MT, Gardner JF,1991.
Evidence:	[PM] Polar mutation
Reference(s):	[1] Lynn SP., et al., 1987 [2] Parsot C., et al., 1983 [3] Theze J., et al., 1974
Promoter
Name:	thrLp
+1:	148
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	42
Sequence:	gccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcAtagcgcacagacagataaaa -35 -10 +1
Evidence:	[ICWHO] [IHBCE] [IMP] [RS-EPT-CBR] [TIM]
Reference(s):	[4] Gardner JF. 1982 [5] Huerta AM., et al., 2003 [6] Lynn SP., et al., 1982 [7] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	atctattcatTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATtatggagaaa
Reference(s):	[8] Feng CQ., et al., 2019 [9] Lesnik EA., et al., 2001

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	activation	thrLp	nd		[APPH] [IEP]	[10] [11]

Evidence:	[APPH] Assay of protein purified to homogeneity [IEP] Inferred from expression pattern
Reference(s):	[10] Lee JH., et al., 2012 [11] Mechold U., et al., 2013

Transcription unit

Name:	thrL
Gene(s):	thrL Genome Browser M3D Gene expression COLOMBOS
Evidence:	[BTEI] Boundaries of transcription experimentally identified
Reference(s):	[12] Gardner JF. 1979 [4] Gardner JF. 1982
Promoter
Name:	thrLp
+1:	148
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	42
Sequence:	gccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcAtagcgcacagacagataaaa -35 -10 +1
Evidence:	[ICWHO] [IHBCE] [IMP] [RS-EPT-CBR] [TIM]
Reference(s):	[4] Gardner JF. 1982 [5] Huerta AM., et al., 2003 [6] Lynn SP., et al., 1982 [7] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	ggaaacacagAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTcgaccaaagg
Reference(s):	[12] Gardner JF. 1979

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	activation	thrLp	nd		[APPH] [IEP]	[10] [11]

Evidence:	[APPH] Assay of protein purified to homogeneity [IEP] Inferred from expression pattern
Reference(s):	[10] Lee JH., et al., 2012 [11] Mechold U., et al., 2013

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	forward
Evidence:	[ICA] Inferred by computational analysis
Reference(s):	[13] Merino E, et al., 2005

Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
terminator	-20.0	276	311	aacacagaaaAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCgaccaaaggt
anti-terminator	-19.41	244	288	acaggtaacgGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCtgacagtgcg
anti-anti-terminator	-14.5	200	255	tgaaacgcatTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGAcgcgtacagg

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"

REGULATION, RNA cis-regulatory element:
Rfam type:	Cis-reg; leader
Strand:	forward
Evidence:	[ICA] Inferred by computational analysis
Reference(s):	[14] null null

	Description	Rfam score	Left Pos	Right Pos	Sequence (RNA-strand)
	Threonine operon leader	122.9	191	310	acaacauccaUGAAACGCAUUAGCACCACCAUUACCACCACCAUCACCAUUACCACAGGUAACGGUGCGGGCUGACGCGUACAGGAAACACAGAAAAAAGCCCGCACCUGACAGUGCGGGCUUUUUUUUUcgaccaaagg

Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"

Evidence
[ICWHO] Inferred computationally without human oversight
[IHBCE] Inferred by a human based on computational evidence
[IMP] Inferred from mutant phenotype
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[TIM] Transcription initiation mapping

Reference(s)
[1] Lynn SP., Burton WS., Donohue TJ., Gould RM., Gumport RI., Gardner JF., 1987, Specificity of the attenuation response of the threonine operon of Escherichia coli is determined by the threonine and isoleucine codons in the leader transcript., J Mol Biol 194(1):59-69
[2] Parsot C., Cossart P., Saint-Girons I., Cohen GN., 1983, Nucleotide sequence of thrC and of the transcription termination region of the threonine operon in Escherichia coli K12., Nucleic Acids Res 11(21):7331-45
[3] Theze J., Saint-Girons I., 1974, Threonine locus of Escherichia coli K-12: genetic structure and evidence for an operon., J Bacteriol 118(3):990-8
[4] Gardner JF., 1982, Initiation, pausing, and termination of transcription in the threonine operon regulatory region of Escherichia coli., J Biol Chem 257(7):3896-904
[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] Lynn SP., Gardner JF., Reznikoff WS., 1982, Attenuation regulation in the thr operon of Escherichia coli K-12: molecular cloning and transcription of the controlling region., J Bacteriol 152(1):363-71
[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] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477
[9] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94
[10] Lee JH., Lennon CW., Ross W., Gourse RL., 2012, Role of the coiled-coil tip of Escherichia coli DksA in promoter control., J Mol Biol 416(4):503-17
[11] Mechold U., Potrykus K., Murphy H., Murakami KS., Cashel M., 2013, Differential regulation by ppGpp versus pppGpp in Escherichia coli., Nucleic Acids Res 41(12):6175-89
[12] Gardner JF., 1979, Regulation of the threonine operon: tandem threonine and isoleucine codons in the control region and translational control of transcription termination., Proc Natl Acad Sci U S A 76(4):1706-10
[13] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.
[14] null, null, null, null

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