RegulonDB

RegulonDB RegulonDB 10.10: Operon Form

rpsLG-fusA-tufA operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	rpsLG-fusA-tufA
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	tufA
Gene(s):	tufA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[LTED] Length of transcript experimentally determined
Reference(s):	[1] Zengel JM., et al., 1990
Promoter
Name:	tufAp2
+1:	3471583
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	254
Sequence:	ggaagagaacaccggtgacgttatcggtgacttgagccgtcgtcgtggtatgctcaaaggTcaggaatctgaagttactgg -35 -10 +1
Note(s):	T1 nuclease mapping was used to identified the tufAp2 promoter; however, the exact position was not determined Zengel JM,1990
Evidence:	[HIPP] [ICWHO] [IHBCE] [RS-EPT-CBR] [TIM]
Reference(s):	[2] Huerta AM., et al., 2003 [3] Salgado H, et al., 2012 [4] Zengel JM., et al., 1984 [1] Zengel JM., et al., 1990

Transcription unit

Name:	tufA
Gene(s):	tufA Genome Browser M3D Gene expression COLOMBOS
Evidence:	[LTED] Length of transcript experimentally determined
Reference(s):	[1] Zengel JM., et al., 1990
Promoter
Name:	tufAp1
+1:	3471724
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	395
Sequence:	tctgcacttcggttcttaccatgacgttgactcctctgaactggcgtttaaactggctgcTtctatcgcctttaaagaagg -35 -10 +1
Note(s):	T1 nuclease mapping was used to identified the tufAp1 promoter; however, the exact position was not determined Zengel JM,1990
Evidence:	[HIPP] [ICWHO] [IEP] [IHBCE] [TIM]
Reference(s):	[2] Huerta AM., et al., 2003 [5] Zaslaver A., et al., 2006 [4] Zengel JM., et al., 1984 [1] Zengel JM., et al., 1990

Transcription unit

Name:	fusA-tufA
Gene(s):	tufA, fusA Genome Browser M3D Gene expression COLOMBOS
Note(s):	FNR represses tufA gene expression under anaerobiosis, but it is not known which transcription unit is affected, or even if this regulation is direct or indirect Salmon K,2003.
Evidence:	[IC] Inferred by curator
Promoter
Name:	fusAp
+1:	3473685
Sigma Factor:	Sigma24 Sigmulon
Distance from start of the gene:	171
Sequence:	gataaatccatggctctgcgcctggcgaacgaactttctgatgctgcagaaaacaaaggtActgcagttaagaaacgtgaa -35 -10 +1
Evidence:	[AIBSCS] [AIPP] [ICWHO] [TIM]
Reference(s):	[2] Huerta AM., et al., 2003 [6] Rezuchova B., et al., 2003 [7] Rhodius VA., et al., 2005

Transcription unit

Name:	rpsLG-fusA-tufA
Gene(s):	tufA, fusA, rpsG, rpsL Genome Browser M3D Gene expression COLOMBOS
Note(s):	FNR represses tufA gene expression under anaerobiosis, but it is not known which transcription unit is affected, or even if this regulation is direct or indirect Salmon K,2003.
Reference(s):	[8] Johanson U., et al., 1992 [9] Post LE., et al., 1978 [10] Saito K., et al., 1994
Promoter
Name:	rpsLp
+1:	3474621
Distance from start of the gene:	69
Sequence:	gtgatggcgggatcgttgtatatttcttgacaccttttcggcatcgccctaaaattcggcGtcctcatattgtgtgaggac
Evidence:	[RPF]
Reference(s):	[11] Post LE., et al., 1978 [9] Post LE., et al., 1978

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	rpsLp	nd		[APPH] [GEA] [IMP]	[12]

Evidence:	[APPH] Assay of protein purified to homogeneity [GEA] Gene expression analysis [IMP] Inferred from mutant phenotype
Reference(s):	[12] Lemke JJ., et al., 2011

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	reverse

Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
terminator	-15.2	3474593	3474623	ctaaaattcgGCGTCCTCATATTGTGTGAGGACGTTTTATtacgtgttta
terminator	-19.7	3471349	3471374	ccaaagtcccGTGCTCTCTCCTGAAGGGGAGAGCActatagtaag
anti-terminator	-5.6	3474619	3474653	tatatttcttGACACCTTTTCGGCATCGCCCTAAAATTCGGCGTcctcatattg
anti-anti-terminator	-9.1	3474637	3474679	atggcctggtGATGGCGGGATCGTTGTATATTTCTTGACACCTTTTCGGCATcgccctaaaa

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
[HIPP] Human inference of promoter position
[ICWHO] Inferred computationally without human oversight
[IHBCE] Inferred by a human based on computational evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[TIM] Transcription initiation mapping
[IEP] Inferred from expression pattern
[AIBSCS] Automated inference based on similarity to consensus sequences
[AIPP] Automated inference of promoter position
[RPF] RNA polymerase footprinting

Reference(s)
[1] Zengel JM., Lindahl L., 1990, Mapping of two promoters for elongation factor Tu within the structural gene for elongation factor G., Biochim Biophys Acta 1050(1-3):317-22
[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] 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.
[4] Zengel JM., Archer RH., Lindahl L., 1984, The nucleotide sequence of the Escherichia coli fus gene, coding for elongation factor G., Nucleic Acids Res 12(4):2181-92
[5] 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
[6] Rezuchova B., Miticka H., Homerova D., Roberts M., Kormanec J., 2003, New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system., FEMS Microbiol Lett 225(1):1-7
[7] 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
[8] Johanson U., Hughes D., 1992, Comparison of the complete sequence of the str operon in Salmonella typhimurium and Escherichia coli., Gene 120(1):93-8
[9] Post LE., Arfsten AE., Reusser F., Nomura M., 1978, DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli., Cell 15(1):215-29
[10] Saito K., Mattheakis LC., Nomura M., 1994, Post-transcriptional regulation of the str operon in Escherichia coli. Ribosomal protein S7 inhibits coupled translation of S7 but not its independent translation., J Mol Biol 235(1):111-24
[11] Post LE., Arfsten AE., Nomura M., Jaskunas SR., 1978, Isolation and characterization of a promoter mutant in the str ribosomal protein operon in E. coli., Cell 15(1):231-6
[12] Lemke JJ., Sanchez-Vazquez P., Burgos HL., Hedberg G., Ross W., Gourse RL., 2011, Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA., Proc Natl Acad Sci U S A 108(14):5712-7

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