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Standard Name	treR
Gene Synonym(s)	ECK4236, b4241, JW4200^[1], JW4200
Product Desc.	TreR transcriptional repressor^[2]^[3] Repressor of trehalose operon^[4]
Product Synonyms(s)	DNA-binding transcriptional repressor^[1], B4241^[2]^[1], TreR^[2]^[1] , ECK4236, JW4200, b4241
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): treR^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	treR
Mnemonic	Trehalose
Synonyms	ECK4236, b4241, JW4200^[1], JW4200
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	96.22 minutes	MG1655: 4465269..4464322 <gbrowseImage> name=NC_000913:4464322..4465269 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4450523..4449576 <gbrowseImage> name=NC_012967:4449576..4450523 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4403057..4404004 <gbrowseImage> name=NC_012759:4403057..4404004 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4471926..4470979 <gbrowseImage> name=NC_007779:4470979..4471926 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4567077..4566130 <gbrowseImage> name=NC_010473:4566130..4567077 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔtreR (Keio:JW4200)	deletion	deletion			PMID:16738554	Shigen CGSC11023^[5]
ΔtreR788::kan					PMID:16738554	CGSC:103206
treR788(del)::FRTKanFRT			Mutagenesis rate	Decreased stress-induced mutagenesis (SIM) phenotype.	PMID:23224554	Parental Strain: SMR4562 Experimental Strain: SMR12001	Mutation was comparatively weak, to other strains, with decrease only happening to 33-67% of population.
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW4200	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAAATCGGCTGACCATCAA Primer 2:CCGGACAGGGTGGCGGGGATGAT
E1F5	Kohara Phage	Genobase	PMID:3038334
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: 49% ^[6] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: % ^[6] Synonyms:zjj-202::Tn10, zji-202::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12202	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12202	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002090	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948760	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2118	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013875	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	TreR
Synonyms	DNA-binding transcriptional repressor^[1], B4241^[2]^[1], TreR^[2]^[1] , ECK4236, JW4200, b4241
Product description	TreR transcriptional repressor^[2]^[3] Repressor of trehalose operon^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000843	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:7608078	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:9148912	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P03023 UniProtKB:P0ACP7	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000843	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005991	trehalose metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012771	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012771	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:7608078	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:9148912	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P03023 UniProtKB:P0ACP7	F	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:7608078	IDA: Inferred from Direct Assay	UniProtKB:P03023 UniProtKB:P0ACP7	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:9148912	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P03023 UniProtKB:P0ACP7	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1147746
Protein	yciH	PMID:16606699	Experiment(s):EBI-1147746
Protein	pflC	PMID:16606699	Experiment(s):EBI-1147746
Protein	ycgL	PMID:16606699	Experiment(s):EBI-1147746
Protein	rplB	PMID:16606699	Experiment(s):EBI-1147746
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1147746
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MQNRLTIKDI ARLSGVGKST VSRVLNNESG VSQLTRERVE AVMNQHGFSP SRSARAMRGQ SDKVVAIIVT RLDSLSENLA VQTMLPAFYE QGYDPIMMES QFSPQLVAEH LGVLKRRNID GVVLFGFTGI TEEMLAHWQS SLVLLARDAK GFASVCYDDE GAIKILMQRL YDQGHRNISY LGVPHSDVTT GKRRHEAYLA FCKAHKLHPV AALPGLAMKQ GYENVAKVIT PETTALLCAT DTLALGASKY LQEQRIDTLQ LASVGNTPLM KFLHPEIVTV DPGYAEAGRQ AACQLIAQVT GRSEPQQIII PATLS
Length	315
Mol. Wt	34.53 kDa
pI	8.3 (calculated)
Extinction coefficient	18,910 - 19,410 (calc based on 9 Y, 1 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	6..51	PF00356 Bacterial regulatory proteins, lacI family	PMID:19920124
Domain	61..315	PF00532 family	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=treR taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16132063	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948760	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013875	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36673	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12202	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12202	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948760	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002090	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2118	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	237	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	143	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	151	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
treR
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:4465249..4465289 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b4241 (EcoliWiki Page)	NCBI GEO profiles for treR
microarray	GenExpDB:b4241 (EcoliWiki Page)	Summary of data for treR from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to treR Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12202	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2118	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4241
EcoGene	EcoGene:EG12202	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002090	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013875	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000001345 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TRER	From SHIGELLACYC
E. coli O157	TRER	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00356 Bacterial regulatory proteins, lacI family
Superfamily (EcoliWiki Page)	SUPERFAMILY:47413
Superfamily (EcoliWiki Page)	SUPERFAMILY:53822
Pfam (EcoliWiki Page)	PF00532 family
EcoCyc	EcoCyc:EG12202	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12202	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002090	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2118	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013875	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

treR:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to treR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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