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Standard Name	crl
Gene Synonym(s)	ECK0241, b0240, JW0230^[1], JW0230
Product Desc.	Crl transcriptional regulator^[2]^[3] Stimulates RNA polymerase holoenzyme formation; stimulates RpoS activity during stationary phase; mutants display rpoS mutant phenocopy; does not reduce amount of RpoS protein^[4]
Product Synonyms(s)	DNA-binding transcriptional regulator^[1], B0240^[2]^[1], Crl^[2]^[1] , ECK0241, JW0230, b0240
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): crl^[2]
Regulation/Activity
Quick Links
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Notes

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RpoD, RpoS and RpoH sigma factor-containing holoenzyme assembly is stimulated by Crl (Gaal, 2006). Accumulation of Crl during stationary phase at 30C, but not 37C, suggests it is a thermosensor controlling sigma(S) activity. Initially identified due to reduction of RpoS-dependent curlin (csgAB) expression.^[4]

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	crl
Mnemonic	Curli
Synonyms	ECK0241, b0240, JW0230^[1], JW0230
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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	5.56 minutes	MG1655: 257829..258230 <gbrowseImage> name=NC_000913:257829..258230 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 262320..262721 <gbrowseImage> name=NC_012967:262320..262721 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 257828..258229 <gbrowseImage> name=NC_012759:257828..258229 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 257829..258230 <gbrowseImage> name=NC_007779:257829..258230 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 231933..232334 <gbrowseImage> name=NC_010473:231933..232334 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
Coding Start (SO:0000323)	MG1655	257832	Edman degradation	PMID:2649795
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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)	Reference	Availability	Comments
crl(del) (Keio:JW0230)	deletion	deletion	PMID:16738554	Shigen CGSC8465^[5]
crl-758(del)::kan			PMID:16738554	CGSC:100402
	G insertion at genome position 257899		PMID:22081388		polymorphic in different MG1655 isolates
	IS1 insertion at genome position 257899		PMID:22081388		polymorphic in different MG1655 isolates
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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
JW0230	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGTTACCGAGTGGACACCC Primer 2:CCCGCCGTTAACTTCACCGGCTC
8F9	Kohara Phage	Genobase	PMID:3038334
8G4	Kohara Phage	Genobase	PMID:3038334
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 38% ^[6] Synonyms:zae-502::Tn10
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 94% ^[6]
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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:EG11092	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11092	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945077	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001080	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1084	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000821	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	Crl
Synonyms	DNA-binding transcriptional regulator^[1], B0240^[2]^[1], Crl^[2]^[1] , ECK0241, JW0230, b0240
Product description	Crl transcriptional regulator^[2]^[3] Stimulates RNA polymerase holoenzyme formation; stimulates RpoS activity during stationary phase; mutants display rpoS mutant phenocopy; does not reduce amount of RpoS protein^[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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01178	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016987	sigma factor activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01178	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045941	positive regulation of transcription	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01178	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	Notes	References	Evidence
Protein	tatE		PMID:16606699	Experiment(s):EBI-1136001
Protein	rpoS:Gene Product(s)	^[7]
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Notes

Crl enhances RpoS activity in vivo.^[8] Crl has been shown to interact directly with RpoS in vivo and in vitro^[7]. In vitro results sugges that it acts to stimulate RpoS activity by enhancing formation of RNA polymerase sigma 38.^[9] In vitro it has been shown to stimulate formation of RNA polymerase sigma70 and RNA polymerase sigma32.^[9]

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
cytoplasm			From EcoCyc^[3]
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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 MTLPSGHPKS RLIKKFTALG PYIREGKCKD NRFFFDCLAV CVNVKPAPEV REFWGWWMEL EAQESRFTYS YQFGLFDKAG DWKSVPVKDT EVVERLEHTL REFHEKLREL LTTLNLKLEP ADDFRDEPVK LTA
Length	133
Mol. Wt	15.654 kDa
pI	6.7 (calculated)
Extinction coefficient	26,470 - 26,845 (calc based on 3 Y, 4 W, and 3 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	Notes	References
Initiator Methionine	1	Removed	UniProt:P24251
Domain	2..131	PF07417 Transcriptional regulator Crl		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=crl taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Met1 is cleaved to generate mature protein ^[10].

Gene Product Resources

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

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:16128226	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945077	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000821	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P24251	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11092	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11092	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945077	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001080	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1084	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 MC4100	3.48E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	8827	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	5379	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	6819	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)
crl
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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_000913:257809..257849 source=MG1655 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:b0240 (EcoliWiki Page)	NCBI GEO profiles for crl
microarray	GenExpDB:b0240 (EcoliWiki Page)	Summary of data for crl 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
	GFP Fusion	Intergenic region (257690..257844) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:H3^[11]
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Notes

Accessions Related to crl Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11092	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1084	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0240
EcoGene	EcoGene:EG11092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001080	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000821	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
Shigella flexneri	CRL	From SHIGELLACYC
E. coli O157	CRL	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)	PF07417 Transcriptional regulator Crl
EcoCyc	EcoCyc:EG11092	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001080	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1084	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000821	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 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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).
↑ ^7.0 ^7.1 Bougdour, A et al. (2004) Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase. J. Biol. Chem. 279 19540-50 PubMed
↑ Pratt, LA & Silhavy, TJ (1998) Crl stimulates RpoS activity during stationary phase. Mol. Microbiol. 29 1225-36 PubMed
↑ ^9.0 ^9.1 Gaal, T et al. (2006) Crl facilitates RNA polymerase holoenzyme formation. J. Bacteriol. 188 7966-70 PubMed
↑ Arnqvist, A et al. (1992) The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101. Mol. Microbiol. 6 2443-52 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

crl:On One Page

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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 crl Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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