csrA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

csrA

Gene Synonym(s)

ECK2691, b2696, JW2666, zfiA[1], zfiA

Product Desc.

carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties[2][3];

Component of CsrA complex with CsrB RNA[3]

Global regulator of carbon source metabolism; CsrA exerts reciprocal effects on glycolysis versus gluconeogenesis and glycogen biosynthesis; glgC mRNA-binding activity blocks GlgC translation; csrB RNA inhibits csrA[4]

Product Synonyms(s)

pleiotropic regulatory protein for carbon source metabolism[1], B2696[2][1], ZfiA[2][1], CsrA[2][1] , ECK2691, JW2666, zfiA, b2696

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): csrA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Recombinant CsrA-His6 was N-terminally sequenced, but this does not Verify since translation start was forced at ATG: Met is not clipped: MLIL start. CsrA also postively regulates FlhCD post-translationally, and hence is required for motility.[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

csrA

Mnemonic

Carbon storage regulator

Synonyms

ECK2691, b2696, JW2666, zfiA[1], zfiA

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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

60.72 minutes 

MG1655: 2817168..2816983
<gbrowseImage> name=NC_000913:2816983..2817168 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2714005..2713820
<gbrowseImage> name=NC_012967:2713820..2714005 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2702795..2702980
<gbrowseImage> name=NC_012759:2702795..2702980 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2817802..2817617
<gbrowseImage> name=NC_007779:2817617..2817802 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2909710..2909525
<gbrowseImage> name=NC_010473:2909525..2909710 source=DH10B preset=GeneLocation </gbrowseImage>

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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

csrA905

CGSC:72207


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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

JW2666

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCTGATTCTGACTCGTCGAGT

Primer 2:CCGTAACTGGACTGCTGGGATTT

23B7

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: % [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 75% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG11447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001410

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947176

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1416

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008866

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

CsrA

Synonyms

pleiotropic regulatory protein for carbon source metabolism[1], B2696[2][1], ZfiA[2][1], CsrA[2][1] , ECK2691, JW2666, zfiA, b2696

Product description

carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties[2][3];

Component of CsrA complex with CsrB RNA[3]

Global regulator of carbon source metabolism; CsrA exerts reciprocal effects on glycolysis versus gluconeogenesis and glycogen biosynthesis; glgC mRNA-binding activity blocks GlgC translation; csrB RNA inhibits csrA[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:0003723

RNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00167

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003751

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0006109

regulation of carbohydrate metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00167

P

Seeded from EcoCyc (v14.0)

complete

GO:0006109

regulation of carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003751

P

Seeded from EcoCyc (v14.0)

complete

GO:0006402

mRNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00167

P

Seeded from EcoCyc (v14.0)

complete

GO:0006402

mRNA catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003751

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

Subunits of CsrA complex with CsrB RNA

could be indirect

Protein

dnaN

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.462038

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

tig

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.245483

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rho

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.045828

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.860281

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):4.332004

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.648246

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):22.179834

Protein

nagC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.961368

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.527392

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.548305

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):31.398357

Protein

rlmL

PMID:19402753

MALDI(Z-score):25.017977

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

lpxD

PMID:19402753

LCMS(ID Probability):99.3 MALDI(Z-score):5.587843

Protein

rpoA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.391520

Protein

infC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rne

PMID:19402753

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.3 MALDI(Z-score):26.968435

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rhlB

PMID:19402753

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.305076

Protein

rluB

PMID:19402753

MALDI(Z-score):36.330881

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Notes

CsrA-his6 binding recovers mRNA from ~700 genes. CarB and CsrC RNAs titrate out CsrA and compete with mRNA targets.

Localization

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

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 

MLILTRRVGE TLMIGDEVTV TVLGVKGNQV RIGVNAPKEV SVHREEIYQR IQAEKSQQSS Y
Length

61

Mol. Wt

6.855 kDa

pI

9.6 (calculated)

Extinction coefficient

2,980 (calc based on 2 Y, 0 W, and 0 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

Domain

1..54

PF02599 Global regulator protein 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=csrA 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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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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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

NCBI (Protein) (EcoliWiki Page)

GI:16130603

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947176

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008866

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P69913

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11447

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947176

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001410

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1416

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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.

CsrA is indirectly auto regulated.

Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

3.12E+04

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

Ecoli K-12

473.979+/-3.242

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.94454+/-0.02241

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

2.564864865

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

18982

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

7647

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

16543

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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<protect>

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

Transcription unit(s)

csrA

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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_000913:2817148..2817188 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:b2696 (EcoliWiki Page)

NCBI GEO profiles for csrA

microarray

GenExpDB:b2696 (EcoliWiki Page)

Summary of data for csrA 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 csrA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11447

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1416

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2696

EcoGene

EcoGene:EG11447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001410

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008866

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

CSRA

From SHIGELLACYC

E. coli O157

CSRA

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF02599 Global regulator protein family

Superfamily (EcoliWiki Page)

SUPERFAMILY:117130

EcoCyc

EcoCyc:EG11447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001410

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1416

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008866

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

Categories

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