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Carbon storage regulator



Escherichia coli (strain K12)
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli


A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability, initially identified for its effects on central carbon metabolism (PubMed:8393005). Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems (PubMed:21488981, PubMed:28924029). Binds to the 5'-UTR of mRNA to repress or activate translation; 2 binding sites on the homodimer can bridge 2 sites within target RNA (By similarity). Exerts reciprocal effects on enzymes of gluconeogenesis and glycogen biosynthesis versus those of glycolysis (PubMed:7493933, PubMed:16923806). Negatively effects glycogen biosynthesis, gluconeogenesis, alters cell size and surface properties (PubMed:8393005, PubMed:7751274, PubMed:7493933). Activates regulates expression of glycolysis genes (PubMed:7493933). Represses biofilm formation (PubMed:11741870). Regulates glycogen synthesis under both aerobic and anaerobic conditions; overexpression strongly inhibits glycogen accumulation (PubMed:8393005). Binds to 4 sites in its own promoter, including the Shine-Dalgarno sequence, repressing its own translation; mutating the binding-sites decreases repression (PubMed:21696456). Indirectly activates transcription from 1 of its 5 promoters, which is responsible for increased expression during stationary phase (PubMed:21696456). Binds to at least 720 transcripts in strain K12 / CF7789, many of which are also part of the stringent response, including relA, spoT and dksA; slightly represses RelA and slightly activates DskA translation (PubMed:21488981). Binds to and represses the ECF sigma factor rpoE promoter (PubMed:28924029). Accelerates the degradation of glgC gene transcripts; overexpression further decreases glgC transcripts (PubMed:7751274). Binds 2 sites in the glgC mRNA leader, 1 of which overlaps the Shine-Dalgarno sequence, preventing ribosome-binding and thus destabilizing the mRNA (PubMed:12067347). Acts to inhibit interaction between the CcdB (also known as LetD) protein and the A subunit of DNA gyrase (PubMed:8604133). Required to activate motility and flagellum biosynthesis through the post-transcriptional activation of flhDC expression by binding to and stabilizing the flhDC message (PubMed:11298291). Represses translation of iraD mRNA via translational coupling to an upstream open reading frame (PubMed:28851853). Binds to mRNA and reduces levels of probable diguanylate cyclases dgcT and dgcZ (PubMed:18713317).By similarity14 Publications
Binds to and is sequestered by non-coding small RNAs (sRNA) CsrB and CsrC which antagonize the activity of CsrA (PubMed:9211896, PubMed:12694612). The consensus RNA-binding site is CAGGA(U/A/C)G which is located in probable hairpin loops (PubMed:9211896). There are 18 sites in CsrB, which cooperatively binds about 18 copies of CsrA (PubMed:9211896, PubMed:12694612). CsrC has 9 sites, and cooperatively binds multiple copies of CsrA (PubMed:12694612). Indirectly activates expression of CsrB and CsrC, both dependently and independently of the BarA-UvrY two-component system (PubMed:12193630, PubMed:12694612). ppGpp activates transcription of CsrA-antagonistic small RNAs CsrB and CsrC, which downregulates CsrA's action on translation during the stringent response (PubMed:21488981).3 Publications

GO - Molecular functioni

  • mRNA 5'-UTR binding Source: EcoCyc

GO - Biological processi

  • mRNA catabolic process Source: InterPro
  • negative regulation of glycogen biosynthetic process Source: EcoCyc
  • negative regulation of translational initiation Source: EcoCyc


Molecular functionActivator, Repressor, RNA-binding
Biological processTranslation regulation

Enzyme and pathway databases


Names & Taxonomyi

Protein namesi
Recommended name:
Carbon storage regulatorCurated
Alternative name(s):
Translational dual regulator CsrAUniRule annotation
Gene namesi
Name:csrA1 PublicationUniRule annotation
Synonyms:zfiA1 Publication
Ordered Locus Names:b2696, JW2666
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11447. csrA.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc

Keywords - Cellular componenti


Pathology & Biotechi

Disruption phenotypei

Essential, it cannot be deleted when cells grow on LB but cells will grow with pyruvate as the sole carbon source; if glycogen synthesis is impaired then cells become viable (PubMed:19103924). Most deletion experiments use an allele which has a kanamycin-resistance cassette inserted after amino acid 50, which retains about 10% residual activity (PubMed:8393005, PubMed:19103924). Increased levels of glgC transcripts during both exponential and stationary phases (PubMed:7751274). Decreased levels of enzymes involved in glycolysis (PubMed:7493933). Increased biofilm formation (PubMed:11741870). Decreased expression of it antagonistic small RNAs CsrB and CsrC (PubMed:12694612). Allows basal levels of poly-GlcNAc synthesis and biofilm formation; this disrupted strain serves as a model system for biofilm formation (PubMed:19460094). Increased expression of RelA, about 1.5-fold increase in (p)ppGpp levels (PubMed:21488981). Increased levels of ECF sigma factor E (rpoE) (PubMed:28924029).9 Publications


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi2L → A: Loss of in vivo repression and activation, 73-fold decreased affinity for RNA, about 75% wild-type protein levels. 1 Publication1
Mutagenesisi3I → A: 80% loss of in vivo repression and activation, about 20% wild-type protein levels. 1 Publication1
Mutagenesisi4L → A: 90% loss of in vivo repression and activation, 60-fold decreased affinity for RNA, about 60% wild-type protein levels. 1 Publication1
Mutagenesisi6R → A: Nearly complete loss of in vivo repression and activation, 30-fold decreased affinity for RNA, about 175% wild-type protein levels. 1 Publication1
Mutagenesisi7R → A: 70% loss of in vivo repression and activation, 12-fold decreased affinity for RNA, about 125% wild-type protein levels. 1 Publication1
Mutagenesisi19T → A: Increased repression and activation in vivo, about 75% wild-type protein levels. 1 Publication1
Mutagenesisi35N → A: Increased repression and activation in vivo, about 75% wild-type protein levels. 1 Publication1
Mutagenesisi40V → A: 90% loss of in vivo repression and activation, 67-fold decreased affinity for RNA, about 75% wild-type protein levels. 1 Publication1
Mutagenesisi42V → A: Loss of in vivo repression and activation, 135-fold decreased affinity for RNA, about 40% wild-type protein levels. 1 Publication1
Mutagenesisi44R → A: Loss of in vivo repression and activation, 150-fold decreased affinity for RNA, >500% wild-type protein levels. 1 Publication1
Mutagenesisi47I → A: 90% loss of in vivo repression and activation, 67-fold decreased affinity for RNA, about 150% wild-type protein levels. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001770611 – 61Carbon storage regulatorAdd BLAST61

Proteomic databases




Activated by MqsR (PubMed:16352847, PubMed:18713317). Activated by DksA and (p)ppGpp, under partial control of RpoS, the sigma stress factor (at protein level) (PubMed:21488981). Binds to 4 sites in its own mRNA and represses translation (PubMed:21696456). Expressed from 5 promoters; P2 and P5 depend on housekeeping sigma factor 70 (rpoD) while P1 and P3 2 depend on RpoS; indirect activation of P3 leads to increased transcription during the log to stationary phase shift (PubMed:21696456).4 Publications


Subunit structurei

Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (PubMed:15866937, ECO:0000255|HAMAP-Rule:MF_00167).1 Publication

Protein-protein interaction databases

BioGridi4259421. 231 interactors.
IntActiP69913. 10 interactors.


Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 8Combined sources7
Beta strandi12 – 17Combined sources6
Beta strandi19 – 21Combined sources3
Beta strandi27 – 35Combined sources9
Beta strandi38 – 43Combined sources6
Helixi46 – 51Combined sources6

3D structure databases

Select the link destinations:
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum

Miscellaneous databases


Family & Domainsi


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 7Region 1, important for regulation and mRNA-binding1 Publication6
Regioni40 – 47Region 2, important for regulation and mRNA-binding1 Publication8


Two regions important for regulation and RNA-binding are found in the N-terminus (residues 2-7) and middle (residues 40-47). Both are part of the intercalated beta-strands that form the hydrophobic core of the protein; region 1 from one monomer contacts region 2 of the other. The homodimer has 2 distinct RNA-binding regions on opposite, solvent-exposed surface of the protein.1 Publication

Sequence similaritiesi

Belongs to the CsrA/RsmA family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1551. LUCA.

Family and domain databases

HAMAPiMF_00167. CsrA. 1 hit.
InterProiView protein in InterPro
IPR003751. CsrA.
IPR036107. CsrA_sf.
PANTHERiPTHR34984. PTHR34984. 1 hit.
PfamiView protein in Pfam
PF02599. CsrA. 1 hit.
ProDomiView protein in ProDom or Entries sharing at least one domain
PD009007. CsrA. 1 hit.
SUPFAMiSSF117130. SSF117130. 1 hit.
TIGRFAMsiTIGR00202. csrA. 1 hit.


Sequence statusi: Complete.

P69913-1 [UniParc]FASTAAdd to basket

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Mass (Da):6,856
Last modified:January 4, 2005 - v1

Sequence databases

Select the link destinations:
Links Updated
L07596 Unassigned DNA. Translation: AAA71919.1.
D44453 Genomic DNA. Translation: BAA21555.1.
U00096 Genomic DNA. Translation: AAC75738.1.
AP009048 Genomic DNA. Translation: BAA16558.1.
RefSeqiNP_417176.1. NC_000913.3.
WP_000906486.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75738; AAC75738; b2696.
BAA16558; BAA16558; BAA16558.

Similar proteinsi

Entry informationi

Entry nameiCSRA_ECOLI
AccessioniPrimary (citable) accession number: P69913
Secondary accession number(s): P31803
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: February 28, 2018
This is version 104 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program


Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome