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    csrD regulator of CsrB and CsrC decay [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947702, updated on 3-Dec-2024

    Summary

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    Official Symbol
    csrD
    Official Full Name
    regulator of CsrB and CsrC decay
    Primary source
    ECOCYC:EG10018
    Locus tag
    b3252
    See related
    ASAP:ABE-0010663
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK3240; yhdA
    Summary
    In its c-di-GMP domains CsrD has HRSDF instead of GGDEF and ELM instead of EAL and does not appear to have either diguanylate cyclase or cyclic-di-GMP phosphodiesterase activities and the role of CsrD in csrB/C destabilization does not involve cyclic-di-GMP metabolism (Suzuki, 2006). [More information is available at EcoGene: EG10018]. CsrD controls the degradation of the small RNAs CsrB and CsrC, thereby regulating the activity of CsrA and affecting the expression of CsrA-regulated genes. [More information is available at EcoCyc: EG10018].
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    Genomic context

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    Sequence:
    NC_000913.3 (3401392..3403332, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene cell shape determining protein MreD Neighboring gene cell shape determining protein MreC Neighboring gene dynamic cytoskeletal protein MreB Neighboring gene acrylyl-CoA reductase Neighboring gene pseudo

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system. Jonas K, et al. FEMS Microbiol Lett, 2006 Nov. PMID 17064377
    2. The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli. Esquerré T, et al. Sci Rep, 2016 Apr 26. PMID 27112822, Free PMC Article
    3. Regulation of CsrB/C sRNA decay by EIIA(Glc) of the phosphoenolpyruvate: carbohydrate phosphotransferase system. Leng Y, et al. Mol Microbiol, 2016 Feb. PMID 26507976, Free PMC Article
    4. Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells. Doi M, et al. J Bacteriol, 1988 Oct. PMID 3049542, Free PMC Article
    5. Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins. Vakulskas CA, et al. Nucleic Acids Res, 2016 Sep 19. PMID 27235416, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study shows that CsrD is involved in a massive positive transcriptional regulation in Escherichia coli.
      Title: The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli.
    2. CsrD evolution was driven by the selective advantage of decoupling Csr small RNA decay from CsrA binding, connecting it instead to the availability of a preferred carbon source.
      Title: Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins.
    3. Data indicate that CsrA proteins are sequestered by CsrB noncoding RNAs, and the degradation of CsrB RNAs is increased by CsrD proteins.
      Title: Rapid and robust signaling in the CsrA cascade via RNA-protein interactions and feedback regulation.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables cyclic-guanylate-specific phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of RNA metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    regulator of CsrB and CsrC decay

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      3401392..3403332 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417718.1 regulator of CsrB and CsrC decay [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417718.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A376FVU1
      Conserved Domains (1) summary
      PRK11059
      Location:1 → 634
      PRK11059; regulatory protein CsrD; Provisional
    Nucleotide Protein
    Heading Accession and Version

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