Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: regulator of CsrB and CsrC decay



Gene: csrD Accession Numbers: EG10018 (EcoCyc), b3252, ECK3240

Synonyms: yhdA

Regulation Summary Diagram: ?

Summary:
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. CsrD itself does not appear to be a ribonuclease, but may function to selectively target RNA molecules for degradation by RNase E [Suzuki06d].

CsrD contains two predicted transmembrane regions, a HAMP-like domain and GGDEF and EAL signaling domains [Suzuki06d]. The GGDEF and EAL domains do not contain several highly conserved sites thought to be essential for activity [Jonas06, Sommerfeldt09]. While the transmembrane domains are not required for activity of CsrD, the GGDEF and EAL domains are. The regulatory activity of CsrD does not involve the signaling molecule c-di-GMP [Suzuki06d].

csrD is expressed during exponential growth. A csrD mutant shows strongly reduced expression of yaiC, ydaM and the csgBAC curli structural operon, reduced biofilm formation, as well as reduced CsgD accumulation and csgD mRNA levels [Sommerfeldt09].

CsrD: "carbon storage regulator D" [Suzuki06d]

Locations: inner membrane

Map Position: [3,399,414 <- 3,401,354] (73.27 centisomes)
Length: 1941 bp / 646 aa

Molecular Weight of Polypeptide: 73.339 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010663 , DIP:DIP-12292N , EchoBASE:EB0018 , EcoGene:EG10018 , EcoliWiki:b3252 , Mint:MINT-1286606 , OU-Microarray:b3252 , PortEco:csrD , Pride:P13518 , Protein Model Portal:P13518 , RefSeq:NP_417718 , RegulonDB:EG10018 , SMR:P13518 , String:511145.b3252 , UniProt:P13518

Relationship Links: InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR001054 , InterPro:IN-FAMILY:IPR001633 , Pfam:IN-FAMILY:PF00563 , Pfam:IN-FAMILY:PF00990 , Prosite:IN-FAMILY:PS50883 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00052 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 97 (15 members)

GO Terms:

Biological Process: GO:0034661 - ncRNA catabolic process Inferred from experiment [Suzuki06d]
GO:0051252 - regulation of RNA metabolic process Inferred from experiment [Suzuki06d]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: regulation type of regulation posttranscriptional

Essentiality data for csrD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 04-Jun-2009 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 10 -> 30
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 135 -> 155
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 152 -> 219
[UniProt10]
UniProt: HAMP-like; Sequence Annotation Type: region of interest;
Conserved-Region 254 -> 387
[UniProt09]
UniProt: GGDEF;
Conserved-Region 396 -> 644
[UniProt09]
UniProt: EAL;
Mutagenesis-Variant 584
[Suzuki06d, UniProt11]
Alternate sequence: L → A; UniProt: Decreased transcription of csrB.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b3252 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10018; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Jonas06: Jonas K, Tomenius H, Romling U, Georgellis D, Melefors O (2006). "Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system." FEMS Microbiol Lett 264(2);232-7. PMID: 17064377

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Sommerfeldt09: Sommerfeldt N, Possling A, Becker G, Pesavento C, Tschowri N, Hengge R (2009). "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli." Microbiology 155(Pt 4);1318-31. PMID: 19332833

Suzuki06d: Suzuki K, Babitzke P, Kushner SR, Romeo T (2006). "Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E." Genes Dev 20(18);2605-17. PMID: 16980588

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, BIOCYC13B.