Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015 (Sat)

Escherichia coli K-12 substr. MG1655 Protein: DNA replication inhibitor

Gene: cspD Accession Numbers: EG11111 (EcoCyc), b0880, ECK0871

Synonyms: ybjA, cspH

Regulation Summary Diagram: ?

Regulation summary diagram for cspD

Subunit composition of DNA replication inhibitor = [CspD]2
         DNA replication inhibitor = CspD

CspD is a toxin that appears to act by inhibiting replication [Yamanaka01, Kim10d], and which influences persister cell formation [Kim10f]. CspD forms a homodimer in solution and is able to bind single-stranded DNA and RNA and packs ssDNA into structures that are distinguishable from SSB-coated DNA. Binding does not show sequence specificity. In vitro, CspD inhibits initiation and elongation of minichromosome replication [Yamanaka01]. The CspD protein localizes to the nucleoid in stationary-phase cells [Giangrossi01a].

Expression of cspD is not inducible by cold shock [Lee94a] and is inversely correlated with growth rate; it is induced at stationary phase and upon glucose starvation, but is not dependent on σS, the stationary phase sigma factor [Yamanaka97]. cspD is repressed by the MqsR/MqsA toxin/antitoxin complex and MqsA alone, while MqsR overproduction induces cspD expression [Kim10d].

cspD null mutants are viable, but overproduction of the CspD protein is lethal [Yamanaka01].

Reviews: [Yamanaka98, Trun03]

Locations: cytosol

Map Position: [921,589 <- 921,813] (19.86 centisomes, 72°)
Length: 225 bp / 74 aa

Molecular Weight of Polypeptide: 7.969 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002991 , CGSC:31688 , DIP:DIP-47833N , EchoBASE:EB1102 , EcoGene:EG11111 , EcoliWiki:b0880 , Mint:MINT-1219798 , ModBase:P0A968 , OU-Microarray:b0880 , PortEco:cspD , PR:PRO_000022341 , Pride:P0A968 , Protein Model Portal:P0A968 , RefSeq:NP_415401 , RegulonDB:EG11111 , SMR:P0A968 , String:511145.b0880 , Swiss-Model:P0A968 , UniProt:P0A968

Relationship Links: InterPro:IN-FAMILY:IPR002059 , InterPro:IN-FAMILY:IPR011129 , InterPro:IN-FAMILY:IPR012156 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR012751 , InterPro:IN-FAMILY:IPR019844 , Pfam:IN-FAMILY:PF00313 , Prints:IN-FAMILY:PR00050 , Prosite:IN-FAMILY:PS00352 , Smart:IN-FAMILY:SM00357

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for cspD

GO Terms:

Biological Process: GO:0008156 - negative regulation of DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11, Yamanaka01]
GO:0042594 - response to starvation Inferred from experiment [Yamanaka97]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01]
GO:0006950 - response to stress Inferred by computational analysis [GOA01]
Molecular Function: GO:0003697 - single-stranded DNA binding Inferred from experiment [Yamanaka01]
GO:0003723 - RNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Yamanaka01]
GO:0042803 - protein homodimerization activity Inferred from experiment [Yamanaka01]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA01]

MultiFun Terms: information transfer DNA related DNA replication
regulation type of regulation DNA structure level

Essentiality data for cspD 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]

Last-Curated ? 03-Feb-2010 by Keseler I , SRI International

Sequence Features

Protein sequence of DNA replication inhibitor with features indicated

Feature Class Location Citations Comment
Conserved-Region 4 -> 64
UniProt: CSD;
Sequence-Conflict 19
[Wasinger98, UniProt10a]
UniProt: (in Ref. 5; AA sequence);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0880 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11111; confirmed by SwissProt match.


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

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

Giangrossi01a: Giangrossi M, Exley RM, Le Hegarat F, Pon CL (2001). "Different in vivo localization of the Escherichia coli proteins CspD and CspA." FEMS Microbiol Lett 202(2);171-6. PMID: 11520610

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kim10d: Kim Y, Wang X, Zhang XS, Grigoriu S, Page R, Peti W, Wood TK (2010). "Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD." Environ Microbiol 12(5);1105-21. PMID: 20105222

Kim10f: Kim Y, Wood TK (2010). "Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli." Biochem Biophys Res Commun 391(1);209-13. PMID: 19909729

Lee94a: Lee SJ, Xie A, Jiang W, Etchegaray JP, Jones PG, Inouye M (1994). "Family of the major cold-shock protein, CspA (CS7.4), of Escherichia coli, whose members show a high sequence similarity with the eukaryotic Y-box binding proteins." Mol Microbiol 11(5);833-9. PMID: 8022261

Trun03: Trun N, Johnston D (2003). "Folding chromosomes in bacteria: examining the role of Csp proteins and other small nucleic acid-binding proteins." Curr Top Dev Biol 55;173-201. PMID: 12959196

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Wasinger98: Wasinger VC, Humphery-Smith I (1998). "Small genes/gene-products in Escherichia coli K-12." FEMS Microbiol Lett 169(2);375-82. PMID: 9868784

Yamanaka01: Yamanaka K, Zheng W, Crooke E, Wang YH, Inouye M (2001). "CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli." Mol Microbiol 39(6);1572-84. PMID: 11260474

Yamanaka97: Yamanaka K, Inouye M (1997). "Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli." J Bacteriol 1997;179(16);5126-30. PMID: 9260955

Yamanaka98: Yamanaka K, Fang L, Inouye M (1998). "The CspA family in Escherichia coli: multiple gene duplication for stress adaptation." Mol Microbiol 27(2);247-55. PMID: 9484881

Other References Related to Gene Regulation

Uppal14: Uppal S, Shetty DM, Jawali N (2014). "Cyclic AMP receptor protein (CRP) regulates cspD, a bacterial toxin gene, in Escherichia coli." J Bacteriol. PMID: 24509317

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 19.0 on Fri Sep 4, 2015, biocyc14.