Escherichia coli K-12 substr. MG1655 Polypeptide: CspA DNA-binding transcriptional activator

Gene: cspA Accession Numbers: EG10166 (EcoCyc), b3556, ECK3543

Synonyms: major cold shock protein 7.4, CS7.4, F10.6, cold shock protein CspA

Regulation Summary Diagram: ?

Regulation summary diagram for cspA

The "Cold shock protein A," CspA, is a major cold shock protein and was shown to be detected only during early-log-phase growth at 37°C and during log phase after a shift from 37°C to 10°C [Jones87, Goldstein90]. However, studies have shown that although the expression of cspA is reduced during stationary phase, cspA mRNA and CspA are detectable during all growth phases [Brandi12]. CspA acts as a positive transcription factor of at least two cold shock genes: hns [Brandi94, La91, Giangrossi01a] and gyrA [Jones92]. cspA has been shown to negatively regulate its own expression as the result of attenuation of transcription [Bae97]. A model of how CspA might affect the transcription of hns has been proposed [Johnston06]. CspE inhibits the expression of cspA in vitro by increasing pause recognition by RNA polymerase at the cspA "cold box" [Bae99].

CspA belongs to the cold shock family of proteins and was shown to be homologous to eukaryotic Y-box transcription factors [Yamanaka98, Didier88]. The transcription factors of this family recognize a CCAAT sequence in the regulatory region of the genes regulated [Giangrossi01a, Brandi94].

The crystal structure of CspA has been determined by X-ray crystallography to a resolution of 2.0 Å [Schindelin94]; also, the structure of CspA has been determined by NMR spectroscopy [Newkirk94, Feng98].

On other hand, Jiang et al. in 1997 demonstrated that CspA acts as an RNA chaperone that prevents secondary structure formation of RNA at low temperatures [Jiang97, Bae97]. cspA mRNA is very unstable at 37°C and rapidly disappears as the cell density and RNase activity increase [Tanabe92, Brandi99]. The lability of cspA mRNA at high temperatures is mediated by cleavage toward its 3' end; this cleavage is partially dependent on RNase E [Hankins07]. Thus, cspA expression levels change in response to temperature fluctuations [Ivancic13]. The long 5' untranslated region of cspA mRNA contains a feature within the first 25 bases that is responsible for derepression of cspA expression and inhibition of synthesis of cellular proteins other than cold shock proteins following cold shock [Jiang96]. cspA was also shown to be induced by addition of chloramphenicol and was induced even in the absence of protein synthesis [Jiang93, Etchegaray99].

By making use of micro arrays analysis, Constantinidou et al [Constantinidou06] concluded that FNR represses cspA gene expression, but it is not know which of the two promoters (cspAp1, cspA2) is affected. They also identified a putative FNR binding site upstream of the gene, but the sequence was not shown.

Gene Citations: [Xia02, Fang97]

Locations: cytosol

Map Position: [3,718,072 -> 3,718,284] (80.14 centisomes, 288°)
Length: 213 bp / 70 aa

Molecular Weight of Polypeptide: 7.403 kD (from nucleotide sequence), 7.4 kD (experimental) [Goldstein90 ]

pI: 5.66

Unification Links: ASAP:ABE-0011616 , CGSC:29540 , DIP:DIP-31862N , EchoBASE:EB0164 , EcoGene:EG10166 , EcoliWiki:b3556 , Mint:MINT-1220153 , ModBase:P0A9X9 , OU-Microarray:b3556 , PortEco:cspA , PR:PRO_000022338 , Pride:P0A9X9 , Protein Model Portal:P0A9X9 , RefSeq:NP_418012 , RegulonDB:EG10166 , SMR:P0A9X9 , String:511145.b3556 , UniProt:P0A9X9

Relationship Links: InterPro:IN-FAMILY:IPR002059 , InterPro:IN-FAMILY:IPR011129 , InterPro:IN-FAMILY:IPR012156 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR019844 , PDB:Structure:1MJC , PDB:Structure:2BH8 , PDB:Structure:3MEF , Pfam:IN-FAMILY:PF00313 , Prints:IN-FAMILY:PR00050 , Prosite:IN-FAMILY:PS00352 , Smart:IN-FAMILY:SM00357

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Author statement Inferred by computational analysis [UniProtGOA11a, Brandi94, Jiang97, La91, Jones87]
GO:0009409 - response to cold Inferred from experiment [Jones87]
GO:0031564 - transcription antitermination Inferred from experiment [Bae00]
GO:0060567 - negative regulation of DNA-templated transcription, termination Inferred from experiment [Bae00]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0001072 - RNA binding transcription antitermination factor activity Inferred from experiment [Bae00]
GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Brandi94]
GO:0003697 - single-stranded DNA binding Inferred from experiment [Jiang97]
GO:0003723 - RNA binding Inferred from experiment [Jiang97]
GO:0003727 - single-stranded RNA binding Inferred from experiment [Jiang97]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Goldstein90]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: cell processes adaptations temperature extremes
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

DNA binding site length: 7 base-pairs

Symmetry: Asymmetric

Consensus DNA Binding Sequence: ATTGGca

Regulated Transcription Units (2 total): ?


Transcription-unit diagram

Transcription-unit diagram

Essentiality data for cspA 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]

Sequence Features

Protein sequence of CspA DNA-binding transcriptional activator with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
UniProt: Removed.
Chain 2 -> 70
UniProt: Cold shock protein cspA;
Conserved-Region 7 -> 67
UniProt: CSD;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3556 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10166; 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

Bae00: Bae W, Xia B, Inouye M, Severinov K (2000). "Escherichia coli CspA-family RNA chaperones are transcription antiterminators." Proc Natl Acad Sci U S A 97(14);7784-9. PMID: 10884409

Bae97: Bae W, Jones PG, Inouye M (1997). "CspA, the major cold shock protein of Escherichia coli, negatively regulates its own gene expression." J Bacteriol 179(22);7081-8. PMID: 9371456

Bae99: Bae W, Phadtare S, Severinov K, Inouye M (1999). "Characterization of Escherichia coli cspE, whose product negatively regulates transcription of cspA, the gene for the major cold shock protein." Mol Microbiol 1999;31(5);1429-41. PMID: 10200963

Brandi12: Brandi A, Pon CL (2012). "Expression of Escherichia coli cspA during early exponential growth at 37°C." Gene 492(2);382-8. PMID: 22093878

Brandi94: Brandi A, Pon CL, Gualerzi CO (1994). "Interaction of the main cold shock protein CS7.4 (CspA) of Escherichia coli with the promoter region of hns." Biochimie 1994;76(10-11);1090-8. PMID: 7748932

Brandi99: Brandi A, Spurio R, Gualerzi CO, Pon CL (1999). "Massive presence of the Escherichia coli 'major cold-shock protein' CspA under non-stress conditions." EMBO J 18(6);1653-9. PMID: 10075935

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

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

Didier88: Didier DK, Schiffenbauer J, Woulfe SL, Zacheis M, Schwartz BD (1988). "Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box." Proc Natl Acad Sci U S A 85(19);7322-6. PMID: 3174636

Etchegaray99: Etchegaray JP, Inouye M (1999). "CspA, CspB, and CspG, major cold shock proteins of Escherichia coli, are induced at low temperature under conditions that completely block protein synthesis." J Bacteriol 181(6);1827-30. PMID: 10074075

Fang97: Fang L, Jiang W, Bae W, Inouye M (1997). "Promoter-independent cold-shock induction of cspA and its derepression at 37 degrees C by mRNA stabilization." Mol Microbiol 23(2);355-64. PMID: 9044269

Feng98: Feng W, Tejero R, Zimmerman DE, Inouye M, Montelione GT (1998). "Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site." Biochemistry 37(31);10881-96. PMID: 9692981

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, Gualerzi CO, Pon CL (2001). "Mutagenesis of the downstream region of the Escherichia coli hns promoter." Biochimie 83(2);251-9. PMID: 11278076

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Goldstein90: Goldstein J, Pollitt NS, Inouye M (1990). "Major cold shock protein of Escherichia coli." Proc Natl Acad Sci U S A 1990;87(1);283-7. PMID: 2404279

Hankins07: Hankins JS, Zappavigna C, Prud'homme-Genereux A, Mackie GA (2007). "Role of RNA structure and susceptibility to RNase E in regulation of a cold shock mRNA, cspA mRNA." J Bacteriol 189(12);4353-8. PMID: 17416651

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

Ivancic13: Ivancic T, Jamnik P, Stopar D (2013). "Cold shock CspA and CspB protein production during periodic temperature cycling in Escherichia coli." BMC Res Notes 6;248. PMID: 23815967

Jiang93: Jiang W, Jones P, Inouye M (1993). "Chloramphenicol induces the transcription of the major cold shock gene of Escherichia coli, cspA." J Bacteriol 175(18);5824-8. PMID: 8376329

Jiang96: Jiang W, Fang L, Inouye M (1996). "The role of the 5'-end untranslated region of the mRNA for CspA, the major cold-shock protein of Escherichia coli, in cold-shock adaptation." J Bacteriol 178(16);4919-25. PMID: 8759856

Jiang97: Jiang W, Hou Y, Inouye M (1997). "CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone." J Biol Chem 272(1);196-202. PMID: 8995247

Johnston06: Johnston D, Tavano C, Wickner S, Trun N (2006). "Specificity of DNA binding and dimerization by CspE from E. coli." J Biol Chem 281(52);40208-15. PMID: 17088256

Jones87: Jones PG, VanBogelen RA, Neidhardt FC (1987). "Induction of proteins in response to low temperature in Escherichia coli." J Bacteriol 169(5);2092-5. PMID: 3553157

Jones92: Jones PG, Krah R, Tafuri SR, Wolffe AP (1992). "DNA gyrase, CS7.4, and the cold shock response in Escherichia coli." J Bacteriol 1992;174(18);5798-802. PMID: 1325964

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

La91: La Teana A, Brandi A, Falconi M, Spurio R, Pon CL, Gualerzi CO (1991). "Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS." Proc Natl Acad Sci U S A 1991;88(23);10907-11. PMID: 1961761

Newkirk94: Newkirk K, Feng W, Jiang W, Tejero R, Emerson SD, Inouye M, Montelione GT (1994). "Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA." Proc Natl Acad Sci U S A 1994;91(11);5114-8. PMID: 7515185

Schindelin94: Schindelin H, Jiang W, Inouye M, Heinemann U (1994). "Crystal structure of CspA, the major cold shock protein of Escherichia coli." Proc Natl Acad Sci U S A 1994;91(11);5119-23. PMID: 8197194

Tanabe92: Tanabe H, Goldstein J, Yang M, Inouye M (1992). "Identification of the promoter region of the Escherichia coli major cold shock gene, cspA." J Bacteriol 1992;174(12);3867-73. PMID: 1597410

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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

Xia02: Xia B, Ke H, Jiang W, Inouye M (2002). "The Cold Box stem-loop proximal to the 5'-end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature." J Biol Chem 277(8);6005-11. PMID: 11741997

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

Giuliodori10: Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P, Gualerzi CO, Pon CL (2010). "The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA." Mol Cell 37(1);21-33. PMID: 20129052

Hou12: Hou Z, Fink RC, Black EP, Sugawara M, Zhang Z, Diez-Gonzalez F, Sadowsky MJ (2012). "Gene expression profiling of Escherichia coli in response to interactions with the lettuce rhizosphere." J Appl Microbiol 113(5);1076-86. PMID: 22830299

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Marincs06: Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG (2006). "Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor." Biochem J 396(2);227-34. PMID: 16515535

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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