RegulonDB

Gene
Name:	cspA
Synonym(s):	ECK3543, EG10166, b3556
Genome position(nucleotides):	3720049 --> 3720261
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.36
External database links:

ASAP:	ABE-0011616
CGSC:	29540
ECHOBASE:	EB0164
ECOLIHUB:	cspA
OU-MICROARRAY:	b3556
STRING:	511145.b3556
COLOMBOS:	cspA

Product

Name:

cold shock protein CspA

Synonym(s):

CS7.4, CspA, DNA-binding transcriptional activator CspA, F10.6, major cold shock protein 7.4

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

Cold

Cellular location:

cytosol

Molecular weight:

7.403

Isoelectric point:

5.715

Motif(s):

Type	Positions	Sequence	Comment
	2 -> 70	SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL	UniProt: Cold shock protein CspA.
	5 -> 69	MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS
	7 -> 67	GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV	UniProt: CSD.

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
		3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
		5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol
	molecular_function	GO:0003676 - nucleic acid binding GO:0003677 - DNA binding GO:0003697 - single-stranded DNA binding GO:0003723 - RNA binding GO:0003727 - single-stranded RNA binding GO:0001072 - transcription antitermination factor activity, RNA binding
	biological_process	GO:0031564 - transcription antitermination GO:0045893 - positive regulation of transcription, DNA-templated GO:0009409 - response to cold GO:0010468 - regulation of gene expression GO:0060567 - negative regulation of DNA-templated transcription, termination

Note(s):

Note(s): ...[more].

Evidence:

[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP] Inferred from expression pattern

Reference(s):

[1] Jiang W., et al., 1997
[2] Jones PG., et al., 1987
[3] Kram KE., et al., 2020
[4] La Teana A., et al., 1991
[5] Podtelezhnikov AA., et al., 2009
[6] Sharan M., et al., 2017

External database links:

ALPHAFOLD:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PDB:

PDB:

PDB:

PDB:

PFAM:

PRIDE:

PRINTS:

PRODB:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

cspA

Operon arrangement:

Transcription unit	Promoter
cspA	cspAp1
cspA	cspAp2

Transcriptional Regulation
	Display Regulation
Activated by:	Fis
Repressed by:	H-NS

RNA cis-regulatory element

Attenuation:	Translational

Cis-reg; thermoregulator	cspA thermoregulator

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_4160	3719942		forward	nd	[RS-EPT-CBR]	[7]
	promoter	TSS_4161	3720104		forward	nd	[RS-EPT-CBR]	[7]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] 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
[2] Jones PG., VanBogelen RA., Neidhardt FC., 1987, Induction of proteins in response to low temperature in Escherichia coli., J Bacteriol 169(5):2092-5
[3] Kram KE., Henderson AL., Finkel SE., 2020, Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival., mSystems 5(4)
[4] 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 88(23):10907-11
[5] Podtelezhnikov AA., Wild DL., 2009, Reconstruction and stability of secondary structure elements in the context of protein structure prediction., Biophys J 96(11):4399-408
[6] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96
[7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.