Escherichia coli K-12 substr. MG1655 Polypeptide: DpiA-Pasp DNA-binding transcriptional dual regulator

Gene: dpiA Accession Numbers: G6346 (EcoCyc), b0620, ECK0613

Synonyms: citB, criR, mpdA, DpiA-Pasp57, CitB response regulator - phosphorylated, DpiA response regulator - phosphorylated

Regulation Summary Diagram: ?

Regulation summary diagram for dpiA

Alternative forms of DpiA-Pasp DNA-binding transcriptional dual regulator: DpiA

CitB/DpiA is a dual transcriptional regulator involved in anaerobic citrate catabolism. In the presence of citrate and under anaerobic conditions it activates genes for citrate fermentation, the citCDEFXGT operon, the citAB operon, and mdh, as well as the exuTR operon for dissimilation of hexuronate [Yamamoto08].

Due to the ability of CitB/DpiA to bind to A/T-rich sequences, multiple other roles have been assigned to CitB. When overexpressed in E. coli, it destabilizes plasmid inheritance, represses transcription of appY, encoding a regulator of anaerobic metabolism, and induces the SOS response by competing with DnaA and DnaB in binding to A/T-rich sequences at the replication origin [Ingmer98, Miller03]. Moreover, inactivation of penicillin-binding protein 3, FtsI, either chemically or genetically, induces SOS in E. coli. This induction requires dpiBA [Miller04].

CitB/DpiA belongs to the two-component system DpiB/DpiA, or CitBA. The operon containing both genes, citB (dpiA), encoding the response regulator, and citA (dpiB), encoding the sensor kinase, is transcribed divergently to the citCDEFXGT operon. CitA (DpiB) binds citrate with its periplasmic domain [Kaspar02] and senses reduced conditions using a single Cys residue in vitro [Yamamoto09]. The cytoplasmic domain is involved in autophosphorylation and phosphotransfer to CitB (DpiA) [Yamamoto09]. Therefore, it has been suggested that the main role of DpiA/CitB is regulation of citrate fermentation [Kaspar02].

CitB/DpiA shows 47% similarity to the CitB protein from K. pneumoniae, which also controls the citrate fermentation process [Ingmer98]. Like CitB from K. pneumoniae, CitB/DpiA from E. coli contains a helix-turn-helix DNA-binding motif in the C-terminal domain and three well-conserved residues, two aspartates (positions 13 and 57) and one lysine (position 107), in the N-terminal domain [Ingmer98]. CitB/DpiA binds to sequences with a very high A + T content [Meyer97, Yamamoto09].

Dpi: destabilizes plasmid inheritance

Locations: cytosol

Map Position: [653,085 -> 653,765] (14.08 centisomes, 51°)
Length: 681 bp / 226 aa

Unification Links: ASAP:ABE-0002131 , EchoBASE:EB3314 , EcoGene:EG13544 , OU-Microarray:b0620 , PortEco:dpiA , PR:PRO_000025028 , RegulonDB:G6346

In Paralogous Gene Group: 121 (40 members)

Reactions known to produce the compound:

DpiBA Two-Component Signal Transduction System :
DpiB sensory histidine kinase - phosphorylated + DpiA → DpiB + DpiA-Pasp57

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for dpiA

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment [Yamamoto08]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment [Yamamoto08]
Molecular Function: GO:0000156 - phosphorelay response regulator activity Inferred from experiment [Yamamoto08]
GO:0003677 - DNA binding Inferred from experiment [Yamamoto08]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

DNA binding site length: 23 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: tttttaattaatttaattaaaaa

Regulated Transcription Units (8 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Last-Curated ? 27-Jul-2009 by Mackie A , Macquarie University

Sequence Features

Protein sequence of DpiA-Pasp DNA-binding transcriptional dual regulator with features indicated

Feature Class Location Citations Comment State
4-aspartylphosphate-Modification 57
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G498/EG13544 and G6346/citB
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Ingmer98: Ingmer H, Miller CA, Cohen SN (1998). "Destabilized inheritance of pSC101 and other Escherichia coli plasmids by DpiA, a novel two-component system regulator." Mol Microbiol 29(1);49-59. PMID: 9701802

Kaspar02: Kaspar S, Bott M (2002). "The sensor kinase CitA (DpiB) of Escherichia coli functions as a high-affinity citrate receptor." Arch Microbiol 177(4);313-21. PMID: 11889485

Meyer97: Meyer M, Dimroth P, Bott M (1997). "In vitro binding of the response regulator CitB and of its carboxy-terminal domain to A + T-rich DNA target sequences in the control region of the divergent citC and citS operons of Klebsiella pneumoniae." J Mol Biol 269(5);719-31. PMID: 9223636

Miller03: Miller C, Ingmer H, Thomsen LE, Skarstad K, Cohen SN (2003). "DpiA binding to the replication origin of Escherichia coli plasmids and chromosomes destabilizes plasmid inheritance and induces the bacterial SOS response." J Bacteriol 185(20);6025-31. PMID: 14526013

Miller04: Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H, Cohen SN (2004). "SOS response induction by beta-lactams and bacterial defense against antibiotic lethality." Science 305(5690);1629-31. PMID: 15308764

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

Yamamoto08: Yamamoto K, Matsumoto F, Oshima T, Fujita N, Ogasawara N, Ishihama A (2008). "Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli." Biosci Biotechnol Biochem 72(11);3011-4. PMID: 18997424

Yamamoto09: Yamamoto K, Matsumoto F, Minagawa S, Oshima T, Fujita N, Ogasawara N, Ishihama A (2009). "Characterization of CitA-CitB signal transduction activating genes involved in anaerobic citrate catabolism in Escherichia coli." Biosci Biotechnol Biochem 73(2);346-50. PMID: 19202292

Other References Related to Gene Regulation

Mandin09: Mandin P, Gottesman S (2009). "A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system." Mol Microbiol 72(3);551-65. PMID: 19426207

Scheu12: Scheu PD, Witan J, Rauschmeier M, Graf S, Liao YF, Ebert-Jung A, Basche T, Erker W, Unden G (2012). "CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo." J Bacteriol 194(3);636-45. PMID: 22101843

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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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