|Gene:||dpiA||Accession Numbers: G6346 (EcoCyc), b0620, ECK0613|
Synonyms: citB, criR, mpdA, DpiA-Pasp57, CitB response regulator - phosphorylated, DpiA response regulator - phosphorylated
Alternative forms of DpiA-Pasp DNA-binding transcriptional dual regulator: DpiA (summary available)
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 [Yamamoto09a]. The cytoplasmic domain is involved in autophosphorylation and phosphotransfer to CitB (DpiA) [Yamamoto09a]. 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 [Meyer97a, Yamamoto09a].
Dpi: destabilizes plasmid inheritance
|Map Position: [653,085 -> 653,765] (14.08 centisomes, 51°)||Length: 681 bp / 226 aa|
In Paralogous Gene Group: 121 (40 members)
Reactions known to produce the compound:
|Biological Process:||GO:0000160 - phosphorelay signal transduction system
GO:0006355 - regulation of transcription, DNA-templated [Yamamoto08]
|Molecular Function:||GO:0000156 - phosphorelay response regulator activity
GO:0003677 - DNA binding [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
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
Meyer97a: 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
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
Yamamoto09a: 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
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
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493