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Escherichia coli K-12 substr. MG1655 Protein: DksA-ppGpp



Gene: dksA Accession Numbers: EG10230 (EcoCyc), b0145, ECK0144

Synonyms: msmA

Regulation Summary Diagram: ?

Subunit composition of DksA-ppGpp = [DksA][ppGpp]
         RNA polymerase-binding transcription factor DksA = DksA (extended summary available)

Gene Citations: [Dubois04, Kang90, Yamanaka94a, Kawamukai91]

Map Position: [160,149 <- 160,604] (3.45 centisomes)
Length: 456 bp / 151 aa

Unification Links: ASAP:ABE-0000499 , CGSC:30521 , EchoBASE:EB0226 , EcoGene:EG10230 , OU-Microarray:b0145 , PortEco:dksA , RegulonDB:EG10230

In Reactions of unknown directionality:

Not in pathways:
DksA + ppGpp = DksA-ppGpp

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

MultiFun Terms: cell processes adaptations starvation
information transfer protein related translation
regulation type of regulation posttranscriptional translation attenuation and efficiency

Regulated Transcription Units (37 total): ?

Notes:


Subunit of DksA-ppGpp: RNA polymerase-binding transcription factor DksA

Synonyms: MsmA, DksA

Gene: dksA Accession Numbers: EG10230 (EcoCyc), b0145, ECK0144

Locations: cytosol

Sequence Length: 151 AAs

Molecular Weight: 17.528 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0010468 - regulation of gene expression Inferred by computational analysis [GOA06]
Molecular Function: GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: cell processes adaptations starvation
information transfer protein related translation
regulation type of regulation posttranscriptional translation attenuation and efficiency

Unification Links: DIP:DIP-31875N , DisProt:DP00414 , EcoliWiki:b0145 , Mint:MINT-8413451 , PR:PRO_000022453 , Pride:P0ABS1 , Protein Model Portal:P0ABS1 , RefSeq:NP_414687 , SMR:P0ABS1 , String:511145.b0145 , UniProt:P0ABS1

Relationship Links: InterPro:IN-FAMILY:IPR000962 , InterPro:IN-FAMILY:IPR012784 , InterPro:IN-FAMILY:IPR020458 , InterPro:IN-FAMILY:IPR020460 , PDB:Structure:1TJL , Pfam:IN-FAMILY:PF01258 , Prints:IN-FAMILY:PR00618 , Prosite:IN-FAMILY:PS01102 , Prosite:IN-FAMILY:PS51128

In Reactions of unknown directionality:

Not in pathways:
DksA + ppGpp = DksA-ppGpp

Summary:
The DksA protein binds directly to RNA polymerase, affecting transcript elongation and augmenting the effect of the alarmone ppGpp on transcription initiation [Perederina04]. DksA together with ppGpp is required for regulation of transcription of ribosomal RNA promoters [Paul04].

DksA is involved in translational regulation of RpoS [Brown02].

dksA mutants have pleiotropic phenotypes. A null mutant is viable [Kang90]. A dksA mutant exhibited a defect in induction of RpoS production upon entry into stationary phase [Hirsch02] or in the presence of ppGpp [Brown02]. A dksA mutant exhibited a complex phenotype with respect to ppGpp regulation [Brown02].

DksA is required for repair of double-stranded breaks in the chromosome when these breaks occur at two or more locations, but not when there is a single break in the chromosome. This may occur via DksA acting to destabilize transcription complexes, allowing for the replication fork assembly required for double-stranded break repair. DksA works with RecN in this capacity. A recN dksA double mutant became filamentous and was unable to divide after induction of double-stranded breaks. DksA may act by destabilizing transcription complexes, allowing for the replication fork assembly required for double-stranded break repair. [Meddows05].

A dksA mutant exhibited a defect in amino acid biosynthesis that was suppressed by an rpoB T563P mutation [Brown02]. A dksA mutation suppressed the replication defect of a plasmid with mutations at the origin of replication [Ohkubo97]. DksA overproduction suppressed the heat sensitivity of a dnaK or grpE280 mutant [Kang90, Chandrangsu12]. Overproduction also suppressed the heat sensitivity, but not the anucleate cell morphology, of a mukB106 mutant [Yamanaka94a]. Overproduction partially suppressed the filamentous morphology of a dnaK or grpE280 mutant [Kang90]. Overproduction suppressed phenotypes of a prc mutant [Bass96]. Overproduction also suppressed the filamentous morphology and growth defect of a yhhP mutant in low-salt rich medium [Ishii00].

DksA: "dnaK suppressor" [Kang90].

MsmA: "multicopy suppressor of mukB106" [Yamanaka94a].

The crystal structure of DksA has been solved at 2.0 A resolution, and it shows similarity to the structure of GreA, the transcription cleavage factor [Perederina04].

Based on overexpression, deletion, transcription profiling, and RNA polymerase mutant experiments, mutual and antagonistic competition effects between GreA, GreB, and DksA on RNA polymerase activity are observed when ppGpp is absent but are more pronounced when DksA and ppGpp are not present [Vinella12]. DksA overproduction suppressed the temperature-sensitive phenotype of a dnaKJ and a grpE280 mutants [Kang90, Chandrangsu12].

GreA/B factors contribute significantly to complex regulation by DksA and ppGpp. Here, GreA has a major role and GreB has a minor role in the DksA-ppGpp regulatory network [Vinella12]. An interaction network of GreA, GreB, DksA, ppGpp, and RNA polymerase has been proposed [Vinella12].

The aspartic acid residue D74 located in the coiled-coil tip of DksA is crucial for function of both positive and negative control of transcription initiation in vitro and in vivo [Lee12a]. It is also key for distinguishing its functions from those of Gre factors [Lee12a]. A substitution in this residue eliminates DksA function without affecting its apparent affinity [Lee12a]. Two models have been proposed for the DksA-RNAP interaction: i) the coiled-coil tip of DksA, specifically the D74 and A76 residues, interact and stabilize the β trigger loop of RNAP, altering its conformation, and ii) D74 and A76 are affected by the conformation changing the timing required for RNAP [Lee12a].

Expression is increased under low-pH conditions [Stancik02]. Increased ppGpp abundance does not induce DksA production [Brown02].

DksA is stable and long-lived and remains constant under log- and stationary-phase growth conditions [Chandrangsu11].

DksA has a half-life of 44 +/- 9 minutes [Chandrangsu11].

Review: [Paul04a]

Essentiality data for dksA 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]

Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0145 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10230; confirmed by SwissProt match.


References

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

Bass96: Bass S, Gu Q, Christen A (1996). "Multicopy suppressors of prc mutant Escherichia coli include two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated RlpA." J Bacteriol 178(4);1154-61. PMID: 8576052

Brown02: Brown L, Gentry D, Elliott T, Cashel M (2002). "DksA affects ppGpp induction of RpoS at a translational level." J Bacteriol 184(16);4455-65. PMID: 12142416

Chandrangsu11: Chandrangsu P, Lemke JJ, Gourse RL (2011). "The dksA promoter is negatively feedback regulated by DksA and ppGpp." Mol Microbiol 80(5);1337-48. PMID: 21496125

Chandrangsu12: Chandrangsu P, Wang L, Choi SH, Gourse RL (2012). "Suppression of a dnaKJ deletion by multicopy dksA results from non-feedback-regulated transcripts that originate upstream of the major dksA promoter." J Bacteriol 194(6);1437-46. PMID: 22267514

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

Dubois04: Dubois DY, Blaise M, Becker HD, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D (2004). "An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp." Proc Natl Acad Sci U S A 101(20);7530-5. PMID: 15096594

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

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hirsch02: Hirsch M, Elliott T (2002). "Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli." J Bacteriol 184(18);5077-87. PMID: 12193624

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

Ishii00: Ishii Y, Yamada H, Yamashino T, Ohashi K, Katoh E, Shindo H, Yamazaki T, Mizuno T (2000). "Deletion of the yhhP gene results in filamentous cell morphology in Escherichia coli." Biosci Biotechnol Biochem 2000;64(4);799-807. PMID: 10830496

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

Kang90: Kang PJ, Craig EA (1990). "Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation." J Bacteriol 172(4);2055-64. PMID: 2180916

Kawamukai91: Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T (1991). "Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli." J Bacteriol 173(8);2644-8. PMID: 2013578

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lee12a: Lee JH, Lennon CW, Ross W, Gourse RL (2012). "Role of the coiled-coil tip of Escherichia coli DksA in promoter control." J Mol Biol 416(4);503-17. PMID: 22200485

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Meddows05: Meddows TR, Savory AP, Grove JI, Moore T, Lloyd RG (2005). "RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks." Mol Microbiol 57(1);97-110. PMID: 15948952

Ohkubo97: Ohkubo S, Yamaguchi K (1997). "A suppressor of mutations in the region adjacent to iterons of pSC101 ori." J Bacteriol 179(6);2089-91. PMID: 9068662

Paul04: Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL (2004). "DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP." Cell 118(3);311-22. PMID: 15294157

Paul04a: Paul BJ, Ross W, Gaal T, Gourse RL (2004). "rRNA Transcription in Escherichia coli." Annu Rev Genet 38:749-70. PMID: 15568992

Perederina04: Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG (2004). "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell 118(3);297-309. PMID: 15294156

Stancik02: Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL (2002). "pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli." J Bacteriol 184(15);4246-58. PMID: 12107143

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."

Vinella12: Vinella D, Potrykus K, Murphy H, Cashel M (2012). "Effects on Growth by Changes of the Balance between GreA, GreB, and DksA Suggest Mutual Competition and Functional Redundancy in Escherichia coli." J Bacteriol 194(2);261-73. PMID: 22056927

Yamanaka94a: Yamanaka K, Mitani T, Ogura T, Niki H, Hiraga S (1994). "Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli." Mol Microbiol 1994;13(2);301-12. PMID: 7984109

Other References Related to Gene Regulation

Turner11: Turner PC, Miller EN, Jarboe LR, Baggett CL, Shanmugam KT, Ingram LO (2011). "YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance." J Ind Microbiol Biotechnol 38(3);431-9. PMID: 20676725

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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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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