Escherichia coli K-12 substr. MG1655 Enzyme: cardiolipin synthase 1

Gene: clsA Accession Numbers: EG11608 (EcoCyc), b1249, ECK1243

Synonyms: yciJ, nov, cls

Regulation Summary Diagram: ?

Regulation summary diagram for clsA

ClsA is the major cardiolipin synthase in E. coli. Synthesis of cardiolipin during exponential growth is due to the activity of ClsA, while all three cardiolipin synthases, ClsA, ClsB and ClsC, contribute to cardiolipin synthesis in stationary phase [Pluschke78, Shibuya85, Nishijima88, Tan12a].

The ClsA protein appears to undergo posttranslational processing at the N terminus. A Δ2-60 deletion mutant retains activity and membrane association [Guo00, Quigley09].

A clsA mutant is resistant to rac-3,4-dihydroxybutyl 1-phosphonate (DBP) [Hwang84]. clsA mutants have increased sensitivity to novobiocin [Tropp95]. clsA mutations are recovered in strains adapted to freeze-thaw-growth cycles [Sleight08]. Cells with deletions of all three of the genes encoding cardiolipin synthases, ΔclsABC, completely lack cardiolipin [Tan12a]. Expression of clsA is osmoregulated [Romantsov07].

ClsA: "cardiolipin synthase" [Pluschke78]

Reviews: [Tropp97, Romantsov09]

Citations: [Homma82, Shibuya85a, Heber91, Shibuya92, Rakonjac92, Hiraoka93, Babu11a]

Locations: inner membrane

Map Position: [1,305,209 <- 1,306,669] (28.13 centisomes, 101°)
Length: 1461 bp / 486 aa

Molecular Weight of Polypeptide: 54.822 kD (from nucleotide sequence), 46.0 kD (experimental) [Ohta85 ]

Unification Links: ASAP:ABE-0004186 , CGSC:915 , EchoBASE:EB1565 , EcoGene:EG11608 , EcoliWiki:b1249 , ModBase:P0A6H8 , OU-Microarray:b1249 , PortEco:cls , Pride:P0A6H8 , Protein Model Portal:P0A6H8 , RefSeq:NP_415765 , RegulonDB:EG11608 , SMR:P0A6H8 , String:511145.b1249 , UniProt:P0A6H8

Relationship Links: InterPro:IN-FAMILY:IPR001736 , InterPro:IN-FAMILY:IPR022924 , InterPro:IN-FAMILY:IPR027379 , Pfam:IN-FAMILY:PF00614 , Pfam:IN-FAMILY:PF13396 , Prosite:IN-FAMILY:PS50035 , Smart:IN-FAMILY:SM00155

In Paralogous Gene Group: 198 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0032049 - cardiolipin biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Shibuya85, Pluschke78]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0008654 - phospholipid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
Molecular Function: GO:0008808 - cardiolipin synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Ragolia94, Hiraoka91, Pluschke78]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016780 - phosphotransferase activity, for other substituted phosphate groups Inferred by computational analysis [GOA06]
Cellular Component: GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Pluschke78]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell processes protection drug resistance/sensitivity
cell structure membrane
metabolism biosynthesis of macromolecules (cellular constituents) phospholipid

Essentiality data for clsA 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]
Yes [Feist07, Comment 4]

Last-Curated ? 26-Sep-2012 by Keseler I , SRI International

Enzymatic reaction of: cardiolipin synthase

Synonyms: cardiolipin synthetase

EC Number: 2.7.8.-

2 an L-1-phosphatidyl-glycerol <=> a cardiolipin + glycerol

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

Alternative Substrates [Comment 5]:

In Pathways: superpathway of phospholipid biosynthesis I (bacteria) , cardiolipin biosynthesis I

The enzyme can weakly catalyze the reverse reaction with relaxed substrate specificity [Hiraoka91].

Activators (Unknown Mechanism): phosphate [Hiraoka91, Ragolia94] , an L-1-phosphatidyl-inositol [Ragolia94, Comment 6] , an L-1-phosphatidylethanolamine [Ragolia94] , an L-1-phosphatidylserine [Ragolia94]

Inhibitors (Allosteric): a cardiolipin [Ragolia94, Comment 7]

Inhibitors (Unknown Mechanism): dimyristoyl phosphatidate [Ragolia94] , (trans-, trans-)dioleoyl phosphatidate [Ragolia94] , 1-stearoyl-2-stearoyl-sn-glycerol 3-phosphate [Ragolia94] , dipalmitoyl phosphatidate [Ragolia94]

Primary Physiological Regulators of Enzyme Activity: a cardiolipin

Kinetic Parameters:

Specific Activity (U/mg)
an L-1-phosphatidyl-glycerol

pH(opt): 7 [Hiraoka91]

Sequence Features

Protein sequence of cardiolipin synthase 1 with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 2 -> 60
[Tan12a, UniProt14a]
UniProt: Remains membrane associated and retains in vitro and in vivo activity.
Transmembrane-Region 3 -> 23
UniProt: Helical;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 7 -> 8
[Tan12a, UniProt14a]
UniProt: Retains in vitro activity, but loses most of its in vivo activity. Higher apparent molecular mass than wild-type protein.
Mutagenesis-Variant 30 -> 32
[Tan12a, UniProt14a]
UniProt: Undergoes altered post-translational processing and has much lower in vivo and in vitro activity.
Transmembrane-Region 38 -> 58
UniProt: Helical;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 59
[Tan12a, UniProt14a]
UniProt: Does not affect CL synthase processing or activity.
Extrinsic-Sequence-Variant 113
UniProt: In strain: ECOR 60..
Conserved-Region 219 -> 246
UniProt: PLD phosphodiesterase 1;
Active-Site 224
UniProt: Non-Experimental Qualifier: potential;
Active-Site 226
UniProt: Non-Experimental Qualifier: potential;
Active-Site 231
UniProt: Non-Experimental Qualifier: potential;
Extrinsic-Sequence-Variant 283
UniProt: In strain: ECOR 50..
Extrinsic-Sequence-Variant 378
UniProt: In strain: ECOR 16..
Conserved-Region 399 -> 426
UniProt: PLD phosphodiesterase 2;
Active-Site 404
UniProt: Non-Experimental Qualifier: potential;
Active-Site 406
UniProt: Non-Experimental Qualifier: potential;
Active-Site 411
UniProt: Non-Experimental Qualifier: potential;
Extrinsic-Sequence-Variant 426
UniProt: In strain: ECOR 46..

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G721/b1249 and EG11608/cls
10/20/97 Gene b1249 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11608; 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

Babu11a: Babu M, Diaz-Mejia JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A (2011). "Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways." PLoS Genet 7(11);e1002377. PMID: 22125496

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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

GOA01a: 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."

Guo00: Guo D, Tropp BE (2000). "A second Escherichia coli protein with CL synthase activity." Biochim Biophys Acta 1483(2);263-74. PMID: 10634942

Heber91: Heber S, Tropp BE (1991). "Genetic regulation of cardiolipin synthase in Escherichia coli." Biochim Biophys Acta 1129(1);1-12. PMID: 1661609

Hiraoka91: Hiraoka S, Nukui K, Uetake N, Ohta A, Shibuya I (1991). "Amplification and substantial purification of cardiolipin synthase of Escherichia coli." J Biochem (Tokyo) 1991;110(3);443-9. PMID: 1663113

Hiraoka93: Hiraoka S, Matsuzaki H, Shibuya I (1993). "Active increase in cardiolipin synthesis in the stationary growth phase and its physiological significance in Escherichia coli." FEBS Lett 336(2);221-4. PMID: 8262233

Homma82: Homma H, Nojima S (1982). "Synthesis of various phospholipids from 2-acyl lysophospholipids by Escherichia coli extract." J Biochem 91(4);1103-10. PMID: 7047508

Hwang84: Hwang YW, Engel R, Tropp BE (1984). "Correlation of 3,4-dihydroxybutyl 1-phosphonate resistance with a defect in cardiolipin synthesis in Escherichia coli." J Bacteriol 157(3);846-56. PMID: 6321438

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

Nishijima88: Nishijima S, Asami Y, Uetake N, Yamagoe S, Ohta A, Shibuya I (1988). "Disruption of the Escherichia coli cls gene responsible for cardiolipin synthesis." J Bacteriol 170(2);775-80. PMID: 2828323

Ohta85: Ohta A, Obara T, Asami Y, Shibuya I (1985). "Molecular cloning of the cls gene responsible for cardiolipin synthesis in Escherichia coli and phenotypic consequences of its amplification." J Bacteriol 163(2);506-14. PMID: 2991193

Pluschke78: Pluschke G, Hirota Y, Overath P (1978). "Function of phospholipids in Escherichia coli. Characterization of a mutant deficient in cardiolipin synthesis." J Biol Chem 253(14);5048-55. PMID: 353047

Quigley09: Quigley BR, Tropp BE (2009). "E. coli cardiolipin synthase: Function of N-terminal conserved residues." Biochim Biophys Acta. PMID: 19341704

Ragolia94: Ragolia L, Tropp BE (1994). "The effects of phosphoglycerides on Escherichia coli cardiolipin synthase." Biochim Biophys Acta 1994;1214(3);323-32. PMID: 7918616

Rakonjac92: Rakonjac J, Milic M, Ajdic-Predic D, Santos D, Ivanisevic R, Savic DJ (1992). "nov: a new genetic locus that affects the response of Escherichia coli K-12 to novobiocin." Mol Microbiol 6(11);1547-53. PMID: 1625583

Romantsov07: Romantsov T, Helbig S, Culham DE, Gill C, Stalker L, Wood JM (2007). "Cardiolipin promotes polar localization of osmosensory transporter ProP in Escherichia coli." Mol Microbiol 64(6);1455-65. PMID: 17504273

Romantsov09: Romantsov T, Guan Z, Wood JM (2009). "Cardiolipin and the osmotic stress responses of bacteria." Biochim Biophys Acta 1788(10);2092-100. PMID: 19539601

Shibuya85: Shibuya I, Miyazaki C, Ohta A (1985). "Alteration of phospholipid composition by combined defects in phosphatidylserine and cardiolipin synthases and physiological consequences in Escherichia coli." J Bacteriol 161(3);1086-92. PMID: 2982784

Shibuya85a: Shibuya I, Yamagoe S, Miyazaki C, Matsuzaki H, Ohta A (1985). "Biosynthesis of novel acidic phospholipid analogs in Escherichia coli." J Bacteriol 161(2);473-7. PMID: 3918012

Shibuya92: Shibuya I, Hiraoka S (1992). "Cardiolipin synthase from Escherichia coli." Methods Enzymol 209;321-30. PMID: 1323048

Sleight08: Sleight SC, Orlic C, Schneider D, Lenski RE (2008). "Genetic basis of evolutionary adaptation by Escherichia coli to stressful cycles of freezing, thawing and growth." Genetics 180(1);431-43. PMID: 18757947

Tan12a: Tan BK, Bogdanov M, Zhao J, Dowhan W, Raetz CR, Guan Z (2012). "Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates." Proc Natl Acad Sci U S A 109(41);16504-9. PMID: 22988102

Tropp95: Tropp BE, Ragolia L, Xia W, Dowhan W, Milkman R, Rudd KE, Ivanisevic R, Savic DJ (1995). "Identity of the Escherichia coli cls and nov genes." J Bacteriol 1995;177(17);5155-7. PMID: 7665497

Tropp97: Tropp BE (1997). "Cardiolipin synthase from Escherichia coli." Biochim Biophys Acta 1348(1-2);192-200. PMID: 9370333

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 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."

Other References Related to Gene Regulation

Ivanisevic95: Ivanisevic R, Milic M, Ajdic D, Rakonjac J, Savic DJ (1995). "Nucleotide sequence, mutational analysis, transcriptional start site, and product analysis of nov, the gene which affects Escherichia coli K-12 resistance to the gyrase inhibitor novobiocin." J Bacteriol 1995;177(7);1766-71. PMID: 7896699

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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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