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CpgD is a phosphoglycerate cytidylyltransferase required for ceramide diphosphoglycerate synthesis
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Abstract
LPS is essential in most Gram-negative bacteria, but mutants of several species have been isolated that can survive in its absence. Caulobacter crescentus viability in the absence of LPS is partially dependent on the anionic sphingolipid ceramide diphosphoglycerate (CPG2). Genetic analyses showed that ccna_01210, which encodes a nucleotidyltransferase, is required for CPG2 production. Using purified recombinant protein, we determined that CCNA_01210 (CpgD) is a phosphoglycerate cytidylyltransferase that uses CTP and phosphoglycerate to produce CDP-glycerate, which we hypothesize is the phosphoglycerate donor for CPG2 synthesis. CpgD had optimum activity at pH 7.5 to 8 in the presence of magnesium. CpgD exhibited Michaelis-Menten kinetics concerning 3-phosphoglycerate, D-2-phosphoglycerate, and L-2-phosphoglycerate. By contrast, CTP followed Michaelis-Menten kinetics in the presence of 3-phosphoglycerate and L-2-phosphoglycerate but exhibited cooperativity with D-2-phosphoglycerate. Overall, D-2-phosphoglycerate was the preferred substrate in vitro. The characterization of this enzyme uncovers another step in the pathway toward CPG2 synthesis.
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A RAPID METHOD OF TOTAL LIPID EXTRACTION AND PURIFICATION
Bligh, E. G., & Dyer, W. J. (1959) · Canadian Journal of Biochemistry and Physiology · doi:10.1139/o59-099 · Cited by 54,751 · cited 1×
“Lipids were extracted from C . crescentus cells using the method of Bligh and Dyer with minor modi fi cations (27).”
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Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 27
- Silhavy, 2010, The bacterial cell envelope, Cold. Spring. Harb. Perspect. Biol., 2, 10.1101/cshperspect.a000414 · DOI
- Nikaido, 2003, Molecular basis of bacterial outer membrane permeability revisited Microbiol, Mol. Biol. Rev., 67, 593, 10.1128/MMBR.67.4.593-656.2003 · DOI · Paper page
- Boll, 2016, A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficient Acinetobacter baumannii, Proc. Natl. Acad. Sci. U. S. A., 113, E6228, 10.1073/pnas.1611594113 · DOI
- Peng, 2005, Moraxella catarrhalis bacterium without endotoxin, a potential vaccine candidate, Infect. Immun., 73, 7569, 10.1128/IAI.73.11.7569-7577.2005 · DOI
- Steeghs, 1998, Meningitis bacterium is viable without endotoxin, Nature, 392, 449, 10.1038/33046 · DOI
- Zik, 2022, Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids, Cell. Rep., 39, 10.1016/j.celrep.2022.110888 · DOI
- Brown, 2019, Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis, Cell. Host. Microbe., 25, 668, 10.1016/j.chom.2019.04.002 · DOI
- Johnson, 2020, Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels, Nat. Commun., 11, 2471, 10.1038/s41467-020-16274-w · DOI
- Moye, 2016, Synthesis of sphingolipids impacts survival of Porphyromonas gingivalis and the presentation of surface polysaccharides, Front. Microbiol., 7, 1919, 10.3389/fmicb.2016.01919 · DOI
- Stankeviciute, 2019, Caulobacter crescentus adapts to phosphate starvation by synthesizing anionic glycoglycerolipids and a novel glycosphingolipid, mBio, 10, 10.1128/mBio.00107-19 · DOI
- Ahrendt, 2015, Neutral and phospholipids of the Myxococcus xanthus lipodome during fruiting body formation and germination, Appl. Environ. Microbiol., 81, 6538, 10.1128/AEM.01537-15 · DOI
- Olea-Ozuna, 2024, Genes required for phosphosphingolipid formation in Caulobacter crescentus contribute to bacterial virulence, Plos. Pathog., 20, 10.1371/journal.ppat.1012401 · DOI
- Dhakephalkar, 2023, Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus, J. Biol. Chem., 299, 10.1016/j.jbc.2023.104894 · DOI
- Fong, 2006, Crystal structure of CTP:glycerol-3-phosphate cytidylyltransferase from Staphylococcus aureus: examination of structural basis for kinetic mechanism, Biochim. Biophys. Acta, 1764, 63, 10.1016/j.bbapap.2005.10.015 · DOI
- Schertzer, 2003, Purified, recombinant TagF protein from Bacillus subtilis 168 catalyzes the polymerization of glycerol phosphate onto a membrane acceptor in vitro, J. Biol. Chem., 278, 18002, 10.1074/jbc.M300706200 · DOI
- Kurnasov, 2013, Structure of the inositol-1-phosphate cytidylyltransferase from Thermotoga maritima, Acta Crystallogr. D Biol. Crystallogr., 69, 1808, 10.1107/S0907444913015278 · DOI
- Campbell, 2001, The CTP:phosphocholine cytidylyltransferase encoded by the licC gene of Streptococcus pneumoniae: cloning, expression, purification, and characterization, Biochim. Biophys. Acta, 1534, 85, 10.1016/S1388-1981(01)00174-3 · DOI
- Taylor, 2019, Manganese-induced substrate promiscuity in the reaction catalyzed by phosphoglutamine cytidylyltransferase from Campylobacter jejuni, Biochemistry, 58, 2144, 10.1021/acs.biochem.9b00189 · DOI
- Kanzaki, 2017, Phosphoglycerol dihydroceramide, a distinctive ceramide produced by Porphyromonas gingivalis, promotes RANKL-induced osteoclastogenesis by acting on non-muscle myosin II-A (Myh9), an osteoclast cell fusion regulatory factor, Biochim. Biophys. Acta Mol. Cell. Biol. Lipids., 1862, 452, 10.1016/j.bbalip.2017.01.008 · DOI
- Wang, 2023, The conserved domain database in 2023, Nucleic. Acids. Res., 51, D384, 10.1093/nar/gkac1096 · DOI · Paper page
- D'Elia, 2006, Lesions in teichoic acid biosynthesis in Staphylococcus aureus lead to a lethal gain of function in the otherwise dispensable pathway, J. Bacteriol., 188, 4183, 10.1128/JB.00197-06 · DOI
- Park, 1993, Expression, purification, and characterization of CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis, J. Biol. Chem., 268, 16648, 10.1016/S0021-9258(19)85467-4 · DOI
- Bennett, 2009, Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli, Nat. Chem. Biol., 5, 593, 10.1038/nchembio.186 · DOI · Paper page
- Poindexter, 1964, Biological properties and classification of the Caulobacter group, Bacteriol. Rev., 28, 231, 10.1128/br.28.3.231-295.1964 · DOI
- Thanbichler, 2007, A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus, Nucleic. Acids. Res., 35, 10.1093/nar/gkm818 · DOI
- Guan, 2014, Clostridium difficile contains plasmalogen species of phospholipids and glycolipids, Biochim. Biophys. Acta., 1842, 1353, 10.1016/j.bbalip.2014.06.011 · DOI
- van Kempen, 2024, Fast and accurate protein structure search with Foldseek, Nat. Biotechnol., 42, 243, 10.1038/s41587-023-01773-0 · DOI · Paper page
Metadata
- Authors
- Dhakephalkar, T., Guan, Z., & Klein, E. A.
- Affiliations
- Rutgers, The State University of New Jersey (US)
- Duke University (US)
- Corresponding author
- Klein, Eric A.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2025-07
- Volume
- 301
- Issue
- 7
- Pages
- 110386
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC12275187
- OpenAlex
- W4411329567
- Cited by
- 3
- References
- 2
- Citations by year
- 2026: 3
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Institutes of Health National Institute of Allergy and Infectious Diseases (AI178692, AI148366)
- National Institutes of Health
- Rutgers Cancer Institute of New Jersey
- National Science Foundation (MCB-2224195)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Sphingolipid Metabolism and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- nucleotidyltransferase, Caulobacter crescentus, enzyme kinetics, magnesium-dependent enzyme activity
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