CTP synthase 1

CTPS1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2VO1
Identifiers
Aliases	CTPS1, CTPS, IMD24, CTP synthase 1, GATD5
External IDs	OMIM: 123860; MGI: 1858304; HomoloGene: 20446; GeneCards: CTPS1; OMA:CTPS1 - orthologs
Gene location (Human) Chr. Chromosome 1 (human)[1] Band 1p34.2 Start 40,979,335 bp[1] End 41,012,565 bp[1]
Gene location (Mouse) Chr. Chromosome 4 (mouse)[2] Band 4 D2.1|4 56.52 cM Start 120,397,065 bp[2] End 120,427,473 bp[2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in parotid gland ascending aorta left uterine tube right coronary artery left coronary artery gonad body of uterus popliteal artery tibial arteries muscle layer of sigmoid colon Top expressed in hair follicle primitive streak primary oocyte superior cervical ganglion mandibular prominence somite maxillary prominence endothelial cell of lymphatic vessel endocardial cushion zygote More reference expression data BioGPS n/a
Gene ontology Molecular function nucleotide binding ligase activity ATP binding CTP synthase activity identical protein binding Cellular component cytosol membrane cytoplasm cytoophidium Biological process T cell proliferation B cell proliferation nucleobase-containing small molecule interconversion glutamine metabolic process nucleobase-containing compound metabolic process 'de novo' CTP biosynthetic process pyrimidine nucleotide biosynthetic process immune system process CTP biosynthetic process pyrimidine nucleobase biosynthetic process Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 1503 51797 Ensembl ENSG00000171793 ENSMUSG00000028633 UniProt P17812 P70698 RefSeq (mRNA) NM_001301237 NM_001905 NM_016748 NM_001355491 RefSeq (protein) NP_001288166 NP_001896 NP_058028 NP_001342420 Location (UCSC) Chr 1: 40.98 – 41.01 Mb Chr 4: 120.4 – 120.43 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

CTP synthase 1 is an enzyme that is encoded by the CTPS1 gene in humans.[5][6] CTP synthase 1 is an enzyme in the de novo pyrimidine synthesis pathway that catalyses the conversion of uridine triphosphate (UTP) to cytidine triphosphate (CTP). CTP is a key building block for the production of DNA, RNA and some phospholipids.

Structure and function

CTPS1 is an asymmetrical homotetramer with only three of its four monomers contributing to the catalytic domain. The substrates required for enzymatic activity are adenosine triphosphate (ATP), UTP and the amino acid glutamine. The ATP and UTP binding domains are located at the tetramer interface, whereas the glutamine binding domain is located away from the tetramer interface.[7]

Glutamine is hydrolysed by the glutamine amidotransferase domain on the outside of the CTPS1 enzyme. The ammonia produced is channelled through to the synthase domain in the interior of the enzyme, to the tetrameric interface. ATP-dependent phosphorylation of UTP produces 4-phosphoryl UTP, which reacts with the ammonia to produce CTP. The reaction can also take place using ammonia in solution in place of the glutamine-derived ammonia. Guanosine triphosphate (GTP) is an allosteric activator of enzyme activity which stimulates the hydrolysis of glutamine. CTP is an allosteric inhibitor of enzyme activity; the CTP binding site overlaps with and impedes the UTP binding site. Thus, CTPS1 enzymatic activity is sensitive to the levels of all four essential ribonucleotides.[8][9]

De novo pyrimidine synthesis pathway

The conversion of UTP to CTP is the final and rate limiting step in the de novo pyrimidine synthesis pathway. This step is unusual as it is catalysed by two homologous enzymes, CTPS1 and CTPS2, which share 74% homology at the protein level in humans. Human genetics suggest different cellular dependencies on CTPS1 and CTPS2 activity (see below).

Pyrimidines can also be generated by a salvage pathway that recycles DNA. Whilst the salvage pathway is sufficient for pyrimidine production in non-dividing cells, de novo pyrimidine synthesis is required for dividing cells.

Clinical significance

Inherited mutations

Inherited CTPS1 deficiency is associated with a severe immunodeficiency syndrome characterised by life-threatening varicella zoster virus (VZV) and Epstein–Barr virus (EBV) infection in the first decade of life. Several cases of Epstein–Barr virus–associated lymphoproliferative disease have also been observed, including in the central nervous system. Importantly, no phenotype has been observed outside of the blood system, suggesting that CTPS2 is able to compensate for the CTPS1 loss in other tissues.[10][11][12]

All individuals described to date are homozygous for the same splicing mutation in CTPS1, which results in skipping of exon 18 resulting in a severely hypomorphic enzyme. All reported families have ancestry in the North West of England, indicating a founder effect for the causative mutation.

The blood systems of individuals with inherited CTPS1 deficiency are characterised by the following:

1. Normal numbers of T cells, normal T cell subsets
2. Near absence of invariant NKT cells and mucosal associated invariant T cell
3. Normal numbers of total B cells, reduced proportion of memory B cells
4. Reduced numbers of NK cells
5. Severely impaired T cell proliferation response and reduced IL-2 secretion following activation
6. Impaired B cell proliferation response following activation
7. Elevated IgG with selective deficiencies of specific antibodies
8. Normal numbers and subset distribution of myeloid cells and dendritic cells

Inherited CTPS1 deficiency can be cured by allogeneic bone marrow transplantation.[13][14]

Cancer

Increased expression of CTPS1 has been reported to play a role in several different cancer types.

High expression of CTPS1 has been reported to impart a worse prognosis in myeloma, pancreatic cancer and breast cancer.[15][16][17][18][19][20]

miR-125b-5p was identified as a tumour suppressor which is down regulated in squamous cell lung cancer; CTPS1 is a potential target of miR-125b-5p, and loss of expression of this miR is predicted to result in increased expression of CTPS1.[21]

CTPS1 knock down by shRNA inhibited tumour cell growth in a breast cancer model.[22] CTPS1 knock down by CRISPR showed synergy with inhibition of ATR in a model of MYC-driven cancer.[23]

CTPS1 as a therapeutic target

Cancer therapy

The high proliferation rates and metabolic activity of cancer cells are likely to result in a critical dependency on the de novo pyrimidine synthesis pathway. This dependency is exploited therapeutically by several chemotherapy drugs that block de novo pyrimidine synthesis, including the nucleotide analogues cytosine arabinoside (ara-C) and gemcitabine.[24]

Cyclopentenyl cytosine (CPEC) is an inhibitor of both CTPS1 and CTPS2, with activity thought to be mediated by its 5'-triphosphate metabolite CPEC-TP. In phase 1 clinical studies, CPEC administration resulted in unpredictable and refractory hypotension, including fatal events, resulting in discontinuation of clinical development.[25][26]

Recently, selective small molecule inhibitors have been described with a high degree of selectivity for CTPS1 over CTPS2. The binding mode and mechanism of CTPS1 selectivity has been resolved by cryo-EM which showed docking of the compounds to the CTP binding site of the enzyme.[27] A lead clinical candidate from this chemical series has shown efficacy in preclinical models of B and T cell neoplasia.[28]

A first in human clinical trial of a selective CTPS1 inhibitor will open to recruitment for patients with relapsed/refractory B cell lymphoma or T cell lymphoma late summer 2022 (NCT05463263).[29]

Anti-viral therapy

Nucleoside analogues have a long history in the treatment of viral infection.[30][31]

Specific inhibition of CTP synthase has been identified as a target for anti-viral therapies.[32][33]

Epstein–Barr virus (EBV) upregulates the expression of both CTPS1 and CTPS2 in infected B cells, with the expression of CTPS1 increasing earlier than CTPS2. The EBV protein ENBA-LP binds to the CTPS1 promoter, along with MYC and NFκB, to enhance expression of CTPS1.[34]

SARS-CoV-2, the virus that causes COVID-19, uses CTPS1 from infected cells to drive its proliferation; inhibition of CTPS1 has been highlighted as a potential anti-viral therapy.[35]

References

1. GRCh38: Ensembl release 89: ENSG00000171793 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000028633 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. Yamauchi M, Yamauchi N, Phear G, Spurr NK, Martinsson T, Weith A, et al. (December 1991). "Genomic organization and chromosomal localization of the human CTP synthetase gene (CTPS)". Genomics. 11 (4): 1088–1096. doi:10.1016/0888-7543(91)90036-E. PMID 1783378.
6. "Entrez Gene: CTP synthase".
7. Kursula P, Flodin S, Ehn M, Hammarström M, Schüler H, Nordlund P, et al. (July 2006). "Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62 (Pt 7): 613–617. doi:10.1107/S1744309106018136. PMC 2242944. PMID 16820675.
8. Lauritsen I, Willemoës M, Jensen KF, Johansson E, Harris P (February 2011). "Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67 (Pt 2): 201–208. doi:10.1107/S1744309110052334. PMC 3034608. PMID 21301086.
9. Lynch EM, Kollman JM (January 2020). "Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments". Nature Structural & Molecular Biology. 27 (1): 42–48. doi:10.1038/s41594-019-0352-5. PMC 6954954. PMID 31873303.
10. Martin E, Palmic N, Sanquer S, Lenoir C, Hauck F, Mongellaz C, et al. (June 2014). "CTP synthase 1 deficiency in humans reveals its central role in lymphocyte proliferation". Nature. 510 (7504): 288–292. Bibcode:2014Natur.510..288M. doi:10.1038/nature13386. PMC 6485470. PMID 24870241.
11. Martin E, Minet N, Boschat AC, Sanquer S, Sobrino S, Lenoir C, et al. (March 2020). "Impaired lymphocyte function and differentiation in CTPS1-deficient patients result from a hypomorphic homozygous mutation". JCI Insight. 5 (5): 133880. doi:10.1172/jci.insight.133880. PMC 7141395. PMID 32161190.
12. Nademi Z, Wynn RF, Slatter M, Hughes SM, Bonney D, Qasim W, et al. (January 2019). "Hematopoietic stem cell transplantation for cytidine triphosphate synthase 1 (CTPS1) deficiency" (PDF). Bone Marrow Transplantation. 54 (1): 130–133. doi:10.1038/s41409-018-0246-x. PMID 29884857. S2CID 46999914.
13. Nademi Z, Wynn RF, Slatter M, Hughes SM, Bonney D, Qasim W, et al. (January 2019). "Hematopoietic stem cell transplantation for cytidine triphosphate synthase 1 (CTPS1) deficiency" (PDF). Bone Marrow Transplantation. 54 (1): 130–133. doi:10.1038/s41409-018-0246-x. PMID 29884857. S2CID 46999914.
14. Kucuk ZY, Zhang K, Filipovich L, Bleesing JJ (November 2016). "CTP Synthase 1 Deficiency in Successfully Transplanted Siblings with Combined Immune Deficiency and Chronic Active EBV Infection". Journal of Clinical Immunology. 36 (8): 750–753. doi:10.1007/s10875-016-0332-z. PMID 27638562. S2CID 44209317.
15. Huang HY, Wang Y, Wang WD, Wei XL, Gale RP, Li JY, et al. (November 2021). "A prognostic survival model based on metabolism-related gene expression in plasma cell myeloma". Leukemia. 35 (11): 3212–3222. doi:10.1038/s41375-021-01206-4. PMID 33686197. S2CID 232137095.
16. Shukla SK, Purohit V, Mehla K, Gunda V, Chaika NV, Vernucci E, et al. (July 2017). "MUC1 and HIF-1alpha Signaling Crosstalk Induces Anabolic Glucose Metabolism to Impart Gemcitabine Resistance to Pancreatic Cancer". Cancer Cell. 32 (1): 71–87.e7. doi:10.1016/j.ccell.2017.06.004. PMC 5533091. PMID 28697344.
17. Conte F, Sibilio P, Grimaldi AM, Salvatore M, Paci P, Incoronato M (2022). "In silico recognition of a prognostic signature in basal-like breast cancer patients". PLOS ONE. 17 (2): e0264024. Bibcode:2022PLoSO..1764024C. doi:10.1371/journal.pone.0264024. PMC 8846521. PMID 35167614.
18. Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, et al. (January 2022). "CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1". Journal of Translational Medicine. 20 (1): 17. doi:10.1186/s12967-021-03206-5. PMC 8734240. PMID 34991621.
19. Cao W, Jiang Y, Ji X, Guan X, Lin Q, Ma L (February 2021). "Identification of novel prognostic genes of triple-negative breast cancer using meta-analysis and weighted gene co-expressed network analysis". Annals of Translational Medicine. 9 (3): 205. doi:10.21037/atm-20-5989. PMC 7940929. PMID 33708832.
20. Huang SP, Jiang YF, Yang LJ, Yang J, Liang MT, Zhou HF, et al. (March 2022). "Downregulation of miR-125b-5p and Its Prospective Molecular Mechanism in Lung Squamous Cell Carcinoma". Cancer Biotherapy & Radiopharmaceuticals. 37 (2): 125–140. doi:10.1089/cbr.2020.3657. PMID 32614608. S2CID 220327036.
21. Huang SP, Jiang YF, Yang LJ, Yang J, Liang MT, Zhou HF, et al. (March 2022). "Downregulation of miR-125b-5p and Its Prospective Molecular Mechanism in Lung Squamous Cell Carcinoma". Cancer Biotherapy & Radiopharmaceuticals. 37 (2): 125–140. doi:10.1089/cbr.2020.3657. PMID 32614608. S2CID 220327036.
22. Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, et al. (January 2022). "CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1". Journal of Translational Medicine. 20 (1): 17. doi:10.1186/s12967-021-03206-5. PMC 8734240. PMID 34991621.
23. Sun Z, Zhang Z, Wang QQ, Liu JL (March 2022). "Combined Inactivation of CTPS1 and ATR Is Synthetically Lethal to MYC-Overexpressing Cancer Cells". Cancer Research. 82 (6): 1013–1024. doi:10.1158/0008-5472.CAN-21-1707. PMC 9359733. PMID 35022212.
24. Jordheim LP, Durantel D, Zoulim F, Dumontet C (June 2013). "Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases". Nature Reviews. Drug Discovery. 12 (6): 447–464. doi:10.1038/nrd4010. ISSN 1474-1784. PMID 23722347. S2CID 39842610.
25. Schimmel KJ, Gelderblom H, Guchelaar HJ (August 2007). "Cyclopentenyl cytosine (CPEC): an overview of its in vitro and in vivo activity". Current Cancer Drug Targets. 7 (5): 504–509. doi:10.2174/156800907781386579. PMID 17691910.
26. Politi PM, Xie F, Dahut W, Ford H, Kelley JA, Bastian A, et al. (1995). "Phase I clinical trial of continuous infusion cyclopentenyl cytosine". Cancer Chemotherapy and Pharmacology. 36 (6): 513–523. doi:10.1007/BF00685802. PMID 7554044. S2CID 799892.
27. Lynch EM, DiMattia MA, Albanese S, van Zundert GC, Hansen JM, Quispe JD, et al. (October 2021). "Structural basis for isoform-specific inhibition of human CTPS1". Proceedings of the National Academy of Sciences of the United States of America. 118 (40): e2107968118. Bibcode:2021PNAS..11807968L. doi:10.1073/pnas.2107968118. PMC 8501788. PMID 34583994.
28. Asnagli H, Minet N, Pfeiffer C, Hoeben E, Lane R, Laughton D, et al. (April 2023). "CTP Synthase 1 Is a Novel Therapeutic Target in Lymphoma". HemaSphere. 7 (4): e864. doi:10.1097/HS9.0000000000000864. PMC 10060080. PMID 37008165.
29. Clinical trial number NCT05463263 for "An Open-Label, First in Human, Phase 1/2 to Evaluate Safety, Tolerability, Pharmacokinetics, and Preliminary Efficacy of the CTPS1 Inhibitor STP938 In Adult Subjects With Relapsed/Refractory B-Cell and T-Cell Lymphomas" at ClinicalTrials.gov
30. De Clercq E (1994-07-01). "Antiviral Activity Spectrum and Target of Action of Different Classes of Nucleoside Analogues". Nucleosides and Nucleotides. 13 (6–7): 1271–1295. doi:10.1080/15257779408012151. ISSN 0732-8311.
31. Jordheim LP, Durantel D, Zoulim F, Dumontet C (June 2013). "Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases". Nature Reviews. Drug Discovery. 12 (6): 447–464. doi:10.1038/nrd4010. PMID 23722347. S2CID 39842610.
32. De Clercq E, Bernaerts R, Shealy YF, Montgomery JA (January 1990). "Broad-spectrum antiviral activity of carbodine, the carbocyclic analogue of cytidine". Biochemical Pharmacology. 39 (2): 319–325. doi:10.1016/0006-2952(90)90031-f. PMC 7111205. PMID 1689159.
33. De Clercq E, Murase J, Marquez VE (June 1991). "Broad-spectrum antiviral and cytocidal activity of cyclopentenylcytosine, a carbocyclic nucleoside targeted at CTP synthetase". Biochemical Pharmacology. 41 (12): 1821–1829. doi:10.1016/0006-2952(91)90120-t. PMC 7111160. PMID 1710119.
34. Liang JH, Wang C, Yiu SP, Zhao B, Guo R, Gewurz BE (August 2021). "Epstein-Barr Virus Induced Cytidine Metabolism Roles in Transformed B-Cell Growth and Survival". mBio. 12 (4): e0153021. doi:10.1128/mBio.01530-21. PMC 8406234. PMID 34281398.
35. Rao Y, Wang TY, Qin C, Espinosa B, Liu Q, Ekanayake A, et al. (February 2021). "Targeting CTP Synthetase 1 to Restore Interferon Induction and Impede Nucleotide Synthesis in SARS-CoV-2 Infection". bioRxiv: 2021.02.05.429959. doi:10.1101/2021.02.05.429959. PMC 7872357. PMID 33564769.

Further reading

• Thomas PE, Lamb BJ, Chu EH (April 1988). "Purification of cytidine-triphosphate synthetase from rat liver, and demonstration of monomer, dimer and tetramer". Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 953 (3): 334–344. doi:10.1016/0167-4838(88)90042-8. hdl:2027.42/27539. PMID 3355843.
• Jin J, Smith FD, Stark C, Wells CD, Fawcett JP, Kulkarni S, et al. (August 2004). "Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization". Current Biology. 14 (16): 1436–1450. Bibcode:2004CBio...14.1436J. doi:10.1016/j.cub.2004.07.051. PMID 15324660.
• Verschuur AC, Van Gennip AH, Muller EJ, Voûte PA, Vreken P, Van Kuilenburg AB (January 1999). "Cytidine triphosphate synthase activity and mRNA expression in normal human blood cells". Biological Chemistry. 380 (1): 41–46. doi:10.1515/BC.1999.005. PMID 10064135. S2CID 43352567.
• Yamauchi M, Yamauchi N, Meuth M (July 1990). "Molecular cloning of the human CTP synthetase gene by functional complementation with purified human metaphase chromosomes". The EMBO Journal. 9 (7): 2095–2099. doi:10.1002/j.1460-2075.1990.tb07377.x. PMC 551928. PMID 2113467.
• Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (October 1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–156. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
• Higgins MJ, Loiselle D, Haystead TA, Graves LM (June 2008). "Human cytidine triphosphate synthetase 1 interacting proteins". Nucleosides, Nucleotides & Nucleic Acids. 27 (6): 850–857. doi:10.1080/15257770802146502. PMID 18600551. S2CID 33594588.
• Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, et al. (November 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635–648. doi:10.1016/j.cell.2006.09.026. PMID 17081983.
• Higgins MJ, Graves PR, Graves LM (October 2007). "Regulation of human cytidine triphosphate synthetase 1 by glycogen synthase kinase 3". The Journal of Biological Chemistry. 282 (40): 29493–29503. doi:10.1074/jbc.M703948200. PMID 17681942.
• Takahashi E, Yamauchi M, Tsuji H, Hitomi A, Meuth M, Hori T (November 1991). "Chromosome mapping of the human cytidine-5'-triphosphate synthetase (CTPS) gene to band 1p34.1-p34.3 by fluorescence in situ hybridization". Human Genetics. 88 (1): 119–121. doi:10.1007/BF00204942. PMID 1959918. S2CID 21062598.
• Whelan J, Phear G, Yamauchi M, Meuth M (April 1993). "Clustered base substitutions in CTP synthetase conferring drug resistance in Chinese hamster ovary cells". Nature Genetics. 3 (4): 317–322. doi:10.1038/ng0493-317. PMID 7981751. S2CID 34685308.
• Gevaert K, Staes A, Van Damme J, De Groot S, Hugelier K, Demol H, et al. (September 2005). "Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC". Proteomics. 5 (14): 3589–3599. doi:10.1002/pmic.200401217. PMID 16097034. S2CID 895879.
• Maruyama K, Sugano S (January 1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–174. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
• Han GS, Sreenivas A, Choi MG, Chang YF, Martin SS, Baldwin EP, et al. (November 2005). "Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A". The Journal of Biological Chemistry. 280 (46): 38328–38336. doi:10.1074/jbc.M509622200. PMC 1400552. PMID 16179339.
• Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, et al. (August 2004). "Large-scale characterization of HeLa cell nuclear phosphoproteins". Proceedings of the National Academy of Sciences of the United States of America. 101 (33): 12130–12135. Bibcode:2004PNAS..10112130B. doi:10.1073/pnas.0404720101. PMC 514446. PMID 15302935.
• Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.
• Chang YF, Martin SS, Baldwin EP, Carman GM (June 2007). "Phosphorylation of human CTP synthetase 1 by protein kinase C: identification of Ser(462) and Thr(455) as major sites of phosphorylation". The Journal of Biological Chemistry. 282 (24): 17613–17622. doi:10.1074/jbc.M702799200. PMC 2081159. PMID 17463002.

External links

• Human CTPS1 genome location and CTPS1 gene details page in the UCSC Genome Browser.
• Overview of all the structural information available in the PDB for UniProt: P17812 (CTP synthase 1) at the PDBe-KB.

This article incorporates text from the United States National Library of Medicine, which is in the public domain.