RefGenome Electronic Jamboree 2009-02 CPS1

From GONUTS

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Orthoset

Ortholog set at PPOD

EcoliWiki has included the carA gene product annotations. The CarA gene product is a subunit of the E. coli carbamoyl phosphate synthetase, but was not included in the ortholog set.

Participants

CPS1

Notes

New terms requested;
carbomyl phosphate biosynthetic process GO:0070409

There are 3 carbamoyl phosphate synthetases - CPSI, II, & III. Prokaryotes have only 1 type, usually type II. CPSII can utilize glutamine as the nitrogen donor.^[44] CPSI is the only carbamoyl phosphate synthetase that cannot use glutamine. ^[44]

Minutes

CAD activity is separate for genes that have both CPS and CAD. CAD annotations on a separate page RefGenome_Electronic_Jamboree_2009-02_CAD

CPS1

• Issue with Process annotation:

MGI (Harold): CPS1 is involved in the urea cycle from textbooks, but there is no mouse paper directly testing that. In one paper they assayed one step, inferred by testing two steps down, but only possible if there is a urea cycle. Harold extended it to process 'urea cycle' by IC based on the function annotation (carbamoyl-phosphate synthase (ammonia) activity, GO:0004087). Would not have done it if they only had assayed synthesis of.. They knock out the gene and assay for carbamoyl Particulary step is in urea cycle Also tested ammonia, indicative of urea cycle (but no term for it)

• Poll: would you have annotated to urea cycle using IC from evidence from the molecular function carbamoyl-phosphate synthase (ammonia) activity ?
  • 67% yes, 33% Unsure
  • Karen: For IC, it's not experimental, and so we don't need to discuss, as IC is inferred by knowledge of curator. Question is, is the assay good enough for the experimental function to infer the process
  • Note: (Suzi) Anything that's IC will not be used for inference in the Ref Genome.
  • Pascale: How does a Process annotation ever get an IDA? (or an experimental evidence).

• Rama SGD: CPS1 process: Should this be annotated to 'Glutamine metabolic biosynthesis'?

general agreement: If the function term says it's hydrolyzing glutamine it is metabolizing glutamine and the process can be annotated! This is a general principle that applies to all substrates in reactions.

• How does one distinguish between salvage and de novo' pyrimidine base biosynthetic process:

Harold: from the ground up, if you know it's synthesized from scratch. This reaction is only in de novo. Pyrimidine is synthesized from scratch, by definition. (Pascale: Is this then an IC?)

• Rama: carbamoyl-phosphate synthase complex. As yeast has the complex, it's ok to annotate, even though the paper does not call it 'carbamoyl-phosphate synthase complex',

since the description of the complex in that older paper fits the definition of the term.

References

See Help:References for how to manage references in GONUTS.

1. ↑ ^{1.0 1.1} Schofield JP et al. (1999) Mice deficient in the urea-cycle enzyme, carbamoyl phosphate synthetase I, die during the early neonatal period from hyperammonemia. Hepatology 29: 181-5 PubMed GONUTS page
2. ↑ Bhat NK & Avadhani NG (1984) The transport and processing of carbamyl phosphate synthetase-I in mouse hepatic mitochondria. Biochem Biophys Res Commun 118: 514-22 PubMed GONUTS page
3. ↑ ^{3.0 3.1} Corvi MM et al. (2001) Regulation of mitochondrial carbamoyl-phosphate synthetase 1 activity by active site fatty acylation. J Biol Chem 276: 45704-12 PubMed GONUTS page
4. ↑ ^{4.0 4.1} Kim HS et al. (2007) Rat liver 10-formyltetrahydrofolate dehydrogenase, carbamoyl phosphate synthetase 1 and betaine homocysteine S-methytransferase were co-purified on Kunitz-type soybean trypsin inhibitor-coupled sepharose CL-4B. J Biochem Mol Biol 40: 604-9 PubMed GONUTS page
5. ↑ Goss SJ (1984) Arginine synthesis by hepatomas in vitro. II. Isolation and characterization of Morris hepatoma variants unable to convert ornithine to arginine, and modulation of urea-cycle enzymes by dexamethasone and cyclic-AMP. J Cell Sci 68: 305-19 PubMed GONUTS page
6. ↑ ^{6.0 6.1} Tomomura M et al. (1996) Long-chain fatty acids suppress the induction of urea cycle enzyme genes by glucocorticoid action. FEBS Lett 399: 310-2 PubMed GONUTS page
7. ↑ Ryall JC et al. (1986) Rat liver and intestinal mucosa differ in the developmental pattern and hormonal regulation of carbamoyl-phosphate synthetase I and ornithine carbamoyl transferase gene expression. Eur J Biochem 156: 453-8 PubMed GONUTS page
8. ↑ Gelosa P et al. (2009) S 35171 exerts protective effects in spontaneously hypertensive stroke-prone rats by preserving mitochondrial function. Eur J Pharmacol 604: 117-24 PubMed GONUTS page
9. ↑ Nielsen SS et al. (2007) Cirrhosis and endotoxin decrease urea synthesis in rats. Hepatol Res 37: 540-7 PubMed GONUTS page
10. ↑ ^{10.0 10.1 10.2} Finckh U et al. (1998) Prenatal diagnosis of carbamoyl phosphate synthetase I deficiency by identification of a missense mutation in CPS1. Hum Mutat 12: 206-11 PubMed GONUTS page
11. ↑ Moorman AF et al. (1990) Diet- and hormone-induced reversal of the carbamoylphosphate synthetase mRNA gradient in the rat liver lobulus. FEBS Lett 276: 9-13 PubMed GONUTS page
12. ↑ ^{12.0 12.1} Summar ML et al. (2004) Relationship between carbamoyl-phosphate synthetase genotype and systemic vascular function. Hypertension 43: 186-91 PubMed GONUTS page
13. ↑ Brands R & Hoogenraad N (1986) Import of carbamylphosphate synthetase and ornithine transcarbamylase into mitochondria of rat liver: detection of aggregates of enzyme in cytoplasm and mitochondria using immunoelectron microscopy with the protein A-gold method. Aust J Exp Biol Med Sci 64 ( Pt 2): 165-73 PubMed GONUTS page
14. ↑ ^{14.0 14.1} Powers-Lee SG et al. (1987) The interaction of rat liver carbamoyl phosphate synthetase and ornithine transcarbamoylase with inner mitochondrial membranes. J Biol Chem 262: 15683-8 PubMed GONUTS page
15. ↑ Hoshide R et al. (1993) Carbamyl phosphate synthetase I deficiency. One base substitution in an exon of the CPS I gene causes a 9-basepair deletion due to aberrant splicing. J Clin Invest 91: 1884-7 PubMed GONUTS page
16. ↑ Bogenhagen DF et al. (2008) The layered structure of human mitochondrial DNA nucleoids. J Biol Chem 283: 3665-75 PubMed GONUTS page
17. ↑ Struck J et al. (2005) Release of the mitochondrial enzyme carbamoyl phosphate synthase under septic conditions. Shock 23: 533-8 PubMed GONUTS page
18. ↑ Peltier JB et al. (2006) The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol Cell Proteomics 5: 114-33 PubMed GONUTS page
19. ↑ Kleffmann T et al. (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14: 354-62 PubMed GONUTS page
20. ↑ Mitra SK et al. (2007) Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques. J Proteome Res 6: 1933-50 PubMed GONUTS page
21. ↑ ^{21.0 21.1} Hoogenraad NJ et al. (1980) Detection of carbamyl phosphate synthetase 1 deficiency using duodenal biopsy samples. Arch Dis Child 55: 292-5 PubMed GONUTS page
22. ↑ ^{22.0 22.1} Piérard A & Wiame JM (1964) Regulation and mutation affecting a glutamine dependent formation of carbamyl phosphate in Escherichia coli. Biochem Biophys Res Commun 15: 76-81 PubMed GONUTS page
23. ↑ ^{23.0 23.1} Mullins LS et al. (1991) Alterations in the energetics of the carbamoyl phosphate synthetase reaction by site-directed modification of the essential sulfhydryl group. J Biol Chem 266: 8236-40 PubMed GONUTS page
24. ↑ ^{24.0 24.1} Guillou F et al. (1989) Escherichia coli carbamoyl-phosphate synthetase: domains of glutaminase and synthetase subunit interaction. Proc Natl Acad Sci U S A 86: 8304-8 PubMed GONUTS page
25. ↑ ^{25.0 25.1} Kothe M & Powers-Lee SG (2004) Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase. Protein Sci 13: 466-75 PubMed GONUTS page
26. ↑ Serre V et al. (1999) Half of Saccharomyces cerevisiae carbamoyl phosphate synthetase produces and channels carbamoyl phosphate to the fused aspartate transcarbamoylase domain. J Biol Chem 274: 23794-801 PubMed GONUTS page
27. ↑ ^{27.0 27.1} Jund R & Lacroute F (1972) Regulation of orotidylic acid pyrophosphorylase in Saccharomyces cerevisiae. J Bacteriol 109: 196-202 PubMed GONUTS page
28. ↑ Trotta PP et al. (1974) Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits. J Biol Chem 249: 492-9 PubMed GONUTS page
29. ↑ Lue PF & Kaplan JG (1969) The aspartate transcarbamylase and carbamoyl phosphate synthetase of yeast: a multi-functional enzyme complex. Biochem Biophys Res Commun 34: 426-33 PubMed GONUTS page
30. ↑ Rubino SD et al. (1987) In vivo synthesis of carbamyl phosphate from NH3 by the large subunit of Escherichia coli carbamyl phosphate synthetase. J Biol Chem 262: 4382-6 PubMed GONUTS page
31. ↑ Raushel FM et al. (1979) Paramagnetic probes for carbamoyl-phosphate synthetase: metal ion binding studies and preparation of nitroxide spin-labeled derivatives. Biochemistry 18: 5562-6 PubMed GONUTS page
32. ↑ Lacroute F (1968) Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J Bacteriol 95: 824-32 PubMed GONUTS page
33. ↑ ^{33.0 33.1 33.2} Guillou F et al. (1992) Mutational analysis of carbamyl phosphate synthetase. Substitution of Glu841 leads to loss of functional coupling between the two catalytic domains of the synthetase subunit. Biochemistry 31: 1656-64 PubMed GONUTS page
34. ↑ Denis-Duphil M & Kaplan JG (1976) Fine structure of the URA2 locus in Saccharomyces cerevisiae. II. Meiotic and mitotic mapping studies. Mol Gen Genet 145: 259-71 PubMed GONUTS page
35. ↑ Benoist P et al. (2000) The yeast Ura2 protein that catalyses the first two steps of pyrimidines biosynthesis accumulates not in the nucleus but in the cytoplasm, as shown by immunocytochemistry and Ura2-green fluorescent protein mapping. Yeast 16: 1299-312 PubMed GONUTS page
36. ↑ Vorisek J et al. (2002) Enzymatic activities of Ura2 and Ura1 proteins (aspartate carbamoyltransferase and dihydro-orotate dehydrogenase) are present in both isolated membranes and cytoplasm of Saccharomyces cerevisiae. Yeast 19: 449-57 PubMed GONUTS page
37. ↑ Fresquet V et al. (2000) Site-directed mutagenesis of the regulatory domain of Escherichia coli carbamoyl phosphate synthetase identifies crucial residues for allosteric regulation and for transduction of the regulatory signals. J Mol Biol 299: 979-91 PubMed GONUTS page
38. ↑ Lusty CJ et al. (1983) Yeast carbamyl phosphate synthetase. Structure of the yeast gene and homology to Escherichia coli carbamyl phosphate synthetase. J Biol Chem 258: 14466-77 PubMed GONUTS page
39. ↑ ^{39.0 39.1} Mareya SM & Raushel FM (1995) Mapping the structural domains of E. coli carbamoyl phosphate synthetase using limited proteolysis. Bioorg Med Chem 3: 525-32 PubMed GONUTS page
40. ↑ Lim AL & Powers-Lee SG (1996) Requirement for the carboxyl-terminal domain of Saccharomyces cerevisiae carbamoyl-phosphate synthetase. J Biol Chem 271: 11400-9 PubMed GONUTS page
41. ↑ Piérard A & Schröter B (1978) Structure-function relationships in the arginine pathway carbamoylphosphate synthase of Saccharomyces cerevisiae. J Bacteriol 134: 167-76 PubMed GONUTS page
42. ↑ Thoden JB et al. (2004) Long-range allosteric transitions in carbamoyl phosphate synthetase. Protein Sci 13: 2398-405 PubMed GONUTS page
43. ↑ Delannay S et al. (1999) Serine 948 and threonine 1042 are crucial residues for allosteric regulation of Escherichia coli carbamoylphosphate synthetase and illustrate coupling effects of activation and inhibition pathways. J Mol Biol 286: 1217-28 PubMed GONUTS page
44. ↑ ^{44.0 44.1} Hong J et al. (1994) Carbamyl phosphate synthetase III, an evolutionary intermediate in the transition between glutamine-dependent and ammonia-dependent carbamyl phosphate synthetases. J Mol Biol 243: 131-40 PubMed GONUTS page