Reconstruction of Metabolic Pathways for the Cattle Genome

Overview

Journal BMC Syst Biol

Publisher Biomed Central

Specialty Biology

Date 2009 Mar 17

PMID 19284618

Citations 19

Authors

Seongwon Seo

Harris A Lewin

Affiliations

Soon will be listed here.

Abstract

Background: Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement.

Results: An amalgamated cattle genome database was created using the NCBI and Ensembl cattle genome databases (based on build 3.1) as data sources. PathwayTools was used to create a cattle-specific pathway genome database, which was followed by comprehensive manual curation for the reconstruction of metabolic pathways. The curated database, CattleCyc 1.0, consists of 217 metabolic pathways. A total of 64 mammalian-specific metabolic pathways were modified from the reference pathways in MetaCyc, and two pathways previously identified but missing from MetaCyc were added. Comparative analysis of metabolic pathways revealed the absence of mammalian genes for 22 metabolic enzymes whose activity was reported in the literature. We also identified six human metabolic protein-coding genes for which the cattle ortholog is missing from the sequence assembly.

Conclusion: CattleCyc is a powerful tool for understanding the biology of ruminants and other cetartiodactyl species. In addition, the approach used to develop CattleCyc provides a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. It is clear that metabolic pathway analysis strongly reflects the quality of the underlying genome annotations. Thus, having well-annotated genomes from many mammalian species hosted in BioCyc will facilitate the comparative analysis of metabolic pathways among different species and a systems approach to comparative physiology.

Citing Articles

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis.

Marin de Evsikova C, Raplee I, Lockhart J, Jaimes G, Evsikov A J Pers Med. 2019; 9(2).

PMID: 31032818 PMC: 6617151. DOI: 10.3390/jpm9020021.

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.

Foerster H, Bombarely A, Battey J, Sierro N, Ivanov N, Mueller L Database (Oxford). 2018; 2018.

PMID: 29762652 PMC: 5946812. DOI: 10.1093/database/bay035.

Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome.

Kim W, Park H, Seo S PLoS One. 2016; 11(3):e0150974.

PMID: 26992093 PMC: 4798299. DOI: 10.1371/journal.pone.0150974.

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA.

Schultz A, Qutub A PLoS Comput Biol. 2016; 12(3):e1004808.

PMID: 26942765 PMC: 4778931. DOI: 10.1371/journal.pcbi.1004808.

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches.

Srivastava A, Somvanshi P, Mishra B Syst Synth Biol. 2014; 7(1-2):7-22.

PMID: 24432138 PMC: 3641283. DOI: 10.1007/s11693-012-9102-2.

References

Sharan R, Ulitsky I, Shamir R . Network-based prediction of protein function. Mol Syst Biol. 2007; 3:88. PMC: 1847944. DOI: 10.1038/msb4100129. View

Kobes R, Dekker E . Variant properties of bovine liver 2-keto-4-hydroxyglutarate aldolase; its -decarboxylase activity, lack of substrate stereospecificity, and structural requirements for binding substrate analogs. Biochim Biophys Acta. 1971; 250(1):238-50. DOI: 10.1016/0005-2744(71)90139-2. View

Meister A, Radhakrishnan A, Buckley S . Enzymatic synthesis of L-pipecolic acid and L-proline. J Biol Chem. 1957; 229(2):789-800. View

Hayashi S, Watanabe M, Kimura A . Enzymatic determination of free glucuronic acid with glucuronolactone reductase. I. Isolation and purification of glucuronolactone reductase from rat kidney. J Biochem. 1984; 95(1):223-32. DOI: 10.1093/oxfordjournals.jbchem.a134588. View

Puhakainen E, Hanninen O . Pyrophosphatase and glucuronosyltransferase in microsomal UDPglucuronic-acid metabolism in the rat liver. Eur J Biochem. 1976; 61(1):165-9. DOI: 10.1111/j.1432-1033.1976.tb10007.x. View

Petrack B, Greengard P, CRASTON A, SHEPPY F . NICOTINAMIDE DEAMIDASE FROM MAMMALIAN LIVER. J Biol Chem. 1965; 240:1725-30. View

Anderson M, Scholtz J, Schuster S . Rat liver 4-hydroxy-2-ketoglutarate aldolase: purification and kinetic characterization. Arch Biochem Biophys. 1985; 236(1):82-97. DOI: 10.1016/0003-9861(85)90608-3. View

Aigner A, Jager M, Weber P, Wolf S . A nonradioactive assay for microsomal cysteine-S-conjugate N-acetyltransferase activity by high-pressure liquid chromatography. Anal Biochem. 1994; 223(2):227-31. DOI: 10.1006/abio.1994.1578. View

Romero P, Wagg J, Green M, Kaiser D, Krummenacker M, Karp P . Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2005; 6(1):R2. PMC: 549063. DOI: 10.1186/gb-2004-6-1-r2. View

10.

Piller F, Eckhardt A, Hill R . The preparation of UDP-N-acetylgalactosamine from UDP-N-acetylglucosamine employing UDP-N-acetylglucosamine-4-epimerase. Anal Biochem. 1982; 127(1):171-7. DOI: 10.1016/0003-2697(82)90161-0. View

11.

Winkelman J, Lehninger A . Aldono- and uronolactonases of animal tissues. J Biol Chem. 1958; 233(4):794-9. View

12.

Duarte N, Becker S, Jamshidi N, Thiele I, Mo M, Vo T . Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A. 2007; 104(6):1777-82. PMC: 1794290. DOI: 10.1073/pnas.0610772104. View

13.

Urbanczyk-Wochniak E, Sumner L . MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 2007; 23(11):1418-23. DOI: 10.1093/bioinformatics/btm040. View

14.

Glowacka D, Zwierz K, Gindzienski A, GALASINSKI W . The metabolism of UDP-n-acetyl-D-glucosamine in the human gastric mucous membrane. II. The activity of UDP-N-acetylglucosamine 4-epimerase (E.C.5.1.3.7.). Biochem Med. 1978; 19(2):202-10. DOI: 10.1016/0006-2944(78)90021-2. View

15.

Wheeler D, Barrett T, Benson D, Bryant S, Canese K, Chetvernin V . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2006; 35(Database issue):D5-12. PMC: 1781113. DOI: 10.1093/nar/gkl1031. View

16.

Gillam S, Watson J, Chaykin S . Nicotinamide deamidase from rabbit liver. 3. Inhibition and sedimentation studies. Arch Biochem Biophys. 1973; 157(1):268-84. DOI: 10.1016/0003-9861(73)90413-x. View

17.

Bulfield G . Genetic variation in the activity of the histidine catabolic enzymes between inbred strains of mice: a structural locus for a cytosol histidine aminotransferase isozyme (Hat-1). Biochem Genet. 1978; 16(11-12):1233-41. DOI: 10.1007/BF00484543. View

18.

Smith T, Mitoma C . Partial purification and some properties of 4-ketoproline reductase. J Biol Chem. 1962; 237:1177-80. View

19.

Pruitt K, Tatusova T, Maglott D . NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2006; 35(Database issue):D61-5. PMC: 1716718. DOI: 10.1093/nar/gkl842. View

20.

Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D . BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res. 2007; 35(Database issue):D511-4. PMC: 1899097. DOI: 10.1093/nar/gkl972. View