Abstract
Carnitine acetyltransferase (CRAT) is an important enzyme for energy homeostasis and fat metabolism. We characterized the predicted full length cDNA sequence of the porcine CRAT gene. Its structure is very similar to that in humans with respect to the size and organization of the 14 exons. We demonstrated the existence of a porcine alternative transcript resulting from a partial intron-retention at the 5’ end of exon 2. To perform a comparison of the 5’ end variants of the mammalian CRAT gene, we analyzed the Genbank data, and here we propose a new 5’ variant for dog, rat and mouse. In contrast to other mammals where this variant encodes a shorter protein (−21 aa in human, mouse and rat, and −14 aa in dog), the pig variant encodes for a longer protein (+18 aa). In all mammalian species, variant 1 has a high probability of a preferential mitochondrial sub-cellular localization. Nevertheless, it is not evident, in particular in porcine and dog species, that the second variant is associated with a different sub-cellular specificity.
Key words: Pig, CRAT, mRNA, Alternative splicing, Mammals, Fat metabolism, Leader peptide
Full Text
The Full Text of this article is available as a PDF (571.1 KB).
Abbreviations used
- CRAT
carnitine acetyltransferase
- HSA9
human chromosome 9
- EST
expression sequence tag
- v.1
variant n°1
- aa
amino acid
- RT-PCR
reverse transcription PCR
References
- 1.Anderson R.C. Carnitine palmitoyltransferase: a viable target for the treatment of NIDDM? Curr. Pharm. Des. 1998;4:1–16. [PubMed] [Google Scholar]
- 2.Wagman A.S., Nuss J.M. Current therapies and emerging targets for the treatment of diabetes. Curr. Pharm. Des. 2001;7:417–450. doi: 10.2174/1381612013397915. [DOI] [PubMed] [Google Scholar]
- 3.Jogl G., Hsiao Y.S., Tong L. Structure and function of carnitine acyltransferases. Ann. NY Acad. Sci. 2004;1033:17–29. doi: 10.1196/annals.1320.002. [DOI] [PubMed] [Google Scholar]
- 4.Van der Leij F.R., Huijkman N.C., Boomsma C., Kuipers J.R., Bartelds B. Genomics of the human carnitine acyltransferase genes. Mol. Genet. Metab. 2000;71:139–153. doi: 10.1006/mgme.2000.3055. [DOI] [PubMed] [Google Scholar]
- 5.Zeibig J., Karlic H., Lohninger A., Damsgaard R., Smekal G. Do blood cells mimic gene expression profile alterations known to occur in muscular adaptation to endurance training? Eur. J. Appl. Physiol. 2005;95:96–104. doi: 10.1007/s00421-005-1334-3. [DOI] [PubMed] [Google Scholar]
- 6.Markwell M.A., McGroarty E.J., Bieber L.L., Tolbert N.E. The subcellular distribution of carnitine acyltransferases in mammalian liver and kidney. A new peroxisomal enzyme. J. Biol. Chem. 1973;248:3426–3432. [PubMed] [Google Scholar]
- 7.Muller C., Denis M., Gentzbittel L., Faraut T. The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. Nucleic Acids Res. 2004;32:W429–434. doi: 10.1093/nar/gkh460. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Emanuelsson O., Nielsen H., Brunak S., von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 2000;300:1005–1016. doi: 10.1006/jmbi.2000.3903. [DOI] [PubMed] [Google Scholar]
- 9.Small I., Peeters N., Legeai F., Lurin C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics. 2004;4:1581–1590. doi: 10.1002/pmic.200300776. [DOI] [PubMed] [Google Scholar]
- 10.Humphray S.J., Scott C.E., Clark R., Marron B., Bender C., Camm N., Davis J., Jenks A., Noon A., Patel M., Sehra H., Yang F., Rogatcheva M.B., Milan D., Chardon P., Rohrer G., Nonneman D., de Jong P., Meyers S.N., Archibald A., Beever J.E., Schook L.B., Rogers J. A high utility integrated map of the pig genome. Genome Biol. 2007;8:R139. doi: 10.1186/gb-2007-8-7-r139. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Stamm S., Ben-Ari S., Rafalska I., Tang Y., Zhang Z., Toiber D., Thanaraj T.A., Soreq H. Function of alternative splicing. Gene. 2005;344:1–20. doi: 10.1016/j.gene.2004.10.022. [DOI] [PubMed] [Google Scholar]
- 12.Leipzig J., Pevzner P., Heber S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 2004;32:3977–3983. doi: 10.1093/nar/gkh731. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Zhang L., Tao L., Ye L., He L., Zhu Y.Z., Zhu Y.D., Zhou Y. Alternative splicing and expression profile analysis of expressed sequence tags in domestic pig. Genomics Proteomics Bioinformatics. 2007;5:25–34. doi: 10.1016/S1672-0229(07)60011-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Modrek B., Lee C.J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 2003;34:177–180. doi: 10.1038/ng1159. [DOI] [PubMed] [Google Scholar]
- 15.Gorodkin J., Cirera S., Hedegaard J., Gilchrist M.J., Panitz F., Jorgensen C., Scheibye-Knudsen K., Arvin T., Lumholdt S., Sawera M., Green T., Nielsen B.J., Havgaard J.H., Rosenkilde C., Wang J., Li H., Li R., Liu B., Hu S., Dong W., Li W., Yu J., Staefeldt H.H., Wernersson R., Madsen L.B., Thomsen B., Hornshoj H., Bujie Z., Wang X., Bolund L., Brunak S., Yang H., Bendixen C., Fredholm M. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 2007;8:R45. doi: 10.1186/gb-2007-8-4-r45. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Corti O., DiDonato S., Finocchiaro G. Divergent sequences in the 5’ region of cDNA suggest alternative splicing as a mechanism for the generation of carnitine acetyltransferases with different subcellular localizations. Biochem. J. 1994;303:37–41. doi: 10.1042/bj3030037. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Emanuelsson O., Brunak S., von Heijne G., Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2007;2:953–971. doi: 10.1038/nprot.2007.131. [DOI] [PubMed] [Google Scholar]
- 18.Yura K., Shionyu M., Hagino K., Hijikata A., Hirashima Y., Nakahara T., Eguchi T., Shinoda K., Yamaguchi A., Takahashi K., Itoh T., Imanishi T., Gojobori T., Go M. Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene. 2006;380:63–71. doi: 10.1016/j.gene.2006.05.015. [DOI] [PubMed] [Google Scholar]