Abstract
The DNA sequence corresponding to the second exon of the SLC25A3 gene is duplicated in vertebrates. The second exon codes for the first transmembrane segment and parts of the immediately adjoining intermembrane and mitochondrial matrix segments. The two genomic exon 2 sequences are 84% similar in zebrafish (slc25a3b gene), 70% in chicken, 66% in mouse and 67% in human. The amino acid identity is 86% in zebrafish, 77% in chicken and 70% in mouse and human. The two copies of exon 2 are separated by an intronic interval. Translation of both exon 2 sequences would alter the reading frame of the downstream sequence, generating a modified aa sequence which would soon be truncated by a stop codon. As a matter of fact the splicing machinery is tuned in such a way that in some species only one of the two copies is expressed and the other is spliced out, while in other species both copies are expressed but only one at a time, generating two alternative protein products.
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Altschul S. F., Gish W., Miller W., Myers E. W. and Lipman D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Broughton R. E., Betancur R. R., Li C., Arratia G. and Ortí G. 2013 Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr. 2013, 5.
Corpet F. 1988 Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881–10890.
Dolce V., Fiermonte G. and Palmieri F. 1996 Tissue-specific expression of the two isoforms of the mitochondrial phosphate carrier in bovine tissues. FEBS Lett. 399, 95–98.
Dolce V., Iacobazzi V., Palmieri F. and Walker J. E. 1994 The sequences of human and bovine genes of the phosphate carrier from mitochondria contain evidence of alternatively spliced forms. J. Biol. Chem. 269, 10451–10460.
Fiermonte G., Dolce V. and Palmieri F. 1998 Expression in Escherichia coli, functional characterization, and tissue distribution of isoforms A and B of the phosphate carrier from bovine mitochondria. J. Biol. Chem. 273, 22782–22787.
Foote M., Hunter J. P., Janis C. M. and Sepkoski Jr J. J. 1999 Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283, 1310–1314.
Hoskins A. A. and Moore M. J. 2012 The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem. Sci. 37, 179–188.
Lee M. S. 1999 Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 49, 385–391.
Mayr J. A., Merkel O., Kohlwein S. D., Gebhardt B. R., Bohles H., Fotschl U. et al. 2007 Mitochondrial phosphate-carrier deficiency: a novel disorder of oxidative phosphorylation. Am. J. Hum. Genet. 80, 478–484.
Mayr J. A., Zimmermann F. A., Horváth R., Schneider H. C., Schoser B., Holinski-Feder E. et al. 2011 Deficiency of the mitochondrial phosphate carrier presenting as myopathy and cardiomyopathy in a family with three affected children. Neuromuscul. Disord. 21, 803–808.
Nei M., Xu P. and Glazko G. 2001 Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc. Natl. Acad. Sci. USA 98, 2497–2502.
Nobrega M. A. and Pennacchio L. A. 2004 Comparative genomic analysis as a tool for biological discovery. J. Physiol. 554, 31–39.
Palmieri F. 2013 The mitochondrial transporter family SLC25: identification, properties and physiopathology. Mol. Aspects Med. 34, 465–484.
Palmieri F. 2014 Mitochondrial transporters of the SLC25 family and associated diseases: a review. J. Inherit. Metab. Dis. 37, 565–575.
Palmieri F. and Pierri C. L. 2010 Mitochondrial metabolite transport. Essays Biochem. 47, 37–52.
Sethi I., Romano R. A., Gluck C., Smalley K., Vojtesek B., Buck M. J. et al. 2015 A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues. BMC Genomics 16, 584. (https://doi.org/10.1186/s12864-015-1793-9).
Shah S. H. and Pallas J. A. 2009 Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics 10, 26. (https://doi.org/10.1186/1471-2105-10-26).
Shimomura I., Shimano H., Horton J. D., Goldstein J. L. and Brown M. S. 1997 Differential expression of exons 1a and 1c in mRNAs for sterol regulatory element binding protein-1 in human and mouse organs and cultured cells. J. Clin. Invest. 99, 838–845.
Venkatesh B., Lee A. P., Ravi V., Maurya A. K., Lian M. M., Swann J. B. et al. 2014 Elephant shark genome provides unique insights into gnathostome evolution. Nature 505, 174–179.
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Thanks are due to Mrs Mary V. C. Pragnell for linguistic text revision.
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Rosa Calvello and Antonia Cianciulli contributed equally to this work.
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Calvello, R., Cianciulli, A. & Panaro, M.A. Unusual structure and splicing pattern of the vertebrate mitochondrial solute carrier SLC25A3 gene. J Genet 97, 225–233 (2018). https://doi.org/10.1007/s12041-018-0906-z
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DOI: https://doi.org/10.1007/s12041-018-0906-z