Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Liang, Ping ^a   Nair, Jayakumar R ^a   Lei, Song ^a   McGuire, John J ^a   Dolnick, Bruce J ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; MESSENGER RNA; PROTEIN ENOSF1; THYMIDYLATE SYNTHASE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CELL FRACTIONATION; CELL FUNCTION; DOWN REGULATION; ENZYME SYNTHESIS; GENE SEQUENCE; GENE TRANSFER; GENETIC CODE; GENETIC IDENTIFICATION; GENOME ANALYSIS; HUMAN; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENY; PREDICTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; START CODON;

HOMO SAPIENS;

EID: 25444437024     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-125     Document Type: Article

References (33)

1. Babbitt PC, Hasson MS, Wedekind JE, Palmer DR, Barrett WC, Reed GH et al.: The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 1996, 35: 16489-16501.
2. Dolnick BJ: Cloning and characterization of a naturally occurring antisense RNA to human thymidylate synthase mRNA. Nucleic Acids Res 1993, 21: 1747-1752.
3. Dolnick BJ, Black AR, Winkler PM, Schindler K, Hsueh CT: rTS gene expression is associated with altered cell sensitivity to thymidylate synthase inhibitors. Adv Enzyme Regul 1996, 36: 165-180.
4. Dolnick BJ, Black AR: Alternate splicing of the rTS gene product and its overexpression in a 5-fluorouracil-resistant cell line. Cancer Res 1996, 56: 3207-3210.
5. Dolnick BJ, Lu K, Yin MB, Rustum YM: Recent advances in the study of rTS proteins. rTS expression during growth and in response to thymidylate synthase inhibitors in human tumor cells. Adv Enzyme Regul 1997, 37: 95-109.
6. Dolnick BJ, Angelino NJ, Dolnick R, Sufrin JR: A novel function for the rTS gene. Cancer Biol Ther 2003, 2: 364-369.
7. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268: 78-94.
8. Ford T, Graham J, Rickwood D: Iodixanol: a nonionic iso-osmotic centrifugation medium for the formation of self-generated gradients. Anal Biochem 1994, 220: 360-366.
9. Graham J, Ford T, Rickwood D: The preparation of subcellular organelles from mouse liver in self-generated gradients of iodixanol. Anal Biochem 1994, 220: 367-373.
10. Zhou J, Bai Y, Weiner H: Proteolysis prevents in vivo chimeric fusion protein import into yeast mitochondria. Cytosolic cleavage and subcellular distribution. J Biol Chem 1995, 270: 16689-16693.
11. Wagner C: Symposium on the subcellular compartmentation of folate metabolism. J Nutr 1996, 126: 1228S-1234S.
12. Samsonoff WA, Reston J, McKee M, O'Connor B, Galivan J, Maley G et al.: Intracellular location of thymidylate synthase and its state of phosphorylation. J Biol Chem 1997, 272: 13281-13285.
13. Dolnick RY, Wu Q, Angelino NJ, Stephanie LV, Chow K, Sufrin JR et al.: Enhancement of 5-Fluorouracil Sensitivity by an rTS Signaling Mimic in H630 Colon Cancer Cell. Cancer Res 2005, 65: 5917-5924.
14. Wang XQ, Rothnagel JA: 5′-untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation. Nucleic Acids Res 2004, 32: 1382-1391.
15. Wang XQ, Rothnagel JA: 5′-untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation. Nucleic Acids Res 2004, 32: 1382-1391.
16. Kozak M: Pushing the limits of the scanning mechanism for initiation of translation. Gene 2002, 299: 1-34.
17. Lukaszewicz M, Feuermann1 M, Jerouville B, Stas A, Boutry M: In vivo evaluation of the context sequence of the translation initiation codon in plants. Plant Sci 2000, 154: 89-98.
18. Nakao M, Barrero RA, Mukai Y, Motono C, Suwa M, Nakai K: Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nucleic Acids Res 2005, 33: 2355-2363.
19. Philippe H, Douady CJ: Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 2003, 6: 498-505.
20. Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55: 709-742.
21. Gogarten JP, Doolittle WF, Lawrence JG: Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002, 19: 2226-2238.
22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389-3402.
23. Claros MG, Vincens P: Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 1996, 241: 779-786.
24. Emanuelsson O, Nielsen H, Brunak S, von HG: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000, 300: 1005-1016.
25. Nakai K, Horton P: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999, 24: 34-36.
26. Guda C, Guda P, Fahy E, Subramaniam S: MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res 2004, 32: W372-W374.
27. Guda C, Fahy E, Subramaniam S: MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 2004, 20: 1785-1794.
28. McCloskey DE, McGuire JJ, Russell CA, Rowan BG, Bertino JR, Pizzorno G et al.: Decreased folylpolyglutamate synthetase activity as a mechanism of methotrexate resistance in CCRF-CEM human leukemia sublines. J Biol Chem 1991, 266: 6181-6187.
29. McGuire JJ, Russell CA, Balinska M: Human cytosolic and mitochondrial folylpolyglutamate synthetase are electrophoretically distinct. Expression in antifolate-sensitive and -resistant human cell lines. J Biol Chem 2000, 275: 13012-13016.
30. Abmayr SM&WJL: Preparation of nuclear and cytoplasmic extracts from mammalian cells. In Current protocols in molecular biology. 1993:12.11.11-12.11.19.
31. Storrie B, Madden EA: Isolation of subcellular organelles. Methods Enzymol 1990, 182: 203-225.
32. Schmidt E: Glutamate dehydrogenase - UV assay. In Methods in enzymatic analysis. Edited by Bergemeyer HU. New York: Academic Press, Inc; 1974:650-656.
33. BOXSHADE server [http://bioweb.pasteur.fr/seqanal/interfaces/ boxshade-simple.html]