Bio-informatics and trans-genesis are creating organisms with new features



Cite item

Full Text

Abstract

Bioinformatic resources (databases of the gene nets, transcriptional and posttranscriptional expression signals, programs for recognition of functional sites and prediction of their activities) are reviewed in respect of their utility for gene engineering experiments.

About the authors

Aleksey V Kochetov

Institute of Cytology and Genetics SB RAS, Novosibirsk, Novosibirsk Oblast, RF

Email: ak@bionet.nsc.ru

Nadezhda A Omelyanchuk

Institute of Cytology and Genetics SB RAS, Novosibirsk, Novosibirsk Oblast, RF

Email: nadya@bionet.nsc.ru

Elena V Ignateva

Institute of Cytology and Genetics SB RAS, Novosibirsk, Novosibirsk Oblast, RF

Email: eignat@bionet.nsc.ru

Vitaly A Likhoshvay

Institute of Cytology and Genetics SB RAS, Novosibirsk, Novosibirsk Oblast, RF

Email: likho@bionet.nsc.ru

Yuri G Matushkin

Institute of Cytology and Genetics SB RAS, Novosibirsk, Novosibirsk Oblast, RF

Email: mat@bionet.nsc.ru

References

  1. Кочетов А.В., Шумный В.К. Влияние структуры мРНК на процесс инициации трансляции в клетках растений//Успехи совр. биол. -1998. -Vol. 118. -Р. 754-770.
  2. Bagnoli К, Lio P. Selection, mutations and codon usage in bacterial model//J. Thcor. Biol. -1995. -Vol. 173. -P. 71-281.
  3. Biemelt S., Sonnewald U., Galmbacher P., Willmitzer L. еt al. Production of human papillomavirus type 16 viruslike particles in transgenic plants//J. Virol.-2003,-Vol. 77.-P. 9211-9220.
  4. Brendel V., KlejfeJ. Prediction of locally optimal splice sites in plant prc-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA//Nucleic Acids Res. -1998. -Vol. 26. -P. 4748-4757.
  5. Chiapello H., Lisacek E, Caboche M., Henaut A. Codon usage and gene function arc related in sequences of Arabidopsis thaliana//Gene. -1998. -Vol. 209. -GC1-GC38.
  6. DellaPenna D. Plant metabolic engineering//Plant Physiol. -2001.-Vol. 125. -P. 160-163
  7. Diehn S.H., Chiu W-L., De Rocher E.J., Green P.J. Premature polyadcnylation at multiple sites within a Bacillus thuringiensis toxin gene-coding region//Plant Physiol.-1998.-Vol. 117.-P. 1433-1443.
  8. Duret L., Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Cacnorhabditis, Drosophila, and Arabidopsis//Proc. Natl. Acad. Sci. USA. -1999. -Vol. 96. -P. 4482^4487.
  9. Gallie D.R. Controlling gene expression in transgenics//Curr. Opin. Plant Biol.-1998. -Vol. 1, -P. 166-172.
  10. Grec S., Wang Y., Le Guen L. ct al. Cryptic polyadcnylation sites within the coding sequence of three yeast genes expressed in tobacco//Gene. -2000. -Vol. 242. -P. 87-95.
  11. Gutlierez R.A. Macuntosh G.C., Green P.J. Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control//Trends Plant Sci. -1999. -Vol. 4. -P. 429-438.
  12. Jacobs G.H., Rackham O., Stockwell PA. et al. Transterm: a database of mRNAs and translational control elements//Nucleic Acids Res. -2002.-Vol. 30.-P. 310-311
  13. Haselojj J., Siemering K.S., Prasher D.C., Hodge S. Removal of cryptic intron and subcellular localization of green fluorescent protein arc required to mark transgenic Arabidopsis plants brightly//Proc. Natl. Acad. Sci. USA. -1997. -Vol. 94. -P. 2122-2127.
  14. Higo K., Ugawa Ґ., Iwamoto M., Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999//Nucleic Acids Res. -1999. -Vol. 27. -P. 297-300.
  15. Kanehisa M., Goto S., Kawashima S., Nakaya A. The K.EGG databases at GcnomcNet//Nucleic Acids Res. -2002. -Vol. 30. -P. 42-46.
  16. Khanna H.K., Raina S.K. Elite Indica transgenic rice plants expressing modified Cry 1 Ac endotoxin of Bacillus thuringiensis show enhanced resistance to yellow stem borer (Scirpophaga inccrlulas)//Transgenic Res.-2002.-Vol. П. -Р. 411-423
  17. Kochetov A. V, Grigorovich D., Kolchanov N.A., Sarai A. Database on mRNA located cukaryotic expression signals influencing translation efficiency and specificity//Genome Informatics. Scr. 12/Edt: Matsuda ct al. Universal Academy Press: Tokyo, 2001. -P. 492-493.
  18. Kochetov A. V., Ischenko I. V., Vorobiev D. G. KelA.E. ct al. Eukaryotic mRNAs encoding abundant and scarce proteins arc statistically dissimilar in many structural features//FEBS Lett. -1998. -Vol. 440.-P. 351-355.
  19. Kochetov A.V., Ponomarenko M.P., Kisselev L.L., Kolchanov N.A. Prediction of cukaryotic mRNA translational properties//Bioinformatics.-1999.-Vol. 15, -P. 704-712.
  20. Kolchanov N.A., Ananko E.A., Likhoshvai V.A. et al. Gene networks description and modeling in the GcncNct system//Gene Regulation and Metabolism. Postgcnomic Computational Approaches/Eds Collado-Vides J., Hofcstadt R. Cambridge. London: MIT Press, 2000.-P. 149-179.
  21. Kolchanov N.A., Ignatieva E.V., Ananko E.A. ct al. Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res. 2002a. -Vol. 30. -P. 312-317.
  22. KomarA.A, Lesnik Т., Reiss C. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation//FEBS Lett. -1999. -Vol. 462. -P. 387-391
  23. KozakM. Pushing the limits of the scanning mechanism for initiation of translation//Gene. -2002. -Vol. 299. -P. 1-34.
  24. Larrick J. W. Thomas D. W. Producing proteins in transgenic plants and animals//Curr. Opin. Biotcchnol. -2001.-Vol. 12.-P. 411-418.
  25. Le Hir H., Nott A.' Moore M.J. How introns influence and enhance cukaryotic gene expression//Trends Biochcm. Sci. -2003. -Vol. 28, -P. 215-220.
  26. Lescot M., Dehais P., Thijs G. et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences//Nucleic Acids Res. -2002. -Vol. 30. -P. 325-327.
  27. Likhoshvai V.A. Malushkin Yu.G. Theoretical analysis of possible evolutionary trends in codon distribution along the mRNA//Proc. 1st Intern. Conf. of Bioinformatics of genome regulation and structure/Ed. N.A. Kochanov/Novosibirsk, 1998,-Vol. 1.-P. 341-344.
  28. Likhoshvai V.A., Matushkin Yu.G., Valolin Yu.N., Bazhan S.I. A generalized chemical kinetic metod for simulating complex biological systems. A computer model of ? phage ontogenesis//Computational tcchnol. -2000. -Vol. 5. -P. 87-99.
  29. Lukasiewicz M., Feuermann M., Jerouville В., Stas A., Boutry M. In vivo evaluation of the context sequence of the translation initiation codon in plants//Plant Sci. -2000. -Vol. 154. -P. 89-98.
  30. Matushkin Yu.G., Likhoshvai V.A., Kochetov A.V. Local secondary structure may be a critical characteristic influencing translation of unicellular organisms mRNA.//Bioinformatics Of Genome Regulation And Structure/Ed. By N. Kolchanov and R. Hofcstacdt. Kluwer Academic Publishers: Boston/Dordrccht/London. -2003.-P. 103-114.
  31. Mueller L.A., Zhang P., Rhee S.Y. AraCyc. A Biochemical Pathway Database for Arabidopsis//Plant Physiol. -2003. -Vol. 132. -P. 453-460.
  32. Pesole G, Liuni S., Grillo G et al. UTRdb and UTRsitc: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002//Nucleic Acids Res. -2002. -Vol. 30. -P. 335-340.
  33. Pestova T.V., Kolupaeva V.G., Lomakin IB. et al. Molecular mechanisms of translation initiation in cukaryotcs//Proc. Natl. Acad. Sci. USA. -2001. -Vol. 98. -P. 7029-7036.
  34. Rouwendul G.J.A., Mendes O., Wolbert E.J.H., de Boer A.D. Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage//Plant Mol. Biol. -1997. -Vol. 33. -P. 989-999.
  35. Sawant S.V., Kiran K., Singh P.K., Tuli R. Sequence architecture downstream of the initiator codon enhances gene expression and protein stability in plants//Plant Physiol. -2001. -Vol. 126. -P. 1630-1636.
  36. Schacherer R, Choi C, Golze U. et al. The TRANSPATH signal transduction database: a knowledge base on signal transduction networks//Bioinformatics. -2001. -Vol. 17. -P. 1053-1057.
  37. Tolslrup N., Rouze P., Brunak S. A branch point consensus fron Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites//Nucleic Acids Res.-1997.-Vol. 25, -P. 3159-3163.
  38. Tomila M. Whole-cell simulation: a grand challenge of 21" century//Trends Biotcchnol. -2001. -Vol. 19. -P. 205-210.
  39. Wingender E., Chen X., Fricke E. et al. The TRANSFAC system on gene expression regulation//Nucleic Acids Res.-2001.-Vol. 29.-P. 281-283.
  40. Van Hoof A., Green P.J. Rare codons arc not sufficient to destabilize a reporter gene transcript in tobacco//Plant Mol. Biol. -1997. -Vol.35.-P. 383-387.

Supplementary files

Supplementary Files
Action
1. JATS XML

Copyright (c) 2003 Kochetov A.V., Omelyanchuk N.A., Ignateva E.V., Likhoshvay V.A., Matushkin Y.G.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: серия ПИ № ФС 77 - 65617 от 04.05.2016.


This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies