Analiza struktur przestrzennych wiroida wrzecionowatości bulw ziemniaka (PSTVd)

• Autorzy: Folkman W. , Popienda M. , Cajza M.

Warianty tytułu

EN

Analysis of 3D structures of Potato spindle tuber viroid (PSTVd)

• Języki publikacji: PL

Abstrakty

EN

Based on 156 sequences of Potato spindle tuber viroid (PSTVd) taken from GenBank, consensus sequence thereof containing 359 nucleotides was determied by means of CLUSTAL W program. For this sequence the secondary structures were derived by using Mfold program. In linear structure of the lowest two apical loops and 27 internal loops and bulges were found. To define 3D structures of those fragments and double-stranded structures connecting them, an RNA FRABASE ver. 1.0 search engine was used. In this way, their 3D equivalents in resolved crystallographic structures and those derived from measurements of NMR spectra were found. For smaller fragments, full compatibility was observed. Bigger ones required usage of our script to isostericity base replacement for fragments of not full homology. The above procedure did not change torsion angles χ around glycosyl bonds. Then these fragments were connected via superimposition of common canonical base pairs. An integrated structure that obtained was then energetically minimized in torsion angles space and Cartesian coordinates space. Then 7 different 2D structures (2 linear and 5 branched) were taken into account and additional, alternative threedimensional ones were generated for them. The length of whole 3D structure of viroid RNA for corresponding linear 2D structure amounted to 500 Å that was in agreement with the data obtained from electron microscopy. RNA of linear structures, due to their extent is able to easily complex with proteins. Asides from previously found in central conservative domain of PSTVd and described in the literature E loop we found another, similar one in pathogenic domain. Both structures have characteristic of sarcin/ricin RNA motif S-turn of one strain.

Słowa kluczowe

PL

czynniki chorobotworcze; metody badan; sekwencja konsensusowa; sekwencja kwasow nukleinowych; struktura przestrzenna; wiroid wrzecionowatosci bulw ziemniaka; wrzecionowatosc bulw ziemniaka; ziemniaki

EN

pathogenic factor; research method; consensus sequence; nucleic acid sequence; spatial structure; potato spindle tuber viroid; potato spindle tuber; potato

• Wydawca: -
• Czasopismo: Progress in Plant Protection
• Rocznik: 2010
• Tom: 50
• Numer: 2
• Opis fizyczny: s.634-637,rys.,bibliogr.

Twórcy

autor

Folkman W.

• Instytut Ochrony Roślin – Państwowy Instytut Badawczy, ul.Władysława Węgorka 20, 60-318 Poznań

autor

Popienda M.

autor

Cajza M.

Bibliografia

• Diener T.O. 1971. Potato spindle tuber „virus” IV. A replicating, low molecular weight RNA. Virology 45: 411–428.
• Güntert P., Mumenthaler C., Wüthrich K. 1997. Torsion angle dynamics for NMR structure calculation with the new program CYANA. J. Mol. Biol. 273: 283–298.
• Popenda M., Blazewicz M., Szachniuk M., Adamiak R.W. 2008. RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res. 36: D386–D391.
• Schwieters C.D., Kuszewski J.J., Tjandra N., Clore G.M. 2003. The Xplor-NIH NMR Molecular Structure Determination Package. J. Magn. Res. 160: 66–74.
• Schwieters C.D., Kuszewski J.J., Clore G.M. 2006. Using Xplor-NIH for NMR molecular structure determination. Progr. NMR Spectroscopy 48: 47–62.
• Thompson J.D., Gibson T.J., Higgins D.G. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
• Zhong X., Leontis N., Qian S., Haya A., Qi Y., Boris-Lawrie K., Ding B. 2006. Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagnesis reveal its essential role in replication. J. Virol. 80: 8566–8581.
• Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406–3415.