In silico analysis of dicer-like protein (DCLs) sequences from higher plant species

Year 2013, Volume: 72 Issue: 1, 53 - 63, 08.11.2013

Ertugrul Filiz İbrahim Koc

Abstract

Dicer and Dicer like (DCLs) proteins are essential part of small RNA biogenesis pathway, is a type of RNase III digesting long dsRNA (pre-miRNA) to small RNA segments (miRNA). A total of 20 full length of Dicer like proteins (DCL1, DCL2, DCL3 and DCL4) from different organisms available in NCBI were evaluated by bioinformatics tools to investigate properties, structure of DCLs, domain analysis, multiple sequence alignment and phylogenetics tree construction. All DCLs protein sequences have Ribonuclease III protein family that contains RNaseIII domain including Helicase ATP-binding type-1, Helicase C-terminal, Dicer double-stranded RNA-binding fold, PAZ, Ribonuclease III, Double stranded RNA-binding domain (dsRB). Physicochemical analysis offers data such as pI, EC, Al, GRAVY and instability index about these enzymes. Putative phosphorylation sites were also identified which are found to be conserved in plant species and the results showed that the most abundant phosphorylation site is Serine residues in DCLs proteins. Patterns and profile analysis were performed using Prosite and conserved protein motifs subjected to MEME to obtain the best possible matches. The phylogenetics tree represented three major clusters and similar DCLs protein sequences of different plant species clustered together. The obtained results could be used for further in silico analysis and homology modeling studies.

Keywords:

Dicer, DCLs, miRNA, RNase, In silico analysis.

*Corresponding Author:

Ertuğrul Filiz (e-mail: [e-mail]).

(Received: 25.05.2012 Accepted: 24.01.2013)

Keywords

Dicer, DCLs, miRNA, RNase, In silico analysis.

Gelişmiş bitki türlerinde dicer-benzeri protein (DCLs) dizilerinin in silico analizi

Abstract

Dicer ve Dicer benzeri (DCLs) proteinler küçük RNA biyogenezi yolunun bir parçasıdır ve uzun dsRNA (pre-miRNA)’yı küçük RNA parçalarına sindiren RNase III tipi proteinlerdir. NCBI’da kullanılabilir farklı organizmalara ait 20 tam uzunlukta Dicer benzeri proteinler (DCL1, DCL2, DCL3 and DCL4) biyoenformatik araçlar yardımıyla DCLs’lerin özellik ve yapıları, domain analizleri, çoklu dizi hizalanmaları ve filogenetik ağaç yapımının araştırılması için değerlendirilmiştir. Bütün DCLs protein dizileri, RNaseIII domainin kapsadığı helikaz ATP-bağlanma tip–1, helikaz C-terminal, dicer çift zincir RNA, PAZ, ribonükleaz III, çift zincir RNA-bağlanma domain (dsRB) ailesinin bulunduğu ribonükleaz III protein ailesine sahiptir. Fizikokimyasal analizler bu enzimler hakkında pI, EC, Al, GRAVY ve instabilite indeksi gibi bilgileri sunmuştur. Bitki türerinde korunurlu varsayılan fosforilasyon bölgeleri belirlenmiştir ve sonuçlar DCLs proteinlerinde en sık fosforilasyon bölgesinin serin kalıntısında olduğunu göstermiştir. Motif ve profil analizlerinde Prosite, korunurlu protein motiflerinde en iyi muhtemel eşleşmelerin elde etmek için MEME kullanılmıştır. Filogenetik ağaç üç ana kümeyle temsil edilmiş ve farklı bitki türlerindeki DCLs protein dizileri beraber kümelenmiştir. Elde edilen sonuçlar, gelecekteki homoloji modelleme ve in silico analizlerde kullanılabilir.

Keywords

Dicer, DCLs, miRNA, RNase, In silico analiz

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