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

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

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: ertugrulfiliz@gmail.com).

(Received: 25.05.2012 Accepted: 24.01.2013)

References

  • Bartel D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116: 281–297.
  • Bernstein E., Caudy A.A., Hammond S.M. and Hannon G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409: 363-366.
  • Blom N., Gammeltoft S. and Brunak S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Biology, Vol: 294 (5) pp: 1351-1362.
  • Chen X. (2005) microRNA biogenesis and function in plants. FEBS Letters, 579: 5923–5931.
  • Dhar P., Ganguli S. and Datta A. (2010) Molecular modeling of DICER and identification of phosphorylation sites. Bioinformation, 4(9): 412-4
  • Falquet L., Pagni M., Bucher P., Hulo N., Sigrist, C.J. A. Hofmann K. and Bairoch A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Research, 30: 235-238.
  • Gasteiger E. (2005) Protein Identification and Analysis Tools on the ExPASy Server. In: John M. Walker ed. The Proteomics Protocols Handbook Humana Press, 571-607.
  • Gill S.C. and Von Hippel P.H. (1989) Extinction coefficient. Analitical Biochemistry, 182: 3193
  • Groβhans H. and Filipowicz W. (2008) The expanding world of small RNAs. Nature, 451:414–416.
  • Guruprasad K., Reddy B.V.P. and Pandit M.W. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering Design and Selection, 4: 155-164.
  • Ikai A.J. (1980) Thermo stability and aliphatic index of globular proteins. The Journal of Bichemistry, 88: 1895-1898.
  • Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K. and Kapoor S. (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics, 9: 451 doi:10.1186/1471-21649-4
  • Kim V.N. (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nature Reviews Moleculaer Cell Biology, 6: 376–385.
  • Kumar N. and Bhalla T.C. (2011) In silico analysis of amino acid sequences in relation to specificity and physiochemical properties of some aliphatic amidases and kynurenine formamidases. Journal of Bioinformatics and Sequence Analysis, Vol. 3(6), pp. 116-123.
  • Kyte J. and Doolottle R.F. (1982) A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157: 105-1
  • Lamontagne B., Larose S., Boulanger J. and Elela S.A. (2001) The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Current Issues in Molecular Biology, 3: 71-78.
  • Liu Q., Feng Y. and Zhu Z. (2009) Dicer-like (DCL) proteins in plants. Functional & Integrative Genomics, 9: 277–286.
  • MacRae I.J. and Doudna J.A. (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Current Opinion in Structural Biology, 17: 1–8.
  • MacRae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D. and Doudna J.A. (2006) Structural Basis for Double-Stranded RNA Processing by Dicer. Science, Vol 311: 195-1
  • Margis R., Fusaro A.F., Smith N.A., Curtin S.J., Watson J.M., Finnegan E.J. and Waterhouse P.M. (2006) The evolution and diversification of Dicers in plants. FEBS Letters, 580: 2442–2450. Matzke M.A. and Birchler J.A. (2005) RNAimediated pathways in the nucleus. Natural Reviews Genetics, 6(1): 24-35.
  • Moissiard G., Parizotto E.A., Himber C. and Voinnet O. (2007) Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA, 13: 1268–1278.
  • Sahay A. and Shakya M. (2010) In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach. Journal of proteomics & bioinformatics, Volume 3(5): 148-154.
  • Sivakumar K., Balaji S. and Radhakrishnan G. (2007) In silico characterization of antifreeze proteins using computational tools and servers. The Journal of Chemical Sciences, Vol. 119, No. 5: 571–579.
  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28: 2731-2739.
  • Timothy L., Mikael Bodén B., Buske F.A., Frith M., Grant C.E., Clementi L., Ren J., Li W.W. and Noble W.S. (2009) MEME SUITE: tools for motif discovery and searching Nucleic Acids Research, 37: 202-208.
  • Zhang H., Kolb F.A., Jaskiewicz L., Westhof E. and Filipowicz W. (2004) Single processing center models for human Dicer and bacterial RNase III. Cell, 118: 57–68.

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

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

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.

References

  • Bartel D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116: 281–297.
  • Bernstein E., Caudy A.A., Hammond S.M. and Hannon G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409: 363-366.
  • Blom N., Gammeltoft S. and Brunak S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Biology, Vol: 294 (5) pp: 1351-1362.
  • Chen X. (2005) microRNA biogenesis and function in plants. FEBS Letters, 579: 5923–5931.
  • Dhar P., Ganguli S. and Datta A. (2010) Molecular modeling of DICER and identification of phosphorylation sites. Bioinformation, 4(9): 412-4
  • Falquet L., Pagni M., Bucher P., Hulo N., Sigrist, C.J. A. Hofmann K. and Bairoch A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Research, 30: 235-238.
  • Gasteiger E. (2005) Protein Identification and Analysis Tools on the ExPASy Server. In: John M. Walker ed. The Proteomics Protocols Handbook Humana Press, 571-607.
  • Gill S.C. and Von Hippel P.H. (1989) Extinction coefficient. Analitical Biochemistry, 182: 3193
  • Groβhans H. and Filipowicz W. (2008) The expanding world of small RNAs. Nature, 451:414–416.
  • Guruprasad K., Reddy B.V.P. and Pandit M.W. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering Design and Selection, 4: 155-164.
  • Ikai A.J. (1980) Thermo stability and aliphatic index of globular proteins. The Journal of Bichemistry, 88: 1895-1898.
  • Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K. and Kapoor S. (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics, 9: 451 doi:10.1186/1471-21649-4
  • Kim V.N. (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nature Reviews Moleculaer Cell Biology, 6: 376–385.
  • Kumar N. and Bhalla T.C. (2011) In silico analysis of amino acid sequences in relation to specificity and physiochemical properties of some aliphatic amidases and kynurenine formamidases. Journal of Bioinformatics and Sequence Analysis, Vol. 3(6), pp. 116-123.
  • Kyte J. and Doolottle R.F. (1982) A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157: 105-1
  • Lamontagne B., Larose S., Boulanger J. and Elela S.A. (2001) The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Current Issues in Molecular Biology, 3: 71-78.
  • Liu Q., Feng Y. and Zhu Z. (2009) Dicer-like (DCL) proteins in plants. Functional & Integrative Genomics, 9: 277–286.
  • MacRae I.J. and Doudna J.A. (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Current Opinion in Structural Biology, 17: 1–8.
  • MacRae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D. and Doudna J.A. (2006) Structural Basis for Double-Stranded RNA Processing by Dicer. Science, Vol 311: 195-1
  • Margis R., Fusaro A.F., Smith N.A., Curtin S.J., Watson J.M., Finnegan E.J. and Waterhouse P.M. (2006) The evolution and diversification of Dicers in plants. FEBS Letters, 580: 2442–2450. Matzke M.A. and Birchler J.A. (2005) RNAimediated pathways in the nucleus. Natural Reviews Genetics, 6(1): 24-35.
  • Moissiard G., Parizotto E.A., Himber C. and Voinnet O. (2007) Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA, 13: 1268–1278.
  • Sahay A. and Shakya M. (2010) In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach. Journal of proteomics & bioinformatics, Volume 3(5): 148-154.
  • Sivakumar K., Balaji S. and Radhakrishnan G. (2007) In silico characterization of antifreeze proteins using computational tools and servers. The Journal of Chemical Sciences, Vol. 119, No. 5: 571–579.
  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28: 2731-2739.
  • Timothy L., Mikael Bodén B., Buske F.A., Frith M., Grant C.E., Clementi L., Ren J., Li W.W. and Noble W.S. (2009) MEME SUITE: tools for motif discovery and searching Nucleic Acids Research, 37: 202-208.
  • Zhang H., Kolb F.A., Jaskiewicz L., Westhof E. and Filipowicz W. (2004) Single processing center models for human Dicer and bacterial RNase III. Cell, 118: 57–68.
There are 26 citations in total.

Details

Primary Language English
Journal Section Short Communication
Authors

Ertugrul Filiz This is me

İbrahim Koc This is me

Publication Date November 8, 2013
Submission Date November 8, 2013
Published in Issue Year 2013 Volume: 72 Issue: 1

Cite

AMA Filiz E, Koc İ. In silico analysis of dicer-like protein (DCLs) sequences from higher plant species. Eur J Biol. November 2013;72(1):53-63.