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A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana

Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidops...

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Detalles Bibliográficos
Autores principales: Gunawardana, D., Likic, V. A., Gayler, K. R.
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707057/
https://www.ncbi.nlm.nih.gov/pubmed/19590748
http://dx.doi.org/10.1155/2009/820381
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author Gunawardana, D.
Likic, V. A.
Gayler, K. R.
author_facet Gunawardana, D.
Likic, V. A.
Gayler, K. R.
author_sort Gunawardana, D.
collection PubMed
description Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.
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spelling pubmed-27070572009-07-09 A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana Gunawardana, D. Likic, V. A. Gayler, K. R. Comp Funct Genomics Research Article Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily. Hindawi Publishing Corporation 2009 2009-07-02 /pmc/articles/PMC2707057/ /pubmed/19590748 http://dx.doi.org/10.1155/2009/820381 Text en Copyright © 2009 D. Gunawardana et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Gunawardana, D.
Likic, V. A.
Gayler, K. R.
A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title_full A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title_fullStr A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title_full_unstemmed A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title_short A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana
title_sort comprehensive bioinformatics analysis of the nudix superfamily in arabidopsis thaliana
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707057/
https://www.ncbi.nlm.nih.gov/pubmed/19590748
http://dx.doi.org/10.1155/2009/820381
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