In silico identification, phylogenetic and bioinformatic analysis of argonaute genes in plants.

Khaled Mirzaei,Mohammad Hasan Shamsifard,Bahman Bahramnejad,Wahid Zamani

doi:10.1155/2014/967461

Khaled Mirzaei, Mohammad Hasan Shamsifard + Show 2 more

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https://doi.org/10.1155/2014/967461

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Abstract

Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.

Highlights

IntroductionPathways of gene silencing and small regulatory RNAs such as miRNAs (microRNAs) and siRNAs (short interfering RNAs) are widespread in almost all eukaryotic organisms [1, 2]
Pathways of gene silencing and small regulatory RNAs such as miRNAs and siRNAs are widespread in almost all eukaryotic organisms [1, 2]
This domain has marked similarity with RNaseH family of ribonucleases which is carried out by an active site usually carrying an Asp-Asp-His (DDH) motif and it possesses the catalytic amino acid residues required for endonucleolytic cleavage of the target RNA but in some of the Argonaute proteins (HsAgo3) which have DDH domain but do not appear to have slicer activity, it suggests that the presence of a DDH motif does not necessarily imply slicer activity [11,12,13,14]

Summary

Introduction

Pathways of gene silencing and small regulatory RNAs such as miRNAs (microRNAs) and siRNAs (short interfering RNAs) are widespread in almost all eukaryotic organisms [1, 2]. These pathways are known to act in development, heterochromatin formation, regulation of gene expression at transcription, posttranscription, and translation level, or mRNA stability [3,4,5]. In the pathways of gene silencing and small regulatory RNAs, Argonaute proteins have key catalytic role in translational repression or cleavage These proteins are ∼100-kD, highly basic proteins and share the domain structure that comprises an N terminal, PAZ, Mid, and a C-terminal PIWI domain [6, 10, 11]. This domain has marked similarity with RNaseH family of ribonucleases which is carried out by an active site usually carrying an Asp-Asp-His (DDH) motif and it possesses the catalytic amino acid residues required for endonucleolytic cleavage of the target RNA but in some of the Argonaute proteins (HsAgo3) which have DDH domain but do not appear to have slicer activity, it suggests that the presence of a DDH motif does not necessarily imply slicer activity [11,12,13,14]

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