Comparative Analysis of the 5’ Flanking Region in &amp;lt;i&amp;gt;Arabidopsis&amp;lt;/i&amp;gt; and &amp;lt;i&amp;gt;O. sative&amp;lt;/i&amp;gt; RP Genes Revealed Conserved and Divergent Regulating Mechanisms

Donggen Zhou,Jie Luo

doi:10.4236/ajps.2019.106079

Abstract

Ribosome is one of the most abundant organelles in all living cells and plays a crucial role in cell growth. Synthesis of ribosomal components is tightly related with the change of growth conditions. We have comparatively analyzed the 5’ flanking region of ribosomal protein (RP) genes in Arabidopsis and O. sativa. In both Arabidopsis and O. sativa, there are two putative transcriptional factor binding motifs (telo box and site II elements) overrepresented in the proximal promoter region with a strong positional bias in most of the RP genes, which suggests the conserved mechanism of transcription-level control in RP genes of these two organisms. Tri-nucleotide repeats motif CTT and CCG were also common in 5’ flanking region of RP genes in Arabidopsis and O. sativa. However, we only found CCG repeat motif was enriched in O. sativa RP genes and most of them were clustered in the 5’ UTR region. This finding reveals molecular mechanism for divergent regulation of RP genes in Arabidopsis and O. sativa, and gives the possible clue to the mechanism of controlling O. sativa RP genes expression at the translation level.

Highlights

The ribosome is a large ribonucleoprotein complex with high conservation
Microarray analysis of differential gene expression between quiescent and germinated maize embryo stages had found the expression of mRNAs encoding ribosomal proteins to remain mostly unchanged throughout the germination process, suggesting that the transcriptional control is not so important for these genes during this developmental period. Further analysis of these two stages revealed that RP mRNAs largely accumulate in polysomes of the growthstimulated tissues compared to quiescent tissues, indicating a translational control mechanism to account for the rapid ribosomal protein synthesis in this organism [12] [13]
According to materials and methods, we identified 10 motifs in the 5’ flanking region of Arabidopsis RP genes

Summary

Introduction

The ribosome is a large ribonucleoprotein complex with high conservation. Eucaryotic ribosome is composed of four RNA molecules (rRNAs) and about 80 different ribosomal proteins (RPs). Recent studies in Arabidopsis have identified two cis elements presented in most of the RP genes promoters, suggesting that it could be involved in the coordinated expression of this class of genes at transcriptional level [7] One of these cis elements is the proliferating cell nuclear antigen (PCNA) site II motif (5’-GCCCR-3’) [8]. Further analysis of these two stages revealed that RP mRNAs largely accumulate in polysomes of the growthstimulated tissues compared to quiescent tissues, indicating a translational control mechanism to account for the rapid ribosomal protein synthesis in this organism [12] [13] All these indicate that like other organisms, the expression of plant ribosomal protein genes can be regulated at different expression levels. These characters prompt us to analyze the gene structures around transcriptional start site of Arabidopsis and O. sativa RP genes to compare the sequence features in these two organisms and search for the possible mechanisms for co-regulation of RP genes in plant organisms

Methodology

Identification of Putative DNA-Binding Motifs in the 5’

Conclusions