Arabidopsis paralogous genes RPL23aA and RPL23aB encode functionally equivalent proteins

Wei Xiong,Beixin Mo,Xiangze Chen,Lin Liu,Jiancong Zhang,Xuemei Chen,Ting Lan,Chengxin Zhu

doi:10.1186/s12870-020-02672-1

Wei Xiong, Beixin Mo + Show 6 more

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https://doi.org/10.1186/s12870-020-02672-1

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Abstract

BackgroundIn plants, each ribosomal protein (RP) is encoded by a small gene family but it is largely unknown whether the family members are functionally diversified. There are two RPL23a paralogous genes (RPL23aA and RPL23aB) encoding cytoplasmic ribosomal proteins in Arabidopsis thaliana. Knock-down of RPL23aA using RNAi impeded growth and led to morphological abnormalities, whereas knock-out of RPL23aB had no observable phenotype, thus these two RPL23a paralogous proteins have been used as examples of ribosomal protein paralogues with functional divergence in many published papers.ResultsIn this study, we characterized T-DNA insertion mutants of RPL23aA and RPL23aB. A rare non-allelic non-complementation phenomenon was found in the F1 progeny of the rpl23aa X rpl23ab cross, which revealed a dosage effect of these two genes. Both RPL23aA and RPL23aB were found to be expressed almost in all examined tissues as revealed by GUS reporter analysis. Expression of RPL23aB driven by the RPL23aA promoter can rescue the phenotype of rpl23aa, indicating these two proteins are actually equivalent in function. Interestingly, based on the publicly available RNA-seq data, we found that these two RPL23a paralogues were expressed in a concerted manner and the expression level of RPL23aA was much higher than that of RPL23aB at different developmental stages and in different tissues.ConclusionsOur findings suggest that the two RPL23a paralogous proteins are functionally equivalent but the two genes are not. RPL23aA plays a predominant role due to its higher expression levels. RPL23aB plays a lesser role due to its lower expression. The presence of paralogous genes for the RPL23a protein in plants might be necessary to maintain its adequate dosage.

Highlights

In plants, each ribosomal protein (RP) is encoded by a small gene family but it is largely unknown whether the family members are functionally diversified
Sequencing results revealed that rpl23aa contains a TDNA insertion in the 3′ UTR region, 10 bp downstream of the stop codon of the RPL23aA gene (Fig. 1a), while rpl23ab contains a T-DNA insertion in the second exon of RPL23aB (Fig. 1b)
RPL23aA and RPL23aB genes are transcribed in a concerted manner with higher expression levels of RPL23aA than RPL23aB Since the above results indicated that RPL23aA and RPL23aB proteins have equivalent function, we suspected that the difference in phenotype between rpl23aa and rpl23ab is due to the difference in the expression levels of these two genes

Summary

Introduction

Each ribosomal protein (RP) is encoded by a small gene family but it is largely unknown whether the family members are functionally diversified. There are two RPL23a paralogous genes (RPL23aA and RPL23aB) encoding cytoplasmic ribosomal proteins in Arabidopsis thaliana. Knock-down of RPL23aA using RNAi impeded growth and led to morphological abnormalities, whereas knock-out of RPL23aB had no observable phenotype, these two RPL23a paralogous proteins have been used as examples of ribosomal protein paralogues with functional divergence in many published papers. In E. coli, genes encoding RPs are arranged in about 20 operons, with approximately half of the genes mapping to a single locus [3, 4]. In yeast Saccharomyces cerevisiae, about 75% of the RPs are encoded by gene families with more than one member [6]. Substantially functional redundancy was found between paralogous RP genes in yeast, some paralogous RP genes were reported to have non-redundant functions [6,7,8]

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