Arabidopsis paralogous genes RPL23aA and RPL23aB encode functionally equivalent proteins

Abstract

Background 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. 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. Results In 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. Conclusions Our 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.

Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources

“…In more cases, duplication events lead to one or several main genes, and the other redundant gene copies might degenerate and eventually be lost or, alternatively, undergo neospecialization via a modulation of their expression (temporal or spatial) patterns or functions. A clear reduced dosage was observed for Arabidopsis uS7 (AtRPS5A and AtRPS5B), uL23 (RPL23aA and RPL23aB), uL4 (RPL4A and RPL4D), uL18 (RPL5A and RPL5B), eL42 (RPL36aA and RPL36aB) and eS6 (RPS6A and RPS6B) paralogs (Casanova-S aez et al, 2014;Creff et al, 2010;Fujikura et al, 2009;Rosado et al, 2010;Weijers et al, 2001;Xiong et al, 2020). Several studies have also revealed divergent abundance or subcellular localization patterns of the CRP paralogs (Savada & Bonham-Smith, 2014;Whittle & Krochko, 2009;Xiong et al, 2021) or CRPs with extraribosomal functions (Table S10), indicating that they may undergo neofunctionalization and/or subfunctionalization.…”

High resolution RNA‐seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana

“…Gene balance pressures together with dosage effects could explain the high rates of retention of duplicated RP genes in the genome (Birchler et al., 2001, 2007; Conant & Wolfe, 2008; Veitia et al., 2008). The non‐allelic non‐complementation phenomenon, which may indicate dosage effects between paralogous genes, was found in members within RP families, such as RPL5 (Fujikura et al., 2009), RPS6 (Creff et al., 2010), RPL4 (Rosado et al., 2010), RPL36a (Casanova‐Saez et al., 2014), and RPL23a (Xiong et al., 2020). The transcriptional fluctuation trends of some paralogous RP genes across different tissues and developmental stages was found well‐matched although the transcript accumulation levels between them maybe different, suggesting some paralogous RP genes are regulated in the concerted manner.…”

“…Knockdown of RPL23aA resulted in severely developmental phenotypes whereas knockout of RPL23aB has no obvious phenotype (Degenhardt & Bonhamsmith, 2008a, 2008b). Interestingly, RPL23aA and RPL23aB were found to be transcribed in a concerted manner with much higher expression level of RPL23aA than that of RPL23aB, and over‐expression of RPL23aB in rpl23aa could rescue the phenotype of rpl23aa (Xiong et al., 2020). We thought paralogous RP genes with concerted expression patterns may be the evidence supporting the dosage hypothesis which posits that the presence of duplicated RP genes might be necessary to maintain adequate RP dosages with functional redundant.…”