Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia.

Gangqiao Kuang,Shuqing Zheng,Deshou Wang,Wenjing Tao,Xiaoshuang Wang

doi:10.3390/ijms21041230

Gangqiao Kuang, Shuqing Zheng + Show 3 more

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https://doi.org/10.3390/ijms21041230

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Abstract

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates.

Highlights

Ribosomes are absolutely essential for life, generating all proteins required for cell growth and maintenance
The complete set of 92RP genes were randomly distributed throughout the tilapia genome, with each linkage groups (LG) carrying one or more genes, similar to the ribosomal proteins (RPs) gene distribution pattern observed in rice and humans
Transcriptomic analysis revealed that the RP genes expressed in all tissues examined, but their expression levels differed among different tissues in tilapia, indicating their essential roles in various physiological processes

Summary

Introduction

Ribosomes are absolutely essential for life, generating all proteins required for cell growth and maintenance. A mature ribosome consists of four different ribosomal RNAs (rRNAs; 18S in the small subunit and 28S, 5.8S, and 5S in the large subunit), as well as ~80 ribosomal proteins (RPs) [1]. The cellular levels of some RP transcripts change as a function of growth, development and certain tumors [4,5,6]. Mutations in ribosomal proteins or ribosomal biogenesis factors have been identified in patients with varying disease [9,10]. Many ribosomal protein mutations are associated with growth impairment and tumor predisposition [12]. Knockdown of RPS7 causes developmental abnormalities via p53 dependent and independent pathways [13]

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