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Human Tissues Exhibit Diverse Composition of Translation Machinery - PubMed

  • ️Sun Jan 01 2023

Human Tissues Exhibit Diverse Composition of Translation Machinery

Aleksandra S Anisimova et al. Int J Mol Sci. 2023.

Abstract

While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas, we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g., PABP and eRF3 paralogs, eIF2B and eIF3 subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified the testis and brain as organs with the most diverged expression of translation-associated genes.

Keywords: aminoacyl-tRNA synthetases ARSases; cell type-specific translation; gonads; neurons; organ-specific translation; proteome; sexual dimorphism; transcriptional landscape; transcriptome; translation factors.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1

Tissue-specific expression pattern of two human genes encoding eEF1A paralogs, EEF1A1 and EEF1A2. (A) Expression of the EEF1A1 and EEF1A2 genes in various human tissues according to GTEx. (B) Levels of eEF1A1 and eEF1A2 proteins in various human tissues according to high-throughput proteomic analysis [1]. (C) Histograms showing the distribution of the percentage of EEF1A1 (top) and EEF1A2 (bottom) expressions among the genes from the “ELONGATION” complex across various human tissues, according to GTEx. (D) Percentage of EEF1A1 and EEF1A2 expressions among the genes from the “ELONGATION” complex across various human tissues, according to GTEx. TPM, Transcripts Per Kilobase Million; *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

Figure 2
Figure 2

Tissue-specific expression pattern of translation-associated genes localized in sex chromosomes. (A) Percentage of EIF1AX and EIF1AY expression among the genes from the “INITIATION” complex across various human tissues, according to GTEx. (B) Expression of the DDX3X and DDX3Y genes in various human tissues according to GTEx. (C) Expression of the EIF2S3 gene in various human tissues according to GTEx. TPM, Transcripts Per Kilobase Million; *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

Figure 3
Figure 3

Tissue-specific expression pattern of genes encoding PABPC homologs and translation termination factors. (A) Percentage of PABPC1, PABPC1L, PABPC3, PABPC4, and PABPC5 expression among the genes from the “PABPC” complex across various human tissues, according to GTEx. (B) Expression of the ETF1, GSPT1, and GSPT1 genes encoding eRF1, eRF3a/GSPT1, and eRF3b/GSPT2 correspondingly in various human tissues according to GTEx. (C) Percentage of ETF1, GSPT1, and GSPT1 expression among the genes from the “TERMINATION” complex across various human tissues, according to GTEx. TPM, Transcripts Per Kilobase Million; *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

Figure 4
Figure 4

Tissue-specific expression pattern of genes encoding GTPBP1 and GTPBP2 proteins, eIF4G paralogs, and eIF2B subunits. (A) Expression of the GTPBP1 and GTPBP2 genes in various human tissues according to GTEx. (B) Percentage of EIF4G1 and EIF4G3 among the genes from the “INITIATION” complex across various human tissues, according to GTEx. (C) Percentage of EIF2B1, EIF2B2, EIF2B3, EIF2B4, and EIF2B5 expression among the genes encoding components of the “eIF2B” complex across various human tissues, according to GTEx. TPM, Transcripts Per Kilobase Million; *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

Figure 5
Figure 5

Tissue-specific expression pattern of translation-associated genes showing high tissue specificity. (A) Percentage of EIF4E1B expression among the genes from the “INITIATION” complex across various human tissues, according to GTEx. (B) Expression of the EIF4ENIF1 in various human tissues according to GTEx. (C) Expression of the EIF5A, EIF5A2, and EIF5AL1 in various human tissues according to GTEx. (D) Percentage of BZW1 and BZW2 expression among the genes from the “INITIATION+” complex across various human tissues according to GTEx. (E) Percentage of EIF1B expression among the genes from the “INITIATION” complex across various human tissues, according to GTEx. (F) Percentage of PELO and HBS1L expression among the genes from the “TERMINATION+” complex across various human tissues according to GTEx. TPM, Transcripts Per Kilobase Million; *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

Figure 6
Figure 6

Tissue-specific expression pattern of genes encoding several aminoacyl-tRNA-synthetases (ARSases) showing tissue specificity. (A) Percentage of HARS and TARSL2 expression among the genes from the “ARSases” complex across various human tissues, according to GTEx. (B) Percentage of WARS expression among the genes from the “ARSases” complex across various human tissues, according to Gene Atlas [101]. (C) Percentage of AIMP1, AIMP2, and EEF1E1 expression among the genes from the “ARSase COMPLEX” complex across various human tissues, according to GTEx. (D) Percentage of KARS and NARS expression among the genes from the “ARSase COMPLEX” complex across various human tissues, according to GTEx. *, FDR corrected p-value < 0.01 in enrichment analysis (fgsea R package).

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