The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage

A deficiency of ribosomal proteins is a severe stress to the cell. Haploinsufficiency of human ribosomal protein genes, including RPS26, is the cause of ribosomopathies. Here, we reduced the level of ribosomal protein eS26 in HEK293T cells, which caused a decrease in the level of 40S ribosomal subunits and led to a ribosome-shortage state. We show that eS26-deficient cells have lighter polysomes than control cells. Using RNA-sequencing of total and polysome-associated messenger RNA (mRNA) fractions from both cell types, we identify thousands of differentially expressed genes in the transcriptome and translatome, respectively, as well as genes with altered translation efficiency. By analyzing the intrinsic properties of the mRNAs of these genes, we demonstrate that under ribosome-deficient conditions, the translation efficiency of mRNAs that have longer coding sequences, lower GC levels, and higher abundance increases, whereas that of mRNAs with opposite characteristics decreases. We provide a mathematical rationale that describes changes in the translatome at a ribosome-deficient state through alterations in the rate of translation initiation and density of ribosomes on mRNA. We propose that, in ribosome deficiency, the decrease in the translation efficiency of mRNAs of genes critical for cell differentiation, such as GATA1, is determined by the intrinsic properties of these mRNAs.