Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements

Abstract

We describe a novel approach to separate two ribosome populations from the same cells and use this method, and RNA-seq, to identify the mRNAs bound to S. cerevisiae ribosomes with and without Rps26, a protein linked to the pathogenesis of Diamond Blackfan Anemia (DBA). These analyses reveal that Rps26 contributes to mRNA-specific translation by recognition of the Kozak sequence in well-translated mRNAs, and that Rps26-deficient ribosomes preferentially translate mRNA from select stress response pathways. Surprisingly, exposure of yeast to these stresses leads to the formation of Rps26-deficient ribosomes and to the increased translation of their target mRNAs. These results describe a novel paradigm, the production of specialized ribosomes, which play physiological roles in augmenting the well-characterized transcriptional stress response with a heretofore unknown translational response, thereby creating a feed forward loop in gene-expression. Moreover, the simultaneous gain-of-function and loss-of-function phenotypes from Rps26-deficient ribosomes can explain the pathogenesis of DBA.

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

“…This role could be in addition to the role in promoting the rotated state described herein, and is therefore fully consistent with this report, although alternative explanations for the genetic interaction between Fap7 and Tsr2 have been described (Ferretti et al, 2017). …”

A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements

“…Interestingly, RPS26 is involved in the recognition of the Kozak sequence (67). Indeed, ribosomes that lack RPS26 have a greater propensity to translate proteins that do not start with canonical Kozak leader sequences.…”

Ribosome stoichiometry: from form to function.

“…Even the prominent example suggesting ribosome specialization, RPL38 regulating HOX genes [39,42], falls short of direct proof since (i) its exclusive specificity to 3 HOX is implied and not directly measured and (ii) the existence of ribosomes lacking RPL38 in wildtype cells is assumed, not measured. However, more recent data from the Barna lab identified distinct mRNA subsets exhibiting enriched or diminished ribosome association with subsets of ribosomes enriched for RPL10a [24], and Ferretti & colleagues demonstrated a specific role for RPS26-containing ribosomes [37]. These data had the advantage that the ribosomes and their mRNA specificity were identified from transgenic cells, rather than knockouts or a disease state.…”

“…In favor of broader specificity, Zhen Shi and colleagues recently demonstrated this can occur in wild-type cells with ribosomes enriched in RPL10A preferentially translating a subset of mRNAs containing IRES elements [24]. Recent work in yeast also identified RPS26-deficient ribosomes that preferentially bind mRNAs involved in select stress response pathways by selecting mRNAs with deviations in their Kozak sequence at the -4 position [37]. Horos et al, 2012 [38] reported that a single RP, S19, affects the ribosomal density along hundreds of mRNAs essential for the differentiation of murine and human erythroblasts.…”