Stoichiometry Of Ribosomal Proteins Research Articles

A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.

Exploring Ribosome Code: Unveiling A Novel Dimension of Gene Regulation in Carcinogenesis

The central dogma of molecular biology has traditionally viewed ribosomes as uniform entities translating mRNA into proteins with mechanical precision. Recent findings challenge this perspective, revealing unexpected ribosome heterogeneity within cells, thus proposing a novel mechanism for diversifying protein synthesis. This concept parallels the “histone code” hypothesis, leading to the proposition of a “ribosome code” that suggests variations in ribosomal protein stoichiometry, paralogs, and modifications may preferentially translate certain mRNA populations. The role of ribosome heterogeneity in cancer pathogenesis, however, remains a subject of debate. Evidence suggests that alterations in ribosome composition, structure, and activity could influence abnormal protein synthesis, thus contributing to tumorigenesis. This is supported by the correlation between enhanced ribosome biogenesis, protein synthesis, and tumor growth, as well as the observed modifications in cancer ribosomes. Examining the nuances of ribosome heterogeneity, its influence on translational biases, and implications for tumor biology could significantly deepen our understanding of cancer’s molecular landscape, potentially unveiling novel therapeutic targets.

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.

Coordinate regulation of ribosomal protein (RP) genes is key for controlling cell growth. In yeast, it is unclear how this regulation achieves the required equimolar amounts of the different RP components, given that some RP genes exist in duplicate copies, while others have only one copy. Here, we tested whether the solution to this challenge is partly encoded within the DNA sequence of the RP promoters, by fusing 110 different RP promoters to a fluorescent gene reporter, allowing us to robustly detect differences in their promoter activities that are as small as ~10%. We found that single-copy RP promoters have significantly higher activities, suggesting that proper RP stoichiometry is indeed partly encoded within the RP promoters. Notably, we also partially uncovered how this regulation is encoded by finding that RP promoters with higher activity have more nucleosome-disfavoring sequences and characteristic spatial organizations of these sequences and of binding sites for key RP regulators. Mutations in these elements result in a significant decrease of RP promoter activity. Thus, our results suggest that intrinsic (DNA-dependent) nucleosome organization may be a key mechanism by which genomes encode biologically meaningful promoter activities. Our approach can readily be applied to uncover how transcriptional programs of other promoters are encoded.

Variations in stoichiometry of ribosomal proteins in Escherichia coli

Experiments are described in which the Stoichiometry of the ribosomal proteins before and after ribosome release from mRNA is compared. Polysomes labeled with 3H (or 14C) and run-off 70 S particles (Subramanian el al., 1969) labeled with 14C (or 3H) were separately isolated, mixed, and the ribosomal proteins extracted and fractionated by two-dimensional gel electrophoresis. The measurement of the isotopic ratios shows that 47 proteins out of the 53 investigated are present in the same amount in polysomes as in run-off ribosomes indicating that they remain with the ribosome during the release step. Proteins S 1, S 2, S 6, S 21, L 7 L 12 (Wittmann et al., 1971), however, show higher amounts in polysomes than in run-off ribosomes. The significance of these results is discussed.