Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation

Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.

Translatomics to explore dynamic differences in immunocytes in the tumor microenvironment

Protein is an essential component of all living organisms and is primarily responsible for life activities; furthermore, its synthesis depends on a highly complex and accurate translation system. For proteins, the regulation at the translation level exceeds the sum of that during transcription, mRNA degradation, and protein degradation. Therefore, it is necessary to study regulation at the translation level. Imbalance in the translation process may change the cellular landscape, which not only leads to the occurrence, maintenance, progression, invasion, and metastasis of cancer but also affects the function of immune cells and changes the tumor microenvironment. Detailed analysis of transcriptional and protein atlases is needed to better understand how gene translation occurs. However, a more rigorous direct correlation between mRNA and protein levels is needed, which somewhat limits further studies. Translatomics is a technique for capturing and sequencing ribosome-related mRNAs that can effectively identify translation changes caused by ribosome stagnation and local translation abnormalities during cancer occurrence to further understand the changes in the translation landscape of cancer cells themselves and immune cells in the tumor microenvironment, which can provide new strategies and directions for tumor treatment.

Genome-Wide Analysis of Translation in Replicatively Aged Yeast

Protein synthesis is an essential process that affects major cellular functions including growth, energy production, cell signaling, and enzymatic reactions. However, how it is impacted by aging and how the translation of specific proteins is changed during the aging process remain understudied. Although yeast is a widely used model for studying eukaryotic aging, analysis of age-related translational changes using ribosome profiling in this organism has been challenging due to the need for isolating large quantities of old cells. Here, we provide a detailed protocol for genome-wide analysis of protein synthesis using ribosome profiling in replicatively aged yeast. By combining genetic enrichment of old cells with the biotin affinity purification step, this method allows large-scale isolation of aged cells sufficient for generating ribosome profiling libraries. We also describe a strategy for normalization of samples using a spike-in with worm lysates that permits quantitative comparison of absolute translation levels between young and old cells.

Genetic screen identifies adaptive aneuploidy as a key mediator of ER stress resistance in yeast

The yeast genome becomes unstable during stress, which often results in adaptive aneuploidy, allowing rapid activation of protective mechanisms that restore cellular homeostasis. In this study, we performed a genetic screen in Saccharomyces cerevisiae to identify genome adaptations that confer resistance to tunicamycin-induced endoplasmic reticulum (ER) stress. Whole-genome sequencing of tunicamycin-resistant mutants revealed that ER stress resistance correlated significantly with gains of chromosomes II and XIII. We found that chromosome duplications allow adaptation of yeast cells to ER stress independently of the unfolded protein response, and that the gain of an extra copy of chromosome II alone is sufficient to induce protection from tunicamycin. Moreover, the protective effect of disomic chromosomes can be recapitulated by overexpression of several genes located on chromosome II. Among these genes, overexpression of UDP-N-acetylglucosamine-1-P transferase (ALG7), a subunit of the 20S proteasome (PRE7), and YBR085C-A induced tunicamycin resistance in wild-type cells, whereas deletion of all three genes completely reversed the tunicamycin-resistance phenotype. Together, our data demonstrate that aneuploidy plays a critical role in adaptation to ER stress by increasing the copy number of ER stress protective genes. While aneuploidy itself leads to proteotoxic stress, the gene-specific effects of chromosome II aneuploidy counteract the negative effect resulting in improved protein folding.