5PSeq analysis conecting translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using fivepseq pipeline http://pelechanolab.com/software/fivepseq/Related manuscript abstract:Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.Raw data:Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession number GSE114899 and GSE151632

补充材料：关于酿酒酵母（Saccharomyces cerevisiae）中翻译延伸与核糖体出口通道蛋白质折叠之间的功能联系。Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, 核苷酸研究杂志, gkaa1200, https://doi.org/10.1093/nar/gkaa1200。在此，我们提供了5'P mRNA降解谱的浏览式元基因分析。原始及处理后的测序数据已存档于基因表达综合数据库（GEO），访问号为GSE114899。数据分析采用fivepseq流程（http://pelechanolab.com/software/fivepseq/）。相关论文摘要：蛋白质稳态的严格控制对于满足细胞对正确从头折叠的蛋白质的需求，以及避免蛋白质聚集至关重要。尽管翻译速率与共翻译折叠之间的耦合关系，可能涉及核糖体及其相关伴侣之间的相互作用，已明显存在，但其潜在机制和核糖体蛋白的贡献仍有待探究。核糖体蛋白uL3含有一个长的内部环，其尖端区域靠近核糖体的肽基转移酶中心。引人注目的是，rpl3[W255C]等位基因中，与催化位点最近接触的残基发生了突变，该突变影响了核糖体生物发生和功能的多个方面。在此，我们通过使用此等位基因进行合成致死筛选，揭示了翻译与核糖体相关Ssb-RAC伴侣系统介导的新生蛋白质折叠之间的意外联系。我们的结果表明，uL3和Ssb-RAC在翻译延伸早期阶段防止80S核糖体在mRNA 5'区域堆积上协同作用。总之，我们的研究为肽键在肽基转移酶中心形成与新生多肽在肽出口通道溶剂侧的伴侣辅助从头折叠之间的功能联系提供了令人信服的体内证据。原始数据：原始及处理后的测序数据已存档于基因表达综合数据库（GEO），访问号为GSE114899和GSE151632。