2026-10-11T10:17:13Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34003650 2026-09-26T16:07:43Z category_1 category_4 category_7 category_8 category_12 category_13 category_14 category_24 category_45 category_39 category_734 category_132 portal_63 item_type_3 month_year_09_2026

Stress-Induced Reprogramming of tRNA Epitranscriptome in the Industrially Important Yeast Komagataella phaffii Alex Reading (25114830) Chi-Kong Chan (2873678) Rahul Raman (182763) Michael S. DeMott (235117) Thomas J. Begley (8729661) Peter C. Dedon (235122) Biophysics Biochemistry Medicine Microbiology Cell Biology Genetics Molecular Biology Evolutionary Biology Sociology Ecology Biological Sciences not elsewhere classified Infectious Diseases core modification machinery combined comparative genomics small rna isolated nonconventional industrial yeasts supporting lysidine biology putative lysidine synthase industrially important yeast trna modification system trna modification levels modifications regulate codon saccharomyces cerevisiae </ komagataella phaffii </ conserved epitranscriptome machinery 2 </ sup 5 </ sup cerevisiae </ trna epitranscriptome transfer rna industrial applications 2 ′-< phaffii </ structured remodeling specific codon segregated primarily responsive remodeling overall architecture modifying orthologs methyl methanesulfonate liquid chromatography induced reprogramming findings support extensively characterized equitoxic doses epitranscriptomic landscape environmental stresses diverse organisms differentially regulated dependent responses broad conservation biased translation alkylating stresses >- dimethylcytidine >, little Transfer RNA (tRNA) modifications regulate codon-biased translation and enable rapid translational adaptation to environmental stresses in diverse organisms. While these mechanisms have been extensively characterized in Saccharomyces cerevisiae, little is known about the epitranscriptomic landscape of nonconventional industrial yeasts such as Komagataella phaffii. Here, we combined comparative genomics and liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) to define the tRNA epitranscriptome of K. phaffii and compare its stress-responsive remodeling to that of S. cerevisiae under oxidative and alkylating stresses. Comparative genomic analysis identified 65 shared tRNA-modifying orthologs, consistent with broad conservation of core modification machinery. LC-MS/MS profiling identified 33 modified ribonucleosides in small RNA isolated from S. cerevisiae and 35 in K. phaffii, including two modifications, lysidine (k2C) and 5,2′-O-dimethylcytidine (m5Cm), uniquely detected in K. phaffii. Further supporting lysidine biology in K. phaffii was the identification of a putative lysidine synthase in its genome. Exposure to equitoxic doses of methyl methanesulfonate and hydrogen peroxide induced extensive and structured remodeling of tRNA modification levels in both species. Several wobble uridine modifications associated with codon-biased translation exhibited stress- and species-dependent responses, while hierarchical clustering revealed distinct modification signatures that segregated primarily by stress type and secondarily by yeast species. Although the overall architecture of the tRNA modification system was conserved, the magnitude and direction of stress-induced remodeling differed substantially between species. These findings support a model in which conserved epitranscriptome machinery is differentially regulated to shape species-specific codon-biased translation during stress adaptation, which has implications for industrial applications of the yeast species. 2026-09-26T00:00:00Z Dataset Dataset 10.1021/acs.chemrestox.6c00393.s001 https://figshare.com/articles/dataset/Stress-Induced_Reprogramming_of_tRNA_Epitranscriptome_in_the_Industrially_Important_Yeast_Komagataella_phaffii/34003650 CC BY-NC 4.0