Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination
Authors:Jesús Gómez-Montalvo1, Alvaro de Obeso Fernández del Valle1, Luis Fernando De la Cruz Gutiérrez1, Jose Mario Gonzalez-Meljem1 and Christian Quintus Scheckhuber1
doi: 10.15698/mic2024.02.816
Volume 11, pp. 69 to 78, published 23/02/2024.
1 Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., México.
Keywords:
Saccharomyces cerevisiae, intron retention, replicative aging, mRNA processing, mRNA export, ubiquitination, transcription regulation.
Corresponding Author(s):
Conflict of interest statement:
The authors declare no conflict of interest.
Please cite this article as:
Jesús Gómez-Montalvo, Alvaro de Obeso Fernández del Valle, Luis Fernando De la Cruz Gutiérrez, José Mario González-Meljem and Christian Quintus Scheckhuber (2024). Replicative aging in yeast involves dynamic intron retention patterns associ-ated with mRNA processing/export and protein ubiquitination. Microbial Cell 11: 69-78. doi: 10.15698/mic2024.02.816
© 2024 Gómez-Montalvo et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged.
Abstract:
Saccharomyces cerevisiae (baker´s yeast) has yielded relevant insights into some of the basic mechanisms of organismal aging. Among these are genomic instability, oxidative stress, caloric restriction and mitochondrial dysfunction. Several genes are known to have an impact on the aging process, with corresponding mutants exhibiting short- or long-lived phenotypes. Research dedicated to unraveling the underlying cellular mechanisms can support the identification of conserved mechanisms of aging in other species. One of the hitherto less studied fields in yeast aging is how the organism regulates its gene expression at the transcriptional level. To our knowledge, we present the first investigation into alternative splicing, particularly intron retention, during replicative aging of S. cerevisiae. This was achieved by utilizing the IRFinder algorithm on a previously published RNA-seq data set by Janssens et al. (2015). In the present work, 44 differentially retained introns in 43 genes were identified during replicative aging. We found that genes with altered intron retention do not display significant changes in overall transcript levels. It was possible to functionally assign distinct groups of these genes to the cellular processes of mRNA processing and export (e.g., YRA1) in early and middle-aged yeast, and protein ubiquitination (e.g., UBC5) in older cells. In summary, our work uncovers a previously unexplored layer of the transcriptional program of yeast aging and, more generally, expands the knowledge on the occurrence of alternative splicing in baker´s yeast.