RPS12 and UBC4 Are Related to Senescence Signal Production in the Ribosomal RNA Gene Cluster

ABSTRACT

Genome instability causes cellular senescence in many organisms. The rRNA gene cluster (rDNA) is one of the most unstable regions in the genome and this instability might convey a signal that induces senescence in the budding yeast. The instability of rDNA mostly depends on replication fork blocking (RFB) activity which induces recombination and gene amplification. By overexpression of Fob1, responsible for the RFB activity, we found that unstable rDNA induces cell cycle arrest and restricts replicative life span. We isolated yeast mutants that grew normally while Fob1 was overexpressed, expecting that some of the mutated genes would be related to the production of a “senescence signal” that elongates cell cycle, stops cell division and finally restricts replicative life span. Our screen identified three suppressor genes, RPS12, UBC4, and CCR4. Replicative life spans of the rps12 and ubc4 mutants were longer than that of wild-type cells. An increase in the levels of extrachromosomal rDNA circles and noncoding transcripts, known to shorten replicative life span, was observed in ubc4 and rps12 respectively, while DNA double strand-breaks at the RFB that are triggers of rDNA instability were reduced in the rps12 mutant. Overall, our observations indicate that Rps12 and Ubc4 contribute to the connection between rDNA instability and replicative life span.

KEYWORDS:

• ribosomal RNA gene (rDNA)
• life span
• budding yeast
• genome instability
• senescence
• noncoding transcription

Declaration of Interests

The authors declare no conflict of interest.

SUPPLEMENTAL MATERIAL

Supplemental material is available online only.

ACKNOWLEDGMENTS

We thank members of the Laboratory of Genome Regeneration for discussion. We also thank Joachim Griesenbeck (University of Regensburg) for pFA6a-MNase-3HAkanMX, Hironori Niki (National Institute of Genetics) for plasmid with mCherry, Seiji Tanaka (Kochi University of Technology) for yeast strains, and Jun-ichi Nakayama (National Institute for Basic Biology) for yeast marker plasmids. This work was supported by JST CREST (Grant Number JPMJCR19S3 to T.K.), Yamada Science Foundation (to T.I.), Institute for Fermentation Osaka (to T.I.), and in part by grants-in-aid for Scientific Research (17H01443 and 21H04761 to T.K., and 20K06600 to T. I.) from the Japan Society for the Promotion of Science.