Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae

Nucleic Acids Research
Maria G IacovellaPeter De Wulf

Abstract

The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast's protein-protein and protein-DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserv...Continue Reading

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Citations

May 16, 2019·The EMBO Journal·Katherine E Bohnsack, Markus T Bohnsack
Jul 4, 2019·The EMBO Journal·Katherine E Bohnsack, Markus T Bohnsack
Jul 31, 2019·Cells·Emiliano Matos-Perdomo, Félix Machín
Feb 23, 2020·Genes·Sonia Vidushi Gupta, Kristina Hildegard Schmidt

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Datasets Mentioned

BETA
GSE70287

Methods Mentioned

BETA
GTPase
two-hybrid
electron microscopy
dissection
co-immunoprecipitation
Y2H
co-IP
electrophoresis
Chip
RNA-Seq

Software Mentioned

HTSeq
stats
LP Data View
ImageQuant
Genomic Association Test gat run
ResponseNet
Prism
SoftWoRx
SAMtools
TRANSFAC

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