Nucleic Acids Research, 2018 1 doi: 10.1093/nar/gky618 Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae Maria G. Iacovella 1 , Michael Bremang 1,2,† , Omer Basha 3,† , Luciano Giac ` o 1,† , Walter Carotenuto 4 , Cristina Golfieri 1 , Barnabas Szakal 4 , Marianna Dal Maschio 1 , Valentina Infantino 1 , Galina V. Beznoussenko 4 , Chinnu R. Joseph 4 , Clara Visintin 1 , Alexander A. Mironov 4 , Rosella Visintin 1 , Dana Branzei 4,5 ,S´ ebastien Ferreira-Cerca 6 , Esti Yeger-Lotem 3 and Peter De Wulf 1,7,*,‡ 1 Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy, 2 Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom, 3 Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel, 4 The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy, 5 Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy, 6 Lehrstuhl f ¨ ur Biochemie III, Universit ¨ at Regensburg, Universit¨ atsstraße 31, 93053 Regensburg, Germany and 7 Centre for Integrative Biology (CIBIO), University of Trento, ViaSommarive 9, 38123 Trento, Italy Received January 10, 2018; Revised May 29, 2018; Editorial Decision June 26, 2018; Accepted June 28, 2018 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. Like- wise, RIOK1 promotes 40S ribosomal subunit bio- genesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the pro- tein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availabil- ity, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physi- cal 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 computa- tion. We experimentally confirmed network compo- nents 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 expres- sion), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that patho- logical RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, un- restrained metabolism and proliferation; established contributors to cancer. Our study will advance the un- derstanding of numerous processes, here revealed to depend on Rio1 activity. INTRODUCTION The RIO family of atypical protein kinases is found in most archaea, bacteria and eukaryotes (1–5). Lower eukaryotes including the budding yeast Saccharomyces cerevisiae com- prise two subfamilies: Rio1/RIOK1 and Rio2/RIOK2, while higher eukaryotes, including humans, contain an ad- ditional subfamily: RIOK3. From archaea to higher eu- karyotes, Rio1 promotes the 3 ′ -end processing of the small ribosomal subunit pre-rRNA and mediates the release of late biogenesis factors during small ribosomal particle mat- uration. Importantly, as far as the process of ribosome bio- genesis is concerned, Rio1 can act as a kinase as well as an adenosine triphosphatase (ATPase) (6–15). In budding * To whom correspondence should be addressed. Tel: +39 0461285359; Fax: +39 0461283937; Email: peter.dewulf@unitn.it † The authors wish it to be known that, in their opinion, the third and fourth authors should be regarded as Joint Second Authors. ‡ Lead contact. C  The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gky618/5054092 by guest on 16 July 2018