Arnoux I, Willam M, Griesche N, Krummeich J, Watari H, Offermann N, Weber S, Narayan Dey P, Chen C,
Monteiro O, Buettner S, Meyer K, Bano D, Radyushkin K, Langston R, Lambert JJ, Wanker E, Methner A,
Krauss S, Schweiger S, et al. 2018. Metformin reverses early cortical network dysfunction and behavior changes
in Huntington’s disease. eLife 7:e38744. DOI: https://doi.org/10.7554/eLife.38744, PMID: 30179155
Baryshnikova A. 2016. Systematic Functional Annotation and Visualization of Biological Networks. Cell Systems
2:412–421. DOI: https://doi.org/10.1016/j.cels.2016.04.014, PMID: 27237738
Benaroudj N, Zwickl P, Seemüller E, Baumeister W, Goldberg AL. 2003. ATP hydrolysis by the proteasome
regulatory complex PAN serves multiple functions in protein degradation. Molecular Cell 11:69–78. DOI:
https://doi.org/10.1016/s1097-2765(02)00775-x, PMID: 12535522
Bhat AH, Dar KB, Anees S, Zargar MA, Masood A, Sofi MA, Ganie SA. 2015. Oxidative stress, mitochondrial
dysfunction and neurodegenerative diseases; a mechanistic insight. Biomedicine & Pharmacotherapy =
Biomedecine & Pharmacotherapie 74:101–110. DOI: https://doi.org/10.1016/j.biopha.2015.07.025, PMID:
26349970
Carlson M. 1999. Glucose repression in yeast. Current Opinion in Microbiology 2:202–207. DOI: https://doi.org/
10.1016/S1369-5274(99)80035-6, PMID: 10322167
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS,
Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS,
Simison M, et al. 2012. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic
Acids Research 40:D700–D705. DOI: https://doi.org/10.1093/nar/gkr1029, PMID: 22110037
Daignan-Fornier B, Fink GR. 1992. Coregulation of purine and histidine biosynthesis by the transcriptional
activators BAS1 and BAS2. PNAS 89:6746–6750. DOI: https://doi.org/10.1073/pnas.89.15.6746, PMID:
1495962
Denis V, Boucherie H, Monribot C, Daignan-Fornier B. 1998. Role of the myb-like protein bas1p in
Saccharomyces cerevisiae: a proteome analysis. Molecular Microbiology 30:557–566. DOI: https://doi.org/10.
1046/j.1365-2958.1998.01087.x, PMID: 9822821
Takaine et al. eLife 2022;11:e67659. DOI: https://doi.org/10.7554/eLife.67659
22 of 25
A Self-archived copy in
Kyoto University Research Information Repository
https://repository.kulib.kyoto-u.ac.jp
Cell Biology
Research article
Edelman AM, Blumenthal DK, Krebs EG. 1987. Protein serine/threonine kinases. Annual Review of Biochemistry
56:567–613. DOI: https://doi.org/10.1146/annurev.bi.56.070187.003031, PMID: 2956925
Eftekharzadeh B, Hyman BT, Wegmann S. 2016. Structural studies on the mechanism of protein aggregation in
age related neurodegenerative diseases. Mechanisms of Ageing and Development 156:1–13. DOI: https://doi.
org/10.1016/j.mad.2016.03.001, PMID: 27005270
Eisele YS, Monteiro C, Fearns C, Encalada SE, Wiseman RL, Powers ET, Kelly JW. 2015. Targeting protein
aggregation for the treatment of degenerative diseases. Nature Reviews. Drug Discovery 14:759–780. DOI:
https://doi.org/10.1038/nrd4593, PMID: 26338154
Garcia-Esparcia P, Hernández-Ortega K, Ansoleaga B, Carmona M, Ferrer I. 2015. Purine metabolism gene
deregulation in Parkinson’s disease. Neuropathology and Applied Neurobiology 41:926–940. DOI: https://doi.
org/10.1111/nan.12221, PMID: 25597950
Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. 2008. Co-
regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Molecular
Microbiology 68:1583–1594. DOI: https://doi.org/10.1111/j.1365-2958.2008.06261.x, PMID: 18433446
Ghillebert R, Swinnen E, Wen J, Vandesteene L, Ramon M, Norga K, Rolland F, Winderickx J. 2011. The AMPK/
SNF1/SnRK1 fuel gauge and energy regulator: structure, function and regulation. The FEBS Journal 278:3978–
3990. DOI: https://doi.org/10.1111/j.1742-4658.2011.08315.x, PMID: 21883929
Guthrie C, Fink GR. 2002. Guide to Yeast Genetics and Molecular and Cell Biology: Part C. Gulf Professional
Publishing.
Haelterman NA, Yoon WH, Sandoval H, Jaiswal M, Shulman JM, Bellen HJ. 2014. A mitocentric view of
Parkinson’s disease. Annual Review of Neuroscience 37:137–159. DOI: https://doi.org/10.1146/annurev-neuro-
071013-014317, PMID: 24821430
Hanscho M, Ruckerbauer DE, Chauhan N, Hofbauer HF, Krahulec S, Nidetzky B, Kohlwein SD, Zanghellini J,
Natter K. 2012. Nutritional requirements of the BY series of Saccharomyces cerevisiae strains for optimum
growth. FEMS Yeast Research 12:796–808. DOI: https://doi.org/10.1111/j.1567-1364.2012.00830.x, PMID:
22780918
Hardie DG, Carling D, Carlson M. 1998. The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of
the eukaryotic cell? Annual Review of Biochemistry 67:821–855. DOI: https://doi.org/10.1146/annurev.
biochem.67.1.821, PMID: 9759505
Hardie DG, Schaffer BE, Brunet A. 2016. AMPK: An Energy-Sensing Pathway with Multiple Inputs and Outputs.
Trends in Cell Biology 26:190–201. DOI: https://doi.org/10.1016/j.tcb.2015.10.013, PMID: 26616193
Hattingen E, Magerkurth J, Pilatus U, Mozer A, Seifried C, Steinmetz H, Zanella F, Hilker R. 2009. Phosphorus
and proton magnetic resonance spectroscopy demonstrates mitochondrial dysfunction in early and advanced
Parkinson’s disease. Brain 132:3285–3297. DOI: https://doi.org/10.1093/brain/awp293, PMID: 19952056
Hayes MH, Peuchen EH, Dovichi NJ, Weeks DL. 2018. Dual roles for ATP in the regulation of phase separated
protein aggregates in Xenopus oocyte nucleoli. eLife 7:e35224. DOI: https://doi.org/10.7554/eLife.35224,
PMID: 30015615
Hedbacker K, Carlson M. 2008. SNF1/AMPK pathways in yeast. Frontiers in Bioscience 13:2408–2420. DOI:
https://doi.org/10.2741/2854, PMID: 17981722
Herzig S, Shaw RJ. 2018. AMPK: guardian of metabolism and mitochondrial homeostasis. Nature Reviews.
Molecular Cell Biology 19:121–135. DOI: https://doi.org/10.1038/nrm.2017.95, PMID: 28974774
Hoyle NP, Castelli LM, Campbell SG, Holmes LEA, Ashe MP. 2007. Stress-dependent relocalization of
translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies.
The Journal of Cell Biology 179:65–74. DOI: https://doi.org/10.1083/jcb.200707010, PMID: 17908917
Jain S, Wheeler JR, Walters RW, Agrawal A, Barsic A, Parker R. 2016. ATPase-Modulated Stress Granules Contain
a Diverse Proteome and Substructure. Cell 164:487–498. DOI: https://doi.org/10.1016/j.cell.2015.12.038,
PMID: 26777405
Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, Moreno-Borchart A, Doenges G, Schwob E,
Schiebel E. 2004. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more
markers and promoter substitution cassettes. Yeast (Chichester, England) 21:947–962. DOI: https://doi.org/10.
1002/yea.1142
Janssen E, Dzeja PP, Oerlemans F, Simonetti AW, Heerschap A, Haan A, Rush PS, Terjung RR, Wieringa B,
Terzic A. 2000. Adenylate kinase 1 gene deletion disrupts muscle energetic economy despite metabolic
rearrangement. The EMBO Journal 19:6371–6381. DOI: https://doi.org/10.1093/emboj/19.23.6371, PMID:
11101510
Kaganovich D, Kopito R, Frydman J. 2008. Misfolded proteins partition between two distinct quality control
compartments. Nature 454:1088–1095. DOI: https://doi.org/10.1038/nature07195, PMID: 18756251
Kirkwood TBL, Korolchuk VI, Josefson R, Andersson R, Nyström T. 2017. How and why do toxic conformers of
aberrant proteins accumulate during ageing? Essays in Biochemistry 61:317–324. DOI: https://doi.org/10.1042/
EBC20160085, PMID: 28539486
Kruegel U, Robison B, Dange T, Kahlert G, Delaney JR, Kotireddy S, Tsuchiya M, Tsuchiyama S, Murakami CJ,
Schleit J, Sutphin G, Carr D, Tar K, Dittmar G, Kaeberlein M, Kennedy BK, Schmidt M. 2011. Elevated
proteasome capacity extends replicative lifespan in Saccharomyces cerevisiae. PLOS Genetics 7:e1002253.
DOI: https://doi.org/10.1371/journal.pgen.1002253, PMID: 21931558
Lashuel HA, Overk CR, Oueslati A, Masliah E. 2013. The many faces of α-synuclein: from structure and toxicity to
therapeutic target. Nature Reviews. Neuroscience 14:38–48. DOI: https://doi.org/10.1038/nrn3406, PMID:
23254192
Takaine et al. eLife 2022;11:e67659. DOI: https://doi.org/10.7554/eLife.67659
23 of 25
A Self-archived copy in
Kyoto University Research Information Repository
https://repository.kulib.kyoto-u.ac.jp
Cell Biology
Research article
Ljungdahl PO, Daignan-Fornier B. 2012. Regulation of amino acid, nucleotide, and phosphate metabolism in
Saccharomyces cerevisiae. Genetics 190:885–929. DOI: https://doi.org/10.1534/genetics.111.133306, PMID:
22419079
Marini G, Nüske E, Leng W, Alberti S, Pigino G. 2020. Reorganization of budding yeast cytoplasm upon energy
depletion. Molecular Biology of the Cell 31:1232–1245. DOI: https://doi.org/10.1091/mbc.E20-02-0125, PMID:
32293990
Martinez-Ortiz C, Carrillo-Garmendia A, Correa-Romero BF, Canizal-García M, González-Hernández JC,
Regalado-Gonzalez C, Olivares-Marin IK, Madrigal-Perez LA. 2019. SNF1 controls the glycolytic flux and
mitochondrial respiration. Yeast (Chichester, England) 36:487–494. DOI: https://doi.org/10.1002/yea.3399,
PMID: 31074533
Meriin AB, Zhang X, He X, Newnam GP, Chernoff YO, Sherman MY. 2002. Huntington toxicity in yeast model
depends on polyglutamine aggregation mediated by a prion-like protein Rnq1. The Journal of Cell Biology
157:997–1004. DOI: https://doi.org/10.1083/jcb.200112104, PMID: 12058016
Mochel F, Durant B, Meng X, O’Callaghan J, Yu H, Brouillet E, Wheeler VC, Humbert S, Schiffmann R, Durr A.
2012a. Early alterations of brain cellular energy homeostasis in Huntington disease models. The Journal of
Biological Chemistry 287:1361–1370. DOI: https://doi.org/10.1074/jbc.M111.309849, PMID: 22123819
Mochel F, N’Guyen TM, Deelchand D, Rinaldi D, Valabregue R, Wary C, Carlier PG, Durr A, Henry PG. 2012b.
Abnormal response to cortical activation in early stages of Huntington disease. Movement Disorders 27:907–
910. DOI: https://doi.org/10.1002/mds.25009, PMID: 22517114
Nakano M, Imamura H, Sasaoka N, Yamamoto M, Uemura N, Shudo T, Fuchigami T, Takahashi R, Kakizuka A.
2017. ATP Maintenance via Two Types of ATP Regulators Mitigates Pathological Phenotypes in Mouse Models
of Parkinson’s Disease. EBioMedicine 22:225–241. DOI: https://doi.org/10.1016/j.ebiom.2017.07.024, PMID:
28780078
Outeiro TF, Lindquist S. 2003. Yeast cells provide insight into alpha-synuclein biology and pathobiology. Science
(New York, N.Y.) 302:1772–1775. DOI: https://doi.org/10.1126/science.1090439, PMID: 14657500
Parsell DA, Kowal AS, Lindquist S. 1994. Saccharomyces cerevisiae Hsp104 protein Purification and
characterization of ATP-induced structural changes. The Journal of Biological Chemistry 269:4480–4487 PMID:
8308017.,
Patel A, Malinovska L, Saha S, Wang J, Alberti S, Krishnan Y, Hyman AA. 2017. ATP as a biological hydrotrope.
Science (New York, N.Y.) 356:753–756. DOI: https://doi.org/10.1126/science.aaf6846, PMID: 28522535
Pathak D, Berthet A, Nakamura K. 2013. Energy failure: does it contribute to neurodegeneration? Annals of
Neurology 74:506–516. DOI: https://doi.org/10.1002/ana.24014, PMID: 24038413
Persson LB, Ambati VS, Brandman O. 2020. Cellular Control of Viscosity Counters Changes in Temperature and
Energy Availability. Cell 183:1572-1585.. DOI: https://doi.org/10.1016/j.cell.2020.10.017, PMID: 33157040
Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E,
Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M,
DeRango-Adem E, van Leeuwen J, Shirahige K, et al. 2017. Functional annotation of chemical libraries across
diverse biological processes. Nature Chemical Biology 13:982–993. DOI: https://doi.org/10.1038/nchembio.
2436, PMID: 28759014
Poirier MA, Jiang H, Ross CA. 2005. A structure-based analysis of huntingtin mutant polyglutamine aggregation
and toxicity: evidence for A compact beta-sheet structure. Human Molecular Genetics 14:765–774. DOI:
https://doi.org/10.1093/hmg/ddi071, PMID: 15689354
Pu Y, Li Y, Jin X, Tian T, Ma Q, Zhao Z, Lin S-Y, Chen Z, Li B, Yao G, Leake MC, Lo C-J, Bai F. 2019. ATP-
Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic
Tolerance. Molecular Cell 73:143-156.. DOI: https://doi.org/10.1016/j.molcel.2018.10.022, PMID: 30472191
R Development Core Team. 2017. R: A Language and Environment for Statistical Computing. Vienna, Austria. R
Foundation for Statistical Computing. http://www.r-project.org
Rotermund C, Machetanz G, Fitzgerald JC. 2018. The Therapeutic Potential of Metformin in Neurodegenerative
Diseases. Frontiers in Endocrinology 9:400. DOI: https://doi.org/10.3389/fendo.2018.00400, PMID: 30072954
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S,
Schmid B, Tinevez J-Y, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. 2012. Fiji: an open-source
platform for biological-image analysis. Nature Methods 9:676–682. DOI: https://doi.org/10.1038/nmeth.2019,
PMID: 22743772
Seo AY, Lau PW, Feliciano D, Sengupta P, Gros MAL, Cinquin B, Larabell CA, Lippincott-Schwartz J. 2017. AMPK
and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under
glucose starvation. eLife 6:e21690. DOI: https://doi.org/10.7554/eLife.21690, PMID: 28394250
Sharma N, Brandis KA, Herrera SK, Johnson BE, Vaidya T, Shrestha R, DebBurman SK. 2006. α-synuclein budding
yeast model. Journal of Molecular Neuroscience 28:161–178. DOI: https://doi.org/10.1385/JMN:28:2:161,
PMID: 16679556
Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM. 2019. Proteome-
wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. Nature Communications
10:1155. DOI: https://doi.org/10.1038/s41467-019-09107-y, PMID: 30858367
Takaine M. 2019. QUEEN-based Spatiotemporal ATP Imaging in Budding and Fission Yeast. Bio-Protocol
9:e3320. DOI: https://doi.org/10.21769/BioProtoc.3320, PMID: 33654827
Takaine M, Ueno M, Kitamura K, Imamura H, Yoshida S. 2019. Reliable imaging of ATP in living budding and
fission yeast. Journal of Cell Science 132:jcs230649. DOI: https://doi.org/10.1242/jcs.230649, PMID: 30858198
Takaine et al. eLife 2022;11:e67659. DOI: https://doi.org/10.7554/eLife.67659
24 of 25
A Self-archived copy in
Kyoto University Research Information Repository
https://repository.kulib.kyoto-u.ac.jp
Cell Biology
Research article
Tanaka K, Waxman L, Goldberg AL. 1983. ATP serves two distinct roles in protein degradation in reticulocytes,
one requiring and one independent of ubiquitin. The Journal of Cell Biology 96:1580–1585. DOI: https://doi.
org/10.1083/jcb.96.6.1580, PMID: 6304111
Tofaris GK, Kim HT, Hourez R, Jung JW, Kim KP, Goldberg AL. 2011. Ubiquitin ligase Nedd4 promotes
α-synuclein degradation by the endosomal–lysosomal pathway. PNAS 108:17004–17009. DOI: https://doi.org/
10.1073/pnas.1109356108, PMID: 21953697
Usaj M, Tan Y, Wang W, VanderSluis B, Zou A, Myers CL, Costanzo M, Andrews B, Boone C. 2017. TheCellMap.
org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network. G3:
Genes, Genomes, Genetics 7:1539–1549. DOI: https://doi.org/10.1534/g3.117.040220, PMID: 28325812
Wijayanti I, Watanabe D, Oshiro S, Takagi H. 2015. Isolation and functional analysis of yeast ubiquitin ligase Rsp5
variants that alleviate the toxicity of human α-synuclein. The Journal of Biochemistry 157:251–260. DOI:
https://doi.org/10.1093/jb/mvu069
Willingham S, Outeiro TF, DeVit MJ, Lindquist SL, Muchowski PJ. 2003. Yeast Genes That Enhance the Toxicity of
a Mutant Huntingtin Fragment or α-Synuclein. Science 302:1769–1772. DOI: https://doi.org/10.1126/science.
1090389, PMID: 14657499
Wilson WA, Hawley SA, Hardie DG. 1996. Glucose repression/derepression in budding yeast: SNF1 protein
kinase is activated by phosphorylation under derepressing conditions, and this correlates with a high AMP:ATP
ratio. Current Biology: CB 6:1426–1434. DOI: https://doi.org/10.1016/S0960-9822(96)00747-6
Xiao B, Heath R, Saiu P, Leiper FC, Leone P, Jing C, Walker PA, Haire L, Eccleston JF, Davis CT, Martin SR,
Carling D, Gamblin SJ. 2007. Structural basis for AMP binding to mammalian AMP-activated protein kinase.
Nature 449:496–500. DOI: https://doi.org/10.1038/nature06161, PMID: 17851531
Xie Y, Varshavsky A. 2001. RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a
negative feedback circuit. PNAS 98:3056–3061. DOI: https://doi.org/10.1073/pnas.071022298, PMID:
11248031
Yaginuma H, Kawai S, Tabata KV, Tomiyama K, Kakizuka A, Komatsuzaki T, Noji H, Imamura H. 2014. Diversity in
ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging. Scientific
Reports 4:6522. DOI: https://doi.org/10.1038/srep06522, PMID: 25283467
Takaine et al. eLife 2022;11:e67659. DOI: https://doi.org/10.7554/eLife.67659
25 of 25
...