{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T11:04:26Z","timestamp":1776683066512,"version":"3.51.2"},"reference-count":107,"publisher":"Shared Science Publishers OG","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"Abstract<\/jats:title>\n \n The Juvenile form of Batten disease is a neurodegenerative disease with symptoms starting in the first decade and ending in death in the third decade of life.\u00a0The gene defective in this form of Batten disease,\n CLN3<\/jats:italic>\n , is conserved in eukaryotes, suggesting that the gene product serves a basic function in the cell, though the function is unknown. We have investigated the expression and regulation of the yeast homolog BTN1.\u00a0Reanalysis of publicly available gene expression data suggests that transcription of BTN1 increases in response to oxidative stress, treatment with rapamycin or arsenate, amino acid starvation, and sporulation conditions. Similar to GCN4, there are upstream open reading frames (uORF) in front of BTN1, suggesting translational regulation. We developed reporter strains in which the HIS3 open reading frame replaced that of the BTN1 gene, with and without the uORFs.\u00a0These reporters show that one or more of the uORFs decrease the expression of the HIS3 reporter.\u00a0When expressed in the reporter strain using a high copy vector, GCN3, tRNA\n \n \n \n \n \n Arg<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msup>\n <\/mml:math>\n <\/jats:inline-formula>\n , and tRNA\n \n \n \n \n \n Leu<\/mml:mi>\n <\/mml:mrow>\n <\/mml:msup>\n <\/mml:math>\n <\/jats:inline-formula>\n , increase expression, suggesting the involvement of the TORC1 pathway.\u00a0BIT61 abuts BTN1 but is encoded on the opposite strand; 3\u2019 RACE analysis indicates that the mRNA of BIT61 overlaps with that of BTN1.\u00a0BIT61 is involved in the TORC2 pathway, which interacts with the TORC1 pathway, suggesting a possible cis-acting mechanism of co-regulation.\u00a0Lastly, we demonstrate that a yeast strain with a null mutation in BTN1 is sensitive to selective amino acid starvation, further supporting the association of BTN1 with TORC1.\n <\/jats:p>","DOI":"10.15698\/mic2026.03.872","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T10:21:17Z","timestamp":1776680477000},"page":"131-147","source":"Crossref","is-referenced-by-count":0,"title":["TOR-dependent regulation of\u00a0the yeast homolog of the juvenile Batten\u00a0Disease-associated gene CLN3"],"prefix":"10.15698","volume":"13","author":[{"given":"Vijaykumar","family":"Pillalamarri","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel W.M.","family":"Gatesy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda E.","family":"Grassel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucienna","family":"Wolf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin P.","family":"Whalley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"6394","published-online":{"date-parts":[[2026,3,11]]},"reference":[{"issue":"8","key":"b00f1f","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1007\/s11910-013-0366-z","article-title":"Neuronal ceroid lipofuscinosis: impact of recent genetic advances and expansion of the clinicopathologic spectrum","volume":"13","author":"Cotman","year":"2013","journal-title":"Curr Neurol Neurosci 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Disease)","author":"\u212bberg","year":"2011"},{"key":"b0132d","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1093\/med\/9780199590018.003.0002","article-title":"2 NCL Nomenclature and Classification","volume-title":"The Neuronal Ceroid Lipofuscinoses (Batten Disease)","author":"Williams","year":"2011"},{"key":"b013ee","article-title":"Mutation and Patient Datasheets for Human NCL genes [Internet]","author":"University College London","year":"2023"},{"issue":"710","key":"b01431","article-title":"Patterns of Retinal Ganglion Cell Damage in Neurodegenerative Disorders: Parvocellular vs Magnocellular Degeneration in Optical Coherence Tomography Studies","volume":"8","author":"La\u00a0Morgia","year":"2017","journal-title":"Front Neurol"},{"issue":"3","key":"b014a9","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1042\/bj2680751","article-title":"The sequence of the major protein stored in ovine ceroid lipofuscinosis is identical with that of the dicyclohexylcarbodiimide-reactive proteolipid of mitochondrial ATP synthase","volume":"268","author":"Fearnley","year":"1990","journal-title":"Biochem J"},{"issue":"4","key":"b01544","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1002\/ajmg.1320420428","article-title":"Mitochondrial ATP synthase subunit c storage in the ceroid-lipofuscinoses (Batten disease)","volume":"42","author":"Palmer","year":"1992","journal-title":"Am J Med Genet"},{"key":"b015df","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2023.104628","article-title":"Juvenile CLN3 disease is a lysosomal cholesterol storage disorder: similarities with Niemann-Pick type C disease","volume":"92","author":"Chen","year":"2023","journal-title":"EBioMedicine"},{"issue":"Pt 23","key":"b01674","doi-asserted-by":"crossref","first-page":"5525","DOI":"10.1242\/jcs.02656","article-title":"btn1, the Schizosaccharomyces pombe homologue of the human Batten disease gene CLN3, regulates vacuole homeostasis","volume":"118","author":"Gachet","year":"2005","journal-title":"J Cell Sci"},{"issue":"6","key":"b016f6","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1111\/j.1600-0854.2008.00735.x","article-title":"btn1 affects endocytosis, polarization of sterol-rich membrane domains and polarized growth in Schizosaccharomyces pombe","volume":"9","author":"Codlin","year":"2008","journal-title":"Traffic"},{"issue":"12","key":"b01769","doi-asserted-by":"crossref","first-page":"e859","DOI":"10.1002\/mgg3.859","article-title":"The CLN3 gene and protein: What we know","volume":"7","author":"Mirza","year":"2019","journal-title":"Mol Genet Genomic Med"},{"issue":"2","key":"b01801","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1006\/bbrc.1998.9272","article-title":"The subcellular location of the yeast Saccharomyces cerevisiae homologue of the protein defective in the juvenile form of Batten 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Res"},{"issue":"11","key":"b01b5e","first-page":"2375","article-title":"Immunochemical localization of the Batten disease (CLN3) protein in retina","volume":"38","author":"Katz","year":"1997","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"6","key":"b01bf8","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1111\/j.1471-4159.2007.04920.x","article-title":"Increased expression of lysosomal acid phosphatase in CLN3-defective cells and mouse brain tissue","volume":"103","author":"Pohl","year":"2007","journal-title":"J Neurochem"},{"issue":"22","key":"b01c94","doi-asserted-by":"crossref","first-page":"5851","DOI":"10.1046\/j.0014-2956.2001.02530.x","article-title":"Elevated lysosomal pH in neuronal ceroid lipofuscinoses (NCLs)","volume":"268","author":"Holopainen","year":"2001","journal-title":"Eur J Biochem"},{"issue":"23","key":"b01d14","doi-asserted-by":"crossref","first-page":"3759","DOI":"10.1093\/hmg\/ddi406","article-title":"Defective lysosomal arginine transport in 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Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1","volume":"347","author":"Wang","year":"2015","journal-title":"Science"},{"issue":"3","key":"b02698","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyae185","article-title":"Saccharomyces Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements","volume":"229","author":"Engel","year":"2025","journal-title":"Genetics"},{"issue":"26","key":"b0272e","doi-asserted-by":"crossref","first-page":"14866","DOI":"10.1073\/pnas.96.26.14866","article-title":"Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins","volume":"96","author":"Hardwick","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"24","key":"b027bb","doi-asserted-by":"crossref","first-page":"2696","DOI":"10.1101\/gad.207407.112","article-title":"Aneuploidy causes proteotoxic stress in 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