tRNA wobble-uridine modifications as amino acid sensors and regulators of cellular metabolic state

Current Genetics - Tập 66 Số 3 - Trang 475-480 - 2020
Ritu Gupta1, Sunil Laxman1
1InStem-Institute for Stem Cell Science and Regenerative Medicine, GKVK Post Bellary Road, Bangalore, 560065, India

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Boer VM, De Winde JH, Pronk JT, Piper MDW (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem. https://doi.org/10.1074/jbc.M209759200

Boer VMVM, Crutchfield CACA, Bradley PHPH et al (2010) Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell 21:198–211. https://doi.org/10.1091/mbc.E09-07-0597

Brauer MJMJ, Huttenhower C, Airoldi EMEM et al (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 19:267–352. https://doi.org/10.1091/mbc.E07-08-0779

Broach JR (2012) Nutritional control of growth and development in yeast. Genetics 192:73–105. https://doi.org/10.1534/genetics.111.135731

Cai L, Tu BP (2011) On acetyl-CoA as a gauge of cellular metabolic state. Cold Spring Harb Perspect Biol 76:195–202

Cai L, Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28:59–87. https://doi.org/10.1146/annurev-cellbio-092910-154010

Candiracci J, Migeot V, Chionh Y-H et al (2019) Reciprocal regulation of TORC signaling and tRNA modifications by Elongator enforces nutrient-dependent cell fate. Sci Adv 5:eaav0184. https://doi.org/10.1126/sciadv.aav0184

Chou H-J, Donnard E, Gustafsson HT et al (2017) Transcriptome-wide analysis of roles for tRNA modifications in translational regulation. Mol Cell. https://doi.org/10.1016/j.molcel.2017.11.002

Eskes E, Deprez MA, Wilms T, Winderickx J (2018) pH homeostasis in yeast; the phosphate perspective. Curr, Genet

Glatt S, Zabel R, Kolaj-Robin O et al (2016) Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Nat Struct Mol Biol 23:794–802. https://doi.org/10.1038/nsmb.3265

Goehring AS (2003) Urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast. Mol Biol Cell. https://doi.org/10.1091/mbc.E03-02-0079

González A, Hall MN (2017) Nutrient sensing and TOR signaling in yeast and mammals. EMBO J 8:e201696010. https://doi.org/10.15252/embj.201696010

Gresham D, Boer VM, Caudy A et al (2011) System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. https://doi.org/10.1534/genetics.110.120766

Gupta R, Walvekar AS, Liang S et al (2019) A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis. Elife 8:e44795. https://doi.org/10.7554/eLife.44795

Han L, Guy MP, Kon Y, Phizicky EM (2018) Lack of 2′-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway. PLoS Genet 14:1–25. https://doi.org/10.1371/journal.pgen.1007288

Hesketh A, Oliver SG (2019) High-energy guanine nucleotides as a signal capable of linking growth to cellular energy status via the control of gene transcription. Curr, Genet

Hesketh A, Vergnano M, Oliver SG (2019) Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides. MBio 10:e02500–e02518. https://doi.org/10.1128/mBio.02500-18

Hinnebusch AG (2005) translational regulation of GCN4 and the general amino acid control of yeast*. Annu Rev Microbiol 59:407–450. https://doi.org/10.1146/annurev.micro.59.031805.133833

Kankipati HN, Rubio-Texeira M, Castermans D et al (2015) Sul1 and Sul2 sulfate transceptors signal to protein kinase A upon exit of sulfur starvation. J Biol Chem 290:10430–10446. https://doi.org/10.1074/jbc.M114.629022

Klassen R, Ciftci A, Funk J et al (2016) TRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast. Nucleic Acids Res. https://doi.org/10.1093/nar/gkw705

Kudlicki A, Rowicka M, Otwinowski Z (2007) SCEPTRANS: an online tool for analyzing periodic transcription in yeast. Bioinformatics 23:1559–1561

Laxman S, Tu BP (2011) Multiple TORC1-associated proteins regulate nitrogen starvation-dependent cellular differentiation in Saccharomyces cerevisiae. PLoS One. https://doi.org/10.1371/journal.pone.0026081

Laxman S, Sutter BMBM, Wu XX et al (2013) Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation. Cell 154:416–429. https://doi.org/10.1016/j.cell.2013.06.043

Leidel S, Pedrioli PGA, Bucher T et al (2009) Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature. https://doi.org/10.1038/nature07643

Li Q, Fazly AM, Zhou H et al (2009) The elongator complex interacts with PCNA and modulates transcriptional silencing and sensitivity to DNA damage agents. PLoS Genet 5:e1000684. https://doi.org/10.1371/journal.pgen.1000684

Lin TY, Abbassi NEH, Zakrzewski K et al (2019) The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun. https://doi.org/10.1038/s41467-019-08579-2

Liu N-N, Flanagan PR, Zeng J et al (2017) Phosphate is the third nutrient monitored by TOR in Candida albicans and provides a target for fungal-specific indirect TOR inhibition. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.1617799114

Nakai Y, Umeda N, Suzuki T et al (2004) Yeast Nfs1p is involved in thio-modification of both mitochondrial and cytoplasmic tRNAs. J Biol Chem 279:12363–12368. https://doi.org/10.1074/jbc.M312448200

Nakai Y, Nakai M, Lill R et al (2007) Thio modification of yeast cytosolic tRNA is an iron-sulfur protein-dependent pathway. Mol Cell Biol 27:2841–2847. https://doi.org/10.1128/MCB.01321-06

Nakai Y, Nakai M, Hayashi H (2008) Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems. J Biol Chem 283:27469–27476. https://doi.org/10.1074/jbc.M804043200

Nedialkova DD, Leidel SA (2015) Optimization of codon translation rates via tRNA modifications maintains proteome integrity. Cell 161:1–13. https://doi.org/10.1016/j.cell.2015.05.022

Phizicky EM, Hopper AK (2010) tRNA biology charges to the front. Genes Dev 24:1832–1860. https://doi.org/10.1101/gad.1956510

Rapino F, Delaunay S, Rambow F et al (2018) Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature. https://doi.org/10.1038/s41586-018-0243-7

Saldanha A, Brauer M, Botstein D (2004) Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. https://doi.org/10.1091/mbc.E04-04-0306

Scheidt V, Juedes A, Baer C et al (2014) Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling. Microb Cell 1:416–424. https://doi.org/10.15698/mic2014.12.179

Schmelzle T, Hall MN (2000) TOR, a central controller of cell growth. Cell 103:253–262

Schmitz J, Chowdhury MM, Hänzelmann P et al (2008) The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins. Biochemistry 47:6479–6489. https://doi.org/10.1021/bi800477u

Schneper L, Düvel K, Broach JR (2004) Sense and sensibility: nutritional response and signal integration in yeast. Curr Opin Microbiol 7:624–630. https://doi.org/10.1016/j.mib.2004.10.002

Slavov N, Botstein D (2011) Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol Biol Cell 22:1997–2009. https://doi.org/10.1091/mbc.E11-02-0132

Teng X, Hardwick JM (2019) Whi2: a new player in amino acid sensing. Curr, Genet

Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005a) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310:1152–1158. https://doi.org/10.1126/science.1120499

Tu BP, Tu BP, Kudlicki A et al (2005b) Logic of the yeast metabolic cycle: of cellular processes. Science. https://doi.org/10.1126/science.1120499

Tu BP, Mohler RE, Liu JC et al (2007) Cyclic changes in metabolic state during the life of a yeast cell. Proc Natl Acad Sci USA 104:16886–16891. https://doi.org/10.1073/pnas.0708365104

Walvekar AS, Srinivasan R, Gupta R, Laxman S (2018) Methionine coordinates a hierarchically organized anabolic program enabling proliferation. Mol Biol Cell 29:3183–3200. https://doi.org/10.1091/mbc.E18-08-0515

Wellen KE, Thompson CB (2012) A two-way street: reciprocal regulation of metabolism and signalling. Nat Rev Mol Cell Biol 13:270–276. https://doi.org/10.1038/nrm3305

Wullschleger S, Loewith R, Hall MN (2006) TOR signaling in growth and metabolism. Cell 124:471–484. https://doi.org/10.1016/j.cell.2006.01.016

Zinshteyn B, Gilbert WV (2013) Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet 9:e1003675. https://doi.org/10.1371/journal.pgen.1003675