Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32
Cells have evolved a variety of mechanisms to control the permeability of the plasma membrane to face environmental perturbations. Transcriptional regulation, endocytosis, gating and activity control of channels and transporters enable global or specific responses to stressful conditions and focused variations in nutrient availability. Emerging data from the yeast model reveal that the conserved TORC1 pathway regulates arrestin-mediated endocytosis of amino-acid transporters. We provide genetic and biochemical evidence for a novel mechanism enabling TORC1 to regulate the inherent activity of transport proteins via the Amu1/Par32 regulator intermediate. This low complexity protein mediates inhibition of specific proteins dedicated to the transport of ammonium, a favored nitrogen source, underscoring that TORC1 selects transporters to be degraded or transiently inactivated and preserved at the cell surface according to the environmental situation. The here-revealed mechanism of transport inhibition by Amu/Par32 is reminiscent to the inhibition of prokaryotic ammonium transport proteins mediated by PII-type proteins, key nitrogen signal transducers widespread in bacteria and Archaea.
Vyšlo v časopise:
Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32. PLoS Genet 11(7): e32767. doi:10.1371/journal.pgen.1005382
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005382
Souhrn
Cells have evolved a variety of mechanisms to control the permeability of the plasma membrane to face environmental perturbations. Transcriptional regulation, endocytosis, gating and activity control of channels and transporters enable global or specific responses to stressful conditions and focused variations in nutrient availability. Emerging data from the yeast model reveal that the conserved TORC1 pathway regulates arrestin-mediated endocytosis of amino-acid transporters. We provide genetic and biochemical evidence for a novel mechanism enabling TORC1 to regulate the inherent activity of transport proteins via the Amu1/Par32 regulator intermediate. This low complexity protein mediates inhibition of specific proteins dedicated to the transport of ammonium, a favored nitrogen source, underscoring that TORC1 selects transporters to be degraded or transiently inactivated and preserved at the cell surface according to the environmental situation. The here-revealed mechanism of transport inhibition by Amu/Par32 is reminiscent to the inhibition of prokaryotic ammonium transport proteins mediated by PII-type proteins, key nitrogen signal transducers widespread in bacteria and Archaea.
Zdroje
1. Marini AM, Vissers S, Urrestarazu A, Andre B. Cloning and expression of the MEP1 gene encoding an ammonium transporter in Saccharomyces cerevisiae. EMBO J. 1994;13: 3456–3463. 8062822
2. Biver S, Belge H, Bourgeois S, Van VP, Nowik M, Scohy S, et al. A role for Rhesus factor Rhcg in renal ammonium excretion and male fertility. Nature. 2008;456: 339–343. doi: 10.1038/nature07518 19020613
3. Marini AM, Urrestarazu A, Beauwens R, Andre B. The Rh (rhesus) blood group polypeptides are related to NH4+ transporters. Trends Biochem. 1997;22: 460–461.
4. Huang CH, Peng J. Evolutionary conservation and diversification of Rh family genes and proteins. ProcNatlAcadSciUSA 2005;102: 15512–15517.
5. Auron A, Brophy PD. Hyperammonemia in review: pathophysiology, diagnosis, and treatment. Pediatr Nephrol. 2012;27: 207–22. doi: 10.1007/s00467-011-1838-5 21431427
6. Von Wiren N, Merrick M. Regulation and function of ammonium carriers in bacteria, fungi, and plants. Molecular mechanisms controlling transmembrane transport. Topics in Current Genetics 9; 2004. pp. 95–120.
7. Weiner ID, Verlander JW. Molecular physiology of the Rh ammonia transport proteins. Curr Opin Nephrol Hypertens. 2010;19: 471–7. doi: 10.1097/MNH.0b013e32833bfa4e 20539225
8. Zheng L, Kostrewa D, Berneche S, Winkler FK, Li XD. The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. ProcNatlAcadSciUSA. 2004;101: 17090–17095.
9. Khademi S, O’Connell J III, Remis J, Robles-Colmenares Y, Miercke LJ, Stroud RM. Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science 2004;305: 1587–1594. 15361618
10. Andrade SL, Dickmanns A, Ficner R, Einsle O. Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. ProcNatlAcadSciUSA. 2005;102: 14994–14999.
11. Li X, Jayachandran S, Nguyen HH, Chan MK. Structure of the Nitrosomonas europaea Rh protein. ProcNatlAcadSciUSA. 2007;104: 19279–19284.
12. Lupo D, Li XD, Durand A, Tomizaki T, Cherif-Zahar B, Matassi G, et al. The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. ProcNatlAcadSciUSA. 2007;104: 19303–19308.
13. Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho C-M, et al. Function of human Rh based on structure of RhCG at 2.1 A. Proc Natl Acad Sci U S A. 2010;107: 9638–43. doi: 10.1073/pnas.1003587107 20457942
14. Deschuyteneer A, Boeckstaens M, De Mees C, Van Vooren P, Wintjens R, Marini AM. SNPs altering ammonium transport activity of human Rhesus factors characterized by a yeast-based functional assay. PLoS One. 2013;8: e71092. doi: 10.1371/journal.pone.0071092 23967154
15. Gruswitz F, O’Connell J III, Stroud RM. Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. ProcNatlAcadSciUSA. 2007;104: 42–47.
16. Conroy MJ, Durand A, Lupo D, Li X-D, Bullough P a, Winkler FK, et al. The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci U S A. 2007;104: 1213–8. 17220269
17. Huergo LF, Chandra G, Merrick M. P(II) signal transduction proteins: nitrogen regulation and beyond. FEMS Microbiol Rev. 2013;37: 251–83. doi: 10.1111/j.1574-6976.2012.00351.x 22861350
18. Boeckstaens M, Llinares E, Van Vooren P, Marini AM. The TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium transport protein. Nat Commun. 2014;5: 3101. doi: 10.1038/ncomms4101 24476960
19. Marini AM, Soussi-Boudekou S, Vissers S, Andre B. A family of ammonium transporters in Saccharomyces cerevisiae. MolCell Biol. 1997;17: 4282–4293.
20. MacGurn JA, Hsu P-C, Smolka MB, Emr SD. TORC1 Regulates Endocytosis via Npr1-Mediated Phosphoinhibition of a Ubiquitin Ligase Adaptor. Cell. 2011;147: 1104–1117. doi: 10.1016/j.cell.2011.09.054 22118465
21. Merhi A, André B. Internal Amino Acids Promote Gap1 Permease Ubiquitylation via TORC1/Npr1/14-3-3-Dependent Control of the Bul Arrestin-Like Adaptors. Mol Cell Biol. 2012;32: 4510–22. doi: 10.1128/MCB.00463-12 22966204
22. Boeckstaens M, Andre B, Marini AM. The yeast ammonium transport protein Mep2 and its positive regulator, the Npr1 kinase, play an important role in normal and pseudohyphal growth on various nitrogen media through retrieval of excreted ammonium. Mol Microbiol. 2007;64: 534–546. 17493133
23. Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J. A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Mol Biol Cell. 2008;19: 3028–3039. doi: 10.1091/mbc.E08-01-0033 18434596
24. Neuhäuser B, Dunkel N, Satheesh S V, Morschhäuser J. Role of the Npr1 kinase in ammonium transport and signaling by the ammonium permease Mep2 in Candida albicans. Eukaryot Cell. 2011;10: 332–42. doi: 10.1128/EC.00293-10 21278231
25. Dubois E, Grenson M. Methylamine/ammonia uptake systems in saccharomyces cerevisiae: multiplicity and regulation. MolGenGenet. 1979;175: 67–76.
26. Grenson M, Acheroy B. Mutations affecting the activity and the regulation of the general amino-acid permease of Saccharomyces cerevisiae. Localisation of the cis-acting dominant pgr regulatory mutation in the structural gene of this permease. Mol Gen Genet. 1982;188: 261–5. 6759873
27. Hein C, Springael JY, Volland C, Haguenauer-Tsapis R, Andre B. NPl1, an essential yeast gene involved in induced degradation of Gap1 and Fur4 permeases, encodes the Rsp5 ubiquitin-protein ligase. Mol Microbiol. 1995;18: 77–87. 8596462
28. Springael JY, Galan JM, Haguenauer-Tsapis R, Andre B. NH4+-induced down-regulation of the Saccharomyces cerevisiae Gap1p permease involves its ubiquitination with lysine-63-linked chains. J Cell Sci. 1999;112: 1375–1383. 10194416
29. Springael JY, Nikko E, Andre B, Marini AM. Yeast Npi3/Bro1 is involved in ubiquitin-dependent control of permease trafficking. FEBS Lett. 2002;517: 103–109. 12062418
30. Yang B, Kumar S. Nedd4 and Nedd4-2: closely related ubiquitin-protein ligases with distinct physiological functions. Cell Death Differ. 2010;17: 68–77. doi: 10.1038/cdd.2009.84 19557014
31. Bissig C, Gruenberg J. ALIX and the multivesicular endosome: ALIX in Wonderland. Trends Cell Biol. 2014;24: 19–25. doi: 10.1016/j.tcb.2013.10.009 24287454
32. Nikko E, Marini A-MM, André B, Andre B. Permease recycling and ubiquitination status reveal a particular role for Bro1 in the multivesicular body pathway. J Biol Chem. 2003;278: 50732–50743. 14523026
33. MacGurn JA, Hsu P-C, Emr SD. Ubiquitin and membrane protein turnover: from cradle to grave. Annu Rev Biochem. 2012;81: 231–59. doi: 10.1146/annurev-biochem-060210-093619 22404628
34. De Craene JO, Soetens O, Andre B. The Npr1 kinase controls biosynthetic and endocytic sorting of the yeast Gap1 permease. J Biol Chem. 2001;276: 43939–43948. 11500493
35. Grenson M. Study of the positive control of the general amino-acid permease and other ammonia-sensitive uptake systems by the product of the NPR1 gene in the yeast Saccharomyces cerevisiae. EurJBiochem. 1983;133: 141–144.
36. Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, et al. Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 2009;23: 1929–43. doi: 10.1101/gad.532109 19684113
37. Van Damme P, Lasa M, Polevoda B, Gazquez C, Elosegui-Artola A, Kim DS, et al. N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB. Proc Natl Acad Sci U S A. 2012;109: 12449–54. doi: 10.1073/pnas.1210303109 22814378
38. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2011;39: D214–9. doi: 10.1093/nar/gkq1020 21051339
39. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215: 403–10. 2231712
40. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16: 276–7. 10827456
41. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23: 2947–8. 17846036
42. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. 1999;41: 95–98.
43. Gander S, Bonenfant D, Altermatt P, Martin DE, Hauri S, Moes S, et al. Identification of the rapamycin-sensitive phosphorylation sites within the Ser / Thr-rich domain of the yeast Npr1 protein kinase. Rapid Commun Mass Spectrom. 2008; 3743–3753. doi: 10.1002/rcm.3790 18980262
44. Neklesa TK, Davis RW. A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex. PLoS Genet. 2009;5: e1000515. doi: 10.1371/journal.pgen.1000515 19521502
45. Schmidt A, Beck T, Koller A, Kunz J, Hall MN. The TOR nutrient signalling pathway phosphorylates NPR1 and inhibits turnover of the tryptophan permease. EMBO J. 1998;17: 6924–6931. 9843498
46. Soulard A, Cremonesi A, Moes S, Schütz F, Jenö P, Hall MN. The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates. Mol Biol Cell. 2010;21: 3475–86. doi: 10.1091/mbc.E10-03-0182 20702584
47. Iesmantavicius V, Weinert BT, Choudhary C. Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol Cell Proteomics. 2014;13: 1979–92. doi: 10.1074/mcp.O113.035683 24961812
48. Soufi B, Kelstrup CD, Stoehr G, Fröhlich F, Walther TC, Olsen J V. Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol Biosyst. 2009;5: 1337–46. doi: 10.1039/b902256b 19823750
49. Holt LJ, Tuch BB, Villen J, Johnson AD, Gygi SP, Morgan DO. Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution. Science (80-). 2009;325: 1682–1686.
50. Helbig AO, Rosati S, Pijnappel PWWM, van Breukelen B, Timmers MHTH, Mohammed S, et al. Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics. 2010;11: 685. doi: 10.1186/1471-2164-11-685 21126336
51. Gnad F, de Godoy LMF, Cox J, Neuhauser N, Ren S, Olsen J V, et al. High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics. 2009;9: 4642–52. doi: 10.1002/pmic.200900144 19795423
52. Breitkreutz a., Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, et al. A Global Protein Kinase and Phosphatase Interaction Network in Yeast. Science (80-). 2010;328: 1043–1046.
53. Fasolo J, Sboner A, Sun MGF, Yu H, Chen R, Sharon D, et al. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. 2011;25: 767–78. doi: 10.1101/gad.1998811 21460040
54. Loqué D, Lalonde S, Looger LL, von Wirén N, Frommer WB. A cytosolic trans-activation domain essential for ammonium uptake. Nature. 2007;446: 195–8. 17293878
55. Yuan L, Gu R, Xuan Y, Smith-Valle E, Loqué D, Frommer WB, et al. Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo. Plant Cell. 2013;25: 974–84. doi: 10.1105/tpc.112.108027 23463773
56. Thomas G, Coutts G, Merrick M. The glnKamtB operon. A conserved gene pair in prokaryotes. Trends Genet. 2000;16: 11–14. 10637624
57. Sant’Anna FH, Trentini DB, de Souto Weber S, Cecagno R, da Silva SC, Schrank IS. The PII superfamily revised: a novel group and evolutionary insights. J Mol Evol. 2009;68: 322–36. doi: 10.1007/s00239-009-9209-6 19296042
58. Javelle A, Severi E, Thornton J, Merrick M. Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J Biol Chem. 2004;279: 8530–8538. 14668330
59. Truan D, Huergo LF, Chubatsu LS, Merrick M, Li X-D, Winkler FK. A new P(II) protein structure identifies the 2-oxoglutarate binding site. J Mol Biol. 2010;400: 531–9. doi: 10.1016/j.jmb.2010.05.036 20493877
60. Radchenko M V, Thornton J, Merrick M. P(II) signal transduction proteins are ATPases whose activity is regulated by 2-oxoglutarate. Proc Natl Acad Sci U S A. 2013;110: 12948–53. doi: 10.1073/pnas.1304386110 23818625
61. Bah A, Vernon RM, Siddiqui Z, Krzeminski M, Muhandiram R, Zhao C, et al. Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch. Nature. 2014;519: 106–9. doi: 10.1038/nature13999 25533957
62. Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997;387: 708–713. 9192896
63. Boeckstaens M, Andre B, Marini AM. Distinct transport mechanisms in yeast ammonium transport/sensor proteins of the mep/amt/rh family and impact on filamentation. J Biol Chem. 2008;283: 21362–21370. doi: 10.1074/jbc.M801467200 18508774
64. Lorenz MC, Heitman J. The MEP2 ammonium permease regulates pseudohyphal differentiation in Saccharomyces cerevisiae. EMBO J. 1998;17: 1236–1247. 9482721
65. Pfannmüller A, Wagner D, Sieber C, Schönig B, Boeckstaens M, Marini AM, et al. The General Amino Acid Permease FfGap1 of Fusarium fujikuroi Is Sorted to the Vacuole in a Nitrogen-Dependent, but Npr1 Kinase-Independent Manner. PLoS One. 2015;10: e0125487. doi: 10.1371/journal.pone.0125487 25909858
66. Bechet J, Grenson M, Wiame JM. Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae. EurJBiochem. 1970;12: 31–39.
67. Gietz D, St JA, Woods RA, Schiestl RH. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992;20: 1425. 1561104
68. Wach A, Brachat A, Pohlmann R, Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994;10: 1793–1808. 7747518
69. Lee S, Lim WA, Thorn KS. Improved blue, green, and red fluorescent protein tagging vectors for S. cerevisiae. PLoS One. 2013;8: e67902. doi: 10.1371/journal.pone.0067902 23844123
70. Longtine MS, McKenzie A, Demarini DJ, Shah NG, Wach A, Brachat A, et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998;14: 953–61. 9717241
71. Jacobs P, Jauniaux JC, Grenson M. A cis-dominant regulatory mutation linked to the argB-argC gene cluster in Saccharomyces cerevisiae. JMolBiol. 1980;139: 691–704.
72. Vandenbol M, Jauniaux JC, Vissers S, Grenson M. Isolation of the NPR1 gene responsible for the reactivation of ammonia-sensitive amino-acid permeases in Saccharomyces cerevisiae. RNA analysis and gene dosage effects. EurJBiochem. 1987;164: 607–612.
73. Feller A, Boeckstaens M, Marini AM, Dubois E. Transduction of the nitrogen signal activating Gln3-mediated transcription is independent of Npr1 kinase and Rsp5-Bul1/2 ubiquitin ligase in Saccharomyces cerevisiae. J Biol Chem. 2006;281: 28546–54. 16864574
74. Bonneaud N, Ozier-Kalogeropoulos O, Li GY, Labouesse M, Minvielle-Sebastia L, Lacroute F. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast. 1991;7: 609–615. 1767589
75. Volland C, Urban-Grimal D, Geraud G, Haguenauer-Tsapis R, Géraud G, Haguenauer-Tsapis R. Endocytosis and degradation of the yeast uracil permease under adverse conditions. J Biol Chem. 1994;269: 9833–41. 8144575
76. Schagger H, von Jagow G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. AnalBiochem. 1987;166: 368–379.
77. Marini AM, Andre B. In vivo N-glycosylation of the mep2 high-affinity ammonium transporter of Saccharomyces cerevisiae reveals an extracytosolic N-terminus. MolMicrobiol. 2000;38: 552–564.
78. Copic A, Starr TL, Schekman R. Ent3p and Ent5p exhibit cargo-specific functions in trafficking proteins between the trans-Golgi network and the endosomes in yeast. Mol Biol Cell. 2007;18: 1803–15. 17344475
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