Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae

English version

Autoři: Bianca M. Esch ^aff001; Sergej Limar ^aff001; André Bogdanowski ^aff002; Christos Gournas ^aff004; Tushar More ^aff005; Celine Sundag ^aff001; Stefan Walter ^aff006; Jürgen J. Heinisch ^aff007; Christer S. Ejsing ^aff005; Bruno André ^aff004; Florian Fröhlich ^aff001
Působiště autorů: Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany ^aff001; Department of Biology/Chemistry, Ecology Group, University of Osnabrück, Osnabrück, Germany ^aff002; UFZ–Helmholtz Centre for Environmental Research Ltd, Department for Ecological Modelling, Leipzig, Germany ^aff003; Molecular Physiology of the Cell, Université Libre de Bruxelles (ULB), Institut de Biologie et de Médecine Moléculaires, Gosselies, Belgium ^aff004; Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark ^aff005; Center of Cellular Nanoanalytics Osnabrück, Osnabrück, Germany ^aff006; Department of Biology/Chemistry, Division of Genetics, University of Osnabrück, Osnabrück, Germany ^aff007; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ^aff008
Vyšlo v časopise: Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae. PLoS Genet 16(8): e1008745. doi:10.1371/journal.pgen.1008745
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008745

Souhrn

Sphingolipids are abundant and essential molecules in eukaryotes that have crucial functions as signaling molecules and as membrane components. Sphingolipid biosynthesis starts in the endoplasmic reticulum with the condensation of serine and palmitoyl-CoA. Sphingolipid biosynthesis is highly regulated to maintain sphingolipid homeostasis. Even though, serine is an essential component of the sphingolipid biosynthesis pathway, its role in maintaining sphingolipid homeostasis has not been precisely studied. Here we show that serine uptake is an important factor for the regulation of sphingolipid biosynthesis in Saccharomyces cerevisiae. Using genetic experiments, we find the broad-specificity amino acid permease Gnp1 to be important for serine uptake. We confirm these results with serine uptake assays in gnp1Δ cells. We further show that uptake of exogenous serine by Gnp1 is important to maintain cellular serine levels and observe a specific connection between serine uptake and the first step of sphingolipid biosynthesis. Using mass spectrometry-based flux analysis, we further observed imported serine as the main source for de novo sphingolipid biosynthesis. Our results demonstrate that yeast cells preferentially use the uptake of exogenous serine to regulate sphingolipid biosynthesis. Our study can also be a starting point to analyze the role of serine uptake in mammalian sphingolipid metabolism.

Klíčová slova:

Amino acid analysis – Biosynthesis – Cell membranes – Homeostasis – Saccharomyces cerevisiae – Serine – Sphingolipids – Yeast

Zdroje

1. Van Meer G, Voelker DR, Feigenson GW. Membrane lipids: Where they are and how they behave. Nat Rev Mol Cell Biol. 2008;9 : 112–124. doi: 10.1038/nrm2330 18216768

2. Dickson RC, Lester RL. Yeast sphingolipids. Biochim Biophys Acta—Gen Subj. 1999;1426 : 347–357. doi: 10.1016/S0304-4165(98)00135-4

3. Hanada K, Kumagai K, Yasuda S, Miura Y, Kawano M, Fukasawa M, et al. Molecular machinery for non-vesicular trafficking of ceramide. Nature. 2003;426 : 803–809. doi: 10.1038/nature02188 14685229

4. Liu LK, Choudhary V, Toulmay A, Prinz WA. An inducible ER-Golgi tether facilitates ceramide transport to alleviate lipotoxicity. J Cell Biol. 2017;216 : 131–147. doi: 10.1083/jcb.201606059 28011845

5. Klemm RW, Ejsing CS, Surma MA, Kaiser HJ, Gerl MJ, Sampaio JL, et al. Segregation of sphingolipids and sterols during formation of secretory vesicles at the trans-Golgi network. J Cell Biol. 2009. doi: 10.1083/jcb.200901145 19433450

6. Heinisch JJ, Rodicio R. Protein kinase C in fungi-more than just cell wall integrity. FEMS Microbiology Reviews. Oxford University Press; 2018. pp. 22–39. doi: 10.1093/femsre/fux051 29069410

7. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, et al. Orm family proteins mediate sphingolipid homeostasis. Nature. 2010;463 : 1048–1053. doi: 10.1038/nature08787 20182505

8. Berchtold D, Piccolis M, Chiaruttini N, Riezman I, Riezman H, Roux A, et al. Plasma membrane stress induces relocalization of Slm proteins and activation of TORC2 to promote sphingolipid synthesis. Nat Cell Biol. 2012;14 : 542–547. doi: 10.1038/ncb2480 22504275

9. Roelants FM, Breslow DK, Muir A, Weissman JS, Thorner J. Protein kinase Ypk1 phosphorylates regulatory proteins Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2011;108 : 19222–7. doi: 10.1073/pnas.1116948108 22080611

10. Muir A, Ramachandran S, Roelants FM, Timmons G, Thorner J. TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. Elife. 2014;3 : 1–34. doi: 10.7554/eLife.03779 25279700

11. Fröhlich F, Moreira K, Aguilar PS, Hubner NC, Mann M, Walter P, et al. A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling. J Cell Biol. 2009;185 : 1227–1242. doi: 10.1083/jcb.200811081 19564405

12. Olson DK, Fröhlich F, Christiano R, Hannibal-bach HK, Ejsing CS, Walther TC. Rom2-dependent Phosphorylation of Elo2 Controls the Abundance of Very Long-chain Fatty Acids * □. J Biol Chem. 2015;290 : 4238–4247. doi: 10.1074/jbc.M114.629279 25519905

13. Zimmermann C, Santos A, Gable K, Epstein S, Gururaj C, Chymkowitch P, et al. TORC1 Inhibits GSK3-Mediated Elo2 Phosphorylation to Regulate Very Long Chain Fatty Acid Synthesis and Autophagy. Cell Rep. 2013;5 : 1036–1046. doi: 10.1016/j.celrep.2013.10.024 24239358

14. Fröhlich F, Olson DK, Christiano R, Farese R V., Walther TC. Proteomic and phosphoproteomic analyses of yeast reveal the global cellular response to sphingolipid depletion. Proteomics. 2016;16 : 2759–2763. doi: 10.1002/pmic.201600269 27717283

15. Albers E, Laizé V, Blomberg A, Hohmann S, Gustafsson L. Ser3p (Yer081wp) and Ser33p (Yil074cp) are phosphoglycerate dehydrogenases in Saccharomyces cerevisiae. J Biol Chem. 2003;278 : 10264–10272. doi: 10.1074/jbc.M211692200 12525494

16. Kastanos EK, Woldman YY, Appling DR. Role of mitochondrial and cytoplasmic serine hydroxymethyltransferase isozymes in de Novo purine synthesis in Saccharomyces cerevisiae. Biochemistry. 1997;36 : 14956–14964. doi: 10.1021/bi971610n 9398220

17. Regenberg B, Düring-Olsen L, Kielland-Brandt MC, Holmberg S. Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae. Curr Genet. 1999;36 : 317–328. doi: 10.1007/s002940050506 10654085

18. Cowart LA, Hannun YA. Selective substrate supply in the regulation of yeast de novo sphingolipid synthesis. J Biol Chem. 2007;282 : 12330–12340. doi: 10.1074/jbc.M700685200 17322298

19. Montefusco DJ, Newcomb B, Gandy JL, Brice SE, Matmati N, Cowart LA, et al. Sphingoid bases and the serine catabolic enzyme CHA1 define a novel feedforward/feedback mechanism in the response to serine availability. J Biol Chem. 2012;287 : 9280–9. doi: 10.1074/jbc.M111.313445 22277656

20. Gournas C, Prévost M, Krammer EM, André B. Function and regulation of fungal amino acid transporters: Insights from predicted structure. Advances in Experimental Medicine and Biology. Springer, Cham; 2016. pp. 69–106. doi: 10.1007/978-3-319-25304-6_4

21. Ulane R, Ogur M. Genetic and Physiological Control of Serine and Glycine Biosynthesis in Saccharomyces1. J Bacteriol. 1972;109 : 34–43. doi: 10.1128/JB.109.1.34-43.1972 4333378

22. Fröhlich F, Petit C, Kory N, Christiano R, Hannibal-Bach HK, Graham M, et al. The GARP complex is required for cellular sphingolipid homeostasis. Elife. 2015;4. doi: 10.7554/eLife.08712 26357016

23. Wadsworth JM, Clarke DJ, McMahon SA, Lowther JP, Beattie AE, Langridge-Smith PRR, et al. The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin. J Am Chem Soc. 2013;135 : 14276–14285. doi: 10.1021/ja4059876 23957439

24. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. The genetic landscape of a cell. Science (80-). 2010;327 : 425–431. doi: 10.1126/science.1180823 20093466

25. Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 2005;15 : 1456–61. doi: 10.1101/gr.3672305 16169922

26. RAMOS F, WIAME J -M. Occurrence of a Catabolic l-Serine (l-Threonine) Deaminase in Saccharomyces cerevisiae. Eur J Biochem. 1982;123 : 571–576. doi: 10.1111/j.1432-1033.1982.tb06570.x 7042346

27. Bae-Lee MS, Carman GM. Phosphatidylserine Synthesis in Saccharomyces cerevisiae. Society. 1984;259 : 10857–10862.

28. Ishinaga M, Kito M. Participation of Soluble Phophatidylserine Synthetase in Phosphatidylethanolamine Biosynthesis in Escherichia coli Membrane. Eur J Biochem. 1974;42 : 483–487. doi: 10.1111/j.1432-1033.1974.tb03362.x 4597846

29. Summers EF, Letts VA, McGraw P, Henry SA. Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis. Genetics. 1988;120 : 909–22. Available: http://www.ncbi.nlm.nih.gov/pubmed/3066687 3066687

30. Ong S-E, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002;1 : 376–86. doi: 10.1074/mcp.m200025-mcp200 12118079

31. Schmidt O, Weyer Y, Baumann V, Widerin MA, Eising S, Angelova M, et al. Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism. EMBO J. 2019;38. doi: 10.15252/embj.2018101433 31368600

32. Forsberg H, Gilstring CF, Zargari A, Martínez P, Ljungdahl PO. The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol Microbiol. 2008;42 : 215–228. doi: 10.1046/j.1365-2958.2001.02627.x 11679080

33. Götzke H, Kilisch M, Martínez-Carranza M, Sograte-Idrissi S, Rajavel A, Schlichthaerle T, et al. The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications. Nat Commun. 2019;10 : 4403. doi: 10.1038/s41467-019-12301-7 31562305

34. Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, et al. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast. 2004;21 : 947–962. doi: 10.1002/yea.1142 15334558

35. Han S, Lone MA, Schneiter R, Chang A. Orm1 and Orm2 are conserved endoplasmic reticulum membrane proteins regulating lipid homeostasis and protein quality control. Proc Natl Acad Sci U S A. 2010;107 : 5851–5856. doi: 10.1073/pnas.0911617107 20212121

36. Lee JCY, Tsoi A, Kornfeld GD, Dawes IW. Cellular responses to L -serine in Saccharomyces cerevisiae: roles of general amino acid control, compartmentalization, and aspartate synthesis. FEMS Yeast Res. 2013;13 : 618–634. doi: 10.1111/1567-1364.12063 23837815

37. Mülleder M, Calvani E, Alam MT, Wang RK, Eckerstorfer F, Zelezniak A, et al. Functional Metabolomics Describes the Yeast Biosynthetic Regulome. Cell. 2016;167 : 553-565.e12. doi: 10.1016/j.cell.2016.09.007 27693354

38. Klionsky DJ, Herman PK, Emr SD. The fungal vacuole: Composition, function, and biogenesis. Microbiological Reviews. 1990. pp. 266–292. doi: 10.1128/mmbr.54.3.266–292.1990 2215422

39. Kitamoto K, Yoshizawa K, Ohsumi Y, Anraku Y. Dynamic aspects of vacuolar and cytosolic amino acid pools of Saccharomyces cerevisiae. J Bacteriol. 1988;170 : 2683–2686. doi: 10.1128/jb.170.6.2683-2686.1988 3131304

40. Collado J, Kalemanov M, Martinez-Sanchez A, Campelo F, Baumeister W, Stefan CJ, et al. Tricalbin-Mediated Contact Sites Control ER Curvature to Maintain Plasma Membrane Integrity. SSRN Electron J. 2019; 476–487. doi: 10.2139/ssrn.3371409

41. Hoffmann PC, Wozny MR, Boulanger J, Miller EA, Kukulski W, Hoffmann PC, et al. Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod -⁠ Article Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures. Dev Cell. 2019;51 : 488-502.e8. doi: 10.1016/j.devcel.2019.09.019 31743663

42. Omnus DJ, Manford AG, Bader JM, Emr SD, Stefan CJ. Phosphoinositide kinase signaling controls ER-PM cross-talk. Mol Biol Cell. 2016;27 : 1170–1180. doi: 10.1091/mbc.E16-01-0002 26864629

43. Csordás G, Várnai P, Golenár T, Roy S, Purkins G, Schneider TG, et al. Imaging Interorganelle Contacts and Local Calcium Dynamics at the ER-Mitochondrial Interface. Mol Cell. 2010;39 : 121–132. doi: 10.1016/j.molcel.2010.06.029 20603080

44. Schütter M, Giavalisco P, Brodesser S, Graef M. Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy. Cell. 2020;180 : 135-149.e14. doi: 10.1016/j.cell.2019.12.005 31883797

45. Iraqui I, Vissers S, Bernard F, de Craene J-O, Boles E, Urrestarazu A, et al. Amino Acid Signaling in Saccharomyces cerevisiae: a Permease-Like Sensor of External Amino Acids and F-Box Protein Grr1p Are Required for Transcriptional Induction of the AGP1 Gene, Which Encodes a Broad-Specificity Amino Acid Permease. Mol Cell Biol. 1999;19 : 989–1001. doi: 10.1128/mcb.19.2.989 9891035

46. 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

47. Merhi A, Andre 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 : 4510–4522. doi: 10.1128/MCB.00463-12 22966204

48. Gournas C, Saliba E, Krammer EM, Barthelemy C, Prévost M, André B. Transition of yeast Can1 transporter to the inward-facing state unveils an α-arrestin target sequence promoting its ubiquitylation and endocytosis. Mol Biol Cell. 2017;28 : 2819–2832. doi: 10.1091/mbc.E17-02-0104 28814503

49. Shimobayashi M, Oppliger W, Moes S, Jenö P, Hall MN. TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Riezman H, editor. Mol Biol Cell. 2013;24 : 870–881. doi: 10.1091/mbc.E12-10-0753 23363605

50. Adachi K, Kohara T, Nakao N, Arita M, Chiba K, Mishina T, et al. Design, synthesis, and structure-activity relationships of 2-substituted-2-amino-1,3-propanediols: Discovery of a novel immunosuppressant, FTY720. Bioorg Med Chem Lett. 1995;5 : 853–856. doi: 10.1016/0960-894X(95)00127-F

51. Barthelemy C, Barry AO, Twyffels L, André B. FTY720-induced endocytosis of yeast and human amino acid transporters is preceded by reduction of their inherent activity and TORC1 inhibition. Sci Rep. 2017. doi: 10.1038/s41598-017-14124-2 29062000

52. Welsch CA, Hagiwara S, Goetschy JF, Movva NR. Ubiquitin pathway proteins influence the mechanism of action of the novel immunosuppressive drug FTY720 in Saccharomyces cerevisiae. J Biol Chem. 2003. doi: 10.1074/jbc.M213144200 12709439

53. Busto J V, Elting A, Haase D, Spira F, Kuhlman J, Schäfer-Herte M, et al. Lateral plasma membrane compartmentalization links protein function and turnover. [cited 9 Aug 2018]. doi: 10.15252/embj.201899473

54. Berdyshev E V., Gorshkova I, Skobeleva A, Bittman R, Lu X, Dudek SM, et al. FTY720 inhibits ceramide synthases and up-regulates dihydrosphingosine 1-phosphate formation in human lung endothelial cells. J Biol Chem. 2009;284 : 5467–5477. doi: 10.1074/jbc.M805186200 19119142

55. Lahiri S, Park H, Laviad EL, Lu X, Bittman R, Futerman AH. Ceramide Synthesis Is Modulated by the Sphingosine Analog FTY720 via a Mixture of Uncompetitive and Noncompetitive Inhibition in an Acyl-CoA Chain Length-de pend ent Manner. J Biol Chem. 2009;284 : 16090–16098. doi: 10.1074/jbc.M807438200 19357080

56. Merrill AH, Wang E, Mullins RE. Kinetics of long-chain (sphingoid) base biosynthesis in intact LM cells: effects of varying the extracellular concentrations of serine and fatty acid precursors of this pathway. Biochemistry. 1988;27 : 340–345. doi: 10.1021/bi00401a051 3126810

57. Gao X, Lee K, Reid MA, Li S, Liu J, Correspondence JWL. Serine Availability Influences Mitochondrial Dynamics and Function through Lipid Metabolism. Cell Rep. 2018;22 : 3507–3520. doi: 10.1016/j.celrep.2018.03.017 29590619

58. Yamamoto T, Nishizaki I, Nukada T, Kamegaya E, Furuya S, Hirabayashi Y, et al. Functional identification of ASCT1 neutral amino acid transporter as the predominant system for the uptake of L-serine in rat neurons in primary culture. Neurosci Res. 2004. doi: 10.1016/j.neures.2004.02.004 15099708

59. Damseh N, Simonin A, Jalas C, Picoraro JA, Shaag A, Cho MT, et al. Mutations in SLC1A4, encoding the brain serine transporter, are associated with developmental delay, microcephaly and hypomyelination. J Med Genet. 2015;1 : 541–547. doi: 10.1136/jmedgenet-2015-103104 26041762

60. Heimer G, Marek-Yagel D, Eyal E, Barel O, Oz Levi D, Hoffmann C, et al. SLC1A4 mutations cause a novel disorder of intellectual disability, progressive microcephaly, spasticity and thin corpus callosum. Clin Genet. 2015;88 : 327–335. doi: 10.1111/cge.12637 26138499

61. Kaplan E, Zubedat S, Radzishevsky I, Valenta AC, Rechnitz O, Sason H, et al. ASCT1 (Slc1a4) transporter is a physiologic regulator of brain D-serine and neurodevelopment. 2018;5. doi: 10.1073/pnas.1722677115

62. Auranen M, Toppila J, Suriyanarayanan S, Lone MA, Paetau A, Tyynismaa H, et al. Clinical and metabolic consequences of L-serine supplementation in hereditary sensory and autonomic neuropathy type 1C. Cold Spring Harb Mol case Stud. 2017;3. doi: 10.1101/mcs.a002212 29042446

63. Fridman V, Suriyanarayanan S, Novak P, David W, Macklin EA, McKenna-Yasek D, et al. Randomized trial of l -serine in patients with hereditary sensory and autonomic neuropathy type 1. Neurology. 2019;92: E359–E370. doi: 10.1212/WNL.0000000000006811 30626650

64. Ghaddar K, Krammer E-M, Mihajlovic N, Brohée S, André B, Prévost M. Converting the yeast arginine can1 permease to a lysine permease. J Biol Chem. 2014;289 : 7232–46. doi: 10.1074/jbc.M113.525915 24448798

65. Fröhlich F, Christiano R, Walther TC. Native SILAC: Metabolic Labeling of Proteins in Prototroph Microorganisms Based on Lysine Synthesis Regulation. Mol Cell Proteomics. 2013;12 : 1995–2005. doi: 10.1074/mcp.M112.025742 23592334

66. Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009;6 : 359–62. doi: 10.1038/nmeth.1322 19377485

67. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26 : 1367–72. doi: 10.1038/nbt.1511 19029910

68. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen J V., Mann M. Andromeda: A peptide search engine integrated into the MaxQuant environment. J Proteome Res. 2011;10 : 1794–1805. doi: 10.1021/pr101065j 21254760

69. Ejsing CS, Sampaio JL, Surendranath V, Duchoslav E, Ekroos K, Klemm RW, et al. Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. Proc Natl Acad Sci U S A. 2009;106 : 2136–41. doi: 10.1073/pnas.0811700106 19174513

70. Eising S, Thiele L, Fröhlich F. A systematic approach to identify recycling endocytic cargo depending on the GARP complex. Elife. 2019;8. doi: 10.7554/eLife.42837 30694181

71. Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5 : 264–276. doi: 10.1016/j.ymben.2003.09.002 14642354

72. Aung HW, Henry SA, Walker LP. Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism. Ind Biotechnol. 2013;9 : 215–228. doi: 10.1089/ind.2013.0013 24678285

73. Duarte NC, Herrgård MJ, Palsson BØ. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004;14 : 1298–309. doi: 10.1101/gr.2250904 15197165

74. Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc. 2019;14 : 639–702. doi: 10.1038/s41596-018-0098-2 30787451

75. Gudmundsson S, Thiele I. Computationally efficient flux variability analysis. BMC Bioinformatics. 2010;11 : 10–12. doi: 10.1186/1471-2105-11-10

76. Almeida R, Pauling JK, Sokol E, Hannibal-Bach HK, Ejsing CS. Comprehensive lipidome analysis by shotgun lipidomics on a hybrid quadrupole-orbitrap-linear ion trap mass spectrometer. J Am Soc Mass Spectrom. 2015;26 : 133–48. doi: 10.1007/s13361-014-1013-x 25391725

77. Almeida R, Berzina Z, Arnspang EC, Baumgart J, Vogt J, Nitsch R, et al. Quantitative spatial analysis of the mouse brain lipidome by pressurized liquid extraction surface analysis. Anal Chem. 2015;87 : 1749–1756. doi: 10.1021/ac503627z 25548943

78. Ellis SR, Paine MRL, Eijkel GB, Pauling JK, Husen P, Jervelund MW, et al. Automated, parallel mass spectrometry imaging and structural identification of lipids. Nat Methods. 2018;15 : 515–518. doi: 10.1038/s41592-018-0010-6 29786091

79. Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B, et al. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS One. 2017;12. doi: 10.1371/journal.pone.0188394 29161304

80. Husen P, Tarasov K, Katafiasz M, Sokol E, Vogt J, Baumgart J, et al. Analysis of lipid experiments (ALEX): A software framework for analysis of high-resolution shotgun lipidomics data. PLoS One. 2013;8. doi: 10.1371/journal.pone.0079736 24244551

81. Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O, et al. One library to make them all: Streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods. 2016;13 : 371–378. doi: 10.1038/nmeth.3795 26928762

82. Sikorski RS, Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989;122 : 19–27. doi: 10.1080/00362178385380431 2659436

Článek Immediate activation of chemosensory neuron gene expression by bacterial metabolites is selectively induced by distinct cyclic GMP-dependent pathways in Caenorhabditis elegans

Článek Phospho-regulation of the Shugoshin - Condensin interaction at the centromere in budding yeast

Článek Gα/GSA-1 works upstream of PKA/KIN-1 to regulate calcium signaling and contractility in the Caenorhabditis elegans spermatheca

Článek Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia

Článek Transcriptional regulators of the Golli/myelin basic protein locus integrate additive and stealth activities

Článek Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics

Článek DAnkrd49 and Bdbt act via Casein kinase Iε to regulate planar polarity in Drosophila

Článek Costly Genes

Článek Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

Článek Epistatic interactions between killer immunoglobulin-like receptors and human leukocyte antigen ligands are associated with ankylosing spondylitis

Článek Endogenization and excision of human herpesvirus 6 in human genomes

Článek A subset of broadly responsive Type III taste cells contribute to the detection of bitter, sweet and umami stimuli