Leveraging a gain-of-function allele of Caenorhabditis elegans paqr-1 to elucidate membrane homeostasis by PAQR proteins

English version

Autoři: Kiran Busayavalasa ^aff001; Mario Ruiz ^aff001; Ranjan Devkota ^aff001; Marcus Ståhlman ^aff002; Rakesh Bodhicharla ^aff001; Emma Svensk ^aff001; Nils-Olov Hermansson ^aff003; Jan Borén ^aff002; Marc Pilon ^aff001
Působiště autorů: Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden ^aff001; Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden ^aff002; Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden ^aff003
Vyšlo v časopise: Leveraging a gain-of-function allele of Caenorhabditis elegans paqr-1 to elucidate membrane homeostasis by PAQR proteins. PLoS Genet 16(8): e32767. doi:10.1371/journal.pgen.1008975
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008975

Souhrn

The C. elegans proteins PAQR-2 (a homolog of the human seven-transmembrane domain AdipoR1 and AdipoR2 proteins) and IGLR-2 (a homolog of the mammalian LRIG proteins characterized by a single transmembrane domain and the presence of immunoglobulin domains and leucine-rich repeats in their extracellular portion) form a complex that protects against plasma membrane rigidification by promoting the expression of fatty acid desaturases and the incorporation of polyunsaturated fatty acids into phospholipids, hence increasing membrane fluidity. In the present study, we leveraged a novel gain-of-function allele of PAQR-1, a PAQR-2 paralog, to carry out structure-function studies. We found that the transmembrane domains of PAQR-2 are responsible for its functional requirement for IGLR-2, that PAQR-1 does not require IGLR-2 but acts via the same pathway as PAQR-2, and that the divergent N-terminal cytoplasmic domains of the PAQR-1 and PAQR-2 proteins serve a regulatory function and may regulate access to the catalytic site of these proteins. We also show that overexpression of human AdipoR1 or AdipoR2 alone is sufficient to confer increased palmitic acid resistance in HEK293 cells, and thus act in a manner analogous to the PAQR-1 gain-of-function allele.

Klíčová slova:

Alleles – Caenorhabditis elegans – Cell membranes – Fluorescence recovery after photobleaching – Lipids – Membrane proteins – Phenotypes – Protein domains

Zdroje

1. Covino R, Hummer G, Ernst R. Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response. Mol Cell. 2018;71(3):458–67. Epub 2018/08/04. doi: 10.1016/j.molcel.2018.07.019 30075144.

2. de Mendoza D, Pilon M. Control of membrane lipid homeostasis by lipid-bilayer associated sensors: A mechanism conserved from bacteria to humans. Prog Lipid Res. 2019;76:100996. Epub 2019/08/27. doi: 10.1016/j.plipres.2019.100996 31449824.

3. Inda ME, Oliveira RG, de Mendoza D, Cybulski LE. The Single Transmembrane Segment of Minimal Sensor DesK Senses Temperature via a Membrane-Thickness Caliper. J Bacteriol. 2016;198(21):2945–54. Epub 2016/08/17. doi: 10.1128/JB.00431-16 27528507; PubMed Central PMCID: PMC5055599.

4. Saita E, Abriata LA, Tsai YT, Trajtenberg F, Lemmin T, Buschiazzo A, et al. A coiled coil switch mediates cold sensing by the thermosensory protein DesK. Mol Microbiol. 2015;98(2):258–71. Epub 2015/07/15. doi: 10.1111/mmi.13118 26172072.

5. Cybulski LE, Martin M, Mansilla MC, Fernandez A, de Mendoza D. Membrane thickness cue for cold sensing in a bacterium. Curr Biol. 2010;20(17):1539–44. Epub 2010/08/14. doi: 10.1016/j.cub.2010.06.074 20705470.

6. Albanesi D, Martin M, Trajtenberg F, Mansilla MC, Haouz A, Alzari PM, et al. Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci U S A. 2009;106(38):16185–90. Epub 2009/10/07. doi: 10.1073/pnas.0906699106 19805278; PubMed Central PMCID: PMC2738621.

7. Covino R, Ballweg S, Stordeur C, Michaelis JB, Puth K, Wernig F, et al. A Eukaryotic Sensor for Membrane Lipid Saturation. Mol Cell. 2016;63(1):49–59. Epub 2016/06/21. doi: 10.1016/j.molcel.2016.05.015 27320200.

8. Shimano H, Sato R. SREBP-regulated lipid metabolism: convergent physiology—divergent pathophysiology. Nat Rev Endocrinol. 2017;13(12):710–30. Epub 2017/08/30. doi: 10.1038/nrendo.2017.91 28849786.

9. Attard GS, Templer RH, Smith WS, Hunt AN, Jackowski S. Modulation of CTP:phosphocholine cytidylyltransferase by membrane curvature elastic stress. Proc Natl Acad Sci U S A. 2000;97(16):9032–6. Epub 2000/07/26. doi: 10.1073/pnas.160260697 10908674; PubMed Central PMCID: PMC16816.

10. Haider A, Wei YC, Lim K, Barbosa AD, Liu CH, Weber U, et al. PCYT1A Regulates Phosphatidylcholine Homeostasis from the Inner Nuclear Membrane in Response to Membrane Stored Curvature Elastic Stress. Dev Cell. 2018;45(4):481–95 e8. Epub 2018/05/15. doi: 10.1016/j.devcel.2018.04.012 29754800; PubMed Central PMCID: PMC5971203.

11. Lee J, Taneva SG, Holland BW, Tieleman DP, Cornell RB. Structural basis for autoinhibition of CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in phosphatidylcholine synthesis, by its membrane-binding amphipathic helix. J Biol Chem. 2014;289(3):1742–55. Epub 2013/11/28. doi: 10.1074/jbc.M113.526970 24275660; PubMed Central PMCID: PMC3894351.

12. Halbleib K, Pesek K, Covino R, Hofbauer HF, Wunnicke D, Hanelt I, et al. Activation of the Unfolded Protein Response by Lipid Bilayer Stress. Mol Cell. 2017;67(4):673–84 e8. Epub 2017/07/12. doi: 10.1016/j.molcel.2017.06.012 28689662.

13. Ruiz M, Stahlman M, Boren J, Pilon M. AdipoR1 and AdipoR2 Maintain Membrane Fluidity in Most Human Cell Types and Independently of Adiponectin. J Lipid Res. 2019;60:995–1004. Epub 2019/03/21. doi: 10.1194/jlr.M092494 30890562.

14. Ruiz M, Bodhicharla R, Svensk E, Devkota R, Busayavalasa K, Palmgren H, et al. Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2. Elife. 2018;7:e40686. Epub 2018/12/05. doi: 10.7554/eLife.40686 30509349; PubMed Central PMCID: PMC6279351.

15. Bodhicharla R, Devkota R, Ruiz M, Pilon M. Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditis elegans PAQR-2 and Its Mammalian Homolog AdipoR2. Genetics. 2018;210(1):189–201. Epub 2018/07/13. doi: 10.1534/genetics.118.301272 29997234; PubMed Central PMCID: PMC6116961.

16. Devkota R, Svensk E, Ruiz M, Stahlman M, Boren J, Pilon M. The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids. PLoS Genet. 2017;13(9):e1007004. Epub 2017/09/09. doi: 10.1371/journal.pgen.1007004 28886012; PubMed Central PMCID: PMC5607217.

17. Svensk E, Devkota R, Stahlman M, Ranji P, Rauthan M, Magnusson F, et al. Caenorhabditis elegans PAQR-2 and IGLR-2 Protect against Glucose Toxicity by Modulating Membrane Lipid Composition. PLoS Genet. 2016;12(4):e1005982. Epub 2016/04/16. doi: 10.1371/journal.pgen.1005982 27082444; PubMed Central PMCID: PMC4833288.

18. Svensk E, Stahlman M, Andersson CH, Johansson M, Boren J, Pilon M. PAQR-2 regulates fatty acid desaturation during cold adaptation in C. elegans. PLoS Genet. 2013;9(9):e1003801. Epub 2013/09/27. doi: 10.1371/journal.pgen.1003801 24068966; PubMed Central PMCID: PMC3772066.

19. Tang YT, Hu T, Arterburn M, Boyle B, Bright JM, Emtage PC, et al. PAQR proteins: a novel membrane receptor family defined by an ancient 7-transmembrane pass motif. J Mol Evol. 2005;61(3):372–80. Epub 2005/07/27. doi: 10.1007/s00239-004-0375-2 16044242.

20. Pei J, Millay DP, Olson EN, Grishin NV. CREST—a large and diverse superfamily of putative transmembrane hydrolases. Biol Direct. 2011;6:37. Epub 2011/07/08. doi: 10.1186/1745-6150-6-37 21733186; PubMed Central PMCID: PMC3146951.

21. Tanabe H, Fujii Y, Okada-Iwabu M, Iwabu M, Nakamura Y, Hosaka T, et al. Crystal structures of the human adiponectin receptors. Nature. 2015;520(7547):312–6. Epub 2015/04/10. doi: 10.1038/nature14301 25855295; PubMed Central PMCID: PMC4477036.

22. Vasiliauskaite-Brooks I, Sounier R, Rochaix P, Bellot G, Fortier M, Hoh F, et al. Structural insights into adiponectin receptors suggest ceramidase activity. Nature. 2017;544(7648):120–3. Epub 2017/03/23. doi: 10.1038/nature21714 28329765; PubMed Central PMCID: PMC5595237.

23. Karpichev IV, Cornivelli L, Small GM. Multiple regulatory roles of a novel Saccharomyces cerevisiae protein, encoded by YOL002c, in lipid and phosphate metabolism. J Biol Chem. 2002;277(22):19609–17. Epub 2002/03/28. doi: 10.1074/jbc.M202045200 11916977.

24. Lyons TJ, Villa NY, Regalla LM, Kupchak BR, Vagstad A, Eide DJ. Metalloregulation of yeast membrane steroid receptor homologs. Proc Natl Acad Sci U S A. 2004;101(15):5506–11. Epub 2004/04/03. doi: 10.1073/pnas.0306324101 15060275; PubMed Central PMCID: PMC397413.

25. Mattiazzi Usaj M, Prelec M, Brloznik M, Primo C, Curk T, Scancar J, et al. Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis. Metallomics. 2015;7(9):1338–51. Epub 2015/06/13. doi: 10.1039/c5mt00095e 26067383.

26. Villa NY, Kupchak BR, Garitaonandia I, Smith JL, Alonso E, Alford C, et al. Sphingolipids function as downstream effectors of a fungal PAQR. Mol Pharmacol. 2009;75(4):866–75. Epub 2008/12/11. doi: 10.1124/mol.108.049809 19066337; PubMed Central PMCID: PMC2684929.

27. Kupchak BR, Garitaonandia I, Villa NY, Smith JL, Lyons TJ. Antagonism of human adiponectin receptors and their membrane progesterone receptor paralogs by TNFalpha and a ceramidase inhibitor. Biochemistry. 2009;48(24):5504–6. Epub 2009/05/21. doi: 10.1021/bi9006258 19453184; PubMed Central PMCID: PMC2789275.

28. Holland WL, Miller RA, Wang ZV, Sun K, Barth BM, Bui HH, et al. Receptor-mediated activation of ceramidase activity initiates the pleiotropic actions of adiponectin. Nat Med. 2011;17(1):55–63. Epub 2010/12/28. doi: 10.1038/nm.2277 21186369; PubMed Central PMCID: PMC3134999.

29. Holland WL, Xia JY, Johnson JA, Sun K, Pearson MJ, Sharma AX, et al. Inducible overexpression of adiponectin receptors highlight the roles of adiponectin-induced ceramidase signaling in lipid and glucose homeostasis. Mol Metab. 2017;6(3):267–75. Epub 2017/03/09. doi: 10.1016/j.molmet.2017.01.002 28271033; PubMed Central PMCID: PMC5323887.

30. Svensson E, Olsen L, Morck C, Brackmann C, Enejder A, Faergeman NJ, et al. The adiponectin receptor homologs in C. elegans promote energy utilization and homeostasis. PLoS One. 2011;6(6):e21343. Epub 2011/06/30. doi: 10.1371/journal.pone.0021343 21712952; PubMed Central PMCID: PMC3119701.

31. Svensk E, Biermann J, Hammarsten S, Magnusson F, Pilon M. Leveraging the withered tail tip phenotype in C. elegans to identify proteins that influence membrane properties. Worm. 2016;5(3):e1206171. Epub 2016/10/04. doi: 10.1080/21624054.2016.1206171 27695656; PubMed Central PMCID: PMC5022664.

32. Chen YL, Tao J, Zhao PJ, Tang W, Xu JP, Zhang KQ, et al. Adiponectin receptor PAQR-2 signaling senses low temperature to promote C. elegans longevity by regulating autophagy. Nat Commun. 2019;10(1):2602. Epub 2019/06/15. doi: 10.1038/s41467-019-10475-8 31197136; PubMed Central PMCID: PMC6565724.

33. Lee D, An SWA, Jung Y, Yamaoka Y, Ryu Y, Goh GYS, et al. MDT-15/MED15 permits longevity at low temperature via enhancing lipidostasis and proteostasis. PLoS Biol. 2019;17(8):e3000415. Epub 2019/08/14. doi: 10.1371/journal.pbio.3000415 31408455.

34. Kyriakakis E, Charmpilas N, Tavernarakis N. Differential adiponectin signalling couples ER stress with lipid metabolism to modulate ageing in C. elegans. Sci Rep. 2017;7(1):5115. Epub 2017/07/13. doi: 10.1038/s41598-017-05276-2 28698593; PubMed Central PMCID: PMC5505976.

35. Ruiz M, Bodhicharla R, Stahlman M, Svensk E, Busayavalasa K, Palmgren H, et al. Evolutionarily conserved long-chain Acyl-CoA synthetases regulate membrane composition and fluidity. Elife. 2019;8:e47733. Epub 2019/11/27. doi: 10.7554/eLife.47733 31769755.

36. Aldrich RW. Fifty years of inactivation. Nature. 2001;411(6838):643–4. Epub 2001/06/08. doi: 10.1038/35079705 11395746.

37. Armstrong CM, Bezanilla F. Inactivation of the sodium channel. II. Gating current experiments. J Gen Physiol. 1977;70(5):567–90. Epub 1977/11/01. doi: 10.1085/jgp.70.5.567 591912; PubMed Central PMCID: PMC2228472.

38. Zhou M, Morais-Cabral JH, Mann S, MacKinnon R. Potassium channel receptor site for the inactivation gate and quaternary amine inhibitors. Nature. 2001;411(6838):657–61. Epub 2001/06/08. doi: 10.1038/35079500 11395760.

39. Juhl C, Kosel D, Beck-Sickinger AG. Two motifs with different function regulate the anterograde transport of the adiponectin receptor 1. Cell Signal. 2012;24(9):1762–9. Epub 2012/05/16. doi: 10.1016/j.cellsig.2012.05.002 22584118.

40. Keshvari S, Whitehead JP. Characterisation of the adiponectin receptors: Differential cell-surface expression and temporal signalling profiles of AdipoR1 and AdipoR2 are regulated by the non-conserved N-terminal trunks. Mol Cell Endocrinol. 2015;409:121–9. Epub 2015/04/22. doi: 10.1016/j.mce.2015.04.003 25892445.

41. Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD. Arginine-mediated RNA recognition: the arginine fork. Science. 1991;252(5009):1167–71. Epub 1991/05/24. doi: 10.1126/science.252.5009.1167 1709522.

42. Matsuo M, Huang CH, Huang LC. Evidence for an essential arginine recognition site on adenosine 3':5'-cyclic monophosphate-dependent protein kinase of rabbit skeletal muscle. Biochem J. 1978;173(2):441–7. Epub 1978/08/01. doi: 10.1042/bj1730441 212013; PubMed Central PMCID: PMC1185797.

43. Neves MA, Yeager M, Abagyan R. Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B. 2012;116(23):7006–13. Epub 2012/04/14. doi: 10.1021/jp3009699 22497303; PubMed Central PMCID: PMC3613333.

44. Williams ML, Gready JE. Guanidinium-Type Resonance Stabilization and Its Biological Implications .1. The Guanidine and Extended-Guanidine Series. J Comput Chem. 1989;10(1):35–54. doi: 10.1002/jcc.540100105 WOS:A1989R755300004.

45. Barlow DJ, Thornton JM. Ion-pairs in proteins. J Mol Biol. 1983;168(4):867–85. Epub 1983/08/25. doi: 10.1016/s0022-2836(83)80079-5 6887253.

46. Burley SK, Petsko GA. Amino-aromatic interactions in proteins. FEBS Lett. 1986;203(2):139–43. Epub 1986/07/28. doi: 10.1016/0014-5793(86)80730-x 3089835.

47. Flocco MM, Mowbray SL. Planar stacking interactions of arginine and aromatic side-chains in proteins. J Mol Biol. 1994;235(2):709–17. Epub 1994/01/14. doi: 10.1006/jmbi.1994.1022 8289290.

48. Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins. 2005;60(3):353–66. Epub 2005/05/21. doi: 10.1002/prot.20433 15906321.

49. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. PIER: protein interface recognition for structural proteomics. Proteins. 2007;67(2):400–17. Epub 2007/02/15. doi: 10.1002/prot.21233 17299750.

50. Kupchak BR, Garitaonandia I, Villa NY, Mullen MB, Weaver MG, Regalla LM, et al. Probing the mechanism of FET3 repression by Izh2p overexpression. Biochim Biophys Acta. 2007;1773(7):1124–32. Epub 2007/06/08. doi: 10.1016/j.bbamcr.2007.04.003 17553578; PubMed Central PMCID: PMC1994572.

51. Zhang J, Wang C, Shen Y, Chen N, Wang L, Liang L, et al. A mutation in ADIPOR1 causes nonsyndromic autosomal dominant retinitis pigmentosa. Hum Genet. 2016;135(12):1375–87. Epub 2016/09/23. doi: 10.1007/s00439-016-1730-2 27655171.

52. Sluch VM, Banks A, Li H, Crowley MA, Davis V, Xiang C, et al. ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrp(rd6) mouse. Sci Rep. 2018;8(1):14339. Epub 2018/09/27. doi: 10.1038/s41598-018-32579-9 30254279; PubMed Central PMCID: PMC6156493.

53. Xu M, Eblimit A, Wang J, Li J, Wang F, Zhao L, et al. ADIPOR1 Is Mutated in Syndromic Retinitis Pigmentosa. Hum Mutat. 2016;37(3):246–9. Epub 2015/12/15. doi: 10.1002/humu.22940 26662040; PubMed Central PMCID: PMC5383450.

54. Gur G, Rubin C, Katz M, Amit I, Citri A, Nilsson J, et al. LRIG1 restricts growth factor signaling by enhancing receptor ubiquitylation and degradation. EMBO J. 2004;23(16):3270–81. Epub 2004/07/30. doi: 10.1038/sj.emboj.7600342 15282549; PubMed Central PMCID: PMC514515.

55. Hedman H, Henriksson R. LRIG inhibitors of growth factor signalling—double-edged swords in human cancer? Eur J Cancer. 2007;43(4):676–82. Epub 2007/01/24. doi: 10.1016/j.ejca.2006.10.021 17239582.

56. Lindquist D, Kvarnbrink S, Henriksson R, Hedman H. LRIG and cancer prognosis. Acta Oncol. 2014;53(9):1135–42. Epub 2014/09/03. doi: 10.3109/0284186X.2014.953258 25180912; PubMed Central PMCID: PMC4438349.

57. Peltola MA, Kuja-Panula J, Lauri SE, Taira T, Rauvala H. AMIGO is an auxiliary subunit of the Kv2.1 potassium channel. EMBO Rep. 2011;12(12):1293–9. Epub 2011/11/08. doi: 10.1038/embor.2011.204 22056818; PubMed Central PMCID: PMC3245694.

58. Anbazhagan V, Schneider D. The membrane environment modulates self-association of the human GpA TM domain—implications for membrane protein folding and transmembrane signaling. Biochim Biophys Acta. 2010;1798(10):1899–907. Epub 2010/07/07. doi: 10.1016/j.bbamem.2010.06.027 20603102.

59. Cymer F, Veerappan A, Schneider D. Transmembrane helix-helix interactions are modulated by the sequence context and by lipid bilayer properties. Biochim Biophys Acta. 2012;1818(4):963–73. Epub 2011/08/11. doi: 10.1016/j.bbamem.2011.07.035 21827736.

60. Radanovic T, Reinhard J, Ballweg S, Pesek K, Ernst R. An Emerging Group of Membrane Property Sensors Controls the Physical State of Organellar Membranes to Maintain Their Identity. Bioessays. 2018;40(5):e1700250. Epub 2018/03/27. doi: 10.1002/bies.201700250 29574931.

61. Yamauchi T, Kamon J, Ito Y, Tsuchida A, Yokomizo T, Kita S, et al. Cloning of adiponectin receptors that mediate antidiabetic metabolic effects. Nature. 2003;423(6941):762–9. Epub 2003/06/13. doi: 10.1038/nature01705 12802337.

62. Kosel D, Heiker JT, Juhl C, Wottawah CM, Bluher M, Morl K, et al. Dimerization of adiponectin receptor 1 is inhibited by adiponectin. J Cell Sci. 2010;123(Pt 8):1320–8. Epub 2010/03/25. doi: 10.1242/jcs.057919 20332107.

63. Almabouada F, Diaz-Ruiz A, Rabanal-Ruiz Y, Peinado JR, Vazquez-Martinez R, Malagon MM. Adiponectin receptors form homomers and heteromers exhibiting distinct ligand binding and intracellular signaling properties. J Biol Chem. 2013;288(5):3112–25. Epub 2012/12/21. doi: 10.1074/jbc.M112.404624 23255609; PubMed Central PMCID: PMC3561534.

64. Pilon M. Revisiting the membrane-centric view of diabetes. Lipids Health Dis. 2016;15(1):167. Epub 2016/09/28. doi: 10.1186/s12944-016-0342-0 27671740; PubMed Central PMCID: PMC5037885.

65. Gianfrancesco MA, Paquot N, Piette J, Legrand-Poels S. Lipid bilayer stress in obesity-linked inflammatory and metabolic disorders. Biochem Pharmacol. 2018;153:168–83. Epub 2018/02/21. doi: 10.1016/j.bcp.2018.02.022 29462590.

66. Baenke F, Peck B, Miess H, Schulze A. Hooked on fat: the role of lipid synthesis in cancer metabolism and tumour development. Dis Model Mech. 2013;6(6):1353–63. Epub 2013/11/10. doi: 10.1242/dmm.011338 24203995; PubMed Central PMCID: PMC3820259.

67. Mounier C, Bouraoui L, Rassart E. Lipogenesis in cancer progression (review). Int J Oncol. 2014;45(2):485–92. Epub 2014/05/16. doi: 10.3892/ijo.2014.2441 24827738.

68. Peck B, Schulze A. Lipid desaturation—the next step in targeting lipogenesis in cancer? FEBS J. 2016;283(15):2767–78. Epub 2016/02/18. doi: 10.1111/febs.13681 26881388.

69. Vriens K, Christen S, Parik S, Broekaert D, Yoshinaga K, Talebi A, et al. Evidence for an alternative fatty acid desaturation pathway increasing cancer plasticity. Nature. 2019. Epub 2019/02/08. doi: 10.1038/s41586-019-0904-1 30728499.

70. Sulston J, Hodgkin J. Methods. In: Wood W, editor. The nematode Caenorhabditis elegans. New York: Cold Spring Harbor Laboratory Press; 1988. p. 587–606.

71. Sarin S, Prabhu S, O'Meara MM, Pe'er I, Hobert O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods. 2008;5(10):865–7. Epub 2008/08/05. doi: 10.1038/nmeth.1249 18677319; PubMed Central PMCID: PMC2574580.

72. Bigelow H, Doitsidou M, Sarin S, Hobert O. MAQGene: software to facilitate C. elegans mutant genome sequence analysis. Nat Methods. 2009;6(8):549. Epub 2009/07/22. doi: 10.1038/nmeth.f.260 19620971; PubMed Central PMCID: PMC2854518.

73. Zuryn S, Le Gras S, Jamet K, Jarriault S. A strategy for direct mapping and identification of mutations by whole-genome sequencing. Genetics. 2010;186(1):427–30. Epub 2010/07/09. doi: 10.1534/genetics.110.119230 20610404; PubMed Central PMCID: PMC2940307.

74. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9(7):671–5. Epub 2012/08/30. doi: 10.1038/nmeth.2089 22930834; PubMed Central PMCID: PMC5554542.

75. Liu DW, Thomas JH. Regulation of a periodic motor program in C. elegans. J Neurosci. 1994;14(4):1953–62. Epub 1994/04/01. doi: 10.1523/JNEUROSCI.14-04-01953.1994 8158250.

76. Axang C, Rauthan M, Hall DH, Pilon M. The twisted pharynx phenotype in C. elegans. BMC Dev Biol. 2007;7:61. Epub 2007/06/02. doi: 10.1186/1471-213X-7-61 17540043; PubMed Central PMCID: PMC1904197.

77. Tajsharghi H, Pilon M, Oldfors A. A Caenorhabditis elegans model of the myosin heavy chain IIa E706R mutation. Ann Neurol. 2005;58(3):442–8. doi: 10.1002/ana.20594 WOS:000231679200014. 16130113

78. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 2000;408(6810):325–30. Epub 2000/12/01. doi: 10.1038/35042517 11099033.

79. Davis MW, Morton JJ, Carroll D, Jorgensen EM. Gene activation using FLP recombinase in C. elegans. PLoS Genet. 2008;4(3):e1000028. Epub 2008/03/29. doi: 10.1371/journal.pgen.1000028 18369447; PubMed Central PMCID: PMC2265415.

80. Mello CC, Kramer JM, Stinchcomb D, Ambros V. Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 1991;10(12):3959–70. Epub 1991/12/01. 1935914; PubMed Central PMCID: PMC453137.

81. Yochem J, Gu T, Han M. A new marker for mosaic analysis in Caenorhabditis elegans indicates a fusion between hyp6 and hyp7, two major components of the hypodermis. Genetics. 1998;149(3):1323–34. Epub 1998/07/03. 9649523; PubMed Central PMCID: PMC1460238.

82. Hiatt SM, Shyu YJ, Duren HM, Hu CD. Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in Caenorhabditis elegans. Methods. 2008;45(3):185–91. Epub 2008/07/01. doi: 10.1016/j.ymeth.2008.06.003 18586101; PubMed Central PMCID: PMC2570267.

83. Lofgren L, Forsberg GB, Stahlman M. The BUME method: a new rapid and simple chloroform-free method for total lipid extraction of animal tissue. Sci Rep. 2016;6:27688. Epub 2016/06/11. doi: 10.1038/srep27688 27282822; PubMed Central PMCID: PMC4901324.

84. Jung HR, Sylvanne T, Koistinen KM, Tarasov K, Kauhanen D, Ekroos K. High throughput quantitative molecular lipidomics. Biochim Biophys Acta. 2011;1811(11):925–34. Epub 2011/07/20. doi: 10.1016/j.bbalip.2011.06.025 21767661.

85. 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(7):2136–41. Epub 2009/01/29. doi: 10.1073/pnas.0811700106 19174513; PubMed Central PMCID: PMC2650121.

86. Ekroos K, Ejsing CS, Bahr U, Karas M, Simons K, Shevchenko A. Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation. J Lipid Res. 2003;44(11):2181–92. Epub 2003/08/19. doi: 10.1194/jlr.D300020-JLR200 12923235.

87. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25(4):402–8. Epub 2002/02/16. doi: 10.1006/meth.2001.1262 11846609.

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