1. Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat Biotechnol. 2003;21(3):255-261. doi:10.1038/nbt0303-255
2. Larsen MR, Trelle MB, Thingholm TE, Jensen ON. Analysis of posttranslational modifications of proteins by tandem mass spectrometry. Biotechniques. 2006;40(6):790-798. doi:10.2144/000112201
3. Cohen P. The regulation of protein function by multisite phosphorylation - A 25 year update. Trends Biochem Sci. 2000;25(12):596-601. doi:10.1016/S0968- 0004(00)01712-6
4. Wu D, Jin J, Qiu Z, Liu D, Luo H. Functional Analysis of O-GlcNAcylation in Cancer Metastasis. Front Oncol. 2020;10(October):1-11. doi:10.3389/fonc.2020.585288
5. Ohtsubo K, Marth JD. Glycosylation in Cellular Mechanisms of Health and Disease. Cell. 2006;126(5):855-867. doi:10.1016/j.cell.2006.08.019
6. Cherepanova N, Shrimal S, Gilmore R. N-linked glycosylation and homeostasis of the endoplasmic reticulum. Curr Opin Cell Biol. 2016;41:57-65. doi:10.1016/j.ceb.2016.03.021
7. Aebi M. N-linked protein glycosylation in the ER. Biochim Biophys Acta - Mol Cell Res. 2013;1833(11):2430-2437. doi:10.1016/j.bbamcr.2013.04.001
8. Breitling J, Aebi M. N-linked protein glycosylation in the endoplasmic reticulum. Cold Spring Harb Perspect Biol. 2013;5(8):a013359. doi:10.1101/cshperspect.a013359
9. Hartley MD, Imperiali B. At the membrane frontier: A prospectus on the remarkable evolutionary conservation of polyprenols and polyprenyl-phosphates. Arch Biochem Biophys. 2012;517(2):83-97. doi:10.1016/j.abb.2011.10.018
10. Kohda D. Structural basis of protein asn-glycosylation by oligosaccharyltransferases. Adv Exp Med Biol. 2018;1104:171-199. doi:10.1007/978-981-13-2158-0_9
11. Harada Y, Buser R, Ngwa EM, Hirayama H, Aebi M, Suzuki T. Eukaryotic oligosaccharyltransferase generates free oligosaccharides during N-glycosylation. J Biol Chem. 2013;288(45):32673-32684. doi:10.1074/jbc.M113.486985
12. Harada Y, Masahara-Negishi Y, Suzuki T. Cytosolic-free oligosaccharides are predominantly generated by the degradation of dolichol-linked oligosaccharides in mammalian cells. Glycobiology. 2015;25(11):1196-1205. doi:10.1093/glycob/cwv055
13. Rolf Apweiler HH, Nathan Sharon. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta. 1999;1(2):4-8. doi:10.1097/00013611-198607000-00004
14. Frappaolo A, Karimpour-Ghahnavieh A, Sechi S, Giansanti MG. The Close Relationship between the Golgi Trafficking Machinery and Protein Glycosylation. Cells. 2020;9(12):2652. doi:10.3390/cells9122652
15. Ondruskova N, Cechova A, Hansikova H, Honzik T, Jaeken J. Congenital disorders of glycosylation: Still “hot” in 2020. Biochim Biophys Acta - Gen Subj. 2021;1865(1). doi:10.1016/j.bbagen.2020.129751
16. Chantret I, Moore SEH. Free oligosaccharide regulation during mammalian protein N-glycosylation. Glycobiology. 2008;18(3):210-224. doi:10.1093/glycob/cwn003
17. Chantret I, Kodali VP, Lahmouich C, Harvey DJ, Moore SEH. Endoplasmic reticulum-associated degradation (ERAD) and free oligosaccharide generation in Saccharomyces cerevisiae. J Biol Chem. 2011;286(48):41786-41800. doi:10.1074/jbc.M111.251371
18. Hirayama H, Seino J, Kitajima T, Jigami Y, Suzuki T. Free oligosaccharides to monitor glycoprotein endoplasmic reticulum-associated degradation in Saccharomyces cerevisiae. J Biol Chem. 2010;285(16):12390-12404. doi:10.1074/jbc.M109.082081
19. Fermaintt CS, Sano K, Liu Z, et al. A bioactive mammalian disaccharide associated with autoimmunity activates STING-TBK1-dependent immune response. Nat Commun. 2019;10(1):2377. doi:10.1038/s41467-019-10319-5
20. Lu H, Fermaintt CS, Cherepanova NA, Gilmore R, Yan N, Lehrman MA. Mammalian STT3A/B oligosaccharyltransferases segregate N-glycosylation at the translocon from lipid-linked oligosaccharide hydrolysis. Proc Natl Acad Sci U S A. 2018;115(38):9557-9562. doi:10.1073/pnas.1806034115
21. Katsube M, Ebara N, Maeda M, Kimura Y. Cytosolic Free N-Glycans Are Retro- Transported Into the Endoplasmic Reticulum in Plant Cells. Front Plant Sci. 2021;11(January). doi:10.3389/fpls.2020.610124
22. Wang Y, Hirata T, Maeda Y, Murakami Y, Fujita M, Kinoshita T. Free, unlinked glycosylphosphatidylinositols on mammalian cell surfaces revisited. J Biol Chem. 2019;294(13):5038-5049. doi:10.1074/jbc.RA119.007472
23. Hirayama H, Matsuda T, Tsuchiya Y, et al. Free glycans derived from O- mannosylated glycoproteins suggest the presence of an O-glycoprotein degradation pathway in yeast. J Biol Chem. 2019;294(44):15900-15911. doi:10.1074/jbc.RA119.009491
24. Kimura N, Uchida M, Nishimura S, Yamaguchi H. Promotion of polypeptide folding by interactions with Asn-glycans. J Biochem. 1998;124(4):857-862. doi:10.1093/oxfordjournals.jbchem.a022190
25. Jitsuhara Y, Toyoda T, Itai T, Yamaguchi H. Chaperone-like functions of high- mannose type and complex-type N-glycans and their molecular basis. J Biochem. 2002;132(5):803-811. doi:10.1093/oxfordjournals.jbchem.a003290
26. Kelleher DJ, Karaoglu D, Mandon EC, Gilmore R. Oligosaccharyltransferase isoforms that contain different catalytic STT3 subunits have distinct enzymatic properties. Mol Cell. 2003;12(1):101-111. doi:10.1016/S1097-2765(03)00243-0
27. Niu G, Shao Z, Liu C, Chen T, Jiao Q, Hong Z. Comparative and evolutionary analyses of the divergence of plant oligosaccharyltransferase STT3 isoforms. FEBS Open Bio. 2020;10(3):468-483. doi:10.1002/2211-5463.12804
28. Nasab FP, Schulz BL, Gamarro F, Parodi AJ, Aebi M. All in one: Leishmania major STT3 proteins substitute for the whole oligosaccharyltransferase complex in Saccharomyces cerevisiae. Mol Biol Cell. 2008;19(9):3758-3768. doi:10.1091/mbc.e08-05-0467
29. Kelleher DJ, Gilmore R. An evolving view of the eukaryotic oligosaccharyltransferase. Glycobiology. 2006;16(4):47-62. doi:10.1093/glycob/cwj066
30. Schwarz M, Knauer R, Lehle L. Yeast oligosaccharyltransferase consists of two functionally distinct sub-complexes, specified by either the Ost3p or Ost6p subunit. FEBS Lett. 2005;579(29):6564-6568. doi:10.1016/j.febslet.2005.10.063
31. Knauer R, Lehle L. The oligosaccharyltransferase complex from Saccharomyces cerevisiae. Isolation of the OST6 gene, its synthetic interaction with OST3, and analysis of the native complex. J Biol Chem. 1999;274(24):17249-17256. doi:10.1074/jbc.274.24.17249
32. Nothaft H, Liu X, McNally DJ, Li J, Szymanski CM. Study of free oligosaccharides derived from the bacterial N-glycosylation pathway. Proc Natl Acad Sci U S A. 2009;106(35):15019-15024. doi:10.1073/pnas.0903078106
33. Chung CY, Majewska NI, Wang Q, Paul JT, Betenbaugh MJ. SnapShot: N- Glycosylation Processing Pathways across Kingdoms. Cell. 2017;171(1):258-258.e1. doi:10.1016/j.cell.2017.09.014
34. Bai L, Wang T, Zhao G, Kovach A, Li H. The atomic structure of a eukaryotic oligosaccharyltransferase complex. Nature. 2018;555(7696):328-333. doi:10.1038/nature25755
35. Wild R, Kowal J, Eyring J, Ngwa EM, Aebi M, Locher KP. Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Science (80- ). 2018;359(6375):545-550. doi:10.1126/science.aar5140
36. Poljak K, Selevsek N, Ngwa E, Grossmann J, Losfeld ME, Aebi M. Quantitative profiling of N-linked glycosylation machinery in yeast Saccharomyces cerevisiae. Mol Cell Proteomics. 2018;17(1):18-30. doi:10.1074/mcp.RA117.000096
37. Kung LA, Tao SC, Qian J, Smith MG, Snyder M, Zhu H. Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol. 2009;5(308):1-11. doi:10.1038/msb.2009.64
38. Hossain TJ, Harada Y, Hirayama H, Tomotake H, Seko A, Suzuki T. Structural analysis of free N-glycans in α-glucosidase mutants of Saccharomyces cerevisiae: Lack of the evidence for the occurrence of catabolic α-glucosidase acting on the N-glycans. PLoS One. 2016;11(3). doi:10.1371/journal.pone.0151891
39. Igura M, Maita N, Kamishikiryo J, et al. Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. EMBO J. 2008;27(1):234-243. doi:10.1038/sj.emboj.7601940
40. Li G, Yan Q, Nita-Lazar A, Haltiwanger RS, Lennarz WJ. Studies on the N- glycosylation of the subunits of oligosaccharyl transferase in Saccharomyces cerevisiae. J Biol Chem. 2005;280(3):1864-1871. doi:10.1074/jbc.M410969200
41. Hese K, Otto C, Routier FH, Lehle L. The yeast oligosaccharyltransferase complex can be replaced by STT3 from Leishmania major. Glycobiology. 2009;19(2):160-171. doi:10.1093/glycob/cwn118
42. Sikorski RS, Boeke JD. [20] In vitro mutagenesis and plasmid shuffling: From cloned gene to mutant yeast. In: Methods in Enzymology. Vol 194. ; 1991:302-318. doi:10.1016/0076-6879(91)94023-6
43. Karaoglu D, Kelleher DJ, Gilmore R. The highly conserved Stt3 protein is a subunit of the yeast oligosaccharyltransferase and forms a subcomplex with Ost3p and Ost4p. J Biol Chem. 1997;272(51):32513-32520. doi:10.1074/jbc.272.51.32513
44. Spirig U, Glavas M, Bodmer D, et al. The STT3 protein is a component of the yeast oligosaccharyltransferase complex. Mol Gen Genet. 1997;256(6):628-637. doi:10.1007/s004380050611
45. Chavan M, Chen Z, Li G, Schindelin H, Lennarz WJ, Li H. Dimeric organization of the yeast oligosaccharyl transferase complex. Proc Natl Acad Sci U S A. 2006;103(24):8947-8952. doi:10.1073/pnas.0603262103
46. Chavan M, Rekowicz M, Lennarz W. Insight into functional aspects of Stt3p, a subunit of the oligosaccharyl transferase: Evidence for interaction of the N- terminal domain of Stt3p with the protein kinase C cascade. J Biol Chem. 2003;278(51):51441-51447. doi:10.1074/jbc.M310456200
47. Spirig U, Bodmer D, Wacker M, Burda P, Aebi M. The 3.4-kDa Ost4 protein is required for the assembly of two distinct oligosaccharyltransferase complexes in yeast. Glycobiology. 2005;15(12):1396-1406. doi:10.1093/glycob/cwj025
48. Funakoshi M, Hochstrasser M. Small epitope-linker modules for PCR-based C- terminal tagging in Saccharomyces cerevisiae. Yeast. 2009;26(3):185-192. doi:10.1002/yea.1658
49. Matsumoto S, Shimada A, Nyirenda J, Igura M, Kawano Y, Kohda D. Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation. Proc Natl Acad Sci U S A. 2013;110(44):17868-17873. doi:10.1073/pnas.1309777110
50. Harada Y, Ohkawa Y, Kizuka Y, Taniguchi N. Oligosaccharyltransferase: A gatekeeper of health and tumor progression. Int J Mol Sci. 2019;20(23). doi:10.3390/ijms20236074
51. Igura M, Kohda D. Quantitative assessment of the preferences for the amino acid residues flanking archaeal N-linked glycosylation sites. Glycobiology. 2011;21(5):575-583. doi:10.1093/glycob/cwq196
52. Yamasaki T, Kohda D. A Radioisotope-free Oligosaccharyltransferase Assay Method. BIO-PROTOCOL. 2019;9(5). doi:10.21769/BioProtoc.3186
53. Studier FW. Protein production by auto-induction in high density shaking cultures. Protein Expr Purif. 2005;41(1):207-234. doi:10.1016/j.pep.2005.01.016
54. Widlund PO, Davis TN. A high-efficiency method to replace essential genes with mutant alleles in yeast. Yeast. 2005;22(10):769-774. doi:10.1002/yea.1244
55. Gadaleta MC, Iwasaki O, Noguchi C, Noma KI, Noguchi E. New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe. Biotechniques. 2013;55(5):257-263. doi:10.2144/000114100
56. Fujii Y, Kaneko M, Neyazaki M, Nogi T, Kato Y, Takagi J. PA tag: A versatile protein tagging system using a super high affinity antibody against a dodecapeptide derived from human podoplanin. Protein Expr Purif. 2014;95:240-247. doi:10.1016/j.pep.2014.01.009
57. Einhauer A, Jungbauer A. Affinity of the monoclonal antibody M1 directed against the FLAG peptide. J Chromatogr A. 2001;921(1):25-30. doi:10.1016/S0021-9673(01)00831-7
58. Locatelli-Hoops SC, Gorshkova I, Gawrisch K, Yeliseev AA. Expression, surface immobilization, and characterization of functional recombinant cannabinoid receptor CB2. Biochim Biophys Acta. 2013;1834(10):2045-2056. doi:10.1016/j.bbapap.2013.06.003
59. Shrimal S, Gilmore R. Oligosaccharyltransferase structures provide novel insight into the mechanism of asparagine-linked glycosylation in prokaryotic and eukaryotic cells. Glycobiology. 2019;29(4):288-297. doi:10.1093/glycob/cwy093
60. Matsumoto S, Taguchi Y, Shimada A, Igura M, Kohda D. Tethering an N- glycosylation sequon-containing peptide creates a catalytically competent oligosaccharyltransferase complex. Biochemistry. 2017;56(4):602-611. doi:10.1021/acs.biochem.6b01089
61. Kushnirov V V. Rapid and reliable protein extraction from yeast. Yeast. 2000;16(9):857-860. doi:10.1002/1097-0061(20000630)16:9<857::AID- YEA561>3.0.CO;2-B
62. Zielinska DF, Gnad F, Schropp K, Wiśniewski JR, Mann M. Mapping N- Glycosylation Sites across Seven Evolutionarily Distant Species Reveals a Divergent Substrate Proteome Despite a Common Core Machinery. Mol Cell. 2012;46(4):542-548. doi:10.1016/j.molcel.2012.04.031
63. Dwivedi R, Nothaft H, Reiz B, Whittal RM, Szymanski CM. Generation of free oligosaccharides from bacterial protein N-linked glycosylation systems. Biopolymers. 2013;99(10):772-783. doi:10.1002/bip.22296
64. Hou J, Tang H, Liu Z, Österlund T, Nielsen J, Petranovic D. Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast. FEMS Yeast Res. 2014;14(3):481-494. doi:10.1111/1567-1364.12125
65. Guerra-Moreno A, Ang J, Welsch H, Jochem M, Hanna J. Regulation of the unfolded protein response in yeast by oxidative stress. FEBS Lett. 2019:1873- 3468.13389. doi:10.1002/1873-3468.13389
66. Cui HJ, Cui XG, Jing X, et al. GAS1 deficient enhances UPR activity in saccharomyces cerevisiae. Biomed Res Int. 2019;2019. doi:10.1155/2019/1238581
67. Nakamura T, Ando A, Takagi H, Shima J. EOS1, whose deletion confers sensitivity to oxidative stress, is involved in N-glycosylation in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2007;353(2):293-298. doi:10.1016/j.bbrc.2006.12.012
68. Schulz BL, Stirnimann CU, Grimshaw JPA, et al. Oxidoreductase activity of oligosaccharyltransferase subunits Ost3p and Ost6p defines site-specific glycosylation efficiency. Proc Natl Acad Sci U S A. 2009;106(27):11061-11066. doi:10.1073/pnas.0812515106
69. Ron D, Walter P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol. 2007;8(7):519-529. doi:10.1038/nrm2199
70. Shrimal S, Cherepanova NA, Mandon EC, Venev S V., Gilmore R. Asparagine- linked glycosylation is not directly coupled to protein translocation across the endoplasmic reticulum in Saccharomyces cerevisiae. Mol Biol Cell. 2019;30(21):2626-2638. doi:10.1091/mbc.E19-06-0330
71. Zheng SQ, Palovcak E, Armache JP, Verba KA, Cheng Y, Agard DA. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo- electron microscopy. Nat Methods. 2017;14(4):331-332. doi:10.1038/nmeth.4193
72. Rohou A, Grigorieff N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015;192(2):216-221. doi:10.1016/j.jsb.2015.08.008
73. Wagner T, Merino F, Stabrin M, et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun Biol. 2019;2(1):1-13. doi:10.1038/s42003-019-0437-z
74. Scheres SHW. A bayesian view on cryo-EM structure determination. J Mol Biol. 2012;415(2):406-418. doi:10.1016/j.jmb.2011.11.010
75. Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605-1612. doi:10.1002/jcc.20084
76. Ramírez AS, Kowal J, Locher KP. Cryo–electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Science (80- ). 2019;366(6471):1372-1375. doi:10.1126/SCIENCE.AAZ3505
77. Cherepanova NA, Shrimal S, Gilmore R. Oxidoreductase activity is necessary for N-glycosylation of cysteine-proximal acceptor sites in glycoproteins. J Cell Biol. 2014;206(4):525-539. doi:10.1083/jcb.201404083
78. Stevens KLP, Black AL, Wells KM, et al. Diminished Ost3-dependent N- glycosylation of the BiP nucleotide exchange factor Sil1 is an adaptive response to reductive ER stress. Proc Natl Acad Sci. 2017;114(47):12489-12494. doi:10.1073/pnas.1705641114
79. Kanda Y. Investigation of the freely available easy-to-use software “EZR” for medical statistics. Bone Marrow Transplant. 2013;48(3):452-458. doi:10.1038/bmt.2012.244
80. R Core Team. R: A language and environment for statistical computing. 2020. https://www.r-project.org/.
81. Fox J. The R Commander: A Basic-Statistics Graphical User Interface to R. J Stat Softw. 2005;14(9):1902. doi:10.18637/jss.v014.i09