Darwinian selection for sites of Asn-linked glycosylation in phylogenetically disparate eukaryotes and viruses

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 32, 2009, Pages 13421-13426

  Cui, Jike ^a   Smith, Temple ^a,b   Robbins, Phillips W ^a   Samuelson, John ^a  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

Asn linked glycan; Evolution; Influenza; N glycan dependent quality control; Sequon

Indexed keywords

ASPARAGINE; GLYCAN; MEMBRANE PROTEIN; SERINE; THREONINE; VIRUS GLYCOPROTEIN; VIRUS HEMAGGLUTININ;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; EUKARYOTE; FUNGUS; GENETIC SELECTION; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; INFLUENZA VIRUS A H5N1; METAZOON; PHYLOGENY; PRIORITY JOURNAL; PROTEIN GLYCOSYLATION; RETROVIRUS;

AMINO ACIDS; ASPARAGINE; AT RICH SEQUENCE; EUKARYOTIC CELLS; GLYCOPROTEINS; GLYCOSYLATION; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HIV ENVELOPE PROTEIN GP120; HOST-PATHOGEN INTERACTIONS; HUMANS; LIKELIHOOD FUNCTIONS; OPEN READING FRAMES; ORTHOMYXOVIRIDAE; PHYLOGENY; POLYSACCHARIDES; PROTEIN FOLDING; SELECTION (GENETICS); TIME FACTORS; VIRUSES;

EUKARYOTA; FUNGI; ORTHOMYXOVIRIDAE; PROTISTA; SUIDAE;

EID: 69449094891     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0905818106     Document Type: Article

References (42)

1. Helenius A, Aebi M (2004) Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 73:1019-1049. (Pubitemid 39050393)
2. Samuelson J, et al. (2005) The diversity of protist and fungal dolichol-linked precursors to Asn-linked glycans likely results from secondary loss of sets of glycosyltransferases. Proc Natl Acad Sci USA 102:1548-1553. (Pubitemid 40209206)
3. Kornfeld R, Kornfeld S (1985) Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 54:631-664.
4. Apweiler R, Hermjakob H, Sharon N (1999) On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta 1473:4-8.
5. Ben-Dor S, Esterman N, Rubin E, Sharon N (2004) Biases and complex patterns in the residues flanking protein N-glycosylation sites. Glycobiology 14:95-101. (Pubitemid 38263094)
6. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR (2004) Statistical analysis of the protein environment of N-glycosylation sites: Implications for occupancy, structure, and folding. Glycobiology 14:103-114.
7. Breuer W, Klein RA, Hardt B, Bartoschek A, Bause E (2001) Oligosaccharyltransferase is highly specific for the hydroxy amino acid in Asn-Xaa-Thr/Ser. FEBS Lett 501:106-110. (Pubitemid 32695472)
8. Kasturi L, Eshleman JR, Wunner WH, Shakin-Eshleman SH (1995) The hydroxy amino acid in an Asn-X-Ser/Thr sequon can influence N-linked core glycosylation efficiency and the level of expression of a cell surface glycoprotein. J BiolChem270:14756-14761.
9. Ratner DM, et al. (2008) Changes in the N-glycome, glycoproteins with Asn-linked glycans, of Giardia lamblia with differentiation from trophozoites to cysts. Eukaryot Cell 7:1930-1940.
10. Trombetta ES, Parodi AJ (2003) Quality control and protein folding in the secretory pathway. Annu Rev Cell Dev Biol 19:649-676. (Pubitemid 37487364)
11. Hebert DN, Molinari M (2007) In and out of the ER: Protein folding, quality control, degradation, and related human diseases. Physiol Rev 87:1377-1408.
12. Banerjee S, et al. (2007) Evolution of quality control of protein-folding in the ER lumen. Proc Natl Acad Sci USA 104:11676-11681.
13. Bastien O, et al. (2004) Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference. Gene 336:163-173. (Pubitemid 38891734)
14. Singer GA, Hickey DA (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17:1581-1588.
15. Zhang M, et al. (2004) Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology 14:1229-1246. (Pubitemid 39585357)
16. Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8:196-205.
17. Kwong PD, et al. (2002) HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420:678-682.
18. Poon AF, Lewis FI, Pond SL, Frost SD (2007) Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Biol 3:e11.
19. Jones DC, Mehlert A, Güther ML, Ferguson MA (2005) Deletion of the glucosidase II gene in Trypanosoma brucei reveals novel N-glycosylation mechanisms in the biosynthesis of variant surface glycoprotein. J Biol Chem 280:35929-35942. (Pubitemid 41633861)
20. Peiris JS, de Jong MD (2007) Guan Y Avian influenza virus (H5N1): A threat to human health. Clin Microbiol Rev 20:243-267. (Pubitemid 46709304)
21. Wallace RG, Hodac H, Lathrop RH, Fitch WM (2007) A statistical phylogeography of influenza A H5N1. Proc Natl Acad Sci USA 104:4473-4478.
22. Garten RJ, et al. (2009) Antigenic and genetic characteristics of Swine-origin 2009 A(H1N1) Influenza viruses circulating in humans. Science 325:197-201.
23. Shinde V, et al. (2009) Triple-reassortant swine influenza A (H1) in humans in the United States, 2005-2009. N Engl J Med 360:2616-2625.
24. Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM (1999) Predicting the evolution of human influenza A. Science 286:1921-1925.
25. Fitch WM, Leiter JM, Li XQ, Palese P (1991) Positive Darwinian evolution in human influenza A viruses. Proc Natl Acad Sci USA 88:4270-4274.
26. Goffard A, et al. (2005) Role of N-linked glycans in the functions of hepatitis C virus envelope glycoproteins. J Virol 79:8400-8409. (Pubitemid 40853542)
27. Helle F, et al. (2007) The neutralizing activity of anti-hepatitis C virus antibodies is modulated by specific glycans on the E2 envelope protein. J Virol 81:8101-8111. (Pubitemid 47101496)
28. Dowling W, et al. (2007) Influences of glycosylation on antigenicity, immunogenicity, and protective efficacy of Ebola virus GP DNA vaccines. J Virol 81:1821-1837. (Pubitemid 46214455)
29. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE (2005) Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 33:1141-1153. (Pubitemid 41439907)
30. Paz A, Mester D, Baca I, Nevo E, Korol A (2004) Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc Natl Acad Sci USA 101:2951-2956. (Pubitemid 38327717)
31. Stanley P (2007) Regulation of Notch signaling by glycosylation. Curr Opin Struct Biol 17:530-535.
32. Zhao Y, et al. (2008) Branched N-glycans regulate the biological functions of integrins and cadherins. FEBS J 275:1939-1948. (Pubitemid 351569538)
33. Lau KS, Dennis JW (2008) N-Glycans in cancer progression. Glycobiology 18:750-760.
34. Daniels R, Kurowski B, Johnson AE, Hebert DN (2003) N-linked glycans direct the cotranslational folding pathway of influenza hemagglutinin. Mol Cell 11:79-90. (Pubitemid 36126592)
35. Hong PW, Nguyen S, Young S, Su SV, Lee B (2007) Identification of the optimal DC-SIGN binding site on human immunodeficiencyvirus type 1 gp120. J Virol 81:8325-8336.
36. Vigerust DJ, et al. (2007) N-linked glycosylation attenuates H3N2 influenza viruses. J Virol 81:8593-8600. (Pubitemid 47242833)
37. Freeze HH, Westphal V (2001) Balancing N-linked glycosylation to avoid disease. Biochimie 83:791-799.
38. Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17:282-283. (Pubitemid 32288218)
39. Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554-571. (Pubitemid 26165889)
40. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: Signal P 3.0. J Mol Biol 340:783-795. (Pubitemid 38829638)
41. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305:567-580. (Pubitemid 33032862)
42. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.