Skip to main content
SpringerLink
Log in

A Practical Approach to Reconstruct Evolutionary History of Animal Sialyltransferases and Gain Insights into the Sequence–Function Relationships of Golgi-Glycosyltransferases

  • Protocol
  • First Online:
Glycosyltransferases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1022))

Abstract

In higher vertebrates, sialyltransferases catalyze the transfer of sialic acid residues, either Neu5Ac or Neu5Gc or KDN from an activated sugar donor, which is mainly CMP-Neu5Ac in human tissues, to the hydroxyl group of another saccharide acceptor. In the human genome, 20 unique genes have been described that encode enzymes with remarkable specificity with regards to their acceptor substrates and the glycosidic linkage formed. A systematic search of sialyltransferase-related sequences in genome and EST databases and the use of bioinformatic tools enabled us to investigate the evolutionary history of animal sialyltransferases and propose original models of divergent evolution of animal sialyltransferases. In this chapter, we extend our phylogenetic studies to the comparative analysis of the environment of sialyltransferase gene loci (synteny and paralogy studies), the variations of tissue expression of these genes and the analysis of amino-acid position evolution after gene duplications, in order to assess their sequence–function relationships and the molecular basis underlying their functional divergence.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kikuchi N, Narimatsu H (2006) Bioinformatics for comprehensive finding and analysis of glycosyltransferases. Biochim Biophys Acta 1760:578–583. doi:10.1016/j.bbagen.2005.12.024

    Article  PubMed  CAS  Google Scholar 

  2. Harduin-Lepers A, Stokes DC, Steelant WF, Samyn-Petit B, Krzewinski-Recchi MA, Vallejo-Ruiz V, Zanetta JP, Augé C, Delannoy P (2000) Cloning, expression and gene organization of a human Neu5Ac alpha 2-3Gal beta 1-3GalNAc alpha 2,6-sialyltransferase: hST6GalNAcIV. Biochem J 352(Pt 1):37–48

    Article  PubMed  CAS  Google Scholar 

  3. Harduin-Lepers A (2010) Comprehensive analysis of sialyltransferases in vertebrate genomes. Glycobiol Insights 29. doi:10.4137/GBI.S3123

    Google Scholar 

  4. Harduin-Lepers A, Petit D, Mollicone R, Delannoy P, Petit J-M, Oriol R (2008) Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes. BMC Evol Biol 8:258. doi:10.1186/1471-2148-8-258

    Article  PubMed  Google Scholar 

  5. Varki A (2009) Ajit Varki: on the origin of maladies. Interviewed by Amy Maxmen. J Exp Med 206:1836–1837. doi:10.1084/jem.2069pi

    Article  PubMed  Google Scholar 

  6. Schauer R (2009) Sialic acids as regulators of molecular and cellular interactions. Curr Opin Struct Biol 19:507–514. doi:10.1016/j.sbi.2009.06.003

    Article  PubMed  CAS  Google Scholar 

  7. Hu H, Eggers K, Chen W, Garshasbi M, Motazacker MM, Wrogemann K, Kahrizi K, Tzschach A, Hosseini M, Bahman I, Hucho T, Mühlenhoff M, Gerardy-Schahn R, Najmabadi H, Ropers HH, Kuss AW (2011) ST3GAL3 mutations impair the development of higher cognitive functions. Am J Hum Genet 89:407–414. doi:10.1016/j.ajhg.2011.08.008

    Article  PubMed  CAS  Google Scholar 

  8. Harduin-Lepers A (2012) Sialyltransferases functions in cancers. Front Biosci E4:499. doi:10.2741/396

    CAS  Google Scholar 

  9. Rao FV, Rich JR, Rakić B, Buddai S, Schwartz MF, Johnson K, Bowe C, Wakarchuk WW, Defrees S, Withers SG, Strynadka NCJ (2009) Structural insight into mammalian sialyltransferases. Nat Struct Mol Biol 16:1186–1188. doi:10.1038/nsmb.1685

    Article  PubMed  CAS  Google Scholar 

  10. Audry M, Jeanneau C, Imberty A, Harduin-Lepers A, Delannoy P, Breton C (2011) Current trends in the structure-activity relationships of sialyltransferases. Glycobiology 21:716–726. doi:10.1093/glycob/cwq189

    Article  PubMed  CAS  Google Scholar 

  11. Chang L-Y, Harduin-Lepers A, Kitajima K, Sato C, Huang C-J, Khoo K-H, Guérardel Y (2009) Developmental regulation of oligosialylation in zebrafish. Glycoconj J 26:247–261. doi:10.1007/s10719-008-9161-5

    Article  PubMed  CAS  Google Scholar 

  12. Chang L-Y, Mir A-M, Thisse C, Guérardel Y, Delannoy P, Thisse B, Harduin-Lepers A (2009) Molecular cloning and characterization of the expression pattern of the zebrafish alpha2, 8-sialyltransferases (ST8Sia) in the developing nervous system. Glycoconj J 26:263–275. doi:10.1007/s10719-008-9165-1

    Article  PubMed  CAS  Google Scholar 

  13. Guérardel Y, Chang L-Y, Fujita A, Coddeville B, Maes E, Sato C, Harduin-Lepers A, Kubokawa K, Kitajima K (2012) Sialome analysis of the cephalochordate Branchiostoma belcheri, a key organism for vertebrate evolution. Glycobiology 22:479–491. doi:10.1093/glycob/cwr155

    Article  PubMed  Google Scholar 

  14. Petit D, Mir A-M, Petit J-M, Thisse C, Delannoy P, Oriol R, Thisse B, Harduin-Lepers A (2010) Molecular phylogeny and functional genomics of beta-galactoside alpha2,6-sialyltransferases that explain ubiquitous expression of st6gal1 gene in amniotes. J Biol Chem 285:38399–38414. doi:10.1074/jbc.M110.163931

    Article  PubMed  CAS  Google Scholar 

  15. Harduin-Lepers A, Mollicone R, Delannoy P, Oriol R (2005) The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach. Glycobiology 15:805–817. doi:10.1093/glycob/cwi063

    Article  PubMed  CAS  Google Scholar 

  16. Felsenstein J (2002) PHYLIP: phylogeny inference package, Ver 3.6. University of Washington, Seattle, WA

    Google Scholar 

  17. Guindon S, Gascuel O (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704. doi:10.1080/10635150390235520

    Article  PubMed  Google Scholar 

  18. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121

    Article  PubMed  CAS  Google Scholar 

  19. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analyses. Palaeontol Electron 4:9

    Google Scholar 

  20. Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217. doi:10.1006/jmbi.2000.4042

    Article  PubMed  CAS  Google Scholar 

  21. Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA (2010) Genenames.org: the HGNC resources in 2011. Nucleic Acids Res 39:D514–D519. doi:10.1093/nar/gkq892

    Article  PubMed  Google Scholar 

  22. Page RDM (1996) Tree view: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358. doi:10.1093/bioinformatics/12.4.357

    PubMed  CAS  Google Scholar 

  23. Datta AK (2009) Comparative sequence analysis in the sialyltransferase protein family: analysis of motifs. Curr Drug Targets 10:483–498

    Article  PubMed  CAS  Google Scholar 

  24. Datta AK, Paulson JC (1997) Sialylmotifs of sialyltransferases. Indian J Biochem Biophys 34:157–165

    PubMed  CAS  Google Scholar 

  25. Datta AK, Chammas R, Paulson JC (2001) Conserved cysteines in the sialyltransferase sialylmotifs form an essential disulfide bond. J Biol Chem 276:15200–15207. doi:10.1074/jbc.M010542200

    Article  PubMed  CAS  Google Scholar 

  26. Datta AK, Paulson JC (1995) The sialyltransferase « sialylmotif » participates in binding the donor substrate CMP-NeuAc. J Biol Chem 270:1497–1500

    Article  PubMed  CAS  Google Scholar 

  27. Datta AK, Sinha A, Paulson JC (1998) Mutation of the sialyltransferase S-sialylmotif alters the kinetics of the donor and acceptor substrates. J Biol Chem 273:9608–9614. doi:10.1074/jbc.273.16.9608

    Article  PubMed  CAS  Google Scholar 

  28. Geremia RA, Harduin-Lepers A, Delannoy P (1997) Identification of two novel conserved amino acid residues in eukaryotic sialyltransferases: implications for their mechanism of action. Glycobiology 7:v–vii

    Article  PubMed  CAS  Google Scholar 

  29. Jeanneau C, Chazalet V, Augé C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C (2004) Structure-function analysis of the human sialyltransferase ST3Gal I: role of n-glycosylation and a novel conserved sialylmotif. J Biol Chem 279:13461–13468. doi:10.1074/jbc.M311764200

    Article  PubMed  CAS  Google Scholar 

  30. Tsuji S, Datta AK, Paulson JC (1996) Systematic nomenclature for sialyltransferases. Glycobiology 6:v–vii

    Article  PubMed  CAS  Google Scholar 

  31. Patel RY, Balaji PV (2006) Identification of linkage-specific sequence motifs in sialyltransferases. Glycobiology 16:108–116. doi:10.1093/glycob/cwj046

    Article  PubMed  CAS  Google Scholar 

  32. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233–D238. doi:10.1093/nar/gkn663

    Article  PubMed  CAS  Google Scholar 

  33. Kent WJ (2002) BLAT—The BLAST-like alignment tool. Genome Res 12:656–664. doi:10.1101/gr.229202

    PubMed  CAS  Google Scholar 

  34. Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E (2007) Ensembl 2007. Nucleic Acids Res 35:D610–D617. doi:10.1093/nar/gkl996

    Article  PubMed  CAS  Google Scholar 

  35. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877. doi:10.1101/gr.9.9.868

    Article  PubMed  CAS  Google Scholar 

  36. Burge CB, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8:346–354. doi:10.1016/S0959-440X(98)80069-9

    Article  PubMed  CAS  Google Scholar 

  37. Breathnach R, Chambon P (1981) Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 50:349–383. doi:10.1146/annurev.bi.50.070181.002025

    Article  PubMed  CAS  Google Scholar 

  38. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. doi:10.1093/nar/22.22.4673

    Article  PubMed  CAS  Google Scholar 

  39. Higgins DG, Thompson JD, Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266:383–402

    Article  PubMed  CAS  Google Scholar 

  40. Morgenstern B (2004) DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res 32:W33–W36. doi:10.1093/nar/gkh373

    Article  PubMed  CAS  Google Scholar 

  41. Harduin-Lepers A, Vallejo-Ruiz V, Krzewinski-Recchi M-A, Samyn-Petit B, Julien S, Delannoy P (2001) The human sialyltransferase family. Biochimie 83:727–737. doi:10.1016/S0300-9084(01)01301-3

    Article  PubMed  CAS  Google Scholar 

  42. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788. doi:10.1093/nar/gkg563

    Article  PubMed  CAS  Google Scholar 

  43. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222. doi:10.1093/nar/gkp985

    Article  PubMed  CAS  Google Scholar 

  44. Murphy LR, Wallqvist A, Levy RM (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng 13:149–152. doi:10.1093/protein/13.3.149

    Article  PubMed  CAS  Google Scholar 

  45. Mollicone R, Moore SEH, Bovin N, Garcia-Rosasco M, Candelier J-J, Martinez-Duncker I, Oriol R (2009) Activity, splice variants, conserved peptide motifs and phylogeny of two new alpha1,3-fucosyltransferase families (FUT10 and FUT11). J Biol Chem 284:4723–4738. doi:10.1074/jbc.M809312200

    Article  PubMed  CAS  Google Scholar 

  46. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  PubMed  CAS  Google Scholar 

  47. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577. doi:10.1080/10635150701472164

    Article  PubMed  CAS  Google Scholar 

  48. Müller KF (2005) The efficiency of different search strategies in estimating parsimony jackknife, bootstrap and Bremer support. BMC Evol Biol 5:58. doi:10.1186/1471-2148-5-58

    Article  PubMed  Google Scholar 

  49. Battistuzzi FU, Filipski A, Hedges SB, Kumar S (2010) Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol 27:1289–1300. doi:10.1093/molbev/msq014

    Article  PubMed  CAS  Google Scholar 

  50. Blair JE, Hedges SB (2005) Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 22:2275–2284. doi:10.1093/molbev/msi225

    Article  PubMed  CAS  Google Scholar 

  51. Kumar S, Hedges SB (2011) TimeTree2: species divergence times on the iPhone. Bioinformatics 27:2023–2024. doi:10.1093/bioinformatics/btr315

    Article  PubMed  CAS  Google Scholar 

  52. McLysaght A, Hokamp K, Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nat Genet 31:200–204. doi:10.1038/ng884

    Article  PubMed  CAS  Google Scholar 

  53. Catchen JM, Conery JS, Postlethwait JH (2009) Automated identification of conserved synteny after whole-genome duplication. Genome Res 19:1497–1505. doi:10.1101/gr.090480.108

    Article  PubMed  CAS  Google Scholar 

  54. Muffato M, Louis A, Poisnel C-E, Crollius HR (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26:1119–1121. doi:10.1093/bioinformatics/btq079

    Article  PubMed  CAS  Google Scholar 

  55. Martin R, Gallet P-F, Rocha D, Petit D (2009) Polymorphism of the prion protein in mammals: a phylogenetic approach. Recent Pat DNA Gene Seq 3:63–71

    Article  PubMed  CAS  Google Scholar 

  56. Petit D, Maftah A, Julien R, Petit J-M (2006) En bloc duplications, mutation rates and densities of amino acid changes clarify the evolution of vertebrate alpha-1,3/4-fucosyltransferases. J Mol Evol 63:353–364. doi:10.1007/s00239-005-0189-x

    Article  PubMed  CAS  Google Scholar 

  57. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591. doi:10.1093/molbev/msm088

    Article  PubMed  CAS  Google Scholar 

  58. Bielawski JP, Yang Z (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics 3:201–212. doi:10.1023/A:1022642807731

    Article  PubMed  CAS  Google Scholar 

  59. Yang Z, Nielsen R (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46:409–418. doi:10.1007/PL00006320

    Article  PubMed  CAS  Google Scholar 

  60. Ermonval M, Petit D, Le Duc A, Kellermann O, Gallet PF (2009) Glycosylation-related genes are variably expressed depending on the differentiation state of a bioaminergic neuronal cell line: implication for the cellular prion protein. Glycoconj J 26:477–493. doi:10.1007/s10719-008-9198-5

    Article  PubMed  CAS  Google Scholar 

  61. Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2004) The EMBL nucleotide sequence database. Nucleic Acids Res 32:D27–D30. doi:10.1093/nar/gkh120

    Article  PubMed  CAS  Google Scholar 

  62. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2003) GenBank. Nucleic Acids Res 31:23–27. doi:10.1093/nar/gkg057

    Article  PubMed  CAS  Google Scholar 

  63. Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H, Gojobori T (2002) DNA data bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res 30:27–30. doi:10.1093/nar/30.1.27

    Article  PubMed  CAS  Google Scholar 

  64. Consortium, T. U (2007) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195. doi:10.1093/nar/gkm895

    Article  Google Scholar 

  65. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29:159–164. doi:10.1093/nar/29.1.159

    Article  PubMed  CAS  Google Scholar 

  66. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389

    Article  PubMed  CAS  Google Scholar 

  67. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224. doi:10.1093/molbev/msp259

    Article  PubMed  CAS  Google Scholar 

  68. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. doi:10.1093/nar/gkh340

    Article  PubMed  CAS  Google Scholar 

  69. Apweiler R (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:115D–119D. doi:10.1093/nar/gkh131

    Article  Google Scholar 

  70. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I (2011) The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 1–7. doi:10.1093/nar/gkr947

    Google Scholar 

  71. Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46. doi:10.1093/nar/30.1.42

    Article  PubMed  CAS  Google Scholar 

  72. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. doi:10.1093/nar/28.1.27

    Article  PubMed  CAS  Google Scholar 

  73. Raman R, Venkataraman M, Ramakrishnan S, Lang W, Raguram S, Sasisekharan R (2006) Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 16:82R–90R. doi:10.1093/glycob/cwj080

    Article  PubMed  CAS  Google Scholar 

  74. Sprague J (2006) The Zebrafish information network: the Zebrafish model organism database. Nucleic Acids Res 34:D581–D585. doi:10.1093/nar/gkj086

    Article  PubMed  CAS  Google Scholar 

  75. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res 39:D670–D676. doi:10.1093/nar/gkq1089

    Article  PubMed  CAS  Google Scholar 

  76. Kikuno R (2004) HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. Nucleic Acids Res 32:502D–504D. doi:10.1093/nar/gkh035

    Article  Google Scholar 

  77. Mcwilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R (2009) Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res 37:W6–W10. doi:10.1093/nar/gkp302

    Article  PubMed  CAS  Google Scholar 

  78. Reese MG, Eeckman FH, Kulp D, Haussler D (1997) Improved splice site detection in genie. J Comput Biol 4:311–323

    Article  PubMed  CAS  Google Scholar 

  79. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. doi:10.1093/nar/25.24.4876

    Article  PubMed  CAS  Google Scholar 

  80. Crooks GE, Hon G, Chandonia J-M, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190. doi:10.1101/gr.849004

    Article  PubMed  CAS  Google Scholar 

  81. Otsuka J, Sugaya N (2003) Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals. J Theor Biol 222:447–460. doi:10.1016/S0022-5193(03)00057-2

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The project was financially supported by the University of Lille1 (ppf bioinformatique de Lille1), by the French Centre National de la Recherche Scientifique (CNRS), and by the Agence Nationale de la Recherche (ANR) project GalFish (ANR-2010-BLAN-120401). An Erasmus Mundus doctoral fellowship was attributed to R.E. Teppa.

Author information

Authors and Affiliations

  1. Unité de Génétique Moléculaire Animale, INRA/Université de Limoges, Limoges, France

    Daniel Petit & Jean-Michel Petit

  2. Unité de Glycobiologie Structurale et Fonctionnelle, Université Lille Nord de France, Lille 1, Villeneuve d’Ascq, France

    Roxana Elin Teppa & Anne Harduin-Lepers

Authors
  1. Daniel Petit
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Roxana Elin Teppa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jean-Michel Petit
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anne Harduin-Lepers
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Medicine, Queen's University, Kingston, Ontario, Canada

    Inka Brockhausen

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Petit, D., Teppa, R.E., Petit, JM., Harduin-Lepers, A. (2013). A Practical Approach to Reconstruct Evolutionary History of Animal Sialyltransferases and Gain Insights into the Sequence–Function Relationships of Golgi-Glycosyltransferases. In: Brockhausen, I. (eds) Glycosyltransferases. Methods in Molecular Biology, vol 1022. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-465-4_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-465-4_7

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-464-7

  • Online ISBN: 978-1-62703-465-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation