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Designing Glycosyltransferase Expression Constructs for Improved Purification, Protein Yield, and Crystallization

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Bacterial Polysaccharides

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1954))

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Abstract

Glycosyltransferases in bacteria are built using only four known architectures, but this structural core is often supplemented by fusions with a wide variety of other domains, including those that help recruit them to the membrane. Structural and functional characterization of these proteins is often simplified by making a subconstruct that is better behaved in solution, and perhaps monofunctional. In this chapter we review bioinformatics tools and strategies that can be used for designing such constructs of glycosyltransferases.

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References

  1. Elshahawi SI, Shaaban KA, Kharel MK et al (2015) A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 44:7591–7697

    Article  CAS  Google Scholar 

  2. Holst O, Moran AP, Brennan PJ (2010) Overview of the glycosylated components of the bacterial cell envelope. In: Microbial glycobiology. London, Elsevier, pp 1–13

    Google Scholar 

  3. Greenfield LK, Whitfield C (2012) Synthesis of lipopolysaccharide O-antigens by ABC transporter-dependent pathways. Carbohydr Res 356:12–24

    Article  CAS  Google Scholar 

  4. Albesa-Jové D, Giganti D, Jackson M et al (2014) Structure-function relationships of membrane-associated GT-B glycosyltransferases. Glycobiology 24:108–124

    Article  Google Scholar 

  5. Hu Y, Chen L, Ha S et al (2003) Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases. Proc Natl Acad Sci U S A 100:845–849

    Article  CAS  Google Scholar 

  6. Schmidt H, Hansen G, Singh S et al (2012) Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis. Proc Natl Acad Sci 109:6253–6258

    Article  CAS  Google Scholar 

  7. Guerin ME, Kordulakova J, Schaeffer F et al (2007) Molecular recognition and interfacial catalysis by the essential phosphatidylinositol mannosyltransferase PimA from mycobacteria. J Biol Chem 282:20705–20714

    Article  CAS  Google Scholar 

  8. Wheatley RW, Zheng RB, Richards MR et al (2012) Tetrameric structure of the GlfT2 galactofuranosyltransferase reveals a scaffold for the assembly of mycobacterial arabinogalactan. J Biol Chem 287:28132–28143

    Article  CAS  Google Scholar 

  9. Ramírez AS, Boilevin J, Mehdipour AR et al (2018) Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nat Commun 9:445

    Article  Google Scholar 

  10. Hagelueken G, Clarke BR, Huang H et al (2015) A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat Struct Mol Biol 22:50–56

    Article  CAS  Google Scholar 

  11. Williams DM, Ovchinnikova OG, Koizumi A et al (2017) Single polysaccharide assembly protein that integrates polymerization, termination, and chain-length quality control. Proc Natl Acad Sci U S A 114:E1215–E1223

    Article  CAS  Google Scholar 

  12. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738

    Article  CAS  Google Scholar 

  13. Moretti R, Lyskov S, Das R et al (2018) Web-accessible molecular modeling with Rosetta: the Rosetta online server that includes everyone (ROSIE). Protein Sci 27:259–268

    Article  CAS  Google Scholar 

  14. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202

    Article  CAS  Google Scholar 

  15. Drozdetskiy A, Cole C, Procter J et al (2015) JPred4: a protein secondary structure prediction server. Nucleic Acids Res 43:W389–W394

    Article  CAS  Google Scholar 

  16. Yoo PD, Sikder AR, Taheri J et al (2008) DomNet: protein domain boundary prediction using enhanced general regression network and new profiles. IEEE Trans Nanobioscience 7:172–181

    Article  CAS  Google Scholar 

  17. Marchler-Bauer A, Bo Y, Han L et al (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203

    Article  CAS  Google Scholar 

  18. Ishida T, Kinoshita K (2007) PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 35:W460–W464

    Article  Google Scholar 

  19. Saidijam M, Azizpour S, Patching SG (2018) Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure. J Biomol Struct Dyn 36:443–464

    Article  CAS  Google Scholar 

  20. Reeb J, Kloppmann E, Bernhofer M et al (2015) Evaluation of transmembrane helix predictions in 2014. Proteins 83:473–484

    Article  CAS  Google Scholar 

  21. Nugent T, Jones DT (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 10:159

    Article  Google Scholar 

  22. Käll L, Krogh A, Sonnhammer ELL (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21(Suppl 1):i251–i257

    Article  Google Scholar 

  23. Gautier R, Douguet D, Antonny B et al (2008) HELIQUEST: a web server to screen sequences with specific alpha-helical properties. Bioinformatics 24:2101–2102

    Article  CAS  Google Scholar 

  24. Sapay N, Guermeur Y, Deléage G (2006) Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. BMC Bioinformatics 7:255

    Article  Google Scholar 

  25. Ovchinnikova OG, Mallette E, Koizumi A et al (2016) Bacterial β-Kdo glycosyltransferases represent a new glycosyltransferase family (GT99). Proc Natl Acad Sci 113:E3120–E3129

    Article  CAS  Google Scholar 

  26. Ovchinnikova OG, Doyle L, Huang B-S et al (2016) Biochemical characterization of Bifunctional 3-Deoxy-β-d-manno-oct-2-ulosonic acid (β-Kdo) Transferase KpsC from Escherichia coli involved in capsule biosynthesis. J Biol Chem 291:21519–21530

    Article  CAS  Google Scholar 

  27. Lin LYC, Rakic B, Chiu CPC et al (2011) Structure and mechanism of the lipooligosaccharide sialyltransferase from Neisseria meningitidis. J Biol Chem 286:37237–37248

    Article  CAS  Google Scholar 

  28. Osawa T, Sugiura N, Shimada H et al (2009) Crystal structure of chondroitin polymerase from Escherichia coli K4. Biochem Biophys Res Commun 378:10–14

    Article  CAS  Google Scholar 

  29. Huynh N, Li Y, Yu H et al (2014) Crystal structures of sialyltransferase from Photobacterium damselae. FEBS Lett 588:4720–4729

    Article  CAS  Google Scholar 

  30. Iwatani T, Okino N, Sakakura M et al (2009) Crystal structure of alpha/beta-galactoside alpha2,3-sialyltransferase from a luminous marine bacterium, Photobacterium phosphoreum. FEBS Lett 583:2083–2087

    Article  CAS  Google Scholar 

  31. Tsukamoto H, Takakura Y, Yamamoto T (2007) Purification, cloning, and expression of an alpha/beta-galactoside alpha-2,3-sialyltransferase from a luminous marine bacterium, Photobacterium phosphoreum. J Biol Chem 282:29794–29802

    Article  CAS  Google Scholar 

  32. Chiu CPC, Watts AG, Lairson LL et al (2004) Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog. Nat Struct Mol Biol 11:163–170

    Article  CAS  Google Scholar 

  33. Chiu C, Lairson LL, Gilbert M et al (2007) Structural analysis of the α-2,3-sialyltransferase Cst-I from Campylobacter jejuni in apo and substrate-analogue bound forms. Biochemistry 46:7196–7204

    Article  CAS  Google Scholar 

  34. Zhang H, Zhu F, Yang T et al (2014) The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold. Nat Commun 5:4339

    Article  CAS  Google Scholar 

  35. Zhang H, Zhou M, Yang T et al (2016) New helical binding domain mediates a glycosyltransferase activity of a bifunctional protein. J Biol Chem 291:22106–22117

    Article  CAS  Google Scholar 

  36. Flint J, Taylor E, Yang M et al (2005) Structural dissection and high-throughput screening of mannosylglycerate synthase. Nat Struct Mol Biol 12:608–614

    Article  CAS  Google Scholar 

  37. Nielsen MM, Suits MDL, Yang M et al (2011) Substrate and metal ion promiscuity in mannosylglycerate synthase. J Biol Chem 286:15155–15164

    Article  CAS  Google Scholar 

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Acknowledgments

This work was funded by grants from the National Science and Engineering Research Council of Canada (NSERC) and from the Canadian Glycomics Network, National Centers of Excellence (GlycoNet) to MSK and JSL.

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Correspondence to Matthew S. Kimber .

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Forrester, T.J.B., El Osta, L., Lam, J.S., Kimber, M.S. (2019). Designing Glycosyltransferase Expression Constructs for Improved Purification, Protein Yield, and Crystallization. In: Brockhausen, I. (eds) Bacterial Polysaccharides. Methods in Molecular Biology, vol 1954. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9154-9_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9154-9_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9153-2

  • Online ISBN: 978-1-4939-9154-9

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