Identification of eukaryotic secreted and cell surface proteins using the yeast secretion trap screen

Nature Protocols

Volumn 1, Issue 5, 2006, Pages 2439-2447

  Lee, Sang Jik ^a,b   Kim, Byung Dong ^b   Rose, Jocelyn K C ^a  

^a Department of Obstetrics Gynecology   (United States)

^b School of Agricultural Biotechnology Center for Plant Molecular Genetics and Breeding Research   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BETA FRUCTOFURANOSIDASE; MEMBRANE PROTEIN;

ARTICLE; ESCHERICHIA COLI; EUKARYOTIC CELL; GENE LIBRARY; GENE TRANSFER; GENETICS; METHODOLOGY; PROTEOMICS; REPORTER GENE; SACCHAROMYCES CEREVISIAE; SECRETION;

BETA-FRUCTOFURANOSIDASE; ESCHERICHIA COLI; EUKARYOTIC CELLS; GENE LIBRARY; GENE TRANSFER TECHNIQUES; GENES, REPORTER; MEMBRANE PROTEINS; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

EID: 34548825632     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.373     Document Type: Article

References (46)

1. Diehn, M., Eisen, M.B., Botstein, D. & Brown, P.O. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat. Genet. 25, 58-62 (2000).
2. Clark, H.F. et al. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: A bioinformatics assessment. Genome Res. 13, 2265-2270 (2003).
3. Lee, S.-J., Saravanan, R.S., Damasceno, C.M.B., Yamane, H., Kim, B.-D. & Rose, J.K.C. Digging deeper into the plant cell wall proteome. Plant Physiol. Biochem. 42, 979-988 (2004).
4. De Groot, P.W.J., Ram, A.F. & Klis, F.M. Features and functions of covalently linked proteins in fungal cell walls. Fungal Gen. Biol. 42, 657-675 (2005).
5. Yin, Q.Y. et al. Comprehensive proteomic analysis of Saccharomyces cerevisiae cell walls. J. Biol Chem. 280, 20894-20901 (2005).
6. Jamet, E., Canut, H., Boudart, G. & Pont-Lezica, R.F. Cell wall proteins: A new insight through proteomics. Trends Plant. Sci. 11, 33-39 (2006).
7. von Heijne, G. Signal sequences: The limits of variation. J. Mol. Biol. 184, 99-105 (1985).
8. Martoglio, B. & Dobbertein, B. Signal sequences: More than just greasy peptides. Trends Cell Biol. 8, 410-415 (1998).
9. Plath, K., Mothes, W., Wilkinson, B.M., Stirling, C.J. & Rapoport, T.A. Signal sequence recognition in posttranslational protein transport across the yeast ER membrane. Cell 94, 795-807 (1998).
10. Nielsen, H., Brunak, S. & von Heijne, G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12, 3-9 (1999).
11. Ladunga, I. Large-scale predictions of secretory proteins from mammalian genomic and EST sequences. Curr. Opin. Biotechnol. 11, 13-18 (2000).
12. Fariselli, P., Finocchiaro, G. & Casadio, R. SPEPlip: The detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19, 2498-2499 (2003).
13. Bendtsen, J.D., Nielsen, H., von Heijne, G. & Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340 783-795 (2004).
14. Hiller, K., Grote, A., Scheer, M., Munch, R. & Jahn, D. PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 32, W375-W379 (2004).
15. Kall, L., Krogh, A. & Sonnhammer, E.L.L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338, 1027-1036 (2004).
16. Small, I., Peeters, N., Legeai, F. & Lurin, C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4, 1581-1590 (2004).
17. Levine, T. & Rabouille, C. Endoplasmic reticulum: One continuous network compartmentalized by extrinsic cues. Curr. Opin. Cell Biol. 17 362-368 (2005).
18. Robinson, D.G., Oliviusson, P. & Hinz, G. Protein sorting to the storage vacuoles of plants: A critical appraisal. Traffic 6, 615-625 (2005).
19. Nickel, W. Unconventional secretory routes: Direct protein export across the plasma membrane of mammalian cells. Traffic 6, 607-614 (2005).
20. Nombela, C., Gil, C. & Chaffin, W.L. Non-conventional protein secretion in yeast. Trends Microbiol. 14, 15-21 (2006).
21. Bendtsen, J.D., Jensen, L.J., Blom, N., von Heijne, G. & Brunak, S. Feature-based prediction of non-classical and leaderless protein secretion. Prot. Eng. Des. Select. 17, 349-356 (2004).
22. Tashiro, K. et al. Signal sequence trap: A cloning strategy for secreted proteins and type I membrane proteins. Science 261, 600-603 (1993).
23. Imai, T. et al. Molecular cloning of a novel T cell-directed CC chemokine expressed in thymus by signal sequence trap using Epstein-Barr virus vector. J. Biol. Chem. 271, 21514-21521 (1996).
24. Skarnes, W.C., Moss, J.E., Hurtley, S.M. & Beddington, R.S.P. Capturing genes encoding membrane and secreted proteins important for mouse development. Proc. Natl. Acad. Sci. USA 92, 6592-6596 (1995).
25. Hoffman, C.S. & Wright, A. Fusions of secreted proteins to alkaline phosphatase: An approach for studying protein secretion. Proc. Natl. Acad. Sci. USA 82, 5107-5111 (1985).
26. Chen, H. & Leder, P. A new signal sequence trap using alkaline phosphatase as a reporter. Nucleic Acids Res. 27, 1219-1222 (1999).
27. Kojima, T. & Kitamura, T. A signal sequence trap based on a constitutively active cytokine receptor. Nat. Biotechnol. 17 487-490 (1999).
28. Klein, R.D., Gu, Q., Goddard, A. & Rosenthal, A. Selection for genes encoding secreted proteins and receptors. Proc. Natl. Acad. Sci. USA 93, 7108-7113 (1996).
29. Jacobs, K.A. et al. A genetic selection for isolating cDNAs encoding secreted proteins. Gene 198, 289-296 (1997).
30. Kristoffersen, P., Teichmann, T., Stracke, R. & Palme, K. Signal sequence trap to clone cDNAs encoding secreted or membrane-associated plant proteins. Anal. Biochem. 243, 127-132 (1996).
31. Goo, J.H., Park, A.R., Park, W.J. & Park, O.K. Selection of Arabidopsis genes encoding secreted and plasma membrane proteins. Plant Mol. Biol. 41, 415-423 (1999).
32. Belanger, K.D., Wyman, A.J., Sudol, M.N., Singla-Pareek, S.L. & Quatrano, R.S. A signal peptide secretion screen in Fucus distichus embryos reveals expression of glucanase, EGF domain-containing, and LRR receptor kinase-like polypeptides during asymmetric cell growth. Planta 217, 931-950 (2003).
33. Hugot, K. et al. Coordinated regulation of genes for secretion in tobacco at late developmental stages: Association with resistance against oomycetes. Plant Physiol. 134, 1-13 (2004).
34. Yamane, H., Lee, S.-J., Kim, B.-D., Tao, R. & Rose, J.K.C. A coupled yeast signal sequence trap and transient plant expression strategy to identify genes encoding secreted proteins from peach pistils. J. Exp. Bot. 56, 2229-2238 (2005).
35. Lee, S.-J., Kelley, B., Damasceno, C.M.B., St. John, B., Kim, B.-S., Kim, B.-D. & Rose, J.K.C. A functional screen to characterize the secretomes of eukaryotic phytopathogens and their hosts in planta. Mol. Plant Microbe Interact. 12, 1368-1377 (2006).
36. Ito, H., Fukuda, Y., Murata, K. & Kimura, A. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163-168 (1983).
37. Gietz, R.D. & Woods, R.A. Transformation of yeast by the LiAc/SS carrier DNA/PEG method. Methods Enzymol. 350, 87-96 (2002).
38. Hoffman, C.S. & Winston, F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 57, 267-272 (1987).
39. Akada, R., Murakane, T. & Nishizawa, Y. DNA extraction method for screening yeast clones by PCR. BioTechniques 28, 668-674 (2000).
40. Galliciotti, G. et al. Signal-sequence trap in mammalian and yeast cells: A comparison. J. Membr. Biol. 183, 175-182 (2001).
41. Heazlewood, J.L., Tonti-Filippini, J., Verboom, R.E. & Millar, A.H. Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol. 139, 598-609 (2005).
42. Yates, J.R., Gilchrist, A., Howell, K.E. & Bergeron, J.J.M. Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6, 702-714 (2005).
43. Perco, P., Rapberger, R., Siehs, C., Lukas, A., Oberbauer, R., Mayer, G. & Mayer, B. Transforming omics data into context: Bioinformatics on genomics and proteomics raw data. Electrophoresis 27, 2659-2675 (2006).
44. Ausubel, F.M. et al. (eds.) Current Protocols in Molecular Biology (John Wiley & Sons, Hoboken, New Jersey, USA, 2006).
45. Miller, E.M. & Nickoloff, J.A. Escherichia coli electrotransformation. Methods Mol. Biol. 47, 105-114 (1995).
46. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual 2nd edn. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1989).