Abstract
Plant peptides play a number of important roles in defence, development and many other aspects of plant physiology. Identifying additional peptide sequences provides the starting point to investigate their function using molecular, genetic or biochemical techniques. Due to their small size, identifying peptide sequences may not succeed using the default bioinformatic approaches that work well for average-sized proteins. There are two general scenarios related to bioinformatic identification of peptides to be discussed in this paper. In the first scenario, one already has the sequence of a plant peptide and is trying to find more plant peptides with some sequence similarity to the starting peptide. To do this, the Basic Local Alignment Search Tool (BLAST) is employed, with the parameters adjusted to be more favourable for identifying potential peptide matches. A second scenario involves trying to identify plant peptides without using sequence similarity searches to known plant peptides. In this approach, features such as protein size and the presence of a cleavable amino-terminal signal peptide are used to screen annotated proteins. A variation of this method can be used to screen for unannotated peptides from genomic sequences. Bioinformatic resources related to Arabidopsis thaliana will be used to illustrate these approaches.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Farrokhi, N., Whitelegge, J.P., and Brusslan, J.A. (2007) Plant peptides and peptidomics. Plant Biotechnol. J. 6, 105–134.
McGurl, B., Pearce, G., Orozco-Cardenas, M., and Ryan, C.A. (1992) Structure, expression, and antisense inhibition of the systemin precursor gene. Science 255, 1570–1573.
Matsubayashi, Y., and Sakagami, Y. (1996) Phytosulfokine, sulfated peptides that induce the proliferation of single mesophyll cells of Asparagus officinalis L. Proc. Natl. Acad. Sci. USA 93, 7623–7627.
Fletcher, J.C., Brand, U., Running, M.P., Simon, R., and Meyerowitz, E.M. (1999) Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283, 1911–1914.
Kondo, T., Sawa, S., Kinoshita, A., Mizuno, S., Kakimoto, T., Fukuda, H., and Sakagami, Y. (2006) A plant peptide encoded by CLV3 identified by in situ MALDI-TOF MS analysis. Science 313, 845–848.
Schopfer, C.R., Nasrallah, M.E., and Nasrallah, J.B. (1999) The male determinant of self-incompatibility in Brassica. Science 5445, 1697–1700.
Takayama, S., Shiba, H., Iwano, M., Shimosato, H., Che, F.S., Kai, N., Watanabe, M., Suzuki, G., Hinata, K., and Isogai, A. (2000) The pollen determinant of self-incompatibility in Brassica campestris. Proc. Natl. Acad. Sci. USA 97, 1920–1925.
Pearce, G., Moura, D.S., Stratmann, J., and Ryan, C.A. (2001) Production of multiple plant hormones from a single polyprotein precursor. Nature 411, 817–820
Pearce, G., Moura, D.S., Stratmann, J., and Ryan, C.A. (2001) RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. Proc. Natl. Acad. Sci. USA 98, 12843–12847.
Butenko, M.A., Patterson, S.E., Grini, P.E., Stenvik, G.E., Amundsen, S.S., Mandal, A., and Aalen, R.B. (2003) Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants. Plant Cell 15, 2296–2307.
Huffaker, A., Pearce, G., and Ryan, CA (2006) An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc. Natl. Acad. Sci. USA 103, 10098–10103.
Stenvik, G., Tandstad, N.M, Guo, Y., Shi, C., Kristiansen, W., Holmgren, A., Clark, S.E., Aalen, R., and Butenko, M.A. (2008) The EPIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION is sufficient to induce abscission in Arabidopsis through the receptor-like kinases HAESA and HAESA-LIKE2. Plant Cell 20, 1805–1817.
Cho, S.K., Larue, C.T., Chevalier, D., Wang, H., Jinn, T., Zhang, S., and Walker, J.C. (2008). Regulation of floral organ abscission in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 105, 15629–15634.
Vanoosthuyse, V., Miege, C., Dumas, C., and Cock, J.M. (2001) Two large Arabidopsis thaliana gene families are homologous to the Brassica gene superfamily that encodes pollen coat proteins and the male component of the self-incompatibility response. Plant Mol. Biol. 46, 17–34.
Cock, J.M., and McCormick, S. (2001) A large family of genes that share homology with CLAVATA3. Plant Physiol. 126, 939–942.
Yang, H., Matsubayashi, Y., Nakamura, K., Sakagami, Y. (2001) Diversity of Arabidopsis genes encoding precursors for phytosulfakine, a peptide growth factor. Plant Physiol. 127, 842–851.
Olsen, A.N., Mundy, J., and Skriver, K. (2002) Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs. In Silico Biol. 2, 441–451
Oelkers, K., Goffard, N., Weiller, G.F., Gresshoff, P.M., Mathesius, U., and Frickey, T. (2008) Bioinformatic analysis of the CLE signaling peptide family. BMC Plant Biol. 8, 1.
Lease, K.A., and Walker, J.C. (2006) The Arabidopsis unannotated secreted peptide database, a resource for plant peptidomics. Plant Physiol. 142, 831–838.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Poole, R.L. (2007). The TAIR Database. Methods Mol. Biol. 406, 179–212.
Baggerman, G., Cerstiaens, A., De Loof, A., and Schoofs, L. (2002). Peptidomics of the larval Drosophila melanogaster central nervous system. J. Biol. Chem. 277, 40368–40374.
Baggerman, G., Liu, F., Wets, G., and Schoofs, L. (2006) Bioinformatic analysis of peptide precursor proteins. Ann. NY Acad. Sci. 1040, 59–65.
Bendtsen, J.D., Nielsen, H., von Heijne, G., and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783–787.
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Lease, K.A., Walker, J.C. (2010). Bioinformatic Identification of Plant Peptides. In: Soloviev, M. (eds) Peptidomics. Methods in Molecular Biology, vol 615. Humana Press. https://doi.org/10.1007/978-1-60761-535-4_26
Download citation
DOI: https://doi.org/10.1007/978-1-60761-535-4_26
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-534-7
Online ISBN: 978-1-60761-535-4
eBook Packages: Springer Protocols