Abstract
The increasing pace of acquisition of fully sequenced genomes makes desirable a program of discovery and characterization of protein sequences of biologically significant structural classes. An example is protein phosphatases, involved in modulating reversible protein phosphorylation events underlying the whole gamut of cellular biology. The ready availability of software that can be downloaded to run on a personal computer, or accessed on a server via the Web, allows appropriate sequences to be collected and analyzed. A process is outlined here that has been successfully employed in the description of the genomic complement of protein phosphatase catalytic subunits from the model plant Arabidopsis thaliana. However, the methods are general and readily adapted to deal with any desired class of protein, from any organism of interest.
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
Zhang, Z.-Y. (2001) Protein tyrosine phosphatases: prospects for therapeutics. Curr. Opin. Chem. Biol. 5, 416–423.
Alonso, A., Sasin, J., Bottini, N., et al. (2004) Protein tyrosine phosphatases in the human genome. Cell 117, 699–711.
MacKeigan, J.P., Murphy, L.O., and Blenis, J. (2005) Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat. Cell Biol. 7, 591–600.
Kerk, D., Bulgrien, J., Smith, D.W., Barsam, B., Veretnik, S., and Gribskov M. (2002) The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. Plant Physiol. 129, 908–925.
Monroe-Augustus, M., Zolman, B. K., and Bartel, B. (2003) IBR5, a dual-specificity phosphatase-like protein modulating auxin and abscisic acid responsiveness in Arabidopsis. Plant Cell 15, 2979–2991.
Mora-Garcia, S., Vert, G., Yin, Y., Cano-Delgado, A., Cheong, H., and Chory, J. (2004) Nuclear protein phosphatases with Kelch-repeat domains modulate the response to brassinosteroids in Arabidopsis. Genes Dev. 18, 448–460.
Schweighofer, A., Hirt, H., and Meskiene I. (2004) Plant PP2C phosphatases: emerging functions in stress signaling. Trends Plant Sci. 9, 236–243.
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.
Mount, D.W. (2004) Bioinformatics: Sequence and Genome Analysis, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 163–226.
Gribskov, M. and Veretnik, S. (1996) Identification of sequence patterns with profile analysis. Methods Enzymol. 266, 198–211.
Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–763.
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.
D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis (1996) Phylogenetic inference, in Molecular Systematics, 2nd ed. (Hillis, D. M., Moritz, C., and Mable, B. K., eds.), Sinauer Associates, Sunderland, MA, pp. 407–514.
Felsenstein, J. (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266, 418–426.
Luan, S. (2003) Protein phosphatases in plants. Annu. Rev. Plant Biol. 54, 63–92.
Bateman, A., Coin, L., Durbin, R., et al. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138–D141.
Bernal, A., Ear, U., and Kyrpides, N. (2001) Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nuc. Acids Res. 29, 126–127.
Rhee, S. Y., Beavis, W., Berardini, T. Z., et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31, 224–228.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The ClustalX windows interface: flexible strategies for multiple-sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876–4882.
Edgar, R. C. (2004) MUSCLE: multiple-sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.
Poirot, O., Suhre, K., Abergel, C., O’Toole, E., and Notredame, C. (2004) 3DCoffee: a web server for mixing Sequences and Structures into multiple-sequence alignments. Nuc. Acids Res. 32, W37–W40.
Nicholas, K.B., Nicholas, H.B. Jr., and Deerfield, D.W. II. (1997) GeneDoc: analysis and visualization of genetic variation. EMBNEW.NEWS 4, 14.
Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502–504.
Page, R.D.M. (1996) TreeView: An application to display phylogenetic trees on personal computers. Computer Applic. Biol. Sci. 12, 357–358.
Do, C.B., Mahabhashyam, M.S., Brudno, M., and Batzoglou, S. (2005) ProbCons: probabilistic consistency-based multiple-sequence alignment. Genome Res. 15, 330–340.
Shi, L., Potts, M., and Kennelly, P.J. (1998) The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. FEMS Microbiol. Rev. 22, 229–253.
Yu, L.P., Miller, A.K., and Clark, S.E. (2003) POLTERGEIST encodes a protein phosphatase 2C that regulates CLAVATA pathways controlling stem cell identity at Arabidopsis shoot and flower meristems. Curr. Biol. 13, 179–188.
Bork, P., Brown, N.P., Hegri, H., and Schultz, J. (1996) The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues. Prot. Sci. 5, 1421–1425.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Kerk, D. (2007). Genome-Scale Discovery and Characterization of Class-Specific Protein Sequences. In: Moorhead, G. (eds) Protein Phosphatase Protocols. Methods in Molecular Biology, vol 365. Springer, Totowa, NJ. https://doi.org/10.1385/1-59745-267-X:347
Download citation
DOI: https://doi.org/10.1385/1-59745-267-X:347
Publisher Name: Springer, Totowa, NJ
Print ISBN: 978-1-58829-711-2
Online ISBN: 978-1-59745-267-0
eBook Packages: Springer Protocols