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Computational Identification of Candidate Nucleotide Cyclases in Higher Plants

  • Aloysius Wong
  • Chris Gehring
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1016)

Abstract

In higher plants guanylyl cyclases (GCs) and adenylyl cyclases (ACs) cannot be identified using BLAST homology searches based on annotated cyclic nucleotide cyclases (CNCs) of prokaryotes, lower eukaryotes, or animals. The reason is that CNCs are often part of complex multifunctional proteins with different domain organizations and biological functions that are not conserved in higher plants. For this reason, we have developed CNC search strategies based on functionally conserved amino acids in the catalytic center of annotated and/or experimentally confirmed CNCs. Here we detail this method which has led to the identification of >25 novel candidate CNCs in Arabidopsis thaliana, several of which have been experimentally confirmed in vitro and in vivo. We foresee that the application of this method can be used to identify many more members of the growing family of CNCs in higher plants.

Key words

Cyclic nucleotide cyclase Adenylyl cyclase cAMP Guanylyl cyclase cGMP Catalytic center Motif search Homology modeling Basic local alignment search tool Arabidopsis thaliana 

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Aloysius Wong
    • 1
  • Chris Gehring
    • 1
  1. 1.Division of Chemical and Life Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia

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