title: Identification of cyclic nucleotide gated channels using regular expressions.
abstract: Cyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one-pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin-binding domain. Despite their functional similarities, the plant CNGC family members appear to have different conserved amino acid motifs within corresponding functional domains than animal and bacterial CNGCs do. Here we describe the development and application of methods employing plant CNGC-specific sequence motifs as diagnostic tools to identify novel candidate channels in different plants. These methods are used to evaluate the validity of annotations of putative orthologs of CNGCs from plant genomes. The methods detail how to employ regular expressions of conserved amino acids in functional domains of annotated CNGCs and together with Web tools such as PHI-BLAST and ScanProsite to identify novel candidate CNGCs in species including Physcomitrella patens.
authors.affiliation: Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, CT, USA.
authors.forename: Alice K
authors.initials: AK
authors.lastname: Zelman
authors.forename: Adam
authors.initials: A
authors.lastname: Dawe
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Berkowitz
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism; D019068:Bryopsida / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D054815:Cyclic Nucleotide-Gated Cation Channels / Q000737:chemistry / Q000378:metabolism*; D019143:Evolution, Molecular; D015870:Gene Expression; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D029681:Arabidopsis Proteins; D054815:Cyclic Nucleotide-Gated Cation Channels