Computational identification of candidate nucleotide cyclases in higher plants

Handle URI:
http://hdl.handle.net/10754/562967
Title:
Computational identification of candidate nucleotide cyclases in higher plants
Authors:
Wong, Aloysius Tze ( 0000-0002-9105-5845 ) ; Gehring, Christoph A. ( 0000-0003-4355-4591 )
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. © Springer Science+Business Media New York 2013.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Molecular Signalling Group
Publisher:
Humana Press
Journal:
Methods in Molecular Biology
Issue Date:
3-Sep-2013
DOI:
10.1007/978-1-62703-441-8-13
PubMed ID:
23681580
Type:
Article
ISSN:
10643745
ISBN:
9781627034401
Appears in Collections:
Articles; Bioscience Program; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWong, Aloysius Tzeen
dc.contributor.authorGehring, Christoph A.en
dc.date.accessioned2015-08-03T11:17:21Zen
dc.date.available2015-08-03T11:17:21Zen
dc.date.issued2013-09-03en
dc.identifier.isbn9781627034401en
dc.identifier.issn10643745en
dc.identifier.pmid23681580en
dc.identifier.doi10.1007/978-1-62703-441-8-13en
dc.identifier.urihttp://hdl.handle.net/10754/562967en
dc.description.abstractIn 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. © Springer Science+Business Media New York 2013.en
dc.publisherHumana Pressen
dc.subjectAdenylyl cyclaseen
dc.subjectArabidopsis thalianaen
dc.subjectBasic local alignment search toolen
dc.subjectcAMPen
dc.subjectCatalytic centeren
dc.subjectcGMPen
dc.subjectCyclic nucleotide cyclaseen
dc.subjectGuanylyl cyclaseen
dc.subjectHomology modelingen
dc.subjectMotif searchen
dc.titleComputational identification of candidate nucleotide cyclases in higher plantsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentMolecular Signalling Groupen
dc.identifier.journalMethods in Molecular Biologyen
kaust.authorWong, Aloysius Tzeen
kaust.authorGehring, Christoph A.en

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