Criteria for confirming sequence periodicity identified by Fourier transform analysis: Application to GCR2, a candidate plant GPCR?

Abstract

. Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR?. Biophysical Chemistry, Elsevier, 2008, 133 (1-3) This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT2 AbstractMethods to determine peridiodicity in protein sequences are useful for inferring function. Fourier transformation is one approach but care is required to ensure the periodicity is genuine. Here we have shown that empirically-derived statistical tables can be used as a measure of significance.Genuine protein sequences data rather than randomly generated sequences were used as the statistical backdrop. The method has been applied to G-protein coupled receptor (GPCR) sequences, by Fourier transformation of hydrophobicity values, codon frequencies and the extent of over-representation of codon pairs; the latter being related to translational step times. Genuine periodicity was observed in the hydrophobicity whereas the apparent periodicity (as inferred from previously reported measures) in the translation step times was not validated statistically. GCR2 has recently been proposed as the plant GPCR receptor for the hormone abscisic acid. It has homology to the Lanthionine synthetase C-like family of proteins, an observation confirmed by fold recognition. Application of the Fourier transform algorithm to the GCR2 family revealed strongly predicted seven fold periodicity in hydrophobicity, suggesting why GCR2 has been reported to be a GPCR, despite negative indications in most transmembrane prediction algorithms. The underlying multiple sequence alignment, also required for the Fourier transform analysis of periodicity, indicated that the hydrophobic regions around the 7 GXXG motifs commence near the C-terminal end of each of the 7 inner helices of the α-toroid and continue to the N-terminal region of the helix. The results clearly explain why GCR2 has been understandably but erroneously predicted to be a GPCR.

Do Plants Contain G Protein-Coupled Receptors?

“…Indeed, the pitfalls of GPCR identification are illustrated by the high profile (Liu et al, 2007) but erroneous identification of GCR2 as a plant GPCR. It has now been confirmed through crystallization that GCR2 is a lantibiotic cyclase-like protein , as predicted by our fold recognition studies (Illingworth et al, 2008).…”

“…The negative controls were AAU04564.1 Halobiforma lacisalsi (bacteriorhodopsin) and AT2G20770 (Arabidopsis [Arabidopsis thaliana] GCL2 GCR2). Bacteriorhodopsin is a 7TM protein but not a GPCR, while GCR2 has seven hydrophobic helical motifs that are almost long enough to span the membrane, so that its homologs were initially erroneously identified as GPCRs (Illingworth et al, 2008). These sequences were submitted to the following fold recognition servers: I-TASSER (Roy et al, 2010), FUGUE (Shi et al, 2001), Phyre (Bennett-Lovsey et al, 2008), genTHREADER (Jones, 1999a), mgenTHREADER (McGuffin andJones, 2003), HHpred (Söding et al, 2005), LOMETS (Wu and Zhang, 2007), and MUSTER (Wu and Zhang, 2008).…”

Control of stomatal aperture

“…58 However, it is important to mention that the characterization of GCR2 as a GPCR and ABA receptor is still a matter of discussion. [59][60][61] More recently, other GPCR-like proteins (GTG1 and GTG2) were identified and its characterization revealed that the GTG proteins represent a novel class of proteins with topology similar to GPCRs but with classic GTP-binding/GTPase activity. 62 Further analysis providing biochemical and phenotypic evidences suggest that GTG1 and GTG2 proteins are redundantly involved in G protein-coupled ABA signaling and are, or are parts of, ABA receptor complexes 62 and their detailed characterization will likely clarify the mechanism underlying the ABA response.…”

Ruta de transducción de señal del ácido abscísico: Regulación por HAB1 y dianas de interacción. La inactivación combinada de PP2Cs como herramienta biotecnológica para incrementar la tolerancia a sequía en plantas

“…Otro supuesto receptor de ABA aislado, GCR2, se propuso también como un receptor acoplado a proteínas G. Actualmente existe cierta controversia acerca tanto sobre su papel en la señalización por ABA [59,70] como en su inclusión en el grupo de receptores acoplados a proteínas G [87,97]. Por un lado esta proteína muestra cierta similitud con una enzima soluble de bacterias de la superfamilia LanC (lantibiotic synthetase component C) [97].…”

“…Se han identificado muchos de los componentes de la ruta de señalización y se ha estudiado la interconexión existente entre ellos para elucidar la estructura de la cascada de señalización del ABA. Estudios de genética molecular, bioquímica y farmacología han llevado a la identificación de más de 100 loci y numerosos mensajeros secundarios que participan en la ruta Otro supuesto receptor de ABA aislado, GCR2, se propuso también como un receptor acoplado a proteínas G. Actualmente existe cierta controversia acerca tanto sobre su papel en la señalización por ABA [59,70] como en su inclusión en el grupo de receptores acoplados a proteínas G [87,97]. Por un lado esta proteína muestra cierta similitud con una enzima soluble de bacterias de la superfamilia LanC (lantibiotic synthetase component C) [97].…”