Discovery of Novel Conserved Peptide Domains by Ortholog Comparison within Plant Multi-Protein Families

Abstract

Assigning individual functions to the proteins encoded by the genome of the dicotyledonous reference species Arabidopsis thaliana is one of the major challenges in current plant molecular biology. Frequently, Arabidopsis protein families are biocomputationally analyzed by multiple amino acid sequence alignments of the respective family members for detection of conserved peptide motifs that might be of functional relevance. Mere sequence alignment of paralogous sequences may obscure amino acid patches that are highly conserved amongst orthologs and thus potentially relevant for isoform-specific protein function(s). Here I exemplarily illustrate this potential pitfall by amino acid sequence alignments of the heptahelical MLO proteins using either the suite of 15 isoforms (paralogs) encoded by the Arabidopsis genome or a collection of 13 ortholog sequences derived from a set of both monocotyledonous and dicotyledonous plant species. The findings are corroborated by an analogous analysis of the distinct plant multi-protein family of CONSTANS-like transcription regulators. The data reveal that the generally higher sequence similarity of orthologs versus paralogs is not uniformly distributed among the amino acid positions of the orthologs but at least partially clustered in distinct sites/domains, suggesting conservation of isoform-specific functional modules across taxa.

Naturally Occurring Broad-Spectrum Powdery Mildew Resistance in a Central American Tomato Accession Is Caused by Loss of Mlo Function

“…Based on this finding and the presence of a shared distinctive polypeptide motif at the Cterminus of the encoded polypeptides ( Fig. 2B), which is considered to be diagnostic of an orthologous phylogenetic relationship (Panstruga 2005b), SlMlo1 and SlMlo2 likely represent co-orthologs of AtMLO2, AtMLO6, and AtMLO12.…”

“…We thus inoculated susceptible Col-0 wild-type plants and the previously described set of resistant Arabidopsis mlo mutants with O. neolycopersici. In Arabidopsis, three phylogenetically closely related Mlo co-orthologs, AtMLO2, AtMLO6, and AtMLO12, (Panstruga 2005b), exhibit unequal genetic redundancy with respect to powdery mildew infection phenotypes. Atmlo2 mutants are partially resistant to adapted powdery mildews, while Atmlo2 Atmlo6 and Atmlo2 Atmlo12 double mutants exhibit increased, and the Atmlo2 Atmlo6 Atmlo12 triple mutant full resistance (Consonni et al 2006).…”

Two Seven-Transmembrane Domain MILDEW RESISTANCE LOCUS O Proteins Cofunction inArabidopsisRoot Thigmomorphogenesis

“…Functional specificity of MLO paralogs may reside in amino acid sequences of these proteins that are evolutionarily conserved within each phylogenetic clade (Panstruga, 2005). To elucidate this possibility, we focused on the regions that we identified to be of greatest dissimilarity between MLO2 and MLO4: the first extracellular loop (e1) and the cytoplasmic C terminus (c4).…”

Genome-wide Identification, Classification and Expression Analysis of the Mildew Resistance Locus O ( MLO ) Gene Family in Sweet Orange ( Citrus sinensis )

“…Results demonstrated that all MLO proteins except CisMLO6/10/11 had seven TMs and were highly conservative, which are considered to be remarkable features of MLO gene family [ 5 ]. Previous research has also identified a calmodulin-binding domain (CaMBD) and two conserved regions (I and II) that modulate PM infection in the C-terminus of MLO proteins [ 24,25 ]. Peptide domain I is situated at about 15 to 20 residues downstream of the CaMBD and is featured by conserved residues of threonine and serine.…”

“…These show that phylogenetic studies on MLO proteins may predict factor candidates for PM perceptivity. Previous research has also identified a calmodulin-binding domain (CaMBD) and two conserved regions (I and II) characteristic of barley MLO orthologs that modulate PM infection in the Cterminus of MLO proteins [ 24,25 ]. Peptide domain I is situated at about 15 to 20 residues downstream of the CaMBD and is featured by conserved residues of threonine and serine.…”