Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa

Abstract

Some pathogenesis-related proteins (PR proteins) are subject to positive selection, while others are under negative selection. Here, we report the patterns of molecular evolution in thaumatin-like protein (TLP, PR5 protein) genes of Populus trichocarpa. Signs of positive selection were found in 20 out of 55 Populus TLPs using the likelihood ratio test and ML-based Bayesian methods. Due to the connection between the acidic cleft and the antifungal activity, the secondary structure and three-dimensional structure analyses predicted antifungal activity beta-1,3-glucanase activities in these TLPs. Moreover, the coincidence with variable basic sites in the acidic cleft and positively selected sites suggested that fungal diseases may have been the main environmental stress that drove rapid adaptive evolution in Populus.

The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

“…A study conducted on a total of 600 TLPs retrieved from 100 species in international databases revealed a cluster of phylogenetically related TLPs, enriched in poplar and tree sequences, that might represent a specific innovation in perennial species. Beyond the dramatic expansion of these defense-related genes in the poplar genome, diversification and subsequent sub- or neo-functionalisation likely occurred in poplar TLPs as exemplified by diversifying selection observed in this cluster [27, 28]. So far, other PR gene families have not been explored at the genome-wide scale in poplar, and it would be interesting to determine whether other expansions of specific gene family related to plant immunity occurred in trees, representing possible innovations in these long-living species.…”

Cloning and characterization of defense-related genes from Populus szechuanica infected with rust fungus Melampsora larici-populina

“…P. trichocarpa are reported to contain 42 TLP genes with diverse expressions in leaves infected with Melampsora spp (Rinaldi et al, 2007;Miranda et al, 2007;Azaiez et al, 2009;Petre et al, 2011). The length and physicochemical properties of the deduced proteins of PsTLP1 (245) and PsTLP2 (225) were consistent with most of the P. trichocarpa TLPs (~205-288 aa) (Zhao and Su, 2010;Petre et al, 2011). However, there were differences in the properties, such as pI, between PsTLP1 and PsTLP2 as well as different phylogenetic classification (in two groups).…”

The Hidden Chemical Cross-Talk Between Roots and Microbes: A Proteomic Approach

“…The cocktail of proteins secreted into the rhizosphere comprises peroxidases [14,72,73], phosphatases [74,75], esterases [76], proteases [14,[77][78][79], chitinases [14,80], glucanases [14,81] and thaumatin-like proteins [1,82,83] ( Table 2). Some of these enzymes are members of a PR family [14].…”

“…In addition, it has been demonstrated that the transgenic plants were more resistant to abiotic stress [91]. The genes of these proteins are subject to selection, either positive or negative [83]. In Populus, a positive selection in 20 out of 55 thaumatin-like-proteins has been found [83].…”

“…The genes of these proteins are subject to selection, either positive or negative [83]. In Populus, a positive selection in 20 out of 55 thaumatin-like-proteins has been found [83]. Osmotin, also a member of the PR-5 subfamily, is induced by pathogens and osmotic conditions [96].…”