The pectin lyases in Arabidopsis thaliana: evolution, selection and expression profiles

Abstract

Pectin lyases are a group of enzymes that are thought to contribute to many biological processes, such as the degradation of pectin. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene duplication, gene organization, functional divergence, adaptive evolution, expression profiling and functional networks has been reported for Arabidopsis. Sixty-seven pectin lyase genes have been identified, and most of them possess signal sequences targeting the secretory pathway. Phylogenetic analyses identified five gene groups with considerable conservation among groups. Pectin lyase genes were non-randomly distributed across chromosomes and clustering was evident. Functional divergence and adaptive evolution analyses suggested that purifying selection was the main force driving pectin lyase evolution, although some critical sites responsible for functional divergence might be the consequence of positive selection. A stigma- and receptacle-specific expression promoter was identified, and it had increased expression in response to wounding. Two hundred and eighty-eight interactions were identified by functional network analyses, and most of these were involved in cellular metabolism, cellular transport and localization, and stimulus responses. This investigation contributes to an improved understanding of the complexity of the Arabidopsis pectin lyase gene family.

Figure 1. Phylogenetic relationships and exon-intron organization of pectin lyase genes in Arabidopsis.

Phylogeny tree was constructed using full-length pectin lyase protein sequences. Numbers associated with branches showed bootstrap support values for maximum likelihood analyses. Five major groups designated from I to V were marked with different color. Insertion positions of 0 phase intron, 1 phase intron and 2 phase intron were shown in red, blue and emerald green, respectively.

Figure 2. Chromosomal locations of the pectin lyase genes.

67 pectin lyase genes mapped to the five Arabidopsis chromosomes are shown. Paralogous regions in the putative ancestral constituents of the Arabidopsis genome are depicted using the same colors according to Blanc et al. (2000) .

Figure 3. Expression profiles of the Arabidopsis pectin lyase genes.

(left panel) Dynamic expression profiles of pectin lyase genes for nine different development tissues (germinated seed, seedling, young rosette, developed rosette, bolting, young flower, developed flower, flowers and siliques, and mature siliques). Expression patterns of pectin lyase genes under several abiotic stresses are shown in the right panel.

Figure 4. GUS staining of the pBI-P transgenic plants.

(A) Strong GUS expression of the AT1G17150 promoter is observed in floral organs including stigma and receptacle. Moreover, this model of expression can continue during silique development period. (B) Wound can induce the activity of the AT1G17150 promoter. (C) Wound signal can be transported over time to other areas via vein (12h after wound).

Figure 5. Pectin lyase genes interaction network.

Fifteen members of pectin lyase genes are mapped to the protein-protein interaction database. This analysis reveals a total of 235 unique genes (Table S2) that showed 288 interactions, and a network is then assembled based on these interactions.