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.

Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum)

“…Five SlLEA genes are present on chromosomes 1 and 9; four on chromosomes 2 and 10; three on chromosome 6; two on chromosomes 8 and 12; and one on chromosomes 4 and 7. Segmental duplication, tandem duplication and transposition events are the main reasons for gene family expansion (Cao 2012;. To analyze potential duplications and the evolutionary patterns of LEA genes in tomato, we detected 9 pairs of paralogous SlLEA genes based on phylogenetic analysis.…”

Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis

“…GH28 proteins are known to function as PGs in bacteria, fungi and plants (Abbott and Boraston, 2007;Cao, 2012;Sprockett et al, 2011). Arabidopsis mutants defective in GH28 PGs are compromised in developmentally regulated cell separation in pollen and carpel dehiscence (Ogawa et al, 2009;Rhee et al, 2003).…”

“…The Arabidopsis genome contains a total of 67 genes encoding putative pectin lyases (Cao, 2012) and several of these genes appear to be expressed in the root cap (Brady et al, 2007). Although RCPG is the only GH28 member among the identified 60 genes, it is possible that root cap separation is preconditioned by NAC-independent PG activities.…”

RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways

“…PMEs, PMEIs, PGs, PLLs, and PAEs all belong to large multigene families (Louvet et al, 2006;Pelloux et al, 2007;Sun and van Nocker, 2010;Cao, 2012;Wang et al, 2013;de Souza et al, 2014). A large number of these HGmodifying enzymes are differentially expressed and primarily down-regulated in ant ail6 inflorescences, including approximately 58% of PLLs, 55% of PMEIs, 47% of PMEs, and 40% of PGs (Table I; Supplemental Table S1).…”