Abstract
BackgroundThe polyamine oxidases (PAOs) catabolize the oxidative deamination of the polyamines (PAs) spermine (Spm) and spermidine (Spd). Most of the phylogenetic studies performed to analyze the plant PAO family took into account only a limited number and/or taxonomic representation of plant PAOs sequences.ResultsHere, we constructed a plant PAO protein sequence database and identified four subfamilies. Subfamily PAO back conversion 1 (PAObc1) was present on every lineage included in these analyses, suggesting that BC-type PAOs might play an important role in plants, despite its precise function is unknown. Subfamily PAObc2 was exclusively present in vascular plants, suggesting that t-Spm oxidase activity might play an important role in the development of the vascular system. The only terminal catabolism (TC) PAO subfamily (subfamily PAOtc) was lost in Superasterids but it was present in all other land plants. This indicated that the TC-type reactions are fundamental for land plants and that their function could being taken over by other enzymes in Superasterids. Subfamily PAObc3 was the result of a gene duplication event preceding Angiosperm diversification, followed by a gene extinction in Monocots. Differential conserved protein motifs were found for each subfamily of plant PAOs. The automatic assignment using these motifs was found to be comparable to the assignment by rough clustering performed on this work.ConclusionsThe results presented in this work revealed that plant PAO family is bigger than previously conceived. Also, they delineate important background information for future specific structure-function and evolutionary investigations and lay a foundation for the deeper characterization of each plant PAO subfamily.
Highlights
The polyamine oxidases (PAOs) catabolize the oxidative deamination of the polyamines (PAs) spermine (Spm) and spermidine (Spd)
Our results showed that the plant PAO family is composed of at least four subfamilies with distinct evolutionary relationships, structural and functional features
Sequence database construction through a domain architecture approach The election of the remote-homology detection method is an important factor when searching for plant PAOs sequences, since the majority of the known members of this group show low sequence identity (Additional file 1 Table S1)
Summary
The polyamine oxidases (PAOs) catabolize the oxidative deamination of the polyamines (PAs) spermine (Spm) and spermidine (Spd). PAOs are amino oxidases involved in polyamine metabolism. This group of enzymes catalyzes the oxidation of free higher PAs such as Spm and Spd, and their acetylated derivatives at their secondary amino groups through two known reaction modes [1]. PAOs acting in the TC of PAs oxidize the carbon on the endo-side of the N5 of Spm or Spd producing 1,3-diaminopropane (DAP), H2O2, and the respective aldehydes [2]. PAOs functioning in the BC pathway oxidize the carbon on the endo-side of the N5 of Spm and Spd rendering. Whereas three PAO protein crystal structures are available at the PDB database, only one of them represents the plant kingdom: the maize apoplastic
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