The gymnosperm Pinus pinea contains both AOX gene subfamilies, AOX1 and AOX2

Abstract

The gymnosperm Pinus pinea L. (stone pine) is a typical Mediterranean pine used for nuts and timber production, and as an ornamental around the world. Pine genomes are large in comparison to other species. The hypothesis that retrotransposons, such as gymny, made a large contribution to this alteration in genome size was recently confirmed. However, P. pinea is unique in other various aspects. P. pinea demonstrates a different pattern of gymny organization than other Pinus subgenera. Additionally, P. pinea has a highly recalcitrant behaviour in relation to standard conifer protocols for the induction of somatic embryogenesis or rooting. Because such types of cell reprogramming can be explained as a reaction of plant cells to external stress, it is of special interest to study sequence peculiarities in stress-inducible genes, such as the alternative oxidase (AOX). This is the first report containing molecular evidence for the existence of AOX in gymnosperms at the genetic level. P. pinea AOXs were isolated by a polymerase chain reaction (PCR) approach and three genes were identified. Two of the genes belong to the AOX1 subfamily and one belongs to the AOX2 subfamily. The existence of both AOX subfamilies in gymnosperms is reported here for the first time. This discovery supports the hypothesis that AOX1 and AOX2 subfamilies arose prior to the separation of gymnosperms and angiosperms, and indicates that the AOX2 is absent in monocots because of subsequent gene loss events. Polymorphic P. pinea AOX1 sequences from a selected genetic clone are presented indicating non-allelic, non-synonymous and synonymous translation products.

Differential expression and co‐regulation of carrot AOX genes (Daucus carota)

“…AOX1 and AOX2 genes can be discriminated by conserved nucleotide positions near important functional sites, such as the conserved cysteine in position CysI and the di‐iron‐binding sites. These sites have been recently highlighted by Costa et al (2009a) and Frederico et al (2009) (see arrows in Fig. 5).…”

“…Gray arrows indicate the position of a conserved prolin (P) and a conserved methionine (M) in AOX2 sub family identified by Costa et al (2009a). Black arrows indicate the positions of conserved methionine (M) and valine (V) in AOX2 sub family identified by Frederico et al (2009). Helical regions that are assumed to be involved in the formation of a hydroxo‐bridged binuclear iron center (Andersson and Nordlund 1999, Berthold et al 2000) are shown with overlines.…”

“…The occurrence of two subfamilies is species‐dependent. To date, the AOX1 genes were found in monocots and eudicots, whereas AOX2 genes were detected only in eudicot species (Considine et al 2002) and in the gymnosperm Pinus pinea (see Frederico et al 2009). In most of the species studied so far either the AOX1 subgroup was expanded, as in the case of Arabidopsis thaliana (Saisho et al 1997) or only AOX2 , as in the case of Glycine max or Vigna unguiculata (Costa et al 2004).…”

“…The reason why two gene subfamilies evolved and the functional importance across species are not understood. Recently, conserved sequence differences between AOX1 and AOX2 genes were identified that covered also near‐neighbor sequences of the CysI site (Costa et al 2009a, Frederico et al 2009). From in silico conservation analysis it is known that consideration of neighbor sequences can well‐improve the prediction of conserved functional sites (Capra and Singh 2007) indicating the importance of such loci.…”

Unraveling the evolution and regulation of the alternative oxidase gene family in plants

“…(Frederico et al 2009), and Physcomitrella patens (Neimanis et al 2013). The wide distribution of AOX in the plant kingdom raises the question of whether different plant species share common AOX gene structures and expression profiles.…”