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

Abstract

Alternative oxidase (AOX) is a diiron carboxylate protein present in all plants examined to date that couples the oxidation of ubiquinol with the reduction of oxygen to water. The predominant structure of AOX genes is four exons interrupted by three introns. In this study, by analyzing the genomic sequences of genes from different plant species, we deduced that intron/exon loss/gain and deletion of fragments are the major mechanisms responsible for the generation and evolution of AOX paralogous genes. Integrating gene duplication and structural information with expression profiles for various AOXs revealed that tandem duplication/block duplication contributed greatly to the generation and maintenance of the AOX gene family. Notably, the expression profiles based on public microarray database showed highly diverse expression patterns among AOX members in different developmental stages and tissues and that both orthologous and paralogous genes did not have the same expression profiles due to their divergence in regulatory regions. Comparative analysis of genes in six plant species under various perturbations indicated a large number of protein kinases, transcription factors and antioxidant enzymes are co-expressed with AOX. Of these, four sets of transcription factors--WRKY, NAC, bZIP and MYB--are likely involved in the regulating the differential responses of AOX1 genes to specific stresses. Furthermore, divergence of AOX1 and AOX2 subfamilies in regulation might be the main reason for their differential stress responses.

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

“…1 ). Segmental duplication and tandem duplication were the main driving forces for gene acquisition of new functions and family expansion 32 . Among them, MsSPL15-2/MsSPL 15-5 , MsSPL15-2/MsSPL15-3, two pairs of tandem duplication genes (Table 3 ), and 69 pairs of segmental duplication genes, indicating that segmental duplication is the main driving force for the evolutionary expansion of the MsSPL gene family.…”

Plant protein-coding gene families: Their origin and evolution

“…Furthermore, the number of chilling injury-related gene ( CRG ) family members in Cruciferae is affected by polyploidy ( Song et al, 2020 ). On the other hand, evolution of the AOX gene family is primarily mediated by intron/exon loss or gain, and fragment deletion, although gene loss and duplication, as well as tandem blocking, also play essential roles in the origin and maintenance of the family ( Pu et al, 2015 ; Tables 1 , 2 ; Figure 3 ).…”

Analysis of Posttranslational Activation of Alternative Oxidase Isoforms

“…The gene expression of these isoforms is tissue specific, depends on the developmental stage of the plant, changes in cellular metabolism as well as various abiotic and biotic stress conditions, and is highly responsive to dysfunctions in the mitochondrial respiratory metabolism (Juszczuk and Rychter, 2003;Millenaar and Lambers, 2003;Zarkovic et al, 2005;Clifton et al, 2006;Van Aken et al, 2009;Feng et al, 2013;Vanlerberghe, 2013). Arabidopsis (Arabidopsis thaliana) possesses five genes encoding AOX proteins that can be divided into two subfamilies: AOX1A to AOX1D and AOX2 (Polidoros et al, 2009;Pu et al, 2015). Transcripts of the main isoform AOX1A are abundant throughout all tissues and developmental stages of the plant.…”