Submergence response of pyruvate decarboxylase family genes in adzuki bean

Abstract

Pyruvate decarboxylase (PDC) is the main enzyme in ethanol fermentation in plant low-oxygen response. Expression of the PDC gene can be induced by submergence, a low-oxygen state, which has been demonstrated in Arabidopsis, maize and rice among other plants. However, it is unknown whether the gene expression has similar pattern in the Fabaceae family under low-oxygen stress, and unavailability of PDC family member sequences in Fabaceae hindered these studies. We aimed to comprehensively identify PDC genes in adzuki bean, and characterize their phylogenetic relationships and expression profile with the emphasis of expression response to submergence. Based on genome sequences and identified conserved domains, HMMER was used to mine PDC genes in adzuki bean in addition to mung bean, both of which are Vigna species under the Fabaceae family. Sequences were aligned using MUSCLE and Phylogenetic topology was decided by using MrBayes. Tissue expression patterns were decided using publically available RNASeq data. Adzuki bean plants were treated with submergence stress, and expressions under treatments were measured using qRT-PCR. We identified the genes in PDC family in the genomes of adzuki bean and mung bean. The known PDC peptides contain three conserved domains with the same order. Based on the domain composition, we identified four PDC family genes in adzuki bean, and three in mung bean. Phylogenetic reconstruction resolved three major classes. Class I of the family was grouped with PDC gene in Arabidopsis, and thus likely encodes PDC; one gene is present in this class in adzuki bean, whose expression was high in roots and nodules compared to other tissues, and was significantly induced under submergence treatment, reaching highest at 12 h after waterlogging. No Class I gene was identified in mung bean, possibly result of assembly gaps or failure of gene model prediction of mung bean genome. Class II genes are clustered together with larger subunit of acetolactate synthase, which have two representatives in mung bean and adzuki bean, respectively. There is one copy of gene in Class III in the genome of the two Vigna species, respectively, which is grouped with an uncharacterized Arabidopsis gene. Interestingly, the adzuki bean gene in this class was significantly induced by waterlogging, whose expression reaching the highest earlier than the Class I gene, which indicates that both the Class I and Class III genes in the PDC family are involved in low-oxygen stress response in adzuki bean. Pyruvate decarboxylase family genes were mined in adzuki bean and mung bean, whose phylogeny was clarified into three independent classes. Expression of a putative PDC gene was significantly elevated by submergence stress in adzuki bean. The Class III gene in adzuki bean was significantly induced in expression by waterlogging, too, yet its expression reached highest earlier than putative PDC genes, suggesting involvement of the Class III genes in low-oxygen stress response.