Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice

Abstract

The HAD superfamily is named after the halogenated acid dehalogenase found in bacteria, which hydrolyses a diverse range of organic phosphate substrates. Although certain studies have shown the involvement of HAD genes in Pi starvation responses, systematic classification and bioinformatics analysis of the HAD superfamily in plants is lacking. In this study, 41 and 40 HAD genes were identified by genomic searching in rice and Arabidopsis, respectively. According to sequence similarity, these proteins are divided into three major groups and seven subgroups. Conserved motif analysis indicates that the majority of the identified HAD proteins contain phosphatase domains. A further structural analysis showed that HAD proteins have four conserved motifs and specified cap domains. Fewer HAD genes show collinearity relationships in both rice and Arabidopsis, which is consistent with the large variations in the HAD genes. Among the 41 HAD genes of rice, the promoters of 28 genes contain Pi-responsive cis-elements. Mining of transcriptome data and qRT-PCR results showed that at least the expression of 17 HAD genes was induced by Pi starvation in shoots or roots. These HAD proteins are predicted to be involved in intracellular or extracellular Po recycling under Pi stress conditions in plants.

HDF1, a novel flowering time regulator identified in a mutant suppressing sensitivity to red light reduced 1 early flowering

“…We performed a whole sequence alignment of 93 HAD superfamily proteins from a dataset compiled of previously identified HADs 35 , 37 and our own search in the Araport 11 database. We found all four diagnostic motifs to be well conserved.…”

“…This is further strengthened by a recent study that identified 41 HAD genes in rice and 40 HAD genes in Arabidopsis. 17 of the HADs from rice were induced upon phosphate starvation and thus were predicted to be involved in phosphate recycling under Pi stress conditions 37 . As the search was limited to HADs that show a conserved DxD pattern in motif I, HDF1 was omitted from the search.…”

“…To construct the phylogenetic tree of HAD family proteins, a dataset was compiled comprised of 21 genes from (dataset 1) 35 , 55 genes from (dataset 2) 37 , and 58 proteins which were identified as haloacid dehalogenase by textmining Araport 11 genes (dataset 3). Overall, 93 unique genes from the three datasets were used for further analysis.…”

“…Although there are HADs that act on proteins as their substrates, the vast majority targets small molecules whose identities cannot be deduced from the sequence of the catalytic sites but have to be determined experimentally 32 – 34 . In Arabidopsis, about 200 genes encoding HAD enzymes were identified, but to date only few have been characterized 35 – 37 . Our investigation revealed that the mutation in the HAD responsible for the ssm67 phenotype acts to reduce levels of the floral repressor FLC .…”

Rice ACID PHOSPHATASE 1 regulates Pi stress adaptation by maintaining intracellular Pi homeostasis

“…There are at least 41 typical HAD genes in rice, among which the expression of ACID PHOSPHATASE 1 ( OsACP1 , also named as OsHAD2 ) is a fast response to Pi starvation in both leaves and roots (Du, Deng, Wu, & Wang, 2021; Hur et al, 2007). However, biochemical and physiological functions of the OsACP1 are still unknown.…”