Phylogenetic, structure and expression analysis of ABC1Ps gene family in rice

Abstract

The ABC1 protein family (ABC1P), a new family of putative kinases, widely existed in procaryota and eucaryota. A comprehensive genome-wide analysis was carried out in this study to find all ABC1Ps in rice (Oryza sativa subsp. japonica). We identified 15 ABC1P genes in rice. All the ABC1Ps contained an ABC1 domain of about 120 conserved amino acid residues and conserved kinase motifs-VAIK (VAVK, VAMK) and DFG (DEG). The phylogenetic analysis showed that all the ABC1Ps were grouped into three subgroups, and formed a total of 12 sister pairs. Conserved motifs analysed by MEME program indicated that almost all ABC1Ps contains motifs 1, 3, 7, 8 and 9. Predictably, the ABC1Ps were localized in mitochondria or chloroplasts, which implied that the ABC1Ps might be involved in energy metabolism in plants. RT-PCR assays demonstrated that all 15 ABC1P genes were active, and some of them were affected by abiotic stresses (NaCl, high temperature, methyl viologen, abscisic acid and cadmium).

Phylogenetic, Expression, and Bioinformatic Analysis of the ABC1 Gene Family in Populus trichocarpa

“…In addition, the ABC1 domain contained a VAVK-like motif (such as VAVK, VVIK, VAMK, or VVVK) and a DFG-like motif (such as DFG, DHG, or DVG) (Figure 1). Interestingly, these results coincided with those of Yang et al [14]. …”

“…To evaluate the evolutionary relationships of the ABC1 gene family, we constructed a phylogenetic tree from P. trichocarpa and rice protein sequences using MEGA5, which was divided into three groups (groups I, II, and III) (Figure 2) in accordance with the results of Yang et al [14]. In their study, the rice ABC1 genes were also divided into three groups on the basis of orthologs or paralogs, which indicated that most ABC1P genes in this family were not formed by duplication after the divergence of Arabidopsis and rice and might have expanded in a non-species-specific manner.…”

“…Taken together, NJ method was a preferred tool to construct a phylogenetic tree. Rice protein sequences were obtained from the rice annotation database (http://rice.plantbiology.msu.edu/) based on the results of Yang et al [14]. …”

“…Jasinski et al showed that the ABC1 proteins have the most conserved kinase motifs, including the VAIK catalytic motif (VAVK and VAMK) and the VAVK motif exists in the ABC1 domain, which also contains another motif, DFG [11, 14]. Many studies have also examined the ABC1 kinase protein domain.…”

AtSIA1, an ABC1-like kinase, regulates salt response in Arabidopsis

“…Expression analysis of AtSIA1 gene and the salt response In Arabidopsis, there were 17 members of ABC1 proteins (Yang et al 2012b) The expression profiles of Arabidopsis ABC1 genes were analyzed under salt stress treatment by semi-quantitative RT-PCR. One of them (AtSIA1, At3g07700) was induced by salt stress (Fig.…”