Identification and Expression Analysis of Acid Phosphatase Gene (<i>PAP</i>) in <i>Brassica napus</i>: Effects of <i>cis</i>-Acting Elements on Two <i>BnaPAP10</i> Genes in Response to Phosphorus Stress

Purple acid phosphatases (PAPs) play a key role in phosphorus (P) assimilation and redistribution in plants, catalyzing the hydrolysis of phosphate esters to produce inorganic phosphate (Pi). In this study, a total of 77 <i>PAP</i> genes were identified in <i>B. napus</i>. The candidate genes were divided into three groups and ten subgroups based on the phylogenetic analyses and exon-intron organization. Among these 77 BnaPAP proteins, 35 exhibit typical metal-ligating residues characteristic of known PAPs, whereas certain unaltered amino acid residues were absent or displaced in other BnaPAPs. A computational prediction was conducted, revealing that the majority of PAPs contain signal peptide motifs and display a range of N-glycosylation levels, as well as transmembrane helix motifs. An analysis of previously obtained RNA-seq data revealed that 55.84% (43 of 77) of the <i>BnaPAPs</i> responded to Pi deficiency. Moreover, we conducted a preliminary examination of the expression profiles of <i>BnaPAP</i> genes in response to salt stress, and discovered that 42.86% (33 of 77) of these genes were induced under salt stress, either in the shoots or in the roots. Further qRT-PCR and GUS analyses revealed that <i>BnaC9.PAP10</i> and <i>BnaA7.PAP10</i>, two paralogs of <i>BnaPAP10s</i>, were induced by Pi deficiency. Notably, <i>BnaC9.PAP10</i> exhibits robust induction, compared to the relatively mild induction observed in <i>BnaA7.PAP10</i>. Our research shows that <i>BnaA7.PAP10</i> uniquely responds to Pi stress via the W-box, while <i>BnaA7.PAP10</i> predominantly responds via the P1BS element, and the differences in <i>cis</i>-regulatory elements (CREs) within their promoter regions specifically contribute to their distinct expression levels under Pi stress. Our findings provide valuable insights and establish a foundation for future functional studies of <i>BnaPAPs</i>.