Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Abstract

Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.

Genomic Variation Among and Within SixJuglansSpecies

“…Reads were aligned to the genome using bwa mem (Version 0.7.13; Li and Durbin 2009 ). Aligned reads were subsequently converted into bam format using samtools view (Version 1.3; Li et al 2009 ). The bam-formatted files were sorted using samtools sort.…”

“…PPO genes are also implicated in the plant defense response ( Thipyapong et al 2004 ; Li and Steffens 2002 ; Richter et al 2012 ). The number of PPO genes varies from zero in Arabidopsis ( Tran et al 2012 ) to 19 in Salvia miltiorrhiza , an important ingredient in traditional Chinese medicine ( Li et al 2017 ). Previously, genomic resources established that J. regia actually has two PPO genes, JrPPO1 was the first to be found and characterized ( Escobar et al 2008 ), while the complete genome revealed the presence of another gene, expressed at much lower levels ( JrPPO2 ) and in a narrow range of tissue types ( Martínez-García et al 2016 ).…”

Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing

“…The novel LL-miR09 and LL-miR35 were predicted to target polyphenol oxidase, and the cleavage site of LL-miR09 has been identified by degradome sequencing. In Populus and Salvia miltiorrhiza , miR1444 and Smi-miR12112 have been reported to regulate a subset of polyphenol oxidases, which have important roles in plant development and response to biotic and abiotic stresses 60 – 62 . LRR receptor-like serine/threonine-protein kinase FLS2 and ERECTA were predicted as targets of LL-miR21 and miR35, respectively, and the cleavage site of FLS2 has been detected.…”

The Pentatricopeptide Repeat Gene Family in Salvia miltiorrhiza: Genome-Wide Characterization and Expression Analysis

“…Expression patterns of SmPPR genes in different organs were analyzed using the transcriptome datasets of roots, stems, leaves, and flowers of S. miltiorrhiza downloaded from GenBank (SRP051564, SRP028388). The changes of SmPPR expression levels in response to stress treatments were analyzed using the transcriptome datasets of suspension cells treated with salicylic acid (SA, 0.16 mM) (SRX1423774) for 0 h, 2 h, and 8 h and hairy roots treated with yeast extract (100 µg/mL) and Ag + (30 µM) (SRR924662) for 0 h, 12 h, 24 h, and 36 h. RNA-sequence reads were mapped to SmPPRs using SOAP 2.0 [ 51 ] and analyzed as described previously [ 12 ]. Co-expression pattern analysis of SmPPR genes with phenolic acid and tanshinone biosynthetic genes in S. miltiorrhiza was analyzed using the software package of Co-expression Pattern Clustering Analysis in the BMKCloud cloud server ( ).…”

“…Lipophilic diterpenoids such as tanshinone I, tanshinone IIA, tanshinone IIB, dihydrotanshnone I, and cryptotanshinone are diterpene quinines derived from the 2-C-methyl- d -erythritol 4-phosphate (MEP) pathway and/or the mevalonate (MVA) [ 4 , 5 ]. Due to great economic and medicinal value, the biosynthesis of bioactive components and its regulation mechanism in S. miltiorrhiza have attracted widespread interest [ 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 ]. Many genes related to the biosynthetic pathways of tanshinones and phenolic acids have been identified [ 4 , 5 , 13 ] (see Figure 1 ).…”