Genome-wide characterization and comparative analysis of R2R3-MYB transcription factors shows the complexity of MYB-associated regulatory networks in Salvia miltiorrhiza

Li, Caili; Lu, Shanfa

doi:10.1186/1471-2164-15-277

Cited by 98 publications

(88 citation statements)

References 75 publications

(102 reference statements)

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“…However, the regulatory roles of non-coding RNAs in PQ and UQ biosynthesis have not been revealed. In addition to non-coding RNAs, transcription factors, such as MYB, WRKY and SPL, potentially play significant regulatory roles in PQ and UQ biosynthesis (Li and Lu, 2014a,b; Zhang et al, 2014; Li C. et al, 2015), which needs to be further demonstrated. Understanding the regulatory mechanisms of PQ and UQ are important for manipulating the content of PQ and UQ in plants.…”

Section: Discussionmentioning

confidence: 99%

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

Liu

2016

Front. Plant Sci.

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113

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Plastoquinone (PQ) and ubiquinone (UQ) are two important prenylquinones, functioning as electron transporters in the electron transport chain of oxygenic photosynthesis and the aerobic respiratory chain, respectively, and play indispensable roles in plant growth and development through participating in the biosynthesis and metabolism of important chemical compounds, acting as antioxidants, being involved in plant response to stress, and regulating gene expression and cell signal transduction. UQ, particularly UQ10, has also been widely used in people’s life. It is effective in treating cardiovascular diseases, chronic gingivitis and periodontitis, and shows favorable impact on cancer treatment and human reproductive health. PQ and UQ are made up of an active benzoquinone ring attached to a polyisoprenoid side chain. Biosynthesis of PQ and UQ is very complicated with more than thirty five enzymes involved. Their synthetic pathways can be generally divided into two stages. The first stage leads to the biosynthesis of precursors of benzene quinone ring and prenyl side chain. The benzene quinone ring for UQ is synthesized from tyrosine or phenylalanine, whereas the ring for PQ is derived from tyrosine. The prenyl side chains of PQ and UQ are derived from glyceraldehyde 3-phosphate and pyruvate through the 2-C-methyl-D-erythritol 4-phosphate pathway and/or acetyl-CoA and acetoacetyl-CoA through the mevalonate pathway. The second stage includes the condensation of ring and side chain and subsequent modification. Homogentisate solanesyltransferase, 4-hydroxybenzoate polyprenyl diphosphate transferase and a series of benzene quinone ring modification enzymes are involved in this stage. PQ exists in plants, while UQ widely presents in plants, animals and microbes. Many enzymes and their encoding genes involved in PQ and UQ biosynthesis have been intensively studied recently. Metabolic engineering of UQ10 in plants, such as rice and tobacco, has also been tested. In this review, we summarize and discuss recent research progresses in the biosynthetic pathways of PQ and UQ and enzymes and their encoding genes involved in side chain elongation and in the second stage of PQ and UQ biosynthesis. Physiological functions of PQ and UQ played in plants as well as the practical application and metabolic engineering of PQ and UQ are also included.

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Section: Discussionmentioning

confidence: 99%

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

Liu

2016

Front. Plant Sci.

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113

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“…Tcactin was used as a reference gene as described previously [16]. Gene expression levels were calculated according to the 2 -∆∆Ct method for the different tissues and aged xylem samples [17,18].…”

Section: Quantitative Real-time Reverse Transcription-pcr (Qrt-pcr)mentioning

confidence: 99%

Identification of the Genes Involved in Anthocyanin Biosynthesis and Accumulation in Taxus chinensis

Zhang

Sun

Wilson

et al. 2019

Genes

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Taxus chinensis is a precious woody species with significant economic value. Anthocyanin as flavonoid derivatives plays a crucial role in plant biology and human health. However, the genes involved in anthocyanin biosynthesis have not been identified in T. chinensis. In this study, twenty-five genes involved in anthocyanin biosynthesis were identified, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, anthocyanidin synthase, flavonoid 3’-hydroxylase, flavonoid 3’,5’-hydroxylase, dihydroflavonol 4-reductase, anthocyanidin reductase, and leucoanthocyanidin reductase. The conserved domains and phylogenetic relationships of these genes were characterized. The expression levels of these genes in different tissues and different ages of xylem were investigated. Additionally, the anthocyanin accumulation in xylem of different ages of T. chinensis was measured. The results showed the anthocyanin accumulation was correlated with the expression levels of dihydroflavonol 4-reductase, anthocyanidin synthase, flavonoid 3’-hydroxylase, and flavonoid 3’,5’-hydroxylase. Our results provide a basis for studying the regulation of the biosynthetic pathway for anthocyanins and wood color formation in T. chinensis.

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“…High-quantity RNA-seq reads and ESTs were assembled into unigenes using Trinity software. The sequences of 5 SmRDRs (Shao and Lu 2014), 10 SmAGOs (Shao and Lu 2013) and 110 SmMYBs (Li and Lu 2014) were downloaded from GenBank under the accession numbers KF872203-KF872207, KF153679-KF153688, and KF059355-KF059464, respectively. Sequence comparison of the assembled unigenes with SmRDRs, SmAGOs and SmMYBs was analyzed using BLASTN (Altschul et al 1997).…”

Section: Plant Materials and Stress Treatmentmentioning

confidence: 99%

“…S. miltiorrhiza genes involved in secondary metabolism (Ma et al 2012;Li and Lu 2014;Zhang et al 2014a, b), stress response ) and miRNA pathway Lu 2013, 2014) have been intensively studied recently. However, there is no information available for S. miltiorrhiza mlncRNAs.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

Shao

2015

Planta

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Identification and characterization of 5,446 mlncRNAs from Salvia miltiorrhiza showed that the majority of identified mlncRNAs were stress responsive, providing a framework for elucidating mlncRNA functions in S. miltiorrhiza. mRNA-like noncoding RNAs (mlncRNAs) are transcribed by RNA polymerase II and are polyadenylated, capped and spliced. They play important roles in plant development and defense responses. However, there is no information available for mlncRNAs in Salvia miltiorrhiza Bunge, the first Chinese medicinal material entering the international market. To perform a transcriptome-wide identification of S. miltiorrhiza mlncRNAs, we assembled over 8 million RNA-seq reads from GenBank database and 5,624 ESTs from PlantGDB into 44422 unigenes. Using a computational identification pipeline, we identified 5446 S. miltiorrhiza mlncRNA candidates from the assembled unigenes. Of the 5446 mlncRNAs, 2 are primary transcripts of conserved miRNAs, and 2030 can be grouped into 470 families with at least two members in a family. Quantitative real-time PCR analysis of mlncRNAs with at least 900 nt showed that the majority were differentially expressed in roots, stems, leaves and flowers and responsive to methyl jasmonate (MeJA) treatment in S. miltiorrhiza. Analysis of published RNA-seq data showed that a total of 3,044 mlncRNAs were expressed in hairy roots of S. miltiorrhiza and the expression of 1,904 of the 3,044 mlncRNAs was altered by yeast extract and Ag(+) treatment. The results indicate that the majority of mlncRNAs are involved in plant response to stress. This study provides a framework for understanding the roles of mlncRNAs in S. miltiorrhiza.

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Genome-wide characterization and comparative analysis of R2R3-MYB transcription factors shows the complexity of MYB-associated regulatory networks in Salvia miltiorrhiza

Cited by 98 publications

References 75 publications

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

Identification of the Genes Involved in Anthocyanin Biosynthesis and Accumulation in Taxus chinensis

Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

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