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The phenylalanine ammonia-lyase gene family in Salvia miltiorrhiza: genome-wide characterization, molecular cloning and expression analysis

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Abstract

Salvia miltiorrhiza Bunge is a well-known material of traditional Chinese medicine. Hydrophilic phenolic acids, such as rosmarinic acid and salvianolic acid B, are a group of pharmaceutically important compounds in S. miltiorrhiza. The biosynthesis of rosmarinic acid requires the coordination of the phenylpropanoid pathway and the tyrosine-derived pathway. Phenylalanine ammonia-lyase (PAL) is the first key enzyme of the phenylpropanoid pathway. Systematic analysis of the SmPAL gene family has not been carried out. We report here the identification of three SmPALs through searching the recently obtained working draft of the S. miltiorrhiza genome and full-length cDNA cloning. Bioinformatic and phylogenetic analyses showed that SmPAL1 and SmPAL3 clustered in a sub-clade of dicot PALs, whereas SmPAL2 fell into the other one. Some important cis-elements were conserved in three SmPAL promoters, whereas the others were not. SmPAL1 and SmPAL3 were highly expressed in roots and leaves of S. miltiorrhiza, but SmPAL2 were predominately expressed in stems and flowers. It indicates that SmPAL1 and SmPAL3 function redundantly in rosmarinic acid biosynthesis. All SmPALs were induced in roots treated with PEG and MeJA, but the time and degree of responses were different, suggesting the complexity of SmPAL-associated metabolic network in S. miltiorrhiza. This is the first comprehensive study dedicated to SmPAL gene family characterization. The results provide a basis for elucidating the role of SmPAL genes in the biosynthesis of bioactive compounds.

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Abbreviations

4CL:

4-Coumarate:CoA ligase

C4H:

Cinnamic acid 4-hydroxylase

HPPD:

Hydroxyphenylpyruvate dioxygenase

HPPR:

Hydroxyphenylpyruvate reductase

MeJA:

Methyl jasmonate

MW:

Molecular weight

ORF:

Open reading frame

PAL:

Phenylalanine ammonia-lyase

PCR:

Polymerase chain reactions

pI :

Isoelectric point

qRT-PCR:

Quantitative real-time polymerase chain reaction

RACE:

Rapid amplification of cDNA ends

RAS:

Rosmarinic acid synthase

TAT:

Tyrosine aminotransferase

TCM:

Traditional Chinese medicine

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Acknowledgments

We thank Dr. Shilin Chen and the sequencing group in our institute for kindly providing the S. miltiorrhiza genome sequence. This work was supported by grants from the Beijing Natural Science Foundation (Grant No. 5112026 to SL), the Major Scientific and Technological Special Project for Significant New Drugs Creation (Grant No. 2012ZX09301002-001-031 to SL), the Program for Changjiang Scholars and Innovative Research Team in University (IRT1150 to SL), the Research Fund for the Doctoral Program of Higher Education of China (20111106110033 to SL), and the Program for Xiehe Scholars in Chinese Academy of Medical Sciences & Peking Union Medical College (to SL).

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Authors and Affiliations

  1. Institute of Biodiversity, College of Life Sciences, Shanxi Normal University, Linfen, 041004, China

    Xuemin Hou

  2. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China

    Xuemin Hou, Fenjuan Shao, Yimian Ma & Shanfa Lu

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  1. Xuemin Hou
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Correspondence to Shanfa Lu.

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Hou, X., Shao, F., Ma, Y. et al. The phenylalanine ammonia-lyase gene family in Salvia miltiorrhiza: genome-wide characterization, molecular cloning and expression analysis. Mol Biol Rep 40, 4301–4310 (2013). https://doi.org/10.1007/s11033-013-2517-3

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