Abstract
Key message
A high-efficiency protoplast transient system was devised to screen genome editing elements in Salvia miltiorrhiza.
Abstract
Medicinal plants with high-value pharmaceutical ingredients have attracted research attention due to their beneficial effects on human health. Cell wall-free protoplasts of plants can be used to evaluate the efficiency of genome editing mutagenesis. The capabilities of gene editing in medicinal plants remain to be fully explored owing to their complex genetic background and shortfall of suitable transformation. Here, we took the Salvia miltiorrhiza as a representative example for develo** a method to screen favorable gene editing elements with high editing efficiency in medical plants by a PEG-mediated protoplast transformation. Results indicated that using the endogenous SmU6.1 of S. miltiorrhiza to drive sgRNA and the plant codon-optimized Cas9 driven by the promoter SlEF1α can enhance the efficiency of editing. In summary, we uncover an efficacious transient method for screening editing elements and shed new light on increasing gene editing efficiency in medicinal plants.
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References
Alagoz Y, Gurkok T, Zhang B, Unver T (2016) Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep 6:30910. https://doi.org/10.1038/srep30910
Bruce W, Christensen A, Klein T, Fromm M, Quail P (1989) Photoregulation of a phytochrome gene promoter from oat transferred into rice by particle bombardment. Proc Natl Acad Sci U S A 86(24):9692–9696. https://doi.org/10.1073/pnas.86.24.9692
Cao Y, Chen R, Wang W, Wang D, Cao X (2021) SmSPL6 induces phenolic acid biosynthesis and affects root development in Salvia miltiorrhiza. Int J Mol Sci 22(15):7895. https://doi.org/10.3390/ijms22157895
Deng C, Shi M, Fu R, Zhang Y, Wang Q, Zhou Y, Wang Y, Ma X, Kai G (2020) ABA-responsive transcription factor bZIP1 is involved in modulating biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. J Exp Bot 71(19):5948–5962. https://doi.org/10.1093/jxb/eraa295
Di H, Sun J, Hu Z, Jiang Q, Song G, Zhang B, Zhao S, Zhang H (2019) Enhancing the CRISPR/Cas9 system based on multiple GmU6 promoters in soybean. Biochem Biophys Res Commun 519(4):819–823. https://doi.org/10.1016/j.bbrc.2019.09.074
Fu R, Shi M, Deng C, Zhang Y, Zhang X, Wang Y, Kai G (2020) Improved phenolic acid content and bioactivities of Salvia miltiorrhiza hairy roots by genetic manipulation of RAS and CYP98A14. Food Chem 331:127365. https://doi.org/10.1016/j.foodchem.2020.127365
Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109(39):E2579–E2586. https://doi.org/10.1073/pnas.1208507109
Gu X, Chen J, **ao Y, Di P, Xuan H, Zhou X, Zhang L, Chen W (2012) Overexpression of allene oxide cyclase promoted tanshinone/phenolic acid production in Salvia miltiorrhiza. Plant Cell Rep 31(12):2247–2259. https://doi.org/10.1007/s00299-012-1334-9
Gupta V, Guleri R, Gupta M, Kaur N, Kaur K, Kumar P, Anand M, Kaur G, Pati P (2020) Anti-neuroinflammatory potential of Tylophora indica (Burm. f) Merrill and development of an efficient in vitro propagation system for its clinical use. PLoS ONE 15(3):e0230142. https://doi.org/10.1371/journal.pone.0230142
Hashimoto R, Ueta R, Abe C, Osakabe Y, Osakabe K (2018) Efficient multiplex genome editing induces precise, and self-ligated type mutations in tomato plants. Front Plant Sci 9:916. https://doi.org/10.3389/fpls.2018.00916
**ek M, Chylinski K, Fonfara I, Hauer M, Doudna J, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821. https://doi.org/10.1126/science.1225829
Jores T, Tonnies J, Dorrity M, Cuperus J, Fields S, Queitsch C (2020) Identification of plant enhancers and their constituent elements by STARR-seq in tobacco leaves. Plant Cell 32(7):2120–2131. https://doi.org/10.1105/tpc.20.00155
Kai G, Xu H, Zhou C, Liao P, **ao J, Luo X, You L, Zhang L (2011) Metabolic engineering tanshinone biosynthetic pathway in Salvia miltiorrhiza hairy root cultures. Metab Eng 13(3):319–327. https://doi.org/10.1016/j.ymben.2011.02.003
Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, Ashnest J, Mau M, Schranz M, Alcorn J, Laprairie R, McKay J, Burbridge C, Schneider D, Vergara D, Kane N, Sharbel T (2020) The genomics of cannabis and its close relatives. Annu Rev Plant Biol 71:713–739. https://doi.org/10.1146/annurev-arplant-081519-040203
Kui L, Chen H, Zhang W, He S, **ong Z, Zhang Y, Yan L, Zhong C, He F, Chen J, Zeng P, Zhang G, Yang S, Dong Y, Wang W, Cai J (2016) Building a genetic manipulation tool box for orchid biology: identification of constitutive promoters and application of CRISPR/Cas9 in the orchid, Dendrobium officinale. Front Plant Sci 7:2036. https://doi.org/10.3389/fpls.2016.02036
LeBlanc C, Zhang F, Mendez J, Lozano Y, Chatpar K, Irish V, Jacob Y (2018) Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress. Plant J 93(2):377–386. https://doi.org/10.1111/tpj.13782
Li J, Park E, von Arnim A, Nebenführ A (2009) The FAST technique: a simplified Agrobacterium-based transformation method for transient gene expression analysis in seedlings of Arabidopsis and other plant species. Plant Methods 5:6. https://doi.org/10.1186/1746-4811-5-6
Li J, Norville J, Aach J, McCormack M, Zhang D, Bush J, Church G, Sheen J (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31(8):688–691. https://doi.org/10.1038/nbt.2654
Li B, Cui G, Shen G, Zhan Z, Huang L, Chen J, Qi X (2017) Targeted mutagenesis in the medicinal plant Salvia miltiorrhiza. Sci Rep 7:43320. https://doi.org/10.1038/srep43320
Li Z, Xu S, Liu P (2018) Salvia miltiorrhizaBurge (Danshen): a golden herbal medicine in cardiovascular therapeutics. Acta Pharmacol Sin 39(5):802–824. https://doi.org/10.1038/aps.2017.193
Li L, Wang D, Zhou L, Yu X, Yan X, Zhang Q, Li B, Liu Y, Zhou W, Cao X, Wang Z (2020) JA-responsive transcription factor SmMYB97 promotes phenolic acid and tanshinone accumulation in Salvia miltiorrhiza. J Agric Food Chem 68(50):14850–14862. https://doi.org/10.1021/acs.jafc.0c05902
Li S, Wu Z, Zhou Y, Dong Z, Fei X, Zhou C, Li S (2022) Changes in metabolism modulate induced by viroid infection in the orchid Dendrobium officinale. Virus Res 308:198626. https://doi.org/10.1016/j.virusres.2021.198626
Lin C, Hsu C, Yang L, Lee L, Fu J, Cheng Q, Wu F, Hsiao H, Zhang Y, Zhang R, Chang W, Yu C, Wang W, Liao L, Gelvin S, Shih M (2018) Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnol J 16(7):1295–1310. https://doi.org/10.1111/pbi.12870
Liu H, Lu X, Hu Y, Fan X (2020) Chemical constituents of Panax ginseng and Panax notoginseng explain why they differ in therapeutic efficacy. Pharmacol Res 161:105263. https://doi.org/10.1016/j.phrs.2020.105263
Long L, Guo D, Gao W, Yang W, Hou L, Ma X, Miao Y, Botella J, Song C (2018) Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression. Plant Methods 14:85. https://doi.org/10.1186/s13007-018-0353-0
Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y, **e Y, Shen R, Chen S, Wang Z, Chen Y, Guo J, Chen L, Zhao X, Dong Z, Liu Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8(8):1274–1284. https://doi.org/10.1016/j.molp.2015.04.007
Ma Y, Xu D, Li L, Zhang F, Fu X, Shen Q, Lyu X, Wu Z, Pan Q, Shi P, Hao X, Yan T, Chen M, Liu P, He Q, **e L, Zhong Y, Tang Y, Zhao J, Zhang L, Sun X, Tang K (2018) Jasmonate promotes artemisinin biosynthesis by activating the TCP14-ORA complex in Artemisia annua. Sci Adv 4(11):eaas9357. https://doi.org/10.1126/sciadv.aas9357
Ma X, Claus L, Leslie M, Tao K, Wu Z, Liu J, Yu X, Li B, Zhou J, Savatin D, Peng J, Tyler B, Heese A, Russinova E, He P, Shan L (2020) Ligand-induced monoubiquitination of BIK1 regulates plant immunity. Nature 581(7807):199–203. https://doi.org/10.1038/s41586-020-2210-3
Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Wan J, Gu H, Qu L (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23(10):1233–1236. https://doi.org/10.1038/cr.2013.123
Nadakuduti S, Starker C, Ko D, Jayakody T, Buell C, Voytas D, Douches D (2019) Evaluation of methods to assess in vivo activity of engineered genome-editing nucleases in protoplasts. Front Plant Sci 10:110. https://doi.org/10.3389/fpls.2019.00110
Niu Q, Wu S, **e H, Wu Q, Liu P, Xu Y, Lang Z (2023) Efficient A·T to G·C base conversions in dicots using adenine base editors expressed under the tomato EF1α promoter. Plant Biotechnol J 21(1):5–7. https://doi.org/10.1111/pbi.13736
Pfotenhauer A, Occhialini A, Nguyen M, Scott H, Dice L, Harbison S, Li L, Reuter D, Schimel TM, Stewart CN Jr, Beal J, Lenaghan S (2022) Building the plant SynBio toolbox through combinatorial analysis of DNA regulatory elements. ACS Synth Biol 11(8):2741–2755. https://doi.org/10.1021/acssynbio.2c00147
Ren J, Fu L, Nile S, Zhang J, Kai G (2019) Salvia miltiorrhiza in treating cardiovascular diseases: a review on its pharmacological and clinical applications. Front Pharmacol 10:753. https://doi.org/10.3389/fphar.2019.00753
Ren C, Liu Y, Guo Y, Duan W, Fan P, Li S, Liang Z (2021) Optimizing the CRISPR/Cas9 system for genome editing in grape by using grape promoters. Hortic Res 8(1):52. https://doi.org/10.1038/s41438-021-00489-z
Sabzehzari M, Zeinali M, Naghavi M (2020) Alternative sources and metabolic engineering of taxol: advances and future perspectives. Biotechnol Adv 43:107569. https://doi.org/10.1016/j.biotechadv.2020.107569
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, ** J, Qiu J, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688. https://doi.org/10.1038/nbt.2650
Shao Y, Mu D, Pan L, Wilson I, Zheng Y, Zhu L, Lu Z, Wan L, Fu J, Wei S, Song L, Qiu D, Tang Q (2023) Optimization of isolation and transformation of protoplasts from Uncaria rhynchophylla and Its application to transient gene expression analysis. Int J Mol Sci 24(4):3633. https://doi.org/10.3390/ijms24043633
Sheen J (2001) Signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol 127(4):1466–1475
Shi M, Du Z, Hua Q, Kai G (2021) CRISPR/Cas9-mediated targeted mutagenesis of bZIP2 in Salvia miltiorrhiza leads to promoted phenolic acid biosynthesis. Ind Crops Prod 167:113560. https://doi.org/10.1016/j.indcrop.2021.113560
Shi M, Zhu R, Zhang Y, Zhang S, Liu T, Li K, Liu S, Wang L, Wang Y, Zhou W, Hua Q, Kai G (2022) A novel WRKY34-bZIP3 module regulates phenolic acid and tanshinone biosynthesis in Salvia miltiorrhiza. Metab Eng 73:182–191. https://doi.org/10.1016/j.ymben.2022.08.002
Tian W, Huang X, Ouyang X (2022) Genome-wide prediction of activating regulatory elements in rice by combining STARR-seq with FACS. Plant Biotechnol J 20(12):2284–2297. https://doi.org/10.1111/pbi.13907
Tu Y (2011) The discovery of artemisinin (qinghaosu) and gifts from Chinese medicine. Nat Med 17(10):1217–1220. https://doi.org/10.1038/nm.2471
van Der Heijden R, Jacobs D, Snoeijer W, Hallard D, Verpoorte R (2004) The Catharanthus alkaloids: pharmacognosy and biotechnology. Curr Med Chem 11(5):607–628. https://doi.org/10.2174/0929867043455846
Wang Y, Cao L, Zhang Y, Cao C, Liu F, Huang F, Qiu Y, Li R, Lou X (2015) Map-based cloning and characterization of BPH29, a B3 domain-containing recessive gene conferring brown planthopper resistance in rice. J Exp Bot 66(19):6035–6045. https://doi.org/10.1093/jxb/erv318
Wang N, Gent J, Dawe R (2021) Haploid induction by a maize cenh3 null mutant. Sci Adv 7(4):eabe2299. https://doi.org/10.1126/sciadv.abe2299
Wang J, Wang Y, Lü T, Yang X, Liu J, Dong Y, Wang Y (2022) An efficient and universal protoplast isolation protocol suitable for transient gene expression analysis and single-cell RNA sequencing. Int J Mol Sci 23(7):3419. https://doi.org/10.3390/ijms23073419
Wei T, Gao Y, Deng K, Zhang L, Yang M, Liu X, Qi C, Wang C, Song W, Zhang Y, Chen C (2019) Enhancement of tanshinone production in Salvia miltiorrhiza hairy root cultures by metabolic engineering. Plant Methods 15:53. https://doi.org/10.1186/s13007-019-0439-3
Wu J, Liu Q, Geng X, Li K, Luo L, Liu J (2017) Highly efficient mesophyll protoplast isolation and PEG-mediated transient gene expression for rapid and large-scale gene characterization in cassava (Manihot esculenta Crantz). BMC Biotechnol 17(1):29. https://doi.org/10.1186/s12896-017-0349-2
Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, Xu J, Li Y, Song C, Wang B, Sun W, Shen G, Zhang X, Qian J, Ji A, Xu Z, Luo X, He L, Li C, Sun C, Yan H, Cui G, Li X, Li X, Wei J, Liu J, Wang Y, Hayward A, Nelson D, Ning Z, Peters R, Qi X, Chen S (2016) Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza. Mol Plant 9(6):949–952. https://doi.org/10.1016/j.molp.2016.03.010
Xu M, Du Q, Tian C, Wang Y, Jiao Y (2021) Stochastic gene expression drives mesophyll protoplast regeneration. Sci Adv 7(33):eabg8466. https://doi.org/10.1126/sciadv.abg8466
Yang W, Ren J, Liu W, Liu D, **e K, Zhang F, Wang P, Guo W, Wu X (2023) An efficient transient gene expression system for protein subcellular localization assay and genome editing in citrus protoplasts. Hortic Plant J 9(3):425–436. https://doi.org/10.1016/j.hpj.2022.06.006
Yoo S, Cho Y, Sheen J (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2(7):1565–1572. https://doi.org/10.1038/nprot.2007.199
Zhang Y, Su J, Duan S, Ao Y, Dai J, Liu J, Wang P, Li Y, Liu B, Feng D, Wang J, Wang H (2011) A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes. Plant Methods 7(1):30. https://doi.org/10.1186/1746-4811-7-30
Zhang X, Xu G, Cheng C, Lei L, Sun J, Xu Y, Deng C, Dai Z, Yang Z, Chen X, Liu C, Tang Q, Su J (2021) Establishment of an Agrobacterium-mediated genetic transformation and CRISPR/Cas9-mediated targeted mutagenesis in Hemp (Cannabis sativa L.). Plant Biotechnol J 19(10):1979–1987. https://doi.org/10.1111/pbi.13611
Zheng H, Fu X, Shao J, Tang Y, Yu M, Li L, Huang L, Tang K (2023) Transcriptional regulatory network of high-value active ingredients in medicinal plants. Trends Plant Sci 28(4):429–446. https://doi.org/10.1016/j.tplants.2022.12.007
Zhou Y, Sun W, Chen J, Tan H, **ao Y, Li Q, Ji Q, Gao S, Chen S, Zhang L, Chen W (2016) SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza. Sci Rep 6:22852. https://doi.org/10.1038/srep22852
Zhou Z, Tan H, Li Q, Chen J, Gao S, Wang Y, Chen W, Zhang L (2018) CRISPR/Cas9-mediated efficient targeted mutagenesis of RAS in Salvia miltiorrhiza. Phytochemistry 148:63–70. https://doi.org/10.1016/j.phytochem.2018.01.015
Zhou Z, Tan H, Li Q, Li Q, Wang Y, Bu Q, Li Y, Wu Y, Chen W, Zhang L (2020) TRICHOME AND ARTEMISININ REGULATOR 2 positively regulates trichome development and artemisinin biosynthesis in Artemisia annua. New Phytol 228(3):932–945. https://doi.org/10.1111/nph.16777
Zhu F, Luo T, Liu C, Wang Y, Yang H, Yang W, Zheng L, **ao X, Zhang M, Xu R, Xu J, Zeng Y, Xu J, Xu Q, Guo W, Larkin R, Deng CY (2017) An R2R3-MYB transcription factor represses the transformation of α- and β-branch carotenoids by negatively regulating expression of CrBCH2 and CrNCED5 in flavedo of Citrus reticulate. New Phytol 216(1):178–192. https://doi.org/10.1111/nph.14684
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This work was funded by China Academy of Chinese Medical Sciences (CACMS) Innovation Fund (CI2021A041003), The Ability Establishment of Sustainable Use for Valuable Chinese Medicine Resources (2060302), National Key R&D Program of China (2018YFA0900600), Shanghai Jiao Tong University (SJTU) Transmed Awards Research (20190104) and the Bill & Melinda Gates Foundation (grant numbers: OPP1199872 and INV-027291). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.
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JS, HZ, and KT designed the project; JS, BP, YZ, and XY performed most of the experiments; XY, XH, XF, and LL analyzed the data; JS and BP wrote this research manuscript. All the authors have read and approved the manuscript.
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Shao, J., Peng, B., Zhang, Y. et al. A high-efficient protoplast transient system for screening gene editing elements in Salvia miltiorrhiza. Plant Cell Rep 43, 45 (2024). https://doi.org/10.1007/s00299-023-03134-2
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DOI: https://doi.org/10.1007/s00299-023-03134-2