{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:58:55Z","timestamp":1790758735230,"version":"4.1.0"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Japan Society for the Promotion of Science KAKENHI","award":["19H05638"],"award-info":[{"award-number":["19H05638"]}],"id":[{"id":"https:\/\/ror.org\/00hhkn466","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Japan Society for the Promotion of Science KAKENHI","award":["22K05438"],"award-info":[{"award-number":["22K05438"]}],"id":[{"id":"https:\/\/ror.org\/00hhkn466","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Japan Society for the Promotion of Science KAKENHI","award":["25K08838"],"award-info":[{"award-number":["25K08838"]}],"id":[{"id":"https:\/\/ror.org\/00hhkn466","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Japan Science and Technology Agency (JST) SPRING","award":["JPMJSP2110"],"award-info":[{"award-number":["JPMJSP2110"]}],"id":[{"id":"https:\/\/ror.org\/00097mb19","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001863","name":"New Energy and Industrial Technology Development Organization","doi-asserted-by":"publisher","award":["NEDO 16100890-0"],"award-info":[{"award-number":["NEDO 16100890-0"]}],"id":[{"id":"10.13039\/501100001863","id-type":"DOI","asserted-by":"publisher"}]},{"name":"RIKEN Cluster for Science, Technology and Innovation Hub"},{"name":"Institute for the Future of Human Society of Kyoto University for 2023","id":[{"id":"https:\/\/ror.org\/049tcsg76","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Jikei University Research Fund"},{"name":"Humanosphere Science Research on Sustainable Humanosphere Science"},{"DOI":"10.13039\/501100005683","name":"Kyoto University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005683","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Shikonin, a 1,4-naphthoquinone derivative produced by some limited Boraginaceae species, exhibits unique pharmacological properties and is also used as a natural dye. The regulatory factors of shikonin production have been demonstrated using a cell culture system of Lithospermum erythrorhizon. Among these factors, copper is known to be the strongest enhancer of shikonin production, and the copper-requiring biosynthetic step is shikonin-specific, unlike the byproduct benzoquinones. Despite the long history of shikonin biosynthesis studies for over 40\u00a0years, the copper-involved reaction has been still unknown. Here, we explored candidate genes associated with shikonin production using a PCR-select subtraction experiment. Genes encoding PPO, a dicopper-dependent oxidoreductase, was highlighted by the strong synchronous expression with shikonin production. Transcriptome analysis of hairy roots and cultured cells of this plant revealed that, of the five PPO genes expressed in L. erythrorhizon (LePPOs), only LePPO1 showed a close correlation with shikonin production. Then, we generated genome-edited hairy roots of LePPO1 using CRISPR\/Cas9-mediated mutagenesis to analyze its impact on shikonin derivative and other specialized metabolite production. The results showed that shikonin content was markedly reduced in all LePPO1-ge lines, while the content of deoxyshikonofuran, a hydroquinone-type shunt product that branches after 3\u2032\u2032-hydroxygeranylhydroquinone in the shikonin biosynthetic pathway, remained unaffected in the LePPO1-ge lines. These findings address the question of why a copper ion is crucial for shikonin biosynthesis and suggest that LePPO1 participates in naphthalene ring formation. Interestingly, LePPO1 is localized in plastids, whereas shikonin accumulates in the apoplast.<\/jats:p>","DOI":"10.1093\/pcp\/pcag074","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T11:44:07Z","timestamp":1779968647000},"page":"1557-1572","source":"Crossref","is-referenced-by-count":0,"title":["CRISPR\/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in\n                    <i>Lithospermum erythrorhizon<\/i>"],"prefix":"10.1093","volume":"67","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-6769-9845","authenticated-orcid":false,"given":"Kohei","family":"Nakanishi","sequence":"first","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]},{"name":"Institute of Natural Medicine, Toyama University , 2630 Sugitani, Toyama 930-0194 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Takano","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyoko","family":"Yamamoto","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Matsuda","sequence":"additional","affiliation":[{"name":"Graduate School of Science and Technology, Shinshu University , 3-1-1 Asahi, Matsumoto, Nagano 390-8621 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariko","family":"Yano","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koji","family":"Mito","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9058-5660","authenticated-orcid":false,"given":"Takuji","family":"Ichino","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]},{"name":"Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University , 4-19-1 Motoyamakita-machi, Higashinada, Hyogo, Kobe 658-8558 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kanade","family":"Tatsumi","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Li","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuaki","family":"Ohara","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7888-6281","authenticated-orcid":false,"given":"Ryosuke","family":"Munakata","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0233-7008","authenticated-orcid":false,"given":"Hideyuki","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nozomu","family":"Sakurai","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daisuke","family":"Shibata","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6227-6913","authenticated-orcid":false,"given":"Keishi","family":"Osakabe","sequence":"additional","affiliation":[{"name":"Graduate School of Technology, Industrial and Social Science, Tokushima University , 3-18-15 Kuramoto, Tokushima 770-8503 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bunta","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Chemistry Laboratory, The Jikei University School of Medicine , 8-3-1 Kokuryo, Chofu, Tokyo 182-8570 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6375-2443","authenticated-orcid":false,"given":"Takahiro","family":"Okada","sequence":"additional","affiliation":[{"name":"Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University 5-1-1 Nabeshima , Saga, Saga 840-8502 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koichiro","family":"Shimomura","sequence":"additional","affiliation":[{"name":"Graduate School of Life Sciences, Toyo University , 1-1-1 Izumino, Itakura, Ora, Gunma 374-0193 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4867-5619","authenticated-orcid":false,"given":"Kojiro","family":"Takanashi","sequence":"additional","affiliation":[{"name":"Graduate School of Science and Technology, Shinshu University , 3-1-1 Asahi, Matsumoto, Nagano 390-8621 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9643-6639","authenticated-orcid":false,"given":"Akifumi","family":"Sugiyama","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2523-6418","authenticated-orcid":false,"given":"Kazufumi","family":"Yazaki","sequence":"additional","affiliation":[{"name":"Research Institute for Sustainable Humanosphere, Kyoto University , Gokasho, Uji, Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"2026093004122664500_ref1","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026093004122664500_ref3","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/s41438-020-0301-9","article-title":"Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis","volume":"7","author":"Auber","year":"2020","journal-title":"Hortic. Res."},{"key":"2026093004122664500_ref4","doi-asserted-by":"publisher","first-page":"147060","DOI":"10.1016\/j.gene.2022.147060","article-title":"Characterization of plant laccase genes and their functions","volume":"852","author":"Bai","year":"2023","journal-title":"Gene"},{"key":"2026093004122664500_ref5","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Genome analysis trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026093004122664500_ref6","doi-asserted-by":"publisher","first-page":"2661","DOI":"10.1093\/jxb\/eraa074","article-title":"Dynamics of the localization of the plastid terminal oxidase inside the chloroplast","volume":"71","author":"Bolte","year":"2020","journal-title":"J. Exp. Bot."},{"key":"2026093004122664500_ref7","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1104\/pp.119.2.417","article-title":"Cell-specific production and antimicrobial activity of naphthoquinones in roots of Lithospermum erythrorhizon","volume":"119","author":"Brigham","year":"1999","journal-title":"Plant Physiol."},{"key":"2026093004122664500_ref8","doi-asserted-by":"publisher","first-page":"89","DOI":"10.5511\/plantbiotechnology.10.1109b","article-title":"An acyltransferase-like gene obtained by differential gene expression profiles of quinolizidine alkaloid-producing and nonproducing cultivars of Lupinus angustifolius","volume":"28","author":"Bunsupa","year":"2011","journal-title":"Plant Biotechnol."},{"key":"2026093004122664500_ref9","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1105\/tpc.109.071738","article-title":"Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation","volume":"22","author":"Chang","year":"2010","journal-title":"Plant Cell"},{"key":"2026093004122664500_ref10","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1105\/tpc.113.119685","article-title":"Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid: coenzyme A ligase protein complex formation, regulation, and numerical modeling","volume":"26","author":"Chen","year":"2014","journal-title":"Plant Cell"},{"key":"2026093004122664500_ref11","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1016\/S1875-5364(25)60818-1","article-title":"Comprehensive analysis of the antibacterial activity of 5,8-dihydroxy-1.4-naphthoquinone derivatives against methicillin-resistant Staphylococcus aureus","volume":"23","author":"Chen","year":"2025","journal-title":"Chin. J. Nat. Med."},{"key":"2026093004122664500_ref12","doi-asserted-by":"publisher","first-page":"6025","DOI":"10.1073\/pnas.93.12.6025","article-title":"Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries","volume":"93","author":"Diatchenko","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026093004122664500_ref13","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2026093004122664500_ref14","doi-asserted-by":"publisher","first-page":"e3647","DOI":"10.1371\/journal.pone.0003647","article-title":"A one pot, one step, precision cloning method with high throughput capability","volume":"3","author":"Engler","year":"2008","journal-title":"PLoS One"},{"key":"2026093004122664500_ref15","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1007\/s11240-020-01976-2","article-title":"Cloning and functional analysis of EpGHQH1 in shikonin production of Echium plantagineum","volume":"144","author":"Fu","year":"2021","journal-title":"Plant Cell Tissue Organ Cult."},{"key":"2026093004122664500_ref16","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1007\/BF00269273","article-title":"Production of shikonin derivatives by cell suspension cultures of Lithospermum erythrorhizon - II. A new medium for the production of shikonin derivatives","volume":"1","author":"Fujita","year":"1981","journal-title":"Plant Cell Rep."},{"key":"2026093004122664500_ref17","doi-asserted-by":"publisher","first-page":"2398","DOI":"10.1016\/S0031-9422(00)80569-5","article-title":"Two phenolic acids from Lithospermum erythrorhizon cell suspension cultures","volume":"23","author":"Fukui","year":"1984","journal-title":"Phytochemistry"},{"key":"2026093004122664500_ref18","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1093\/pcp\/pcad024","article-title":"A polyphenol oxidase catalyzes aurone synthesis in Marchantia polymorpha","volume":"64","author":"Furudate","year":"2023","journal-title":"Plant Cell Physiol."},{"key":"2026093004122664500_ref19","doi-asserted-by":"publisher","first-page":"104463","DOI":"10.1016\/j.phrs.2019.104463","article-title":"Pharmacological properties and derivatives of shikonin \u2014 a review in recent years","volume":"149","author":"Guo","year":"2019","journal-title":"Pharmacol. Res."},{"key":"2026093004122664500_ref20","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1006\/abio.1996.0334","article-title":"Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate","volume":"240","author":"Gurskaya","year":"1996","journal-title":"Anal. Biochem."},{"key":"2026093004122664500_ref21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/cbdv.202403291","article-title":"Shikonin derivative suppresses colorectal cancer cells growth via reactive oxygen species-mediated mitochondrial ppoptosis and PI3K \/ AKT pathway","volume":"22","author":"Han","year":"2025","journal-title":"Chem. Biodivers."},{"key":"2026093004122664500_ref22","doi-asserted-by":"publisher","first-page":"102184","DOI":"10.1016\/j.pbi.2022.102184","article-title":"Modes of secretion of plant lipophilic metabolites via ABCG transporter-dependent transport and vesicle-mediated trafficking","volume":"66","author":"Ichino","year":"2022","journal-title":"Curr. Opin. Plant Biol."},{"key":"2026093004122664500_ref23","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1007\/s10265-025-01651-7","article-title":"Characterization of two G-type half-size ABC transporter genes from the lipid-secreting medicinal plant Lithospermum erythrorhizon","volume":"138","author":"Ichino","year":"2025","journal-title":"J. Plant Res."},{"key":"2026093004122664500_ref24","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1093\/pcp\/pcad038","article-title":"Letter to the Editor: gromwell, a purple link between traditional Japanese culture and plant science","volume":"64","author":"Ito","year":"2023","journal-title":"Plant Cell Physiol."},{"key":"2026093004122664500_ref25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-70469-1","article-title":"Apple latent spherical virus (ALSV)-induced gene silencing in a medicinal plant, Lithospermum erythrorhizon","volume":"10","author":"Izuishi","year":"2020","journal-title":"Sci. Rep."},{"key":"2026093004122664500_ref26","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1038\/s41586-020-2223-y","article-title":"Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors","volume":"582","author":"Jin","year":"2020","journal-title":"Nature"},{"key":"2026093004122664500_ref27","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/s41594-020-0440-6","article-title":"Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur","volume":"27","author":"Jin","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026093004122664500_ref28","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.ymgme.2003.08.006","article-title":"PCR-select subtraction for characterization of messages differentially expressed in brown compared with white adipose tissue","volume":"80","author":"Kajimoto","year":"2003","journal-title":"Mol. Genet. Metab."},{"key":"2026093004122664500_ref29","doi-asserted-by":"publisher","first-page":"2330","DOI":"10.1080\/09168451.2017.1381017","article-title":"Recombinant expression, purification, and characterization of polyphenol oxidase 2 (VvPPO2) from \u201cShine Muscat\u201d (Vitis labruscana Bailey \u00d7 Vitis vinifera L.)","volume":"81","author":"Katayama-ikegami","year":"2017","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"2026093004122664500_ref30","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2026093004122664500_ref31","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1093\/jmicro\/dfac018","article-title":"Improved chemical fixation of lipid-secreting plant cells for transmission electron microscopy","volume":"71","author":"Kiyoto","year":"2022","journal-title":"Microscopy"},{"key":"2026093004122664500_ref32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/molbev\/msae263","article-title":"MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing","volume":"41","author":"Kumar","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"2026093004122664500_ref33","doi-asserted-by":"publisher","first-page":"794","DOI":"10.3389\/fpls.2019.00794","article-title":"Evolutionary developments in plant specialized metabolism, exemplified by two transferase families","volume":"10","author":"Kusano","year":"2019","journal-title":"Front. Plant Sci."},{"key":"2026093004122664500_ref34","doi-asserted-by":"publisher","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"2026093004122664500_ref35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/dnares\/dsac016","article-title":"Inventory of ATP-binding cassette proteins in Lithospermum erythrorhizon as a model plant producing divergent secondary metabolites","volume":"29","author":"Li","year":"2022","journal-title":"DNA Res."},{"key":"2026093004122664500_ref36","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1007\/s00425-006-0300-6","article-title":"Involvement of AtLAC15 in lignin synthesis in seeds and in root elongation of Arabidopsis","volume":"224","author":"Liang","year":"2006","journal-title":"Planta"},{"key":"2026093004122664500_ref37","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1134\/S0026893306060094","article-title":"Molecular cloning and characterization of the polyphenol oxidase gene from sweetpotato 1","volume":"40","author":"Liao","year":"2006","journal-title":"Mol. Biol."},{"key":"2026093004122664500_ref38","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.molp.2017.01.003","article-title":"CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants","volume":"10","author":"Liu","year":"2017","journal-title":"Mol. Plant"},{"key":"2026093004122664500_ref39","doi-asserted-by":"publisher","first-page":"315","DOI":"10.5511\/plantbiotechnology.24.0303a","article-title":"Tracer experiment revealed that (E)-3\u2033-hydroxygeranylhydroquinone is not an intermediate of the shikonin\/alkannin and shikonofuran biosynthetic pathways in Lithospermum erythrorhizon","volume":"41","author":"Manabe","year":"2024","journal-title":"Plant Biotechnol. (Tokyo)."},{"key":"2026093004122664500_ref40","doi-asserted-by":"publisher","first-page":"2318","DOI":"10.1016\/j.phytochem.2006.08.006","article-title":"Polyphenol oxidases in plants and fungi: going places? A review","volume":"67","author":"Mayer","year":"2006","journal-title":"Phytochemistry"},{"key":"2026093004122664500_ref41","doi-asserted-by":"publisher","first-page":"5620","DOI":"10.1016\/j.cell.2024.08.027","article-title":"A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes","volume":"187","author":"Mehta","year":"2024","journal-title":"Cell"},{"key":"2026093004122664500_ref42","doi-asserted-by":"publisher","first-page":"4982","DOI":"10.1016\/S0021-9258(19)34072-4","article-title":"Sodium dodecyl sulfate activation of a plant polyphenoloxidase. Effect of sodium dodecyl sulfate on enzymatic and physical characteristics of purified broad bean polyphenoloxidase","volume":"265","author":"Moore","year":"1990","journal-title":"J. Biol. Chem."},{"key":"2026093004122664500_ref43","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12896-015-0162-8","article-title":"A simple and efficient seamless DNA cloning method using SLiCE from Escherichia coli laboratory strains and its application to SLiP site-directed mutagenesis","volume":"15","author":"Motohashi","year":"2015","journal-title":"BMC Biotechnol."},{"key":"2026093004122664500_ref44","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1271\/bbb.70216","article-title":"Improved gateway binary vectors: high-performance vectors for creation of fusion constructs in transgenic analysis of plants","volume":"71","author":"Nakagawa","year":"2007","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"2026093004122664500_ref45","doi-asserted-by":"publisher","first-page":"2843","DOI":"10.1093\/plphys\/kiae157","article-title":"Peroxisomal 4-coumaroyl-CoA ligases participate in shikonin production in Lithospermum erythrorhizon","volume":"195","author":"Nakanishi","year":"2024","journal-title":"Plant Physiol."},{"key":"2026093004122664500_ref46","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1126\/science.290.5494.1163","article-title":"Aureusidin synthase: a polyphenol oxidase homolog responsible for flower coloration","volume":"290","author":"Nakayama","year":"2000","journal-title":"Science"},{"key":"2026093004122664500_ref47","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/S0014-5793(01)02529-7","article-title":"Specificity analysis and mechanism of aurone synthesis catalyzed by aureusidin synthase, a polyphenol oxidase homolog responsible for flower coloration","volume":"499","author":"Nakayama","year":"2001","journal-title":"FEBS Lett."},{"key":"2026093004122664500_ref48","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.plaphy.2018.04.026","article-title":"Generation of \u03b1-solanine-free hairy roots of potato by CRISPR\/Cas9 mediated genome editing of the St16DOX gene","volume":"131","author":"Nakayasu","year":"2018","journal-title":"Plant Physiol. Biochem."},{"key":"2026093004122664500_ref49","doi-asserted-by":"publisher","first-page":"100447","DOI":"10.1016\/j.plgene.2024.100447","article-title":"The complete chloroplast genome sequence of Lithospermum erythrorhizon: insights into the phylogenetic relationship among Boraginaceae species and the material linages of purple gromwells","volume":"37","author":"Okada","year":"2024","journal-title":"Plant Gene"},{"key":"2026093004122664500_ref50","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1104\/pp.20.00207","article-title":"Two bahd acyltransferases catalyze the last step in the shikonin\/alkannin biosynthetic pathway","volume":"184","author":"Oshikiri","year":"2020","journal-title":"Plant Physiol."},{"key":"2026093004122664500_ref51","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1093\/pcp\/pcad158","article-title":"Comparative analysis of shikonin and alkannin acyltransferases reveals their functional conservation in Boraginaceae","volume":"65","author":"Oshikiri","year":"2024","journal-title":"Plant Cell Physiol."},{"key":"2026093004122664500_ref52","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1248\/bpb.21.366","article-title":"Study of the accelerating effect of shikonin and alkanine on the proliferation of granulation tissue in rat","volume":"21","author":"Ozaki","year":"1998","journal-title":"Biol. Pharm. Bull."},{"key":"2026093004122664500_ref53","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2026093004122664500_ref54","doi-asserted-by":"publisher","first-page":"2966","DOI":"10.1105\/tpc.105.035154","article-title":"TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat","volume":"17","author":"Pourcel","year":"2005","journal-title":"Plant Cell"},{"key":"2026093004122664500_ref56","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/1471-2229-9-69","article-title":"Isolation, identification and expression analysis of salt-induced genes in Suaeda maritima, a natural halophyte, using PCR-based suppression subtractive hybridization","volume":"9","author":"Sahu","year":"2009","journal-title":"BMC Plant Biol."},{"key":"2026093004122664500_ref57","doi-asserted-by":"publisher","first-page":"e0276041","DOI":"10.1371\/journal.pone.0276041","article-title":"Purification and characterization of novel isoforms of the polyphenol oxidase from Malus domestica fruit pulp","volume":"18","author":"Sajjad","year":"2023","journal-title":"PLoS One"},{"key":"2026093004122664500_ref58","doi-asserted-by":"publisher","first-page":"2392","DOI":"10.1248\/cpb.25.2392","article-title":"Antitumor activity of shikonin and its derivatives","volume":"25","author":"Sankawa","year":"1977","journal-title":"Chem. Pharm. Bull."},{"key":"2026093004122664500_ref59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1126\/sciadv.adf4166","article-title":"Solanoeclepin B, a hatching factor for potato cyst nematode","volume":"9","author":"Shimizu","year":"2023","journal-title":"Sci. Adv."},{"key":"2026093004122664500_ref60","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/B978-0-12-407695-2.00009-3","article-title":"New insights into the transport mechanisms in plant vacuoles","volume":"305","author":"Shitan","year":"2013","journal-title":"Intl. Rev. Cell Mol. Biol."},{"key":"2026093004122664500_ref61","doi-asserted-by":"publisher","first-page":"112375","DOI":"10.1016\/j.phytochem.2020.112375","article-title":"Potential role of two cytochrome P450s obtained from Lithospermum erythrorhizon in catalyzing the oxidation of geranylhydroquinone during shikonin biosynthesis","volume":"175","author":"Song","year":"2020","journal-title":"Phytochemistry"},{"key":"2026093004122664500_ref62","doi-asserted-by":"publisher","first-page":"2455","DOI":"10.1021\/acs.orglett.1c00360","article-title":"CYP82AR subfamily proteins catalyze C-1\u2032 hydroxylations of deoxyshikonin in the biosynthesis of shikonin and alkannin","volume":"23","author":"Song","year":"2021","journal-title":"Org. Lett."},{"key":"2026093004122664500_ref63","doi-asserted-by":"publisher","first-page":"783","DOI":"10.3389\/fpls.2014.00783","article-title":"Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism","volume":"5","author":"Sullivan","year":"2015","journal-title":"Front. Plant Sci."},{"key":"2026093004122664500_ref64","doi-asserted-by":"publisher","first-page":"uhab087","DOI":"10.1093\/hr\/uhab087","article-title":"Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis","volume":"9","author":"Suttiyut","year":"2022","journal-title":"Hortic. Res."},{"key":"2026093004122664500_ref65","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1021\/np50045a014","article-title":"A comparative study on anti-inflammatory activities of the enantiomers, shikonin and alkannin","volume":"49","author":"Tanaka","year":"1986","journal-title":"J. Nat. Prod."},{"key":"2026093004122664500_ref66","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/dnares\/dsab015","article-title":"Exploring the evolutionary process of alkanin\/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome","volume":"28","author":"Tang","year":"2021","journal-title":"DNA Res."},{"key":"2026093004122664500_ref67","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.3389\/fpls.2016.01066","article-title":"Characterization of shikonin derivative secretion in Lithospermum erythrorhizon hairy roots as a model of lipid-soluble metabolite secretion from plants","volume":"7","author":"Tatsumi","year":"2016","journal-title":"Front. Plant Sci."},{"key":"2026093004122664500_ref68","doi-asserted-by":"publisher","first-page":"39","DOI":"10.5511\/plantbiotechnology.19.1212a","article-title":"Highly efficient method of Lithospermum erythrorhizon transformation using domestic Rhizobium rhizogenes strain A13","volume":"37","author":"Tatsumi","year":"2020","journal-title":"Plant Biotechnol."},{"key":"2026093004122664500_ref69","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1093\/jxb\/erac405","article-title":"Excretion of triacylglycerol as a matrix lipid facilitating apoplastic accumulation of a lipophilic metabolite shikonin","volume":"74","author":"Tatsumi","year":"2023","journal-title":"J. Exp. Bot."},{"key":"2026093004122664500_ref70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-13-395","article-title":"The polyphenol oxidase gene family in land plants: lineage-specific duplication and expansion","volume":"13","author":"Tran","year":"2012","journal-title":"BMC Genomics"},{"key":"2026093004122664500_ref71","doi-asserted-by":"publisher","first-page":"1933","DOI":"10.1104\/pp.19.00999","article-title":"A cytosol-localized geranyl diphosphate synthase from Lithospermum erythrorhizon and its molecular evolution","volume":"182","author":"Ueoka","year":"2020","journal-title":"Plant Physiol."},{"key":"2026093004122664500_ref72","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/s41598-017-00501-4","article-title":"Rapid breeding of parthenocarpic tomato plants using CRISPR\/Cas9","volume":"7","author":"Ueta","year":"2017","journal-title":"Sci. Rep."},{"key":"2026093004122664500_ref73","doi-asserted-by":"publisher","first-page":"131958","DOI":"10.1016\/j.foodchem.2021.131958","article-title":"The unexpected flavone synthase-like activity of polyphenol oxidase in tomato","volume":"377","author":"Wei","year":"2022","journal-title":"Food Chem."},{"key":"2026093004122664500_ref74","doi-asserted-by":"publisher","first-page":"16046","DOI":"10.1038\/hortres.2016.46","article-title":"Biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants","volume":"3","author":"Widhalm","year":"2016","journal-title":"Hortic. Res."},{"key":"2026093004122664500_ref76","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1007\/PL00008139","article-title":"P-450 monooxygenase from Lithospermum erythrorhizon cell suspension cultures","volume":"210","author":"Yamamoto","year":"2000","journal-title":"Planta"},{"key":"2026093004122664500_ref77","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0378-4347(99)00473-9","article-title":"Simultaneous analysis of shikimate-derived secondary metabolites in Lithospermum erythrorhizon cell suspension cultures by high-performance liquid chromatography","volume":"738","author":"Yamamoto","year":"2000","journal-title":"J. Chromatogr. B. Biomed. Sci. Appl."},{"key":"2026093004122664500_ref78","doi-asserted-by":"publisher","first-page":"1798","DOI":"10.1093\/pcp\/pcaa108","article-title":"Alcohol dehydrogenase activity converts 3\u2033-hydroxygeranylhydroquinone to an aldehyde intermediate for shikonin and benzoquinone derivatives in Lithospermum erythrorhizon","volume":"61","author":"Yamamoto","year":"2020","journal-title":"Plant Cell Physiol."},{"key":"2026093004122664500_ref79","doi-asserted-by":"publisher","first-page":"3494","DOI":"10.1111\/j.1742-4658.2008.06496.x","article-title":"Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes","volume":"275","author":"Yamazaki","year":"2008","journal-title":"FEBS J."},{"key":"2026093004122664500_ref80","doi-asserted-by":"publisher","first-page":"131","DOI":"10.5511\/plantbiotechnology.17.0823a","article-title":"Lithospermum erythrorhizon cell cultures: present and future aspects","volume":"34","author":"Yazaki","year":"2017","journal-title":"Plant Biotechnol."},{"key":"2026093004122664500_ref81","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.1016\/0031-9422(94)00821-A","article-title":"Intracellular localization of UDPG: p-hydroxybenzoate glucosyltransferase and its reaction product in Lithospermum cell cultures","volume":"38","author":"Yazaki","year":"1995","journal-title":"Phytochemistry"},{"key":"2026093004122664500_ref82","doi-asserted-by":"publisher","first-page":"335","DOI":"10.5511\/plantbiotechnology.16.335","article-title":"Shikonin biosynthesis in Lithospermum erythrorhizon: light-induced negative regulation of secondary metabolism","volume":"16","author":"Yazaki","year":"1999","journal-title":"Plant Biotechnol."},{"key":"2026093004122664500_ref83","doi-asserted-by":"publisher","first-page":"6240","DOI":"10.1074\/jbc.M106387200","article-title":"Geranyl diphosphate:4-hydroxybenzoate geranyltransferase from Lithospermum erythrorhizon. Cloning and characterization of a key enzyme in shikonin biosynthesis","volume":"277","author":"Yazaki","year":"2002","journal-title":"J. Biol. Chem."},{"key":"2026093004122664500_ref84","doi-asserted-by":"publisher","first-page":"1615","DOI":"10.1093\/pcp\/pcx123","article-title":"\u201cHidden\u201d terpenoids in plants: their biosynthesis, localisation and ecological roles","volume":"58","author":"Yazaki","year":"2017","journal-title":"Plant Cell Physiol."},{"key":"2026093004122664500_ref85","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1111\/j.1745-4514.2003.tb00289.x","article-title":"Physicochemical properties and function of plant polyphenol oxidase: a review","volume":"27","author":"Yoruk","year":"2003","journal-title":"J. Food Biochem."},{"key":"2026093004122664500_ref86","doi-asserted-by":"publisher","first-page":"108842","DOI":"10.1016\/j.foodres.2019.108842","article-title":"Transformation of catechins into thea flavins by upregulation of CsPPO3 in preharvest tea (Camellia sinensis) leaves exposed to shading treatment","volume":"129","author":"Yu","year":"2020","journal-title":"Food Res. Int."},{"key":"2026093004122664500_ref87","doi-asserted-by":"publisher","first-page":"e61247","DOI":"10.1371\/journal.pone.0061247","article-title":"Gene silencing of BnTT10 family genes causes retarded pigmentation and lignin reduction in the seed coat of Brassica napus","volume":"8","author":"Zhang","year":"2013","journal-title":"PLoS One"},{"key":"2026093004122664500_ref88","doi-asserted-by":"publisher","first-page":"26936","DOI":"10.1021\/acs.jafc.5c03738","article-title":"Polyphenol oxidase from Dendrobium officinale flowers: characterization and browning-promoting mechanism","volume":"73","author":"Zhong","year":"2025","journal-title":"J. Agric. Food Chem."}],"container-title":["Plant and Cell Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/pcp\/advance-article-pdf\/doi\/10.1093\/pcp\/pcag074\/68431765\/pcag074.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/pcp\/article-pdf\/67\/9\/1557\/71498898\/pcag074.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/pcp\/article-pdf\/67\/9\/1557\/71498898\/pcag074.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:12:38Z","timestamp":1790755958000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/pcp\/article\/67\/9\/1557\/8698015"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,29]]},"references-count":85,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,5,29]]},"published-print":{"date-parts":[[2026,9,29]]}},"URL":"https:\/\/doi.org\/10.1093\/pcp\/pcag074","relation":{},"ISSN":["0032-0781","1471-9053"],"issn-type":[{"value":"0032-0781","type":"print"},{"value":"1471-9053","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,5,29]]}}}