Entry Steps in the Biosynthetic Pathway to Diterpenoid Alkaloids in Delphinium grandiflorum and Aconitum plicatum

. 2025 May 17 ; () : . [epub] 20250517

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic

Typ dokumentu časopisecké články, preprinty

Perzistentní odkaz   https://www.medvik.cz/link/pmid40463143

Grantová podpora
T32 GM110523 NIGMS NIH HHS - United States

Roots from the Aconitum (Wolf's-Bane) and Delphinium (Larkspur) genera have been widely used in traditional medicine owing to the abundance of bioactive diterpenoid alkaloids that they produce. Despite extensive research on these compounds and their potential medicinal applications, their structural complexity precludes their production through total chemical synthesis, and little progress has been made towards elucidation of their biosynthetic pathways. Here, we report the entry steps in the biosynthesis of the diterpenoid alkaloid atisinium, constituting six enzymes identified from the Siberian Larkspur (Delphinium grandiflorum) and garden monkshood (Aconitum plicatum) through a combination of comparative transcriptomics between tissue types and genera and coexpression analysis. This pathway includes a pair of terpene synthases, three cytochromes P450, and a reductase with little homology to other characterized enzymes. We further demonstrate, through incorporation of isotopically labelled substrates, the preference of the reductase for ethanolamine over ethylamine, and similarly that ethanolamine is the preferred source of nitrogen for the majority of detected diterpenoid alkaloids. Identification of these enzymes and production of a key intermediate in a heterologous host paves the way for biosynthetic production of this group of metabolites with promise for medicinal applications.

Zobrazit více v PubMed

Li F.-S.; Weng J.-K. Demystifying Traditional Herbal Medicine with Modern Approach. Nat. Plants 2017, 3 (8), 1–7. 10.1038/nplants.2017.109. PubMed DOI

Alternative sources and metabolic engineering of Taxol: Advances and future perspectives - ScienceDirect. https://www.sciencedirect.com/science/article/pii/S0734975020300665?casa_token=iBcjS8xspLYAAAAA:APTC3Qe63H7BKmM53FMDx2xfMN6pJ_-F-SQOx61BvQYgYXstDi0Xh0fkNQi3kT1s41LYuAnhNyI (accessed 2025–01-02). PubMed

Huang Y.; Yang Y.; Liu G.; Xu M. New Clinical Application Prospects of Artemisinin and Its Derivatives: A Scoping Review. Infect. Dis. Poverty 2023, 12 (1), 115. 10.1186/s40249-023-01152-6. PubMed DOI PMC

Galanie S.; Thodey K.; Trenchard I. J.; Filsinger Interrante M.; Smolke C. D. Complete Biosynthesis of Opioids in Yeast. Science 2015, 349 (6252), 1095–1100. 10.1126/science.aac9373. PubMed DOI PMC

Nett R. S.; Lau W.; Sattely E. S. Discovery and Engineering of Colchicine Alkaloid Biosynthesis. Nature 2020, 584 (7819), 148–153. 10.1038/s41586-020-2546-8. PubMed DOI PMC

Bedewitz M. A.; Jones A. D.; D’Auria J. C.; Barry C. S. Tropinone Synthesis via an Atypical Polyketide Synthase and P450-Mediated Cyclization. Nat. Commun. 2018, 9, 5281. 10.1038/s41467-018-07671-3. PubMed DOI PMC

Wrenbeck E. E.; Bedewitz M. A.; Klesmith J. R.; Noshin S.; Barry C. S.; Whitehead T. A. An Automated Data-Driven Pipeline for Improving Heterologous Enzyme Expression. ACS Synth. Biol. 2019, 8 (3), 474–481. 10.1021/acssynbio.8b00486. PubMed DOI PMC

Biosynthesis of medicinal tropane alkaloids in yeast | Nature. https://www.nature.com/articles/s41586-020-2650-9 (accessed 2024–12-05). PubMed PMC

Pan Q.; Mustafa N. R.; Tang K.; Choi Y. H.; Verpoorte R. Monoterpenoid Indole Alkaloids Biosynthesis and Its Regulation in Catharanthus Roseus: A Literature Review from Genes to Metabolites. Phytochem. Rev. 2016, 15 (2), 221–250. 10.1007/s11101-015-9406-4. DOI

Caputi L.; Franke J.; Farrow S. C.; Chung K.; Payne R. M. E.; Nguyen T.-D.; Dang T.-T. T.; Soares Teto Carqueijeiro I.; Koudounas K.; Dugé de Bernonville T.; Ameyaw B.; Jones D. M.; Vieira I. J. C.; Courdavault V.; O’Connor S. E. Missing Enzymes in the Biosynthesis of the Anticancer Drug Vinblastine in Madagascar Periwinkle. Science 2018, 360 (6394), 1235–1239. 10.1126/science.aat4100. PubMed DOI

Qu Y.; Safonova O.; De Luca V. Completion of the Canonical Pathway for Assembly of Anticancer Drugs Vincristine/Vinblastine in Catharanthus Roseus. Plant J. 2019, 97 (2), 257–266. 10.1111/tpj.14111. PubMed DOI

The alkaloids of species of Garrya. I. Isolation of alkaloids - ScienceDirect. https://www.sciencedirect.com/science/article/abs/pii/S0095955315310581?via%3Dihub (accessed 2024–12-05).

Ma Y.; Mao X.-Y.; Huang L.-J.; Fan Y.-M.; Gu W.; Yan C.; Huang T.; Zhang J.-X.; Yuan C.-M.; Hao X.-J. Diterpene Alkaloids and Diterpenes from Spiraea Japonica and Their Anti-Tobacco Mosaic Virus Activity. Fitoterapia 2016, 109, 8–13. 10.1016/j.fitote.2015.11.019. PubMed DOI

Hart N.; Johns S.; Lamberton J.; Suares H.; Willing R. New Alkaloids of the Ent-Kaurene Type From Anopterus Species (Escalloniaceae). I. The Structure and Reactions of Anopterine. Aust. J. Chem. 1976, 29 (6), 1295–1318. 10.1071/ch9761295. DOI

Yin T.; Cai L.; Ding Z. An Overview of the Chemical Constituents from the Genus Delphinium Reported in the Last Four Decades. RSC Adv. 2020, 10 (23), 13669–13686. 10.1039/D0RA00813C. PubMed DOI PMC

Nyirimigabo E.; Xu Y.; Li Y.; Wang Y.; Agyemang K.; Zhang Y. A Review on Phytochemistry, Pharmacology and Toxicology Studies of Aconitum. J. Pharm. Pharmacol. 2015, 67 (1), 1–19. 10.1111/JPHP.12310. PubMed DOI

Xu J.-B.; Li Y.-Z.; Huang S.; Chen L.; Luo Y.-Y.; Gao F.; Zhou X.-L. Diterpenoid Alkaloids from the Whole Herb of Delphinium Grandiflorum L. Phytochemistry 2021, 190, 112866. 10.1016/j.phytochem.2021.112866. PubMed DOI

Li Y.; Gao F.; Zhang J.-F.; Zhou X.-L. Four New Diterpenoid Alkaloids from the Roots of Aconitum Carmichaelii. Chem. Biodivers. 2018, 15 (7), e1800147. 10.1002/cbdv.201800147. PubMed DOI

Yamashita H.; Takeda K.; Haraguchi M.; Abe Y.; Kuwahara N.; Suzuki S.; Terui A.; Masaka T.; Munakata N.; Uchida M.; Nunokawa M.; Kaneda K.; Goto M.; Lee K.-H.; Wada K. Four New Diterpenoid Alkaloids from Aconitum Japonicum Subsp. Subcuneatum. J. Nat. Med. 2018, 72 (1), 230–237. 10.1007/s11418-017-1139-9. PubMed DOI

Yin T.-P.; Cai L.; Fang H.-X.; Fang Y.-S.; Li Z.-J.; Ding Z.-T. Diterpenoid Alkaloids from Aconitum Vilmorinianum. Phytochemistry 2015, 116, 314–319. 10.1016/j.phytochem.2015.05.002. PubMed DOI

Csupor D.; Wenzig E. M.; Zupkó I.; Wölkart K.; Hohmann J.; Bauer R. Qualitative and Quantitative Analysis of Aconitine-Type and Lipo-Alkaloids of Aconitum Carmichaelii Roots. J. Chromatogr. A 2009, 1216 (11), 2079–2086. 10.1016/j.chroma.2008.10.082. PubMed DOI

Zhou G.; Tang L.; Zhou X.; Wang T.; Kou Z.; Wang Z. A Review on Phytochemistry and Pharmacological Activities of the Processed Lateral Root of Aconitum Carmichaelii Debeaux. J. Ethnopharmacol. 2015, 160, 173–193. 10.1016/j.jep.2014.11.043. PubMed DOI

Wangchuk P.; Bremner J. B.; Samten; Skelton B. W.; White A. H.; Rattanajak R.; Kamchonwongpaisan S. Antiplasmodial Activity of Atisinium Chloride from the Bhutanese Medicinal Plant, Aconitum Orochryseum. J. Ethnopharmacol. 2010, 130 (3), 559–562. 10.1016/j.jep.2010.05.057. PubMed DOI

Shen Y.; Liang W. J.; Shi Y. N.; Kennelly E. J.; Zhao D. K. Structural Diversity, Bioactivities, and Biosynthesis of Natural Diterpenoid Alkaloids†. Nat. Prod. Rep. 2020, 37 (6), 763–796. 10.1039/d0np00002g. PubMed DOI

Liu X.-Y.; Wang F.-P.; Qin Y. Synthesis of Three-Dimensionally Fascinating Diterpenoid Alkaloids and Related Diterpenes. Acc. Chem. Res. 2021, 54 (1), 22–34. 10.1021/acs.accounts.0c00720. PubMed DOI

Gong J.; Chen H.; Liu X.-Y.; Wang Z.-X.; Nie W.; Qin Y. Total Synthesis of Atropurpuran. Nat. Commun. 2016, 7 (1), 12183. 10.1038/ncomms12183. PubMed DOI PMC

Owens K. R.; McCowen S. V.; Blackford K. A.; Ueno S.; Hirooka Y.; Weber M.; Sarpong R. Total Synthesis of the Diterpenoid Alkaloid Arcutinidine Using a Strategy Inspired by Chemical Network Analysis. J. Am. Chem. Soc. 2019, 141 (35), 13713–13717. 10.1021/jacs.9b05815. PubMed DOI PMC

Pang L.; Liu C.-Y.; Gong G.-H.; Quan Z.-S. Synthesis, in Vitro and in Vivo Biological Evaluation of Novel Lappaconitine Derivatives as Potential Anti-Inflammatory Agents. Acta Pharm. Sin. B 2020, 10 (4), 628–645. 10.1016/j.apsb.2019.09.002. PubMed DOI PMC

Cherney E. C.; Baran P. S. Terpenoid-Alkaloids: Their Biosynthetic Twist of Fate and Total Synthesis. Isr. J. Chem. 2011, 51 (3–4), 391–405. 10.1002/ijch.201100005. PubMed DOI PMC

Zhou R.-J.; Dai G.-Y.; Zhou X.-H.; Zhang M.-J.; Wu P.-Z.; Zhang D.; Song H.; Liu X.-Y.; Qin Y. Progress towards the Synthesis of Aconitine: Construction of the AE Fragment and Attempts to Access the Pentacyclic Core. Org. Chem. Front. 2019, 6 (3), 377–382. 10.1039/C8QO01228H. DOI

Li Y.-G.; Mou F.-J.; Li K.-Z. De Novo RNA Sequencing and Analysis Reveal the Putative Genes Involved in Diterpenoid Biosynthesis in Aconitum Vilmorinianum Roots. 3 Biotech 2021, 11 (2), 96. 10.1007/s13205-021-02646-6. PubMed DOI PMC

Pal T.; Malhotra N.; Chanumolu S. K.; Chauhan R. S. Next-Generation Sequencing (NGS) Transcriptomes Reveal Association of Multiple Genes and Pathways Contributing to Secondary Metabolites Accumulation in Tuberous Roots of Aconitum Heterophyllum Wall. Planta 2015, 242 (1), 239–258. 10.1007/S00425-015-2304-6/FIGURES/11. PubMed DOI

Rai M.; Rai A.; Kawano N.; Yoshimatsu K.; Takahashi H.; Suzuki H.; Kawahara N.; Saito K.; Yamazaki M. De Novo RNA Sequencing and Expression Analysis of Aconitum Carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids. Mol. J. Synth. Chem. Nat. Prod. Chem. 2017, 22 (12). 10.3390/MOLECULES22122155. PubMed DOI PMC

Yang Y.; Hu P.; Zhou X.; Wu P.; Si X.; Lu B.; Zhu Y.; Xia Y. Transcriptome Analysis of Aconitum Carmichaelii and Exploration of the Salsolinol Biosynthetic Pathway. Fitoterapia 2020, 140. 10.1016/J.FITOTE.2019.104412. PubMed DOI

Zhao D.; Shen Y.; Shi Y.; Shi X.; Qiao Q.; Zi S.; Zhao E.; Yu D.; Kennelly E. J. Probing the Transcriptome of Aconitum Carmichaelii Reveals the Candidate Genes Associated with the Biosynthesis of the Toxic Aconitine-Type C19-Diterpenoid Alkaloids. Phytochemistry 2018, 152, 113–124. 10.1016/j.phytochem.2018.04.022. PubMed DOI

Mao L.; Jin B.; Chen L.; Tian M.; Ma R.; Yin B.; Zhang H.; Guo J.; Tang J.; Chen T.; Lai C.; Cui G.; Huang L. Functional Identification of the Terpene Synthase Family Involved in Diterpenoid Alkaloids Biosynthesis in Aconitum Carmichaelii. Acta Pharm. Sin. B 2021. 10.1016/J.APSB.2021.04.008. PubMed DOI PMC

Hong Y. J.; Tantillo D. J. Formation of Beyerene, Kaurene, Trachylobane, and Atiserene Diterpenes by Rearrangements That Avoid Secondary Carbocations. J. Am. Chem. Soc. 2010, 132 (15), 5375–5386. 10.1021/ja9084786. PubMed DOI

Andersen-Ranberg J.; Kongstad K. T.; Nielsen M. T.; Jensen N. B.; Pateraki I.; Bach S. S.; Hamberger B.; Zerbe P.; Staerk D.; Bohlmann J.; Møller B. L.; Hamberger B. Expanding the Landscape of Diterpene Structural Diversity through Stereochemically Controlled Combinatorial Biosynthesis. Angew. Chem. - Int. Ed. 2016, 55 (6), 2142–2146. 10.1002/anie.201510650. PubMed DOI PMC

Johnson S. R.; Bhat W. W.; Bibik J.; Turmo A.; Hamberger B.; Hamberger B. A Database-Driven Approach Identifies Additional Diterpene Synthase Activities in the Mint Family (Lamiaceae). J. Biol. Chem. 2019, 294 (4), 1349–1362. 10.1074/jbc.RA118.006025. PubMed DOI PMC

Jin B.; Cui G.; Guo J.; Tang J.; Duan L.; Lin H.; Shen Y.; Chen T.; Zhang H.; Huang L. Functional Diversification of Kaurene Synthase-Like Genes in Isodon Rubescens. Plant Physiol. 2017, 174 (2), 943–955. 10.1104/pp.17.00202. PubMed DOI PMC

Grennan A. K. Gibberellin Metabolism Enzymes in Rice. Plant Physiol. 2006, 141 (2), 524–526. 10.1104/pp.104.900192. PubMed DOI PMC

Kong H.; Zhang Y.; Hong Y.; Barker M. S. Multilocus Phylogenetic Reconstruction Informing Polyploid Relationships of Aconitum Subgenus Lycoctonum (Ranunculaceae) in China. Plant Syst. Evol. 2017, 303 (6), 727–744. 10.1007/s00606-017-1406-y. DOI

Park S.; An B.; Park S. Recurrent Gene Duplication in the Angiosperm Tribe Delphinieae (Ranunculaceae) Inferred from Intracellular Gene Transfer Events and Heteroplasmic Mutations in the Plastid matK Gene. Sci. Rep. 2020, 10 (1), 2720. 10.1038/s41598-020-59547-6. PubMed DOI PMC

Salvado P.; Aymerich Boixader P.; Parera J.; Vila Bonfill A.; Martin M.; Quélennec C.; Lewin J.-M.; Delorme-Hinoux V.; Bertrand J. A. M. Little Hope for the Polyploid Endemic Pyrenean Larkspur (Delphinium Montanum): Evidences from Population Genomics and Ecological Niche Modeling. Ecol. Evol. 2022, 12 (3), e8711. 10.1002/ece3.8711. PubMed DOI PMC

Nelson D.; Werck-Reichhart D. A P450-Centric View of Plant Evolution. Plant J. 2011, 66 (1), 194–211. 10.1111/j.1365-313X.2011.04529.x. PubMed DOI

Lichman B. R. The Scaffold-Forming Steps of Plant Alkaloid Biosynthesis. Nat. Prod. Rep. 2021, 38 (1), 103–129. 10.1039/D0NP00031K. PubMed DOI

Bai P.; Wang L.; Wei K.; Ruan L.; Wu L.; He M.; Ni D.; Cheng H. Biochemical Characterization of Specific Alanine Decarboxylase (AlaDC) and Its Ancestral Enzyme Serine Decarboxylase (SDC) in Tea Plants (Camellia Sinensis). BMC Biotechnol. 2021, 21 (1), 17. 10.1186/s12896-021-00674-x. PubMed DOI PMC

Zhao P.-J.; Gao S.; Fan L.-M.; Nie J.-L.; He H.-P.; Zeng Y.; Shen Y.-M.; Hao X.-J. Approach to the Biosynthesis of Atisine-Type Diterpenoid Alkaloids. J. Nat. Prod. 2009, 72 (4), 645–649. 10.1021/np800657j. PubMed DOI

Dührkop K.; Fleischauer M.; Ludwig M.; Aksenov A. A.; Melnik A. V.; Meusel M.; Dorrestein P. C.; Rousu J.; Böcker S. SIRIUS 4: A Rapid Tool for Turning Tandem Mass Spectra into Metabolite Structure Information. Nat. Methods 2019, 16 (4), 299–302. 10.1038/s41592-019-0344-8. PubMed DOI

Ludwig M.; Nothias L.-F.; Dührkop K.; Koester I.; Fleischauer M.; Hoffmann M. A.; Petras D.; Vargas F.; Morsy M.; Aluwihare L.; Dorrestein P. C.; Böcker S. Database-Independent Molecular Formula Annotation Using Gibbs Sampling through ZODIAC. Nat. Mach. Intell. 2020, 2 (10), 629–641. 10.1038/s42256-020-00234-6. DOI

Dührkop K.; Shen H.; Meusel M.; Rousu J.; Böcker S. Searching Molecular Structure Databases with Tandem Mass Spectra Using CSI:FingerID. Proc. Natl. Acad. Sci. 2015, 112 (41), 12580–12585. 10.1073/pnas.1509788112. PubMed DOI PMC

Dührkop K.; Nothias L.-F.; Fleischauer M.; Reher R.; Ludwig M.; Hoffmann M. A.; Petras D.; Gerwick W. H.; Rousu J.; Dorrestein P. C.; Böcker S. Systematic Classification of Unknown Metabolites Using High-Resolution Fragmentation Mass Spectra. Nat. Biotechnol. 2021, 39 (4), 462–471. 10.1038/s41587-020-0740-8. PubMed DOI

Schmidt H.-L.; Werner R. A.; Eisenreich W. Systematics of 2H Patterns in Natural Compounds and Its Importance for the Elucidation of Biosynthetic Pathways. Phytochem. Rev. 2003, 2 (1–2), 61–85. 10.1023/B:PHYT.0000004185.92648.ae. DOI

Waller G. R.; Burström H. Diterpenoid Alkaloids as Plant Growth Inhibitors. Nature 1969, 222 (5193), 576–578. 10.1038/222576a0. DOI

Bosch i Daniel M.; Simon Pallisé J.; López i Pujol J.; Blanché i Vergés C. DCDB: An Updated on-Line Database of Chromosome Numbers of Tribe Delphinieae (Ranunculaceae). 2016.

Mitka J.; Sutkowska A.; Ilnicki T.; Joachimiak A. Reticulate Evolution of High-Alpine Aconitum (Ranunculaceae) in the Eastern Sudetes and Western Carpathians (Central Europe). Acta Biol. Cracoviensia Ser. Bot. 2007, 49, 15–26.

Molero J.; Rovira A. M.; Bosch M.; Simon J.; Blanché C. Karyological Study of the Genus Aconitum (Ranunculacae) in the W Mediterranean Area. Flora Mediterr. 2016, 26, 229–239. 10.7320/FlMedit26.229. DOI

Morrone D.; Chen X.; Coates R. M.; Peters R. J. Characterization of the Kaurene Oxidase CYP701A3, a Multifunctional Cytochrome P450 from Gibberellin Biosynthesis. Biochem. J. 2010, 431 (3), 337–347. 10.1042/BJ20100597. PubMed DOI

Prisic S.; Xu M.; Wilderman P. R.; Peters R. J. Rice Contains Two Disparate Ent-Copalyl Diphosphate Synthases with Distinct Metabolic Functions. Plant Physiol. 2004, 136 (4), 4228–4236. 10.1104/pp.104.050567. PubMed DOI PMC

Harris L. J.; Saparno A.; Johnston A.; Prisic S.; Xu M.; Allard S.; Kathiresan A.; Ouellet T.; Peters R. J. The Maize An2 Gene Is Induced by Fusarium Attack and Encodesan Ent-Copalyl Diphosphate Synthase. Plant Mol. Biol. 2005, 59 (6), 881–894. 10.1007/s11103-005-1674-8. PubMed DOI

Kumar S.; Stecher G.; Suleski M.; Hedges S. B. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol. Biol. Evol. 2017, 34 (7), 1812–1819. 10.1093/molbev/msx116. PubMed DOI

Pateraki I.; Andersen-Ranberg J.; Jensen N. B.; Wubshet S. G.; Heskes A. M.; Forman V.; Hallström B.; Hamberger B.; Motawia M. S.; Olsen C. E.; Staerk D.; Hansen J.; Møller B. L.; Hamberger B. Total Biosynthesis of the Cyclic AMP Booster Forskolin from Coleus Forskohlii. eLife 2017, 6, e23001. 10.7554/eLife.23001. PubMed DOI PMC

Miller G. P.; Bhat W. W.; Lanier E. R.; Johnson S. R.; Mathieu D. T.; Hamberger B. The Biosynthesis of the Anti-Microbial Diterpenoid Leubethanol in Leucophyllum Frutescens Proceeds via an All-Cis Prenyl Intermediate. Plant J. 2020, 104 (3), 693–705. 10.1111/tpj.14957. PubMed DOI PMC

Grabherr M. G.; Haas B. J.; Yassour M.; Levin J. Z.; Thompson D. A.; Amit I.; Adiconis X.; Fan L.; Raychowdhury R.; Zeng Q.; Chen Z.; Mauceli E.; Hacohen N.; Gnirke A.; Rhind N.; di Palma F.; Birren B. W.; Nusbaum C.; Lindblad-Toh K.; Friedman N.; Regev A. Full-Length Transcriptome Assembly from RNA-Seq Data without a Reference Genome. Nat. Biotechnol. 2011, 29 (7), 644–652. 10.1038/nbt.1883. PubMed DOI PMC

Haas B. J. TransDecoder, 2025. https://github.com/TransDecoder/TransDecoder.

Li W.; Godzik A. Cd-Hit: A Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences. Bioinformatics 2006, 22 (13), 1658–1659. 10.1093/bioinformatics/btl158. PubMed DOI

Fu L.; Niu B.; Zhu Z.; Wu S.; Li W. CD-HIT: Accelerated for Clustering the next-Generation Sequencing Data. Bioinformatics 2012, 28 (23), 3150–3152. 10.1093/bioinformatics/bts565. PubMed DOI PMC

Patro R.; Duggal G.; Love M. I.; Irizarry R. A.; Kingsford C. Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression. Nat. Methods 2017, 14 (4), 417–419. 10.1038/nmeth.4197. PubMed DOI PMC

Altschul S. F.; Gish W.; Miller W.; Myers E. W.; Lipman D. J. Basic Local Alignment Search Tool. J. Mol. Biol. 1990, 215 (3), 403–410. 10.1016/S0022-2836(05)80360-2. PubMed DOI

Shannon P.; Markiel A.; Ozier O.; Baliga N. S.; Wang J. T.; Ramage D.; Amin N.; Schwikowski B.; Ideker T. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res. 2003, 13 (11), 2498–2504. 10.1101/gr.1239303. PubMed DOI PMC

Sievers F.; Wilm A.; Dineen D.; Gibson T. J.; Karplus K.; Li W.; Lopez R.; McWilliam H.; Remmert M.; Söding J.; Thompson J. D.; Higgins D. G. Fast, Scalable Generation of High-quality Protein Multiple Sequence Alignments Using Clustal Omega. Mol. Syst. Biol. 2011, 7 (1), 539. 10.1038/msb.2011.75. PubMed DOI PMC

Stamatakis A. RAxML Version 8: A Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 2014, 30 (9), 1312–1313. 10.1093/bioinformatics/btu033. PubMed DOI PMC

Wisecaver J. H.; Borowsky A. T.; Tzin V.; Jander G.; Kliebenstein D. J.; Rokas A. A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. Plant Cell 2017, 29 (5), 944–959. 10.1105/TPC.17.00009. PubMed DOI PMC

Sainsbury F.; Thuenemann E. C.; Lomonossoff G. P. pEAQ: Versatile Expression Vectors for Easy and Quick Transient Expression of Heterologous Proteins in Plants. Plant Biotechnol. J. 2009, 7 (7), 682–693. 10.1111/j.1467-7652.2009.00434.x. PubMed DOI

Adusumilli R.; Mallick P. Data Conversion with ProteoWizard msConvert. In Proteomics: Methods and Protocols; Comai L., Katz J. E., Mallick P., Eds.; Springer: New York, NY, 2017; pp 339–368. 10.1007/978-1-4939-6747-6_23. PubMed DOI

Chambers M. C.; Maclean B.; Burke R.; Amodei D.; Ruderman D. L.; Neumann S.; Gatto L.; Fischer B.; Pratt B.; Egertson J.; Hoff K.; Kessner D.; Tasman N.; Shulman N.; Frewen B.; Baker T. A.; Brusniak M.-Y.; Paulse C.; Creasy D.; Flashner L.; Kani K.; Moulding C.; Seymour S. L.; Nuwaysir L. M.; Lefebvre B.; Kuhlmann F.; Roark J.; Rainer P.; Detlev S.; Hemenway T.; Huhmer A.; Langridge J.; Connolly B.; Chadick T.; Holly K.; Eckels J.; Deutsch E. W.; Moritz R. L.; Katz J. E.; Agus D. B.; MacCoss M.; Tabb D. L.; Mallick P. A Cross-Platform Toolkit for Mass Spectrometry and Proteomics. Nat. Biotechnol. 2012, 30 (10), 918–920. 10.1038/nbt.2377. PubMed DOI PMC

Integrative analysis of multimodal mass spectrometry data in MZmine 3 | Nature Biotechnology. https://www.nature.com/articles/s41587-023-01690-2 (accessed 2025–01-23). PubMed PMC

Zuntini A. R.; Carruthers T.; Maurin O.; Bailey P. C.; Leempoel K.; Brewer G. E.; Epitawalage N.; Françoso E.; Gallego-Paramo B.; McGinnie C.; Negrão R.; Roy S. R.; Simpson L.; Toledo Romero E.; Barber V. M. A.; Botigué L.; Clarkson J. J.; Cowan R. S.; Dodsworth S.; Johnson M. G.; Kim J. T.; Pokorny L.; Wickett N. J.; Antar G. M.; DeBolt L.; Gutierrez K.; Hendriks K. P.; Hoewener A.; Hu A.-Q.; Joyce E. M.; Kikuchi I. A. B. S.; Larridon I.; Larson D. A.; De Lírio E. J.; Liu J.-X.; Malakasi P.; Przelomska N. A. S.; Shah T.; Viruel J.; Allnutt T. R.; Ameka G. K.; Andrew R. L.; Appelhans M. S.; Arista M.; Ariza M. J.; Arroyo J.; Arthan W.; Bachelier J. B.; Bailey C. D.; Barnes H. F.; Barrett M. D.; Barrett R. L.; Bayer R. J.; Bayly M. J.; Biffin E.; Biggs N.; Birch J. L.; Bogarín D.; Borosova R.; Bowles A. M. C.; Boyce P. C.; Bramley G. L. C.; Briggs M.; Broadhurst L.; Brown G. K.; Bruhl J. J.; Bruneau A.; Buerki S.; Burns E.; Byrne M.; Cable S.; Calladine A.; Callmander M. W.; Cano Á.; Cantrill D. J.; Cardinal-McTeague W. M.; Carlsen M. M.; Carruthers A. J. A.; De Castro Mateo A.; Chase M. W.; Chatrou L. W.; Cheek M.; Chen S.; Christenhusz M. J. M.; Christin P.-A.; Clements M. A.; Coffey S. C.; Conran J. G.; Cornejo X.; Couvreur T. L. P.; Cowie I. D.; Csiba L.; Darbyshire I.; Davidse G.; Davies N. M. J.; Davis A. P.; Van Dijk K.; Downie S. R.; Duretto M. F.; Duvall M. R.; Edwards S. L.; Eggli U.; Erkens R. H. J.; Escudero M.; De La Estrella M.; Fabriani F.; Fay M. F.; Ferreira P. D. L.; Ficinski S. Z.; Fowler R. M.; Frisby S.; Fu L.; Fulcher T.; Galbany-Casals M.; Gardner E. M.; German D. A.; Giaretta A.; Gibernau M.; Gillespie L. J.; González C. C.; Goyder D. J.; Graham S. W.; Grall A.; Green L.; Gunn B. F.; Gutiérrez D. G.; Hackel J.; Haevermans T.; Haigh A.; Hall J. C.; Hall T.; Harrison M. J.; Hatt S. A.; Hidalgo O.; Hodkinson T. R.; Holmes G. D.; Hopkins H. C. F.; Jackson C. J.; James S. A.; Jobson R. W.; Kadereit G.; Kahandawala I. M.; Kainulainen K.; Kato M.; Kellogg E. A.; King G. J.; Klejevskaja B.; Klitgaard B. B.; Klopper R. R.; Knapp S.; Koch M. A.; Leebens-Mack J. H.; Lens F.; Leon C. J.; Léveillé-Bourret É.; Lewis G. P.; Li D.-Z.; Li L.; Liede-Schumann S.; Livshultz T.; Lorence D.; Lu M.; Lu-Irving P.; Luber J.; Lucas E. J.; Luján M.; Lum M.; Macfarlane T. D.; Magdalena C.; Mansano V. F.; Masters L. E.; Mayo S. J.; McColl K.; McDonnell A. J.; McDougall A. E.; McLay T. G. B.; McPherson H.; Meneses R. I.; Merckx V. S. F. T.; Michelangeli F. A.; Mitchell J. D.; Monro A. K.; Moore M. J.; Mueller T. L.; Mummenhoff K.; Munzinger J.; Muriel P.; Murphy D. J.; Nargar K.; Nauheimer L.; Nge F. J.; Nyffeler R.; Orejuela A.; Ortiz E. M.; Palazzesi L.; Peixoto A. L.; Pell S. K.; Pellicer J.; Penneys D. S.; Perez-Escobar O. A.; Persson C.; Pignal M.; Pillon Y.; Pirani J. R.; Plunkett G. M.; Powell R. F.; Prance G. T.; Puglisi C.; Qin M.; Rabeler R. K.; Rees P. E. J.; Renner M.; Roalson E. H.; Rodda M.; Rogers Z. S.; Rokni S.; Rutishauser R.; De Salas M. F.; Schaefer H.; Schley R. J.; Schmidt-Lebuhn A.; Shapcott A.; Al-Shehbaz I.; Shepherd K. A.; Simmons M. P.; Simões A. O.; Simões A. R. G.; Siros M.; Smidt E. C.; Smith J. F.; Snow N.; Soltis D. E.; Soltis P. S.; Soreng R. J.; Sothers C. A.; Starr J. R.; Stevens P. F.; Straub S. C. K.; Struwe L.; Taylor J. M.; Telford I. R. H.; Thornhill A. H.; Tooth I.; Trias-Blasi A.; Udovicic F.; Utteridge T. M. A.; Del Valle J. C.; Verboom G. A.; Vonow H. P.; Vorontsova M. S.; De Vos J. M.; Al-Wattar N.; Waycott M.; Welker C. A. D.; White A. J.; Wieringa J. J.; Williamson L. T.; Wilson T. C.; Wong S. Y.; Woods L. A.; Woods R.; Worboys S.; Xanthos M.; Yang Y.; Zhang Y.-X.; Zhou M.-Y.; Zmarzty S.; Zuloaga F. O.; Antonelli A.; Bellot S.; Crayn D. M.; Grace O. M.; Kersey P. J.; Leitch I. J.; Sauquet H.; Smith S. A.; Eiserhardt W. L.; Forest F.; Baker W. J. Phylogenomics and the Rise of the Angiosperms. Nature 2024, 629 (8013), 843–850. 10.1038/s41586-024-07324-0. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...