†Co-first authors; *Co-corresponding authors; Weng Lab member names are bolded.
73. Weng JK. (2020) How the flame lily synthesizes a therapeutic natural product. Nature. DOI: 10.1038/d41586-020-01675-0
72. Matsumoto T, Harima S, Weng JK, Nihei KI. (2020) Systematic approach to the chemical synthesis of arabidopyrones, the unique α-pyrones of Arabidopsis metabolites. Synth Commun. DOI:10.1080/00397911.2020.1788600
71. Klein IA, Boija A, Afeyan LK, Hawken SW, Fan M, Dall’Agnese A, Oksuz O, Henninger JE, Shrinivas K, Sabari BR, Sagi I, Clark VE, Platt JM, Mrityunjoy Kar M, McCall PM, Zamudio AV, Manteiga JC, Coffey EL, Li CH, Hannett NM, Guo YE, Decker TM, Lee TI, Zhang T, Weng JK, Taatjes DJ, Chakraborty A, Sharp PA, Chang YT, Hyman AA, Gray NS, Young RA. (2020) Partitioning of cancer therapeutics in nuclear condensates. Science. 368:1386–1392.
70. Weng JK. (2020) Plant Solutions for the COVID-19 Pandemic and Beyond: Historical Reflections and Future Perspectives. Mol Plant.
69. Torrens-Spence MP, Chiang YC, Smith T, Vicent MA, Wang Y, Weng JK. (2020) Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. Proc Natl Acad Sci U S A.
News coverage by WI: Making medicine runs in the family.
68. Kim CY, Mitchell AJ, Glinkerman CM, Li FS, Pluskal T, Weng JK. (2020) The chloroalkaloid (−)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants. Nat Commun. 11:1867.
News coverage by Phys.org: Harnessing the moonseed plant’s chemical know-how.
67. Cao Y, Lim E, Xu M, Weng JK, Marelli B. (2020) Precision delivery of multi-scale payloads to tissue-specific targets in plants. Adv Sci. 7:1903551.
Featured cover article
News coverage by Phys.org: Engineers develop precision injection system for plants.
66. Xu SY and Weng JK. (2020) Climate change shapes the future evolution of plant metabolism. Adv Genet. DOI:10.1002/ggn2.10022
65. Jacobowitz J and Weng JK. (2020) Exploring uncharted territories of plant specialized metabolism in the postgenomic era. Annu Rev Plant Biol. 71:631-658.
64. Pluskal T, Fallon TR, Schmid R, Korf A, Smirnov A, Du X, Weng JK. (2020) Metabolomics data analysis using MZmine. in Processing Metabolomics and Proteomics Data with Open Software, edited by Robert Winkler, Royal Society of Chemistry. 232-254.
63. Pluskal T, Hoffmann N, Du X, Weng JK. (2020) Mass Spectrometry Development Kit (MSDK): a Java library for mass spectrometry data processing. in Processing Metabolomics and Proteomics Data with Open Software, edited by Robert Winkler, Royal Society of Chemistry. 399-405.
62. Goodheart JA, Minsky G, Brynjegard-Bialik MN, Drummond MS, Munoz JD, Fallon TR, Schultz DT, Weng JK, Torres E, Oakley TH. (2020) Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence. Sci Rep. 10:10443.
Preprint at bioRxiv: doi:10.1101/708065
61. Torrens-Spence MP, Bobokalonova A, Carballo V, Glinkerman CM, Pluskal T, Shen A, Weng JK. (2019) PBS3 and EPS1 complete salicylic acid biosynthesis from isochorismate in Arabidopsis. Mol Plant. 12:1577-1586.
Preprint at bioRxiv: doi:10.1101/601948
News coverage by WI: Building a roadmap for salicylic acid.
Spotlight by Molecular Plant: Connecting the Dots: A New and Complete Salicylic Acid Biosynthesis Pathway.
60. Torrens-Spence MP†, Liu CT†, Weng JK. (2019) Engineering new branches of the kynurenine pathway to produce oxo-(2-aminophenyl) and quinoline scaffolds in yeast. ACS Synth Biol. 8:2735-2745.
59. Chau Y, Levsh O, Li FS, Weng JK. (2019) Exploration of icariin analog structure space reveals key features driving potent inhibition of human phosphodiesterase-5. Plos One. 14:e0222803.
58. Levsh O, Pluskal T, Carballo V, Mitchell AJ, Weng JK. (2019) Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants. J Bio Chem. 294:15193-15205.
Deposited structure: 6MK2
Featured cover article
57. Christ B†, Xu C†, Xu M†, Li FS, Wada N, Mitchell AJ, Han XL, Wen ML, Fujita M, Weng JK. (2019) Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants. Nat Commun. 10:3206.
Deposited sequencing datasets: PRJNA544308, PRJNA544524
Extended reading: The “Marker degradation” and creation of the Mexican steroid hormone industry.
56. Pluskal T, Torrens-Spence MP, Fallon TR, De Abreu A, Shi CH, Weng JK. (2019) The biosynthetic origin of psychoactive kavalactones in kava. Nat Plants. 5:867-878.
News coverage by MIT News: Uncovering the riches of traditional global medicine.
News coverage by NPR: MIT Scientists Synthesize The Feel-Good Molecules In Kava, ‘Nature’s Xanax’.
News coverage by Ciencia y biología: Kava kava, la planta que alivia el dolor (y el último descubrimiento).
55. Cheng J, Song T, Wang H, Zhou X, Torrens-Spence MP, Wang D*, Weng JK*, Wang Q*. (2019) Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng. 55:23-32.
Preprint at bioRxiv: doi:10.1101/568121
54. Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C. (2019) The reference genome sequence of Scutellaria baicalensis provides insights into the evolution of wogonin biosynthesis. Mol Plant. 12:935-950.
News coverage by Science Daily: Ancient secrets of medicinal mint.
53. Jacobowitz JR, Doyle WC, Weng JK. (2019) PRX9 and PRX40 are extensin peroxidases essential for maintaining tapetum and microspore cell wall integrity during Arabidopsis anther development. Plant Cell. 31:848–861.
Preprint at bioRxiv: doi:10.1101/319020
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News coverage by WI: Scaffolding the nursery of pollen development.
The Plant Cell “In a Nutshell”: Peroxidases prevent tapetum swelling and pollen degeneration.
52. Mitchell AJ and Weng JK. (2019) Unleashing the synthetic power of plant oxygenases: from mechanism to application. Plant Physiol. 179:813-829.
Part of Focus Issue on Synthetic Biology
51. Li FS, Phyo P, Jacobowitz JR, Hong M, Weng JK. (2019) The molecular structure of plant sporopollenin. Nat Plants. 5:41-46.
Preprint at bioRxiv: doi:10.1101/415612
Featured cover article
50. Renault H*, Werck-Reichhart D*, Weng JK*. (2019) Harnessing lignin evolution for biotechnological applications. Curr Opin Biotechnol. 56:105-111.
49. Torrens-Spence MP†, Liu CT†, Pluskal T, Chung YK, Weng JK. (2018) Monoamine biosynthesis via a noncanonical calcium-activatable aromatic amino acid decarboxylase in psilocybin mushroom. ACS Chem Biol. 13:3343-3353.
48. Kersten RD* and Weng JK*. (2018) Gene-guided discovery and engineering of branched cyclic peptides in plants. Proc Natl Acad Sci U S A. 115:E10961-E10969.
Editor’s Highlights by Molecular Plant: Mining Plant Genomes for Rapid Discovery of Nature Products.
News coverage by WI: Heart-healthy plant chemistry.
47. Liou G, Chiang YC, Wang Y, Weng JK. (2018) Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants. J Bio Chem. 293:18601–18612.
46. Christ B, Pluskal T, Aubry S*, Weng JK*. (2018) Contribution of untargeted metabolomics for future assessment of biotech crops. Trends Plant Sci. 23:1047-1056.
45. Chiang YC, Levsh O, CK Lam, Weng JK*, Wang Y*. (2018) Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT). PLoS Comput Biol. 14:e1006511.
Deposited structure: 6DD2
44. Fallon TR†, Lower SE†, Chang CH, Bessho-Uehara M, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Day JC, Suvorov A, Silva CJ, Stanger-Hall KF, Hall DW, Schmitz RJ, Nelson DR, Lewis S, Shigenobu S, Bybee SM, Larracuente AM, Oba Y, Weng JK. (2018) Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife. 7:e36495.
News coverage by STAT: To make better biomedical research tools, a grad student picks apart fireflies’ glow.
News coverage by WI: How many evolutionary events can it take to screw in nature’s lightbulb?
News coverage by NIBB (in Japanese): ホタルのゲノム解読に成功 〜ホタルの光の遺伝子の進化が明らかに〜.
43. Hill M and Weng JK. (2018) Pièce de Self-Résistance: A New Paradigm for Natural-Product Herbicide Discovery. Mol Plant. 11:1115-1116.
42. Ban Z, Qin H, Mitchell AJ, Liu B, Zhang F, Weng JK, Dixon R, Wang G. (2018) Non-catalytic Chalcone Isomerase-fold Proteins in Humulus lupulus are Auxiliary Components in Prenylated Flavonoid Biosynthesis. Proc Natl Acad Sci U S A. 115:E5223-E5232.
Featured cover article
41. Wada N, Kersten RD, Iwai T, Lee S, Sakurai F, Kikuchi T, Fujita D, Fujita M*, Weng JK*. (2018) Crystalline Sponge-based Structural Analysis of Crude Natural Product Extracts. Angew Chem Int Ed. 57:3671 –3675.
40. Pluskal T and Weng JK. (2018) Natural product modulators of human sensations and mood: molecular mechanisms and therapeutic potential. Chem Soc Rev. 47:1592-1637.
Featured cover article
39. Torrens-Spence MP, Pluskal T, Li FS, Carballo V, Weng JK. (2018) Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis. Mol Plant. 11:205–217.
News coverage by WI: Harnessing nature’s riches.
38. Zhao Q, Cui M, Levsh O, Yang D, Liu J, Li J, Hill L, Yang L, Hu Y, Weng JK, Chen X, Martin C. (2017) Two CYP82D enzymes function as flavone hydroxylases in the biosynthesis of root-specific 4′-deoxyflavones in Scutellaria baicelensis. Mol Plant. 11:135–148.
37. Christ B, Hochstrasser R, Guyer L, Francisco R, Aubry S, Hoertensteiner S*, Weng JK*. (2017) Nonspecific activities of the major herbicide-resistance gene BAR. Nat Plants. 3:937–945.
News and Views in Nature Plants: Raising the BAR of specificity.
News coverage by EurekAlert: Large-scale approach reveals imperfect actor in plant biotechnology.
News coverage by MIT News: Revealing an imperfect actor in plant biotechnology.
36. Kersten RD†, Lee S†, Fujita D, Pluskal T, Kram S, Smith JE, Iwai T, Noel JP, Fujita M*, Weng JK*. (2017) A red algal bourbonane sesquiterpene synthase defined by microgram-scale NMR-coupled crystalline sponge XRD analysis. J Am Chem Soc. 139:16838-16844.
News coverage by WI: A new workflow for natural product characterization comes ashore with red algae.
35. Chezem WR, Memon AA, Li FS, Weng JK, Clay NK. (2017) SG2-type R2R3-MYB transcription factor MYB15 controls defense-induced lignification and basal immunity in Arabidopsis. Plant Cell. 29:1907-1926.
34. Li FS and Weng JK. (2017) Rediscovering and demystifying traditional herbal medicine with modern approaches. Nat plants. 3:17109.
33. Edgar S, Li FS, Qiao K, Weng JK*, Stephanopoulos G*. (2017) Engineering of taxadiene synthase for improved selectivity and yield of a key taxol biosynthetic intermediate. ACS Synth Biol. 6:201–205.
32. Al-Wathiqui N†, Fallon TR†, South A, Weng JK*, Lewis SM*. (2016) Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection. Sci Rep. 6:38556.
News coverage by EurekAlert: New research sheds light on postmating sexual selection.
31. Levsh O, Chiang YC, Tung C, Noel JP, Wang Y*, Weng JK*. (2016) Dynamic conformational states dictate selectivity toward native substrate in a substrate-permissive acyltransferase. Biochemistry. 55:6314–6326.
30. Fallon TR, Li FS, Vicent MA, Weng JK. (2016) Sulfoluciferin is biosynthesized by a specialized luciferin sulfotransferase in fireflies. Biochemistry. 55:3341–3344.
29. Torrens-Spence MP†, Fallon TR†, Weng JK. (2016) A workflow for studying specialized metabolism in nonmodel eukaryotic organisms. Methods Enzymol. 576:69-97.
28. Zhao Q, Zhang Y, Wang G, Hill L, Weng JK, Chen XY, Xue H, Martin C. (2016) A specialized flavone biosynthetic pathway has evolved in the medicinal plant, Scutellaria baicalensis. Sci Adv. 2:e1501780.
News coverage by BBC: Chinese medicine plant secrets probed.
27. Fallon TR and Weng JK. (2014) A Molecular Gauge for Nitrogen Economy in Plants. Cell. 159:977-978.
26. Weng JK. (2014) The evolutionary paths towards complexity: a metabolic perspective. New Phytol. 201:1141-1149.
25. Weng JK. (2013) Elegant biochemistry, chaotic origin. New Phytol. 200:592-594.
24. Weng JK, Ye M, Li B, Noel JP. (2016) Co-evolution of hormone metabolism and signaling networks expands plant adaptive plasticity. Cell. 166:881-893.
News coverage by PYSORG: Disregarded plant molecule actually a treasure.
News and Views in Nature Plants: Hormone signalling: ABA has a breakdown.
Spotlight in Molecular Plant: Abscisic Acid Catabolism Generates Phaseic Acid, a Molecule Able to Activate a Subset of ABA Receptors.
23. Weng JK and Noel JP. (2013) Chemodiversity in Selaginella: a reference system for parallel and convergent metabolic evolution in terrestrial plants. Front Plant Sci. 4:119.
22. Weng JK and Noel JP. (2012) The remarkable pliability and promiscuity of specialized metabolism. Cold Spring Harb Symp Quant Biol. 77:309-320.
21. Weng JK, Philippe RN, Noel JP. (2012) The rise of chemodiversity in plants. Science. 336:1667-1670.
Highlighted by the NSF press release: Provocative Prescription for Chemical Evolution in Plants.
20. Weng JK and Noel JP. (2012) Structure-function analyses of plant type III polyketide synthases. Methods Enzymol. 515: 317-335.
19. Weng JK, Li Y, Mo H, Chapple C. (2012) Assembly of an evolutionarily new pathway for α-pyrone biosynthesis in Arabidopsis. Science.337:960-964.
News coverage by PYSORG: Never-before-seen plant metabolites discovered.
18. Bonawitz ND, Soltau WL, Blatchley MR, Powers BL, Hurlock AK, Seals LA, Weng JK, Stout J, Chapple C. (2012) The REF4 and RFR1 subunits of the eukaryotic transcriptional coregulatory complex Mediator are required for phenylpropanoid homeostasis in Arabidopsis. J Bio Chem. 287: 5434-5445.
17. Weng JK, Akiyama T, Ralph J, Chapple C. (2011) Independent recruitment of an O-methyltransferase for syringyl lignin biosynthesis in Selaginella moellendorffii. Plant Cell. 23: 2708–2724.
16. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, Depamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, Debarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theißen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. (2010) The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science. 332:960-963.
News coverage by NPR: Decoding The Platypus Of The Plant Kingdom.
News coverage by DOE: Spikemoss Genome Offers New Paths for Biofuels Research–Bridges Plant Development Gap.
15. Weng JK, Mo H, Chapple C. (2010) Over-expression of F5H in COMT-deficient Arabidopsis leads to enrichment of an unusual lignin and disruption of pollen wall formation. Plant J. 64:898-911.
Featured cover article
14. Weng JK and Chapple C. (2010) The origin and evolution of lignin biosynthesis. New Phytol. 187:273-285.
Also featured in Sir Arthur Tansley’s ecosystem concept (a virtual special issue).
13. Li X, Bonawitz ND, Weng JK, Chapple C. (2010) The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids. Plant Cell. 22:1620-1632.
12. Weng JK, Akiyama T, Bonawitz ND, Li X, Ralph J, Chapple C. (2010) Convergent evolution of syringyl lignin via distinct biosynthetic pathways in the lycophyte Selaginella and flowering plants. Plant Cell. 22:1033-1045.
Highlighted in the Editor’s Choice of Science 328:406-407 (2010). Cell Wall Construction
News release by ScienceDaily: Convergent Evolution in Lignin Biosynthesis: Tools for Re-Engineering Biomass Composition.
11. Schilmiller AL, Stout J, Weng JK, Humphreys J, Ruegger MO, Chapple C. (2009) Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J. 60:771-782.
10. Weng JK, Banks JA, Chapple C. (2008) Parallels in lignin biosynthesis: a study in Selaginella moellendorffii reveals convergence across 400 million years of evolution. Commun Integr Biol. 1:20-22.
9. Weng JK, Li X, Stout J, Chapple C. (2008) Independent origins of syringyl lignin in vascular plants. Proc Natl Acad Sci U S A. 105:7887-7892.
Highlighted by the NSF press release: When Plants “Think” Alike
8. Li X, Weng JK, Chapple C. (2008) Improvement of biomass through lignin modification. Plant J. 54:569-581.
7. Weng JK, Li X, Bonawitz ND, Chapple C. (2008) Emerging strategies of lignin engineering and degradation for cellulosic biofuel production. Curr Opin Biotechnol. 19:166-172.
6. Weng JK, Tanurdzic M, Chapple C. (2005) Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii. BMC Genomics. 6:85.
5. Wang W, Tanurdzic M, Luo M, Sisneros N, Kim HR, Weng JK, Kudrna D, Mueller C, Arumuganathan K, Carlson J, Chapple C, de Pamphilis C, Mandoli D, Tomkins J, Wing RA, Banks JA. (2005) Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Bio. 5:10.
4. Weng HX, Weng JK, Yan AL, Hong CL, Yong WB, Qin YC. (2008) Increment of iodine content in vegetable plants by applying iodized fertilizer and the residual characteristics of iodine in soil. Biol Trace Elem Res. 123:218-228.
3. Weng HX, Sun XW, Weng JK, Qing YC, Dong H. (2008) Crucial roles of iron in the growth of Prorocentrum micans Ehrenberg (Dinophyceae). J Coastal Res. 24:176-183.
2. Weng HX, Qin YC, Weng JK. (2005) Inherent correlation between decreased marine sedimentary phosphorus and glacial atmospheric CO2 decline. Geophys Res Lett. 32: L18606.
1. Weng HX, Weng JK, Yong WB, Sun XW, Zhong H. (2003) Capacity and degree of iodine absorbed and enriched by vegetable from soil. J Environ Sci. 15:107-111.