Publications

†Co-first authors; *Co-corresponding authors.

2018

54.    Torrens-Spence MP, Chiang YC, Smith T, Vicent MA, Wang Y, Weng JK. (2018) Structural basis for independent origins of new catalytic machineries in plant AAAD proteins. (Submitted)

Deposited structures: 6EEI, 6EEM, 6EEQ, 6EEW
Preprint at bioRxiv: doi:10.1101/404970

53.    Jacobowitz J and Weng JK. (2018) PRX9 and PRX40 are extensin peroxidases essential for maintaining tapetum and microspore cell wall integrity during Arabidopsis anther development. (Submitted)

Preprint at bioRxiv: doi:10.1101/319020

52.    Pluskal T, Torrens-Spence MP, Fallon TR, De Abreu A, Shi CH, Weng JK. (2018) The biosynthetic origin of psychoactive kavalactones in kava. (In revision)

Deposited structures: 6CO0, 6CQB
Preprint at bioRxiv: doi:10.1101/294439

51.    Li FS, Phyo P, Jacobowitz J, Hong M, Weng JK. (2018) The molecular structure of plant sporopollenin. Nature Plants. (In press)

Preprint at bioRxiv: doi:10.1101/415612

50.    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. doi:10.1021/acschembio.8b00821

 

Deposited sequencing datasets: SRR7028478, SRR7028479
Deposited structures: 6EBN

 

 

49.    Renault H*, Werck-Reichhart D*, Weng JK*. (2019) Harnessing lignin evolution for biotechnological applications. Curr Opin Biotechnol. 56:105-111.

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.

 

 

Deposited sequencing datasets: SRR6896657
Deposited metabolomics datasets: MSV000082522MSV000082557

 

 

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.

 

Deposited structures: 6DX7, 6DX8, 6DX9, 6DXA, 6DXB, 6DXC, 6DXD, 6DXE, 6DXF
Preprint at bioRxiv: doi:10.1101/429795

 

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.

 

Genomic data access: www.fireflybase.org
Deposited metabolomics datasets: MTBLS698
Preprint at bioRxiv: doi:10.1101/237586
Crowdfunding site: Illuminating the firefly genome

 

 

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. Molecular 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.

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. Molecular Plant. 11:205–217.

 

 

Deposited sequencing datasets: SRR5936536, SRR5936537
Deposited metabolomics datasets: MTBLS566

 

News coverage by WI: Harnessing nature’s riches.


2017

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. Molecular 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. Nature Plants. 3:937–945.

 

 

Deposited structures: 5T7D, 5T7E
Deposited metabolomics datasets: MTBLS553
Preprint at bioRxiv: doi:10.1101/122184

 

 

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 DPluskal 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.

 

Deposited sequencing datasets: SRR5314125, SRR5314126
Deposited plasmid: 89468

 

 

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. Nature Plants. 3:17109.

 

 

 

Courtesy link to the Artemisia story (PDF) in the plant science cartoon series created by Anna Backhaus & Isotta Reichenbach.

 

 

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.


2016

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.

fireflies_nuptial_gift

 

 

Deposited sequencing datasets: PRJNA328865
Deposited proteomics datasets: PXD004005
Deposited metabolomics datasets: MTBLS362

 

 

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.
levsh_et-al_toc_graphic_v1

 

Deposited structures: 5KJS, 5KJT, 5KJU, 5KJV, 5KJW

 

 

30.    Fallon TR, Li FS, Vicent MA, Weng JK. (2016) Sulfoluciferin is biosynthesized by a specialized luciferin sulfotransferase in fireflies. Biochemistry. 55:3341–3344.

bi-2016-004023_0004

 

Deposited sequencing datasets: GEOW00000000
Deposited plasmids: 74121, 74122, 74123

 

 

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.
Scutellaria

 

 

 

News coverage by BBC: Chinese medicine plant secrets probed.


2013-2014

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.


Postdoctoral work

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.
PA_Weng_graphical_abstract

 

 

Deposited structures: 5JNN, 5JO1, 5JO2
Deposited sequencing datasets: GSE65739

 

 

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.


Graduate work

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.
Figure
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 moellendorffiiPlant 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.
Sela

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 moellendorffiiBMC 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.


Undergraduate work

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.