Featured
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| Open AccessA versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing
CRISPR prime editing enables double-strand break free engineering of the genome. Here the authors present a toolkit for prime editing in E. coli.
- Yaojun Tong
- , Tue S. Jørgensen
- & Sang Yup Lee
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Article
| Open AccessA guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria
The metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity remain unclear. Here, the authors report a guanidine degrading enzyme that controls genomic stability of ethylene producing cyanobacterial strains.
- Bo Wang
- , Yao Xu
- & Jianping Yu
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Article
| Open AccessAn integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts
Cell-free systems enable the design of biosynthetic pathways for sustainable chemical synthesis. Here the authors create an integrated framework for accelerating design using extracts from genetically rewired strains.
- Blake J. Rasor
- , Xiunan Yi
- & Michael C. Jewett
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| Open AccessComplete and efficient conversion of plant cell wall hemicellulose into high-value bioproducts by engineered yeast
Cellulosic hydrolysates contain substantial amounts of acetate, which is toxic to fermenting microorganisms. Here, the authors engineer Baker’s yeast to co-consume xylose and acetate for triacetic acid lactone production from a hemicellulose hydrolysate of switchgrass.
- Liang Sun
- , Jae Won Lee
- & Yong-Su Jin
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Article
| Open AccessGenome-scale target identification in Escherichia coli for high-titer production of free fatty acids
Identification of gene targets is one of the major challenges to construct superior microbial cell factory for chemical synthesis. Here, the authors employ CRISPRi and omics analyses for genome-scale target genes identification for high-titer production of free fatty acids in E. coli.
- Lixia Fang
- , Jie Fan
- & Hao Song
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Article
| Open AccessMetabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli
Synthetic pathways represent a metabolic burden on host cells. Here the authors engineer Cra-binding sites to prevent misregulation in glycerol and carotenoid overproducing E. coli strains.
- Chun-Ying Wang
- , Martin Lempp
- & Hannes Link
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Article
| Open AccessA genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics
Formulating metabolic networks mathematically can help researchers study metabolic diseases and optimize the production of industrially important molecules. Here, the authors propose a framework that allows to model eukaryotic metabolism considering gene expression and thermodynamic constraints.
- Omid Oftadeh
- , Pierre Salvy
- & Vassily Hatzimanikatis
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Article
| Open AccessRational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria
An efficient chassis for heterologous expression of biosynthetic gene clusters (BGCs) from Gram-negative bacteria is still unavailable. Here, the authors report rational construction of genome-reduced Burkholderials chassis to facilitate production of a class of new compounds by expressing BGC from Chitinimonas koreensis.
- Jiaqi Liu
- , Haibo Zhou
- & Xiaoying Bian
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Article
| Open AccessRenewable fatty acid ester production in Clostridium
Esters can be used as fuels and specialty chemicals for food flavoring, cosmetic and pharmaceutical industries. Here, the authors systematically engineer clostridia, including discovery and deletion of prophages to increase strain stability, for the production of butyl acetate and butyl butyrate from corn stover at low cost.
- Jun Feng
- , Jie Zhang
- & Yi Wang
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Article
| Open AccessImproved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway
Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.
- Joanne M. L. Ho
- , Corwin A. Miller
- & Matthew R. Bennett
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Article
| Open AccessDesigning an irreversible metabolic switch for scalable induction of microbial chemical production
A promising strategy to increase product synthesis from bacteria uses inducible systems to switch metabolism to production. Here, the authors use models to show how engineering positive feedback loops into the genetic circuitry creates a switch that requires only temporary induction with a cheap nutrient to switch metabolism irreversibly, and so drastically reduce inducer use and cost.
- Ahmad A. Mannan
- & Declan G. Bates
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Article
| Open AccessCharacterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip
Engineered live bacteria could represent a new class of therapeutic treatment for human disease. Here, the authors use a human gut-on-a-chip microfluidics system to characterize an engineered live bacterial therapeutic, designed for the treatment of phenylketonuria, and to construct mathematical models that predict therapeutic strain function in non-human primates.
- M. Tyler Nelson
- , Mark R. Charbonneau
- & Camilla A. Mauzy
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Article
| Open AccessProduction of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion
Lignin conversion to higher value products is essential to the economic viability of lignocellulosic biorefineries. Here, the authors demonstrate the bioconversion of alkali pretreated lignin to itaconic acid by dynamic two stage fermentation using a signal-amplified nitrogen-limitation biosensor.
- Joshua R. Elmore
- , Gara N. Dexter
- & Adam M. Guss
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Article
| Open AccessDirect 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant
Microorganisms cannot naturally produce 1,3-butadiene, an important monomer for synthetic rubber and plastic production, using glucose as carbon source. Here, the authors combine the cis,cis-muconic acid-production pathway and tailor ferulic acid decarboxylase mutations to achieve its production in E. coli.
- Yutaro Mori
- , Shuhei Noda
- & Akihiko Kondo
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Article
| Open AccessCreating enzymes and self-sufficient cells for biosynthesis of the non-natural cofactor nicotinamide cytosine dinucleotide
Nicotinamide cytosine dinucleotide is an NAD mimic that can be used to mediate redox reactions. Here the authors design an NCD synthetase for the intracellular production of NCD.
- Xueying Wang
- , Yanbin Feng
- & Zongbao K. Zhao
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Article
| Open AccessA computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives
The top down cheminformatics method is usually used for the reconstitution of heterologous pathway to produce plant natural products. Here, the authors report a bottom up computational workflow for the identification of potential products and the enzymes required to make them in a noscapine pathway in yeast.
- Jasmin Hafner
- , James Payne
- & Christina Smolke
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Article
| Open AccessHyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis
3-Hydroxypropionic acid (3HP) is an important platform chemical. Here, the authors engineer Halomonas bluephagenesis by deleting newly identified degradation pathway and balancing redox state to achieve high level production of 3HP and its copolymer under open and unsterile conditions.
- Xiao-Ran Jiang
- , Xu Yan
- & Guo-Qiang Chen
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Article
| Open AccessEngineered yeast genomes accurately assembled from pure and mixed samples
The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.
- Joseph H. Collins
- , Kevin W. Keating
- & Eric M. Young
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Article
| Open AccessReversible thermal regulation for bifunctional dynamic control of gene expression in Escherichia coli
Genetic circuits can be built with bifunctional dynamic regulation of gene expression. Here the authors design a thermosensitive switch for spatial and temporal control of colony pattern, cell shape and polymer production.
- Xuan Wang
- , Jia-Ning Han
- & Guo-Qiang Chen
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Article
| Open AccessComplete biosynthesis of a sulfated chondroitin in Escherichia coli
Chondroitin sulfate (CS) is a type of sulfated glycosaminoglycan that is manufactured by extraction from animal tissues for the treatment of osteoarthritis and in drug delivery applications. Here, the authors report the development of single microbial cell factories capable of compete, one-step biosynthesis of animal-free CS production in E. coli.
- Abinaya Badri
- , Asher Williams
- & Mattheos A. G. Koffas
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Article
| Open AccessAuxin-mediated protein depletion for metabolic engineering in terpene-producing yeast
Loss-of-function experiments are used in metabolic engineering to understand and optimise metabolism. Here, the authors apply auxin inducible protein degradation to test different metabolic engineering strategies for improved terpenoid production in yeast.
- Zeyu Lu
- , Bingyin Peng
- & Claudia E. Vickers
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Article
| Open AccessIn-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing
To obtain optimal yield and productivity in bioproduction, expression of pathway genes must be appropriately coordinated. Here, the authors report repurposing of base editors for simultaneous regulation of multiple gene expression and demonstrate its application in industrially important and model microorganisms.
- Yu Wang
- , Haijiao Cheng
- & Yanhe Ma
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Article
| Open AccessMicrobial production of multiple short-chain primary amines via retrobiosynthesis
Short-chain primary amines (SCPAs) are industrially important compounds that are commonly produced under harsh synthetic conditions. Here, the authors report a combination of retrobiosynthesis and precursor selection step for design of biosynthetic pathways leading to production of SCPAs, using valine decarboxylase-expressing Escherichia coli strains.
- Dong In Kim
- , Tong Un Chae
- & Sang Yup Lee
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Comment
| Open AccessSynthetic biology 2020–2030: six commercially-available products that are changing our world
Synthetic biology will transform how we grow food, what we eat, and where we source materials and medicines. Here I have selected six products that are now on the market, highlighting the underlying technologies and projecting forward to the future that can be expected over the next ten years.
- Christopher A. Voigt
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Article
| Open AccessSynthesis of high-titer alka(e)nes in Yarrowia lipolytica is enabled by a discovered mechanism
Alka(e)nes with chain lengths in C5-C23 range are ideal fuel components. Here, the authors report that high-titer production of alak(e)nes in pathway engineered Yarrowia lipolytica, which is enabled by the finding that acyl-CoA is another substrate of fatty acid photodecarboxylase (FAP).
- Jingbo Li
- , Yongshuo Ma
- & Gregory Stephanopoulos
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Article
| Open AccessPathway engineering in yeast for synthesizing the complex polyketide bikaverin
Bikaverin is a fungal-derived tetracyclic polyketide with antibiotic, antifungal and anticancer properties. Here, the authors employ various pathway engineering strategies to achieve high level production of bikaverin in baker’s yeast.
- Meng Zhao
- , Yu Zhao
- & Jef D. Boeke
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Article
| Open AccessPhotosynthetic hydrogen production by droplet-based microbial micro-reactors under aerobic conditions
The development of techniques capable of orchestrating the assembly of living cells into multicellular ensembles with synergistic and function is challenge. Here, the authors construct algal or algal/bacterial cells-based core shell-like structure based on aqueous two-phase system for synergic photosynthetic H2 production.
- Zhijun Xu
- , Shengliang Wang
- & Stephen Mann
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Article
| Open AccessA cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis
Saponins such as glycyrrhizin, a natural sweetener found in licorice root, are a class of triterpenoids synthesized that are characterized by a glucoronic acid moiety at the C-3 position. Here the authors show that saponin glucuronosylation is catalyzed by cellulose-synthase like enzymes and reconstitute glycyrrhizin synthesisin yeast.
- Soo Yeon Chung
- , Hikaru Seki
- & Toshiya Muranaka
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Article
| Open AccessAwakening a latent carbon fixation cycle in Escherichia coli
Current efforts to establish synthetic carbon fixation in model heterotrophs rely on expression of heterologous enzymes. Here, the authors explore the presence and activity of a latent CO2-assimilation pathway in E. coli based only on endogenous enzymes and a reversible decarboxylase.
- Ari Satanowski
- , Beau Dronsella
- & Arren Bar-Even
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Article
| Open AccessAdaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae
Methylotrophic metabolism enables growth on methanol, an alternative to sugar fermentation. Here the authors use adaptive laboratory evolution to uncover native methylotrophy capacity in Saccharomyces cerevisiae.
- Monica I. Espinosa
- , Ricardo A. Gonzalez-Garcia
- & Thomas C. Williams
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Article
| Open AccessDeveloping a pathway-independent and full-autonomous global resource allocation strategy to dynamically switching phenotypic states
A challenge for biological chemical production is the completion between synthetic circuits and host resources. Here the authors the authors use quorum sensing circuits and global mRNA decay to independently control two phenotypic states.
- Junjun Wu
- , Meijiao Bao
- & Zhijun Zhao
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Article
| Open AccessMethanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
The engineering of methanol-dependent growth in Escherichia coli is challenging. Here, the authors predict and experimentally validate methanol-dependent strains with a complete RuMP cycle and high potential for the development of a methylotrophic platform organism.
- Philipp Keller
- , Elad Noor
- & Julia A. Vorholt
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Article
| Open AccessGenome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale
The trade-off between growth and production affects the application of engineered microbes. Here, the authors take the minimal cut set approach to predict metabolic reactions for elimination to couple metabolite production strongly with growth and achieve high production of indigoidine in Pseudomonas putida.
- Deepanwita Banerjee
- , Thomas Eng
- & Aindrila Mukhopadhyay
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Article
| Open AccessGPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery
Expansion of the chemical diversity of glycopeptide antibiotics (GPAs) to deal with the emergence and spread of GPA resistance is challenging. Here, the authors report a GPA synthetic biology platform in Streptomyces coelicolor for Type IV–V glycopeptide antibiotic production and discovery.
- Min Xu
- , Wenliang Wang
- & Gerard D. Wright
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Perspective
| Open AccessMultiplying the efficiency and impact of biofortification through metabolic engineering
Biofortification is an effective means to reduce micronutrient malnutrition. Here, the authors review recent advances in biofortification and propose stacking multiple micronutrient traits into high-yielding varieties through the combination of conventional breeding and genetic engineering approaches.
- Dominique Van Der Straeten
- , Navreet K. Bhullar
- & Howarth Bouis
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Article
| Open AccessFermentative production of Vitamin E tocotrienols in Saccharomyces cerevisiae under cold-shock-triggered temperature control
Tocotrienols are valuable supplementations to α-tocopherol-dominated Vitamin E products. Here, the authors engineer baker’s yeast by combining the heterologous genes from photosynthetic organisms with the endogenous pathway for the production of tocotrienols under cold-shock-triggered temperature control.
- Bin Shen
- , Pingping Zhou
- & Hongwei Yu
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Article
| Open AccessTitrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction
An imbalance between cell growth and bioproduction of engineered microbes often reduces production efficiency. Here, the authors report genetic code expansion-based cell growth and biosynthesis balance engineering to achieve high levels production of N-acetylglucosamine in E. coli and N-acetylneuraminic acid in B. subtilis.
- Rongzhen Tian
- , Yanfeng Liu
- & Jian Chen
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Article
| Open AccessA fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida
Addition of fluorine to organic structures is a unique strategy for tuning molecular properties, but approaches to integrate fluorometabolites into the biochemistry of living cells are scarce. Here, the authors develop a fluoride-responsive genetic circuit to enable in vivo biofluorination in engineered Pseudomonas putida.
- Patricia Calero
- , Daniel C. Volke
- & Pablo I. Nikel
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Article
| Open AccessCombining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
In metabolic engineering, mechanistic models require prior metabolism knowledge of the chassis strain, whereas machine learning models need ample training data. Here, the authors combine the mechanistic and machine learning models to improve prediction performance of tryptophan metabolism in baker’s yeast.
- Jie Zhang
- , Søren D. Petersen
- & Michael K. Jensen
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Article
| Open AccessA machine learning Automated Recommendation Tool for synthetic biology
Synthetic Biology often lacks the predictive power needed for efficient bioengineering. Here the authors present ART, a machine learning and probabilistic predictive tool to guide synthetic biology design in a systematic fashion.
- Tijana Radivojević
- , Zak Costello
- & Hector Garcia Martin
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Article
| Open AccessEngineering and application of a biosensor with focused ligand specificity
Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.
- Dennis Della Corte
- , Hugo L. van Beek
- & Jan Marienhagen
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Article
| Open AccessIsobutanol production freed from biological limits using synthetic biochemistry
A cell free or synthetic biochemistry approach offers a way to circumvent the many constraints of living cells. Here, the authors demonstrate, via enzyme and process enhancements, the production of isobutanol with the metrics exceeding highly developed ethanol fermentation.
- Saken Sherkhanov
- , Tyler P. Korman
- & James U. Bowie
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Article
| Open AccessContinuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway
Biosynthetic gene clusters (BGCs) make small molecules with fitness-enhancing activities that drive BGC evolution. Here, the authors show that synthetic biology can leverage bioactivity to achieve continuous evolution of an antibiotic BGC in the lab and improve antibiotic production in a new host.
- Chad W. Johnston
- , Ahmed H. Badran
- & James J. Collins
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Article
| Open AccessEngineering regulatory networks for complex phenotypes in E. coli
Regulatory networks respond to environmental and genetic perturbations by reprogramming metabolism. Here the authors screen a library of 82 regulators with 110,120 mutations to map the regulatory network of 4000 genes.
- Rongming Liu
- , Liya Liang
- & Ryan T. Gill
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Article
| Open AccessRational flux-tuning of Halomonas bluephagenesis for co-production of bioplastic PHB and ectoine
Halomonas bluephagenesis is a halophilic platform bacterium for next generation industrial biotechnology. Here, the authors employ a stimulus response-based flux-tuning method for coproduction of bioplastic PHB and ectoine under open unsterile and continuous growth conditions.
- Hong Ma
- , Yiqing Zhao
- & Guo-Qiang Chen
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Article
| Open AccessA yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids
Plants synthesize more than 3000 tetrahydroisoquinoline (THIQ) alkaloids, but only a few of them have been produced by engineered microbes and titers are very low. Here, the authors increase (S)-reticuline titer to 4.6 g/L and repurpose the yeast Ehrlich pathway to synthesize a diverse array of THIQ scaffolds.
- Michael E. Pyne
- , Kaspar Kevvai
- & Vincent J. J. Martin
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Article
| Open AccessEliminating the capsule-like layer to promote glucose uptake for hyaluronan production by engineered Corynebacterium glutamicum
Bioproduction of hyaluronan needs increases in yield and greater diversity of the molecular weights. Here, the author increases hyaluronan production and diversifies the molecular weights through engineering the hyaluronan biosynthesis pathway and disruption of Corynebacterium glutamicum encapsulation caused by secreted hyaluronan.
- Yang Wang
- , Litao Hu
- & Zhen Kang
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Article
| Open AccessAnalysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
The complexity of genome-scale metabolic networks (GEMs) hinders their application in specific physiological contexts. Here, the authors introduce a framework to reduce thermodynamically curated GEMs to the subnetworks of interest and demonstrate its application by deriving leukemia-specific models.
- Maria Masid
- , Meric Ataman
- & Vassily Hatzimanikatis
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Article
| Open AccessSynergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism
TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.
- Nan Jiang
- , Aimer Gutierrez-Diaz
- & Erich Grotewold