Featured
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Review Article
| Open Access
Choreographing root architecture and rhizosphere interactions through synthetic biology
Engineering the form and function of root systems and their associated microbiota could provide a means to mitigate adverse climate-driven effects. Here, the authors review the recent developments in plant and rhizobacterial synthetic biology and highlight engineering targets for applications in root systems and rhizosphere.
- Carin J. Ragland
- , Kevin Y. Shih
- & José R. Dinneny
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Article
| Open Access
The synthetic NLR RGA5HMA5 requires multiple interfaces within and outside the integrated domain for effector recognition
An engineered sensor NLR RGA5HMA5 carrying multiple resurfaced interfaces was generated to confer complete resistance to the rice blast fungus strains expressing the non-corresponding effector AVR-PikD, paving a way to broaden the resistance spectra of NLRs.
- Xin Zhang
- , Yang Liu
- & You-Liang Peng
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Article
| Open Access
Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis
Isoflavones are mostly found in the legumes, and little is known about their formation outside of this family. Here, the authors discover an isoflavone synthase gene in wheat, found in a pathogen-induced gene cluster encoding isoflavone biosynthesis.
- Guy Polturak
- , Rajesh Chandra Misra
- & Anne Osbourn
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Article
| Open Access
Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants
The multiplex CRISPR system is the tool of choice for creating targeted tandemly arrayed genes (TAGs) deletions in plants. Here, the authors show that up to 80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion bi-alleles, an unwanted products of targeted TAG deletions.
- Jiuer Liu
- , Feng-Zhu Wang
- & Jian-Feng Li
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Article
| Open Access
Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system
In the field of plant genome engineering, new nucleases with improved editing efficiency and alterative PAM requirements are needed. Here, the authors report a probiotic sourced CRISPR-LrCas9 system with similar PAM requirement to Cas12a and show its high efficiencies in various genome editing applications.
- Zhaohui Zhong
- , Guanqing Liu
- & Yong Zhang
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Article
| Open Access
Understanding the mechanism of red light-induced melatonin biosynthesis facilitates the engineering of melatonin-enriched tomatoes
Melatonin is a physiological regulator in many organisms including plants. Here, the authors demonstrate a molecular mechanism of red light-induced melatonin biosynthesis in tomato fruit which could guide the engineering of melatonin-enriched tomatoes.
- Zixin Zhang
- , Xin Zhang
- & Yang Zhang
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Article
| Open Access
A BAHD-type acyltransferase concludes the biosynthetic pathway of non-bitter glycoalkaloids in ripe tomato fruit
During tomato fruit ripening, bitter and toxic steroidal glycoalkaloids (SGAs) are converted to nonbitter and less toxic forms, but proposed acylating enzyme in pathway remain unknown. Here, authors report BAHD-type acyltransferase that catalyze acylation step in biosynthesis of non-bitter SGAs in tomato.
- Prashant D. Sonawane
- , Sachin A. Gharat
- & Asaph Aharoni
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Article
| Open Access
Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar
Modifying plant lignin pathway to enhance saccharification efficiency is often associated with growth penalty. Here, the authors show that overexpression of Pag-miR408 in poplar leads to enhanced saccharification efficiency and growth in both laboratory and field conditions, and laccase genes are the targets of Pag-miR408.
- Yayu Guo
- , Shufang Wang
- & Jinxing Lin
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Article
| Open Access
Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation
Development of canker-resistant citrus cultivars via traditional approaches is a lengthy and laborious process. Here, the authors report the generation of regulatory approval, transgene-free, canker-resistant sweet orange lines using Cas12a/crRNA ribonucleoprotein-based susceptibility gene editing strategy.
- Hang Su
- , Yuanchun Wang
- & Nian Wang
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Article
| Open Access
Regioselective stilbene O-methylations in Saccharinae grasses
O-methylated stilbenes are promising nutraceutical candidates. Here, the authors reveal that sorghum and wild sugarcane accumulate different types of O-methylated stilbenes due to major differences in catalytic regioselectivities of O-methyltransferases.
- Andy C. W. Lui
- , Kah Chee Pow
- & Clive Lo
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Article
| Open Access
Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis
Engineering carboxysomes into crop chloroplasts is a potential route to improve photosynthesis and crop yield. Here, the authors engineer functional CO2-fixing modules into tobacco chloroplasts to improve their photosynthesis and productivity.
- Taiyu Chen
- , Marta Hojka
- & Lu-Ning Liu
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Article
| Open Access
An integrase toolbox to record gene-expression during plant development
Synthetic circuits that can record in vivo signaling networks is critical in elucidating developmental process. Here, the authors describe the engineering and application of synthetic in vivo recorders with different promoters that can drive spatiotemporally-specific integrase switching during lateral root initiation.
- Sarah Guiziou
- , Cassandra J. Maranas
- & Jennifer L. Nemhauser
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Article
| Open Access
Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens
Antimicrobial peptides (AMPs) are next-generation antibiotics that can be used to combat drugresistant pathogens. Here, the authors report efficient production of bioactive amidated AMPs by transient expression in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase.
- Shahid Chaudhary
- , Zahir Ali
- & Magdy Mahfouz
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Article
| Open Access
High-frequency synthetic apomixis in hybrid rice
Previously, a proof-of-concept for low frequency synthetic apomixis was established in a laboratory strain of rice by combining MiMe mutations with the egg cell expression of the embryogenic trigger - BBM1. Here, the authors achieve clonal seed formation in hybrid rice with almost full penetrance and higher fertility.
- Aurore Vernet
- , Donaldo Meynard
- & Emmanuel Guiderdoni
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Article
| Open Access
Expression strategies for the efficient synthesis of antimicrobial peptides in plastids
Antimicrobial peptides (AMPs) are promising next-generation antibiotics, but are difficult to produce due to the toxicity to bacterial hosts. Here, the authors report the utilization of transplastomic tobacco plants for AMPs production without cytotoxic effects via inducible expression systems and fusions to cleavable carrier protein.
- Matthijs P. Hoelscher
- , Joachim Forner
- & Ralph Bock
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Article
| Open Access
A fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action
Managing herbicide resistance problem needs the identification of new herbicidal modes of action. Here, the authors solve the crystal structures of Arabidopsis HMGR and show HMGR as a potential new herbicide target by identifying plant-specific HMGR inhibitors and engineering tolerant trait in Arabidopsis.
- Joel Haywood
- , Karen J. Breese
- & Joshua S. Mylne
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Article
| Open Access
Nucleotide mismatches prevent intrinsic self-silencing of hpRNA transgenes to enhance RNAi stability in plants
Long hairpin RNA (hpRNA) transgenes are the most widely used RNAi technology in plants, but are potentially subject to self-induced transcriptional silencing. Here, the authors show nucleotide mismatches prevent intrinsic self-silencing of hpRNA transgenes in Arabidopsis and tobacco.
- Daai Zhang
- , Chengcheng Zhong
- & Ming-Bo Wang
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Article
| Open Access
Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria
The delivery of genetic material into plants is challenging due to the cell wall barrier. Here, the authors hybridize polymer-coated carbon nanotubes with functional peptides to deliver plasmid DNA cargo into intact plant mitochondria for transient expression and homologous recombination at high efficiency.
- Simon Sau Yin Law
- , Geoffrey Liou
- & Keiji Numata
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Article
| Open Access
Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation
Agrobacterium infection can cause defense responses in many plants, which leads to transformation recalcitrance. Here, the authors express type III secretion system in Agrobacterium to deliver effector proteins into plant cells to suppress host defense responses and thus enhance transformation in some plant species.
- Vidhyavathi Raman
- , Clemencia M. Rojas
- & Kirankumar S. Mysore
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Article
| Open Access
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
- Guotai Yu
- , Oadi Matny
- & Brande B. H. Wulff
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Article
| Open Access
New recognition specificity in a plant immune receptor by molecular engineering of its integrated domain
Plant NLR proteins trigger immune responses upon recognition of pathogen effectors. Here the authors show that the integrated decoy domain of the rice NLR RGA5 can be engineered to trigger immune responses upon binding a non-cognate effector.
- Stella Cesari
- , Yuxuan Xi
- & Thomas Kroj
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Article
| Open Access
Using CRISPR-Kill for organ specific cell elimination by cleavage of tandem repeats
How double strand breaks (DSBs) are repaired within the plant 45S rDNA repeats is unclear. Here, the authors show that Cas9-mediated DSBs in 45S rDNA are mainly repaired by cNHEJ and describe CRISPR-Kill as a tool for organ-specific cell elimination by targeting functional repetitive DNA in Arabidopsis.
- Angelina Schindele
- , Fabienne Gehrke
- & Holger Puchta
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Article
| Open Access
Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes
The all-flesh type of tomato fruits is caused by mutation of the MBP3 gene, however, knocking down MBP3 in certain genotypes also affect plant and fruit development. Here, the authors show that a natural mutation of AGL11, a close homolog of MBP3, is responsible for the phenotypic divergence.
- Baowen Huang
- , Guojian Hu
- & Mondher Bouzayen
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Comment
| Open Access
Homecoming: rewinding the reductive evolution of the chloroplast genome for increasing crop yields
Developing more productive and sustainable crops will be essential to achieving food security in coming decades. A core process in plant evolution has been the transfer of chloroplast-encoded genes to the nuclear genome. We propose reverting this process as a new approach to improve plant disease resistance and photosynthesis in future crops.
- Briardo Llorente
- , María Eugenia Segretin
- & Nicolás E. Blanco
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Article
| Open Access
Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells
Miniature Cas12f editing systems are well suited for in vivo editing applications. Here the authors characterize the intrinsic activity of SpCas12f1 in plant and animal cells.
- Greta Bigelyte
- , Joshua K. Young
- & Virginijus Siksnys
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Comment
| Open Access
Biotechnological development of plants for space agriculture
The logistical and practical challenges of supplying food for long-term space missions are substantial. In this comment, the authors discuss potential biotechnological approaches that could be used to aid the production of food crops in space.
- Yongming Liu
- , Gengxin Xie
- & Maozhi Ren
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Article
| Open Access
RETRACTED ARTICLE: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis
Unlike insects and mice, CRISPR/Cas9-based gene drives have not been achieved in plants. Here, the authors demonstrate homozygous F1 Arabidopsis plants can be obtained through zygotic conversion using CRISPR/Cas9-mediated homology-directed repair.
- Tao Zhang
- , Michael Mudgett
- & Yunde Zhao
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Article
| Open Access
A Bacillus thuringiensis Cry protein controls soybean cyst nematode in transgenic soybean plants
Genetic resistance to soybean cyst nematode (SCN) is beginning to decline. Here, the authors report that soybean lines expressing the Bacillus thuringiensis protein Cy14Ab have significant levels of protection from SCN in both greenhouse and field trials.
- Theodore W. Kahn
- , Nicholas B. Duck
- & Julia Daum
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Article
| Open Access
A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes
The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
- Jianping Zhang
- , Timothy C. Hewitt
- & Evans S. Lagudah
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Article
| Open Access
Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase
The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin features favorable for efficient gain of methylation.
- Wanlu Liu
- , Javier Gallego-Bartolomé
- & Steven E. Jacobsen
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Article
| Open Access
Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis
Accumulating evidences point to a discrepancy in the epigenetic behaviour of transgenes and endogenous genes. Here, via characterization of mutants impaired in histone demethylases JMJ14 and IBM1, the authors show that transgenes and endogenous genes are regulated by different epigenetic mechanisms in Arabidopsis.
- Nicolas Butel
- , Agnès Yu
- & Hervé Vaucheret
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Article
| Open Access
Versatility in acyltransferase activity completes chicoric acid biosynthesis in purple coneflower
Biosynthetic pathway of chicoric acid in purple coneflower has not been fully elucidated, though the compound has been shown to have potential health benefits. Here, the authors report the involvement of both BAHD and SCPL acyltransferases in its biosynthesis and show the pathway is unique to Echinacea species.
- Rao Fu
- , Pingyu Zhang
- & Yang Zhang
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Article
| Open Access
Towards plant resistance to viruses using protein-only RNase P
New approaches to plant disease control are important for pathogens that are difficult to control by existing methods. Here, the authors report a potential strategy to combat plant viruses by cytosolic expressed protein-only RNase P and show its ability for in vitro cleavage of tRNA-like structures existing in many plant viruses.
- Anthony Gobert
- , Yifat Quan
- & Philippe Giegé
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Article
| Open Access
Plasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis
Improved utilisation of nitrogen and carbon could boost agricultural productivity. Here Zhang et al. show that overexpression of a single gene, encoding the plasma membrane H+ -ATPase 1 OSA1, is able to increase both carbon fixation via photosynthesis and nitrogen assimilation via ammonium uptake in rice.
- Maoxing Zhang
- , Yin Wang
- & Yiyong Zhu
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Article
| Open Access
Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts
Introducing the pyrenoid-based CO2-concentrating mechanism of green algae into crops could greatly improve photosynthesis. Here, the authors show that expression of the algal linker protein EPYC1 and a plant-algal hybrid Rubisco in Arabidopsis chloroplasts leads to formation of a phase separated algal-like proto-pyrenoid.
- Nicky Atkinson
- , Yuwei Mao
- & Alistair J. McCormick
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Article
| Open Access
A 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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Perspective
| Open Access
Multiplying 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 Access
Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele
Plants with reduced amounts of lignin typically suffer from dwarfed growth, which offsets their gain in fermentable sugar yield. Here, the authors show that genome-edited poplar lines with a null and a haploinsufficient allele of CINNAMOYL-COA REDUCTASE2 (CCR2) can be obtained that have a reduced lignin level and normal growth.
- Barbara De Meester
- , Barbara Madariaga Calderón
- & Wout Boerjan
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Article
| Open Access
Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering
The heterochromatic knob (hk4S) on Arabidopsis chromosome 4 prevents the recombination between accessions with and without hk4S. Here, via egg-cell specific expression of the Cas9 nuclease, the authors demonstrate targeted reversal of the 1.1 Mb long hk4S-inversion in Col-0 and restore the crossovers with Ler-1.
- Carla Schmidt
- , Paul Fransz
- & Holger Puchta
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Article
| Open Access
A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering
Fluorescent RNA aptamers could potentially be used as protein-independent reporters of transgene expression in plants. Here, the authors report that an optimized RNA aptamer, developed from Broccoli, can be used to detect transgene expression in stable and transiently transformed plant tissue.
- Jiuyuan Bai
- , Yao Luo
- & Yun Zhao
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Article
| Open Access
Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa
Alfalfa is an important forage crop, but genetic improvement is challenging due to the lack of a reference genome and an efficient genome editing protocol. Here, the authors report the chromosome-level assembly of the autotetraploid genome and a CRISPR/Cas9-based transgene-free genome editing protocol.
- Haitao Chen
- , Yan Zeng
- & Qiang Qiu
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Article
| Open Access
Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9
Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.
- Oliver Xiaoou Dong
- , Shu Yu
- & Pamela C. Ronald
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Article
| Open Access
A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation
Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.
- Kun Zhang
- , Jingjing Su
- & Yongcai Fu
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Article
| Open Access
Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases
Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.
- Pablo D. Cárdenas
- , Prashant D. Sonawane
- & Asaph Aharoni
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Article
| Open Access
Chloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana
Engineering Taxol pathway in microbes needs to overcome the difficulty of expressing plant P450 enzymes. Here, the authors use a compartmentalized metabolic engineering strategy to construct the taxanes production pathway in chloroplasts of Nicotiana benthamiana and realize the production of taxadience-5α-ol.
- Jianhua Li
- , Ishmael Mutanda
- & Yong Wang
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Article
| Open Access
Soybean antiviral immunity conferred by dsRNase targets the viral replication complex
Soybean mosaic virus (SMV) is a potyvirus that reduces soybean yield and seed quality worldwide. Here, the authors reveal that the resistance gene Rsv4 encodes an RNase H family protein with dsRNA-degrading activity, and it can enter the viral replication compartment and degrade viral dsRNA.
- Kazuhiro Ishibashi
- , Masayasu Saruta
- & Akito Kaga
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Article
| Open Access
Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria
The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
- Barney A. Geddes
- , Ponraj Paramasivan
- & Philip S. Poole
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Article
| Open Access
Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems
Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.
- Ashot Papikian
- , Wanlu Liu
- & Steven E. Jacobsen
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Article
| Open Access
Carboxysome encapsulation of the CO2-fixing enzyme Rubisco in tobacco chloroplasts
Previous efforts to assemble Rubisco within a cyanobacterial carboxysome-derived protein shell in plant chloroplasts to concentrate CO2 have been unsuccessful. Here, Long et al. produce carboxysomes in tobacco chloroplasts that encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2.
- Benedict M. Long
- , Wei Yih Hee
- & G. Dean Price
Identification of triacylglycerol remodeling mechanism to synthesize unusual fatty acid containing oils