Targeted editing of tomato carotenoid isomerase reveals the role of 5′ UTR region in gene expression regulation

Jayaraj, K. Lakshmi; Thulasidharan, Nitu; Antony, Aju; John, Moni; Augustine, Rehna; Chakravartty, Navajeet; Sukumaran, Smitha; Maheswari, M. Uma; Abraham, Sweety; Thomas, George; Lachagari, V. B. Reddy; Seshagiri, Somasekar; Narayanan, S. S.; Kuriakose, Boney

doi:10.1007/s00299-020-02659-0

Cited by 16 publications

(4 citation statements)

References 54 publications

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“…The 5' UTR region has been shown to play a role in the regulation of mRNA stability [17] as it harbours the transcription initiation site in many eukaryotes. Therefore the 5'UTR region offers an alternative to the traditional exon targeting for genome editing [18][19][20]. Our data indicate that, by targeting 50% of the alleles in the 5'UTR of VInv, we quantitatively regulate gene expression and retain the desired phenotype of the tubers.…”

Section: Eu Benchmark Valuementioning

confidence: 85%

Mutation of theVinv5′ UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards

Shumbe¹,

Soares²,

Muhovski³

et al. 2023

Preprint

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Protein–coding regions of genes have so far been the preferred targets for trait improvement using CRISPR–Cas9 genome editing in plants. Alteration of the reading frame can result in termination of transcription or translation, hence, loss of function of the encoded protein. 5′ UTR sequences also represent a practical target region to alter gene expression and protein abundance. However, editing of 5′ UTRs has so far been scarcely used to engineer trait in crop plants. Here, we demonstrate that insertion of a single adenine nucleotide mediated by Cas9 in the 5′ UTR region of two alleles from theVacuolar invertasegene (VInv) of the tetraploid potato variety Lady Rosetta (LaRo) is sufficient to substantially lower the content of reducing sugars in the potato under cold–storage conditions. Moreover, the acrylamide content generated during processing of the edited potato lines into crisps was more than three folds lower than the current EU–regulated maximum level of 750 μg/kg in crisps. This gene–editing approach represents a durable strategy to improve food safety of potatoes in varieties widely preferred by the consumers and the industry.

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Section: Eu Benchmark Valuementioning

confidence: 85%

Mutation of theVinv5′ UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards

Shumbe¹,

Soares²,

Muhovski³

et al. 2023

Preprint

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“…5’ untranslation region (UTR) plays an important role in gene expression regulation (Jayaraj et al., 2021). To generate new fzp alleles producing more secondary branches per panicle and grain numbers, CRISPR/Cas9 multiplex editing system was used to target the 5’ UTR of FZP in 'Nipponbare' (NIP; Miao et al., 2013).…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel mutant allele, fzp‐15, involved in panicle branch pattern of rice (Oryza sativa)

et al. 2021

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FRIZZY PANICLE (FZP) is involved in the development of panicle branching in rice. Herein, a novel mutant fzp‐15, demonstrating the sequential rounds of branching and severe defects in SM (spikelet meristem) formation, was identified. Map‐based cloning revealed that the abnormal panicle architecture of fzp‐15 resulted from an amino acid substitution (Glu (E) to Ala (A)) in the N‐terminal ERF domain of rice FZP protein. To generate new advantageous FZP alleles increasing grain numbers, CRISPR/Cas9 multiplex editing system was used to target the 5’ untranslation region (UTR) of FZP in 'Nipponbare' (NIP). The 85‐bp (−156 to ‐72 bp) or 149‐bp (−157 to ‐9 bp) deletion in the upstream region of FZP can significantly increase grain numbers without a decrease in grain size, while the 38‐bp deletion (−44 to −7 bp) in the upstream region of FZP has little effect in changing grain numbers. These results indicated that the 113‐bp fragment (−157 to −45 bp) upstream of FZP is important to its function and deletion of this region can be used to increase grain numbers in rice.

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“…Later on, CRTISO mutants were identified in rice (phs3, zebra2, mit3), melon (yofi), orange flower calendula, and orange color Chinese cabbage, marked with an accumulation of tetra-cis lycopene and reduced lutein content (Fang et al, 2008;Kishimoto and Ohmiya, 2012;Galpaz et al, 2013;Zhao et al, 2014;Su et al, 2015;Liu et al, 2018). CRISPR mutants of CRTISO were also reported in Chinese kale and tomato with similar phenotypes (Dahan-Meir et al, 2018;Sun et al, 2020a;Lakshmi Jayaraj et al, 2021).…”

Section: Desaturation and Isomerization -The Poly-cis Pathwaymentioning

confidence: 99%

“…Arabidopsis) (Dong et al, 2007;Avendaño-Vázquez et al, 2014) alb1, vp-wl2, vp9-8113,vp9-99-2226-R (GRMZM2G454952; Maize) (Chen et al, 2017;Wang et al, 2020b) phs2-1, phs2-2 (Os07g10490; Rice) (Fang et al, 2008) clb5-1 (EMS), clb 5-2 (fast-neutron; At3g04870; Arabidopsis) (Avendaño-Vázquez et al, 2014) ale1 (Os07g10490; EMS; Rice) (Fang et al, 2019) nd-1 HaZDS (GenBank accession no AJ514406; sunflower) (Conti et al, 2004) CRTISO phs3-1, phs3-2 (Os11g36440; Rice) (Fang et al, 2008) ccr2-3 (At1g06820; Arabidopsis) (Park et al, 2002) Chinese kale (Sun et al, 2020a) Tomato (Solyc10g081650) (Dahan-Meir et al, 2018;Lakshmi Jayaraj et al, 2021) t mic (fast-neutron), t3002, t4838, t3406, t9776 (EMS; Solyc10g081650; tomato) (Isaacson et al, 2002;Kachanovsky et al, 2012) ccr2-1 (EMS), ccr2-5 (At1g06820; fast-neutron; Arabidopsis) (Park et al, 2002) yofI (EMS; Genbank accession number JX491496) (Melon) (Galpaz et al, 2013) zb2, mit3-1, mit3-2, mit 3-3, mit3-4 (EMS; Os11g36440; Rice) (Zhao et al, 2014;Liu et al, 2018) phs3-3 (Os11g36440; Rice) (Fang et al, 2008) Orange flowered calendula (Kishimoto and Ohmiya, 2012) t3183, LA0351, LA3002, LA3128 (Solyc10g081650; tomato) (Isaacson et al, 2002;Yoo et al, 2017) Chinese cabbage (Bra031539) (Su et al, 2015) (Continued)…”

Section: Pds (Genbank Accession Jq762260)mentioning

confidence: 99%

The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants

Gupta

Hirschberg

2022

Front. Plant Sci.

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Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.

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Targeted editing of tomato carotenoid isomerase reveals the role of 5′ UTR region in gene expression regulation

Cited by 16 publications

References 54 publications

Mutation of theVinv5′ UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards

Mutation of theVinv5′ UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards

Identification of a novel mutant allele, fzp‐15, involved in panicle branch pattern of rice (Oryza sativa)

The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants

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