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A peer-reviewed article of this preprint also exists.
Submitted:
30 October 2023
Posted:
31 October 2023
You are already at the latest version
A peer-reviewed article of this preprint also exists.
Submitted:
30 October 2023
Posted:
31 October 2023
You are already at the latest version
Proteins | Species | Target genes | Anti-oxidants | Editing type | Result |
---|---|---|---|---|---|
Kaempferol 3-O-rhamnosyl transferase and kaempferol 3-O-glucosyltransferase | A. thaliana |
At1g30530, At5g17050 |
Ubiquinone | Knockout as a result of deletion and insertion | Ubiquinone content in the double knockout represented 160% of wild-type level [141] |
PSY, phytoene synthase |
Oryza sativa | ZmPsy | Carotenoids | Marker-free targeted insertion at pre-determined plant genomic safe harbors (knock-in Erwinia uredovora carotenoid desaturase (SSU-crtI) and maize phytoene synthase (ZmPsy) both driven by the endosperm-specific glutelin promoter) |
High level of β-carotene in the endosperm [139] |
SlCYC-B, lycopene-β-cyclase; SlDDB1, DNA damage UV binding protein 1; SlDET1, de-etiolated 1 |
Solanum lycoper-sycum |
DNA damage SlCYC-B, SlDDB1, SlDET1, | Carotenoids | Target activation-induced cytidine deaminase base-editing technology, substitution of a cytidine with a thymine | Variations in carotenoid accumulation with an additive effect for each single mutation [132,133] |
LCY-E, lycopene ε-cyclase; Blc, beta-lycopene cyclase; LCY-B1, lycopene β-cyclase 1; LCY-B2, lycopene β-cyclase 2; SGR1, Stay-green 1 |
S. lycopersycum |
DQ100158 (SGR1), EU533951 (LCY-E), XM_010313794 (Blc), EF650013 (LCY-B1), AF254793 (LCY-B2) |
Carotenoids | Knockout as a result of deletions, insertion, substitution | Lycopene content in tomato fruit was increased to about 5.1-fold [126] |
LCYE, lycopene ε-cyclase |
O. sativa (rice calli) |
LcyE | Gene replacement using HDR, substitution H523L | Orange-colored line, total carotenoid content was 6.8–9.6 times higher than that of wild-type calli, increased tolerance to salt stress [129] | |
Nicotiana tabacum |
Ntε-LCY1, Ntε-LCY2 |
Knockout as a result of deletions, insertion, substitution | Increase of the total carotenoid and chlorophyll contents, photosynthetic efficiency, and levels of the stress response [131] | ||
Musa sapientum (banana) | GN-LCYε | Knockout as a result of indels | Accumulation of β-carotene content up to 6-fold; absence or a drastic reduction in the levels of lutein and α-carotene [128] | ||
EIL2, Ethylene-Insensitive 3/ Ethylene-Insensitive 3-Likes |
S. lycopersycum | EIL2 | Carotenoids, Ascorbate |
Knockout as a result of insertion | Yellow, orange fruits. 1.62-fold increase of ascorbate content via both the L-galactose and myoinositol pathways [61] |
PDS, phytoene desaturases |
Malus domestica (apple) |
LC10183 (PDS) |
Carotenoids | Knockout as a result of deletions, insertion | Albino phenotypes of regenerated plantlets [44] |
Fragaria sp. | PDS | Knockout as a result of deletions | Albino regenerants [45] | ||
Daucus carota (Orange carrot ‘Kurodagosun’, ‘Deep purple’ carrot) | XM_017385289.1 (DcPDS and DcMYB113-like genes) | Knockout as a result of deletions, insertion, substitution | Albino plants and purple color depigmented plants [48] |
||
Dioscorea rotundata | DrPDS | Knockout as a result of deletions, insertion | Phenotypes of variegated to complete albinism [46] | ||
Allium cepa L. | AcPDS | Knockout as a result of deletions, indels | Regenerated shoots exhibited three distinct phenotypes: albino, chimeric, and pale green [47] | ||
CCDs, carotenoid cleavage dioxygenases | Musa sapientum (banana) | CCDs | Carotenoids | Knockout as a result of deletions | Higher fold β-carotene accumulation in non-green tissue (roots) than in green tissue (leaf) [138] |
βOHase2, β-carotene hydroxylase |
A. thaliana |
At5g52570 (BCH2) |
Xantho-phylls | Knockout as a result of deletions | Prevention of the negative effects of carotenoid overproduction on seed germination [140] |
DnaJ, cysteine-rich zinc-binding domain |
O. sativa (rice calli) |
Orange gene (OsOr) | Chromoplast formation | Knockout as a result of deletions | Orange-colored line accumulated more lutein, β-carotene, and two β-carotene isomers; increased tolerance to salt stress [136] |
F3H, flavanone 3-hydroxylases |
D. carota (Carrot calli, purple-colored) |
F3H | Dihydro-flavonols, leucoantho-cyanidins, proantho-cyanidins, antho-cyanidins, anthocyanins | Knockout as a result of deletions | Blockage of the anthocyanin biosynthesis, discoloration of calli [142] |
F3′H, flavanone 3′-hydroxylase |
Oryza sativa L. (black rice) |
Os10g0320100 (OsF3′H) |
Flavan-3-oles | Knockout as a result of deletions, insertions | Ocher seeds, much lower anthocyanin content [143] |
Euphorbia pulcherrima | F3'H | Increased ratio of pelargonidin to cyanidin, braigt color changed from vivid red to vivid reddish orange [144] | |||
DFR, dihydroflavonol 4-reductase | Zea mays | GRMZM2G026930 (a1), MZM2G013726 (a4) | Leucoantho-cyanidins, proantho-cyanidins, antho-cyanidins, anthocyanins | Knockout as a result of deletions, insertions | Blockage of the anthocyanin biosynthesis [145] |
S. lycopersycum | Solyc02g085020 (DFR) |
Blockage of the anthocyanin biosynthesis, hypocotyls and callus were green [146,147] | |||
Oryza sativa L. (black rice) |
Os01g0633500 (OsDFR) |
Much lower anthocyanin content, ocher seeds [143] |
|||
Ipomoea nil |
AB006793 (InDFR-B) |
Anthocyanin-less white flowers [148] | |||
S. lycopersycum | DFR | Green hypocotyl due to defective anthocyanin accumulation [147] | |||
LDOX, leucoanthocyanidin dioxygenase |
Oryza sativa L. (black rice) |
Os01g0372500 (OsLDOX) |
Prontho-cyanidins, antho-cyanidins, anthocyanins | Knockout as a result of deletions and insertions | Brown seeds, much lower total anthocyanin content [143] |
UGTs, UDP-glucosyltransferases | A. thaliana | UGT79B2 (At4g27560), UGT79B3, (At4g27570) | Anthocyanin | Knockout as a result of deletions and insertions | Reduced levels of flavonoids and increased susceptibility to abiotic stress [149] |
Gt5GT, anthocyanin 5-O-glucosyl transferase; Gt3′GT, anthocyanin 3′-O-glucosyl transferase; Gt5/3′AT, anthocyanin 5/3′-aromatic acyl transferase |
Gentian cv. Albireo (Gentiana-triflora × G. scabra) |
Gt5GT, Gt3′GT, Gt5/3′AT |
Anthocyanin | Knockout as a result of deletions and insertions | Transformants produced pale red violet, dull pink and pale mauve flowers [150] |
PAP1, production of anthocyanin pigment 1 (MYB transcription factor (TF)) |
A. thaliana |
AT1G56650 (PAP1) |
Flavonoids | CRISPR/Cas9 activation system with the p65-HSF activators to increase endogenous transcriptional levels | Purple pigmentation of the leaves under a high light [151] |
ANT1, anthocyanin mutant 1 (Myb TFs) |
S. lycopersicum | ANT1 | Flavonoids | Gene targeting upstream of the ANT1 gene | Overexpression and ectopic accumulation of pigments in tomato tissues [152] |
CRISPR/LbCpf1-based HDR, Gene targeting upstream of the ANT1 gene | Tomato purple phenotype with salinity tolerance [153] | ||||
SlAN2-like, (R2R3-MYB TFs) |
Solyc10g086290 (SlAN2-like) |
Knockout as a result of deletion | Lower accumulation of anthocyanins, downregulation of multiple anthocyanin-related genes [154] | ||
SlAN2 (R2R3-MYB TFs) |
SlAN2 | Knockout as a result of deletion and substitution | Flavonoid content and the relative expression levels of several anthocyanin-related genes in vegetative tissues were significantly lower [155] | ||
DcPDS and DcMYB113-like (R2R3-MYB TFs) |
D. carota ('Deep Purple') |
DcPDS, DcMYB113-like | Knockout as a result of deletions | Regenerated albino shoots [48] |
|
PtrMYB57 (R2R3-MYB TFs) |
Populus tomentosa Carr | PtrMYB57 | Anthocyanin and proantho-cyanidin | Knockout as a result of deletions | High anthocyanin and proanthocyanidin phenotype [156] |
FtMYB45 (R2R3-MYB TFs) |
Fagopyrum tataricum | FtMYB45 | Flavonoids | Knockout as a result of deletions and insertion | Content of rutin, catechin, and other flavonoids was increased in hairy root mutants [157] |
bZIP (basic region/leucine zipper TFs) |
Vitis vinifera | VvbZIP36 | Flavonoids | Knockout as a result of deletions and insertion | Accumulation of metabolites (naringenin chalcone, naringenin, dihydroflavonols and cyanidin-3-O-glucoside). Synthesis of stilbenes (α-viniferin), lignans and some flavonols (including quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and kaempferol-7-O-rhamnoside) was inhibited [158] |
TTG1, Transparent Testa Glabra1 (MYB-bHLH-WD40 TFs) |
A. thaliana | TTG1 | Flavonoids | Knockout as a result of deletion | Mutants produce pale seeds and lack trichomes [159] |
O. sativa L. | OsTTG1 | Decreased falvonoid accumulation in various rice organs [160] | |||
TT, Transparent Testa (bHLH TFs) |
Brassica napus | BnTT8 | Proantho-cyanidin | Knockout as a result of deletion and insertion | The yellow-seeded phenotype, seeds with elevated seed oil and protein content and altered fatty acid composition [161,162] |
N. tabacum L. |
NtAn1a, NtAn1b |
||||
uORFGGP1 | Single nucleotide transversion from C to T in the 5′ UTR of the Solyc06g073320 sequence, leading to a change in the predicted amino acid sequence from serine to phenylalanine | Increased ascorbate content (2- to 5-fold higher), male sterility [163] | |||
GST, Glutathione S-transferase | S. lycopersycum | SlGSTAA | Glutathione | Knockout as a result of deletions | Green hypocotyl owing to anthocyanin deficiency [164,165] |
Gentian cv. Albireo (G. triflora × G. scabra) |
GST | Knockout as a result of deletions | Decreased anthocyanin accumulation in flower petals [150] | ||
F. vesca | RAP, Reduced Anthocyanins in Petioles | Knockout as a result of deletions, insertion | Green stem and white-fruited phenotype [166] | ||
Phosphorylase, GGP | Lactuca sativa | uORFAtVTC2LsGGP1 and LsGGP2 (homologs of AtVTC2) | Ascorbate | Knockout as a result of deletions and indels | Increased ascorbate content by ∼150% and oxidation stress tolerance [167] |
S. lycopersicum | uORFAtVTC2LsGGP2 (homologs of AtVTC2) | Knockout, deletions, indels | Increased ascorbate content [126] |
Genes | Enzymes | Functions | |
---|---|---|---|
At4g23100 | γ-glutamylcysteine synthetase, γ-ECS, ATECS1, ATGSH1, Cinnamyl Alcohol Dehydrogenase Homolog 2, Glutamate-Cysteine Ligase, GSH1, GSHA | Catalysis of the first, and rate-limiting, step of glutathione biosynthesis. | |
At5g27380 | Glutathione Synthetase 2, ATGSH2, GSH2, GSHB | Binding γ-glutamylcysteine and glycine together to form glutathione | |
At4g29130 | Hexokinase 1, HXK1, ATHXK1, GIN2 | Hexose phosphorylation activity | |
At2g19860 | Hexokinase 2, HXK2, ATHXK2 | ||
At1g47840 | Hexokinase 3, HXK3 | ||
At4g24620 | Phosphoglucose Isomerase, PGI, Glucose-6-phosphate isomerase | Transformation of d-glucose-6-phosphate into d-fructose-6-phosphate | |
At3g02570 At1g67070 | Man-6-phosphate Isomerase, Phosphomannose isomerase, PMI | D-mannose-6-P formation from d-fructose-6-phosphate [261] | |
At2g45790 | Phosphomannomutase, PMM | Transformation of D-mannose 6-phosphate into D-mannose 1-phosphate [262,263] | |
At2g39770 | GDP-D-mannose pyrophosphorylase, GMP1, Vitamin C Defective 1, VTC1, Cytokinesis Defective 1, CYT1, Embryo Defective 101, EMB101, Sensitive To Ozone 1, SOZ1, | Guanosine monophosphate transfer from GTP to GDP-D-Mannose [251,264,265] | |
At5g28840 | GDP-D-mannose 3’,5’ Epimerase, GME | The conversion of GDP-D-mannose to GDP-L-galactose (Barber, 1979). GME is also able to catalyze the 3′ epimerization of GDP-mannose, giving GDP-l-gulose, which is the precursor of a possible side-branch biosynthetic pathway (the gulose pathway) for vitamin C synthesis [252,266]. Plays a key role at the intersection of ascorbate and non-cellulosic cell-wall biosynthesis. | |
At5g55120 | VTC5 | GDP-L-Galactose Phosphorylase, GGP | Encodes a novel protein involved in ascorbate biosynthesis, which was shown to catalyze the transfer of GMP from GDP-galactose to a variety of hexose-1-phosphate acceptors [267] |
At4g26850 | VTC2 | ||
At3g02870 | L-Galactose 1-P-phosphatase, GPP, VTC4 |
The conversion of l-Galactose-1-phosphate into l-galactose [268,269,270] | |
At3g07130 | Purple acid phosphatase with phytase activity, PAP15 | ||
At4g33670 | L-Galactose Dehydrogenase, GDH | The conversion of l-galactose into l-galactono-1,4-lactone [251] | |
At3g47930 | L-Galactono 1,4-lactone Dehydrogenase, GLDH | Oxidation of L-galactono-1,4-lactone to AscA [264,271] | |
At3g05620 At5g04970 At5g47500 At5g61680 | Methyl Esterases | The conversion of Methyl-D-Galacturonate into D-Galacturonate in D-Galacturonate pathway [272] | |
At1g14520 At4g26260 |
Myo-Inositol Oxygenase, MIOX1 | Convertion of Myo-inositol into L-Gulono-1,4-lactone Myo-inositol [254] | |
At1g65770 | Ascorbic Acid Mannose Pathway Regulator 1, AMR1, ATFDA7, F-BOX/DUF295 ANCESTRAL 7 | Regulation of the mannose/L-galactose ascorbic acid biosynthetic pathway in response to developmental and environmental factors [273] | |
At3g23230 | Ethylene Response Factor 98, ERF98, AtERF98, Transcriptional Regulator of Defense Response 1, TDR1, TTDR1 | Enhancement of the tolerance to salt through the transcriptional activation of ascorbic acid synthesis [274] |
Genes | Enzymes | Functions | |
---|---|---|---|
At5g16440 | IPPI, isopentenyl diphosphate isomerases | Enzymes with dimethyl allyl diphosphate isomerase activity. It is involved in the biosynthesis of IPP, isopentenyl diphosphate. IPP is a subject for further condensation reactions to form intermediates in the synthesis of plastidic and mitochondrial isoprenoids (carotenoids, tocopherols, PQ, PCr8, UQ) | |
At3g02780 | |||
At4g19010 | AT4G 19010 |
Peroxisomal 4-coumarate CoA ligases | 4-HBA (hydroxybezoic acid) biosynthesis from phenylalanine in peroxisomes for further UQ biosynthesis [10,11] |
At5g38120 | 4CL8 | ||
At5g47770 | FPS1 | Farnesyl diphosphate synthases | Isoprenoid farnesyl diphosphate (FPP) biosynthesis for further UQ biosynthesis [12,13] |
At4g17190 | FPS2 | ||
At2g34630 | CoQ1, SPS3, solanesyl diphosphate synthase | Isoprene polymerization for further UQ biosynthesis [14] | |
At4g23660 | Coq2, PPT1, 4-hydroxybenzoate polyprenyl diphosphate transferase | Rate-limiting enzyme in UQ biosynthesis. Catalysis of benzoquinone ring of 4-HB condensation with polyisoprenoid side chain of polyprenyl-pyrophosphate to form 3-polyprenyl-4-hydroxybenzoate [15] |
|
At3g24200 | Coq6 | Flavin-dependent monooxygenases (Toda et al., 2014; Latimer et al., 2021) | Aromatic hydroxylation of C-H in different positions in UQ biosynthesis |
At1g24340 | CoqF | ||
At2g30920 | Coq3 | S -adenosyl- l -methionine (SAM)-dependent methyl transferases | |
At5g57300 | Coq5 | ||
At2g03690 | Coq4 | Presumably, a scaffold protein, which is responsible for organization of UQ biosynthetic complex [16] | |
At5g17230 | PSY, phytoene synthase | Condensation of two molecules of GGDP to produce phytoene for further carotenoid biosynthesis |
|
At4g14210 | PDS, phytoene desaturase | Desaturation of phytoene to ζ-carotene by introduction of four double bonds into phytoene for further carotenoid biosynthesis | |
At3g04870 | ZDS, ζ-carotene desaturase | Reduction ζ-carotene to lycopene by introduction of four double bonds for further carotenoid biosynthesis | |
At1g06820 | CRTISO, carotenoid isomerase | Catalyzes cis-trans isomerization of poly-cis-carotenoids to all-trans-lycopene. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene for further carotenoid biosynthesis [17,18] | |
At3g10230 | βLCY1, β-carotene cyclase, ATLCY, LYC, Lycopene cyclase | Introduction of a ring at both ends of symmetrical lycopene to form the bicyclic β-carotene [19] | |
At5g57030 | εLCY, ε- carotene cyclase | Required to form lutein [20] | |
At4g25700 | βOHase1 | β-carotene hydroxylases | Conversion of beta-carotene to zeaxanthin via cryptoxanthin [21] |
At5g52570 | βOHase2 | ||
At3g53130 | εOHase, ε-carotene hydroxylase | Involved in epsilon ring hydroxylation to carotene for lutein biosynthesis [22] | |
At5g67030 | ZE, zeaxanthin epoxidase | Introduction of epoxide groups into both rings of zeaxanthin to form violaxanthin [23] | |
At1g08550 | VDE, | De-epoxidation of violaxanthin to zeaxanthin [24] | |
At1g06570 | HPPD, 4-hydroxyphenylpyruvate dioxygenase (α-ketoisocaproate dioxygenase, KIC dioxygenase) |
Homogentisate (HGA) synthesis from hydroxyphenylpyruvate for further biosynthesis of PQ, PCr and tocopherols [25] | |
At5g04490 | VTE5, phytol kinase | Phosphorylation of free phytol for further biosynthesis of tocopherols [26] | |
At1g78620 | VTE6, phytyl-phosphate kinase | A key enzyme for phytol phosphorylation for further biosynthesis of tocopherols and phylloquinone [27] | |
At1g78510 | SPS1 | Solanesyl diphosphate synthases | Solanesyl diphosphate condensation from geranylgeranyl diphosphate (GGDP) and isopentenyl phosphate (IPP) for further biosynthesis of PQ and PCrs [28,29,30] |
At1g17050 | SPS2 | ||
At5g09820 | FBN5-B | Fibrillins | Specifically interacted with solanesyl SPS1 and SPS2 |
At3g11945 | HST, homogentisate solanesyl diphosphate transferase | Condensation of homogentisate (HGA) with solanesyl diphosphate with formation of methyl-solanesyl-benzoquinone (MSBQ) for further biosynthesis of PQ and PCrs | |
At2g18950 | HPT, homogentisate phytyl transferase (VTE2) | Catalysis of condensation of HGA and Phytyl-DP to form dimethyl-phytyl-benzoquinone (MPBQ) for further biosynthesis of tocopherols | |
At3g63410 | VTE3 2-methyl-6-phytyl-1,4-benzoquinol methyltransferase |
Methyl-solanesyl-benzoquinone (MSBQ) conversion to PQ9 and methyl-phytyl-benzoquinone (MPBQ) conversion to DMPBQ for further biosynthesis of tocopherols [31] | |
At4g32770 | VTE1, tocopherol cyclase | Plastochromanol-8 synthesis from reduced plastoquinone-9; α-tocopherol biosynthesis from γ -tocopherol [31] | |
At1g64970 | VTE4, G-TMT, γ-tocopherol methyltransferase |
Conversion of δ- and γ-tocopherols (and tocotrienols) to β- and α-tocopherols [31] |
Genes | Enzymes | Functions |
---|---|---|
At2g37040 | PAL, phenylalanine ammonia lyase | The deamination of phenylalanine to trans-cinnamic acid [172,173] |
At3g53260 | ||
At2g30490 | C4H, Cinnamic acid 4-hydroxylase | The hydroxylation of trans-cinnamic acid [174,175] |
At1g65060 | 4CL, 4-coumarate CoA ligase | Coumaric acid conversion to coumaroyl-CoA, which is the last step of phenylpropanoid pathway [176] |
At5g13930 | CHS, chalcone synthase (ATCHS, Transparent Testa 4, TT4) | The condensation of activated coumaric acid with three molecules of activated malonic acid in the form of malonyl-CoA to the formation of naringenin-chalcone. A key enzyme involved in the biosynthesis of flavonoids [177] |
At3g55120 | CHI, chalcone isomerase (A11, ATCHI, Chalcone flavanone isomerase, Transparent Testa 5, TT5) | Catalysis of the conversion of chalcones into flavanones [177]. At3g55120 is co-expressed with CHS encoding gene [54] |
At3g51240 | F3H, flavanone 3-hydroxylase | Encodes flavanone 3-hydroxylase that is coordinately expressed with CHSs and CHIs and involved in flavonoid biosynthesis [178]. |
At5g07990 | F3’H, flavanone 3’-hydroxylase (CYP75B1, Cytochrome P450 75B1, D501, Transparent Testa 7, TT7) | Hydroxylation of 3’-position of B-ring of flavonoids with catalysis of dihydroquercetin and quercetin formation from dihydrokaempferol and kaempferol, respectively [178] |
At5g24530 | FNS, flavone synthase (AtDMR6, Downy Mildew Resistant6) | The conversion of the flavanones into flavones. This class is also shown to comprise soluble Fe2+/2-oxoglutarate-dependent dioxygenases, which are oxygen- and NADPH-dependent cytochrome P450 membrane-bound monooxygenases [179] |
At5g08640 | FLS, flavonol synthase (ATFLS1) | Encodes a flavonol synthase that catalyzes formation of flavonols from dihydroflavonols. Co-expressed with CHI and CHS (qRT-PCR) |
At5g63590 | ||
At5g42800 | DFR, dihydroflavonol 4-reductase | The reduction of the 4-keto group of dihydroflavonol to the corresponding leucoanthocyanidin (Shirley et al., 1998). Synthesis of phlobaphenes from flavan-4-oles in Zea mays [180] |
At1g61720 | ANR, anthocyanidin reductase | Synthesis of proanthocyanidins (condensed tannins) from leukoanthocyanidins and anthocyanidins [181] |
At4g22880 | ANS, anthocyanidin synthase (LDOX, Leucoanthocyanidin dioxygenase) | Convertion leucoanthocyanidins to anthocyanins [182] |
At5g17050 | FGT, flavonoid glycosyltransferases | Glycosylation of anthocyanidins to anthocyanins [183,184,185,186] |
At1g30530 | ||
At5g17030 | ||
At2g36790 | ||
At1g06000 | ||
At4g14090 | ||
At5g54060 | ||
At2g47460 | MYB domain protein 12, MYB12, ATMYB12, PFG1 | Flavonol synthesis regulators. Strongly activate the promoters of CHS, F3H, FLS and CHI [187] |
At3g62610 | AtMYB11, PFG2 | |
At5g49330 | AtMYB111, PFG3 | |
At2g46510 | bHLH17 (ABA-inducible bHLH-type transcription factor, AIB, ATAIB, JA-associated MYC2-like 1, JAM1 | Positive regulator of flavonoid biosynthesis [188] |
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