Rational design of geranylgeranyl diphosphate synthase enhances carotenoid production and improves photosynthetic efficiency in Nicotiana tabacum.

Restricted genetic diversity can supply only a limited number of elite genes for modern plant cultivation and transgenesis. In this study, we demonstrate that rational design enables the engineering of geranylgeranyl diphosphate synthase (NtGGPPS), an enzyme of the methylerythritol phosphate pathway (MEP) in the model plant Nicotiana tabacum. As the crucial bottleneck in carotenoid biosynthesis, NtGGPPS1 interacts with phytoene synthase (NtPSY1) to channel GGPP into the production of carotenoids. Loss of this enzyme in the ntggpps1 mutant leads to decreased carotenoid accumulation. With the aim of enhancing NtGGPPS1 activity, we undertook structure-guided rational redesign of its substrate binding pocket in combination with sequence alignment. The activity of the designed NtGGPPS1 (a pentuple mutant of five sites V154A/I161L/F218Y/I209S/V233E, d-NtGGPPS1) was measured by a high-throughput colorimetric assay. d-NtGGPPS1 exhibited significantly higher conversion of IPP and each co-substrate (DMAPP ~1995.5-fold, GPP ~25.9-fold, and FPP ~16.7-fold) for GGPP synthesis compared with wild-type NtGGPPS1. Importantly, the transient and stable expression of d-NtGGPPS1 in the ntggpps1 mutant increased carotenoid levels in leaves, improved photosynthetic efficiency, and increased biomass relative to NtGGPPS1. These findings provide a firm basis for the engineering of GGPPS and will facilitate the development of quality and yield traits. Our results open the door for the structure-guided rational design of elite genes in higher plants.

• Publication year

  2021

• Venue

  Science Bulletin

• Publication date

  2021-07-01

• Fields of study

  Biology, Chemistry, Engineering, Environmental Science, Medicine

• Identifiers
  DOI 10.1016/J.SCIB.2021.07.003PMID 36546080
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Characterization and functional analysis of phytoene synthase gene family in tobacco

  2021cited by this paper
• Lycopene β-cyclase expression influences plant physiology, development, and metabolism in tobacco plants

  2021cited by this paper
• Integrative analysis of metabolome and transcriptome reveals the mechanism of color formation in pepper fruit (Capsicum annuum L.).

  2020cited by this paper
• The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes.

  2020cited by this paper
• Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

  2020cited by this paper
• Synthetic conversion of leaf chloroplasts into carotenoid-rich plastids reveals mechanistic basis of natural chromoplast development

  2020cited by this paper
• Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco.

  2020cited by this paper
• Nuclear-encoded synthesis of the D1 subunit of photosystem II increases photosynthetic efficiency and crop yield

  2020cited by this paper
• Base-Editing-Mediated Artificial Evolution of OsALS1 in planta to Develop Novel Herbicide-Tolerant Rice Germplasms.

  2020cited by this paper
• CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit.

  2020cited by this paper
• Statistical Analysis of the Benefits of Focused Saturation Mutagenesis in Directed Evolution Based on Reduced Amino Acid Alphabets

  2019cited by this paper
• Revolutionizing agriculture with synthetic biology

  2019cited by this paper
• Applications of Protein Engineering and Directed Evolution in Plant Research1[OPEN]

  2019cited by this paper
• Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production

  2019cited by this paper
• Heteromeric Geranylgeranyl Diphosphate Synthase Contributes to Carotenoid Biosynthesis in Ripening Fruits of Red Pepper ( Capsicum annuum var. conoides).

  2018cited by this paper
• Carotenoid Metabolism in Plants: The Role of Plastids.

  2018cited by this paper
• A simple and cost-effective method for screening of CRISPR/Cas9-induced homozygous/biallelic mutants

  2018cited by this paper
• A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health.

  2018cited by this paper
• A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice

  2017cited by this paper
• Polyprenols Are Synthesized by a Plastidial cis-Prenyltransferase and Influence Photosynthetic Performance[OPEN]

  2017cited by this paper
• Arabidopsis GERANYLGERANYL DIPHOSPHATE SYNTHASE 11 is a hub isozyme required for the production of most photosynthesis-related isoprenoids.

  2016cited by this paper
• Improving photosynthesis and crop productivity by accelerating recovery from photoprotection

  2016cited by this paper
• Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase

  2016cited by this paper
• SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

  2015cited by this paper
• Heterologous expression of the isopimaric acid pathway in Nicotiana benthamiana and the effect of N-terminal modifications of the involved cytochrome P450 enzyme

  2015cited by this paper
• Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

  2015cited by this paper
• Carotenoid metabolism in plants.

  2015cited by this paper
• Heterologous expression of chloroplast‐localized geranylgeranyl pyrophosphate synthase confers fast plant growth, early flowering and increased seed yield

  2015cited by this paper
• Inducible Repression of Nuclear-Encoded Subunits of the Cytochrome b6f Complex in Tobacco Reveals an Extraordinarily Long Lifetime of the Complex1[W][OPEN]

  2014cited by this paper
• High-level diterpene production by transient expression in Nicotiana benthamiana

  2013cited by this paper
• LCAA, a Novel Factor Required for Magnesium Protoporphyrin Monomethylester Cyclase Accumulation and Feedback Control of Aminolevulinic Acid Biosynthesis in Tobacco1[W][OA]

  2012cited by this paper
• A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana

  2011cited by this paper
• Carotenoids and their cleavage products: biosynthesis and functions.

  2011cited by this paper
• Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control

  2010cited by this paper
• Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods.

  2010cited by this paper
• Structure of a Heterotetrameric Geranyl Pyrophosphate Synthase from Mint (Mentha piperita) Reveals Intersubunit Regulation[W][OA]

  2010cited by this paper
• Heterodimeric geranyl(geranyl)diphosphate synthase from hop (Humulus lupulus) and the evolution of monoterpene biosynthesis

  2009cited by this paper
• Natural Genetic Variation in Lycopene Epsilon Cyclase Tapped for Maize Biofortification

  2008cited by this paper
• Carotenoid metabolism: biosynthesis, regulation, and beyond.

  2008cited by this paper
• Metabolic Engineering of Potato Carotenoid Content through Tuber-Specific Overexpression of a Bacterial Mini-Pathway

  2007cited by this paper
• Determining the limitations and regulation of photosynthetic energy transduction in leaves.

  2007cited by this paper
• Improving the nutritional value of Golden Rice through increased pro-vitamin A content

  2005cited by this paper
• Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation.

  1996cited by this paper
• A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.

  1976cited by this paper

• Beyond pigments and perfumes: engineering in the carotenoid and apocarotenoid spectrum, novel enzymes, and synthetic biology strategies

  2026cites this paper
• Structural insights into the molecular mechanisms of OsFBN5-induced OsSPS3 catalysis

  2026cites this paper
• Lipoxygenase 2 (LOX2) coordinates carotenoid and methyl jasmonate metabolism in Nicotiana tabacum.

  2026cites this paper
• Suppression of microRNAs targeting key MEP pathway genes affects plastid terpenoid content and photosynthesis under variable light conditions

  2026influential citation
• Metabolic engineering for increased nutritional quality in rice

  2026cites this paper
• Reconstruction of the Early Stage Paclitaxel Biosynthesis Pathway in Escherichia coli by Integrating Enzyme and Metabolic Engineering Approaches

  2026cites this paper
• Smart Nanoparticles Disrupting Energy Supply through Triple Mechanisms to Kill Tumors via Dual Disruption of Mitochondria and Lysosomes

  2025cites this paper
• Specific sets of geranylgeranyl diphosphate synthases and phytoene synthases control the production of carotenoids and ABA in different tomato tissues

  2025cites this paper
• Ghβ-LCY1 influences metabolism and photosynthetic in Gossypium hirsutum.

  2025cites this paper
• Manganese‐regulated accumulation of carotenoids and abscisic acid in sweet potato through multi‐omics analysis

  2025cites this paper
• Optimizing carotenoid cleavage dioxygenase 4 (CCD4) for enhanced β-ionone production in Nicotiana tabacum

  2025cites this paper
• Insights into the geranylgeranyl pyrophosphate synthase (GGPPS) gene family in Osmanthus fragrans and the role of OfGGPPS13 in the formation of floral color and aroma

  2025cites this paper
• Overexpression of GhGGPPS10 and GhGGPPS23 Enhances Plant Biomass Accumulation and Optimizes Photosynthetic Performance in Cotton

  2025cites this paper
• Melatonin enhanced photosynthesis efficiency by improving carotenoid biosynthesis and carbon fixation via regulation of transcription factors

  2025influential citation
• Heterologous Biosynthesis of Crocin I in Solanum lycopersicum L.

  2025cites this paper
• Mutations in active surface sites of NtGGPPS1 enhance carotenoid biosynthesis and drought resistance in Nicotiana tabacum

  2025cites this paper
• Genome-Wide Identification of the Glycosyl Hydrolase Family 1 Genes in Brassica napus L. and Functional Characterization of BnBGLU77

  2025cites this paper
• Computer-Aided Techniques in the Engineering of Enzyme Binding Pockets: New Perspectives and Frontiers.

  2025cites this paper
• Orange debittering by a novel thermostable flavonoid glycosidase.

  2025cites this paper
• Genome-Wide Identification and Functional Characterization of the BAHD Acyltransferase Gene Family in Brassica napus L.

  2025cites this paper
• Metabolic Engineering of Methanotrophic Bacteria for De Novo Production of Taxadiene from Methane.

  2025cites this paper
• Construction and optimization of a cell-free metabolic engineering system for lycopene synthesis

  2025cites this paper
• Transcriptomic and Metabolomic Analysis of Isodon suzhouensis Reveals a Potentially IsCPS1 Gene for Glaucocalyxin A Biosynthesis

  2025cites this paper
• LOX5 roles in forming diverse aroma profiles of Nicotiana tabacum via multi-omics analysis

  2025cites this paper
• Expression of WsSQS and WsSQS2 in Tobacco Divergently Regulates Terpenoid Metabolism and Enhances Squalene Accumulation

  2025cites this paper
• Integrated metabolome and transcriptome analyses reveal the formation of seed albinism in Nelumbo nucifera

  2025cites this paper
• From traditional to AI-driven: The evolution of intelligent enzyme engineering for biocatalysis.

  2025cites this paper
• NnLOX1-mediated aroma formation in lotus (Nelumbo nucifera) through multi-omics integration and machine learning.

  2025cites this paper
• Investigation of genes involved in scent and color production in Rosa damascena Mill

  2024cites this paper
• Engineered enzymes for the synthesis of pharmaceuticals and other high-value products

  2024cites this paper
• Correlation study on microbial communities and volatile flavor compounds in cigar tobacco leaves of diverse origins

  2024cites this paper
• Biochemical synthesis of taxanes from mevalonate

  2024cites this paper
• The defensin protein NtCAL1 functions as a positive factor in plant cadmium accumulation and resistance in tobacco

  2024cites this paper
• Proteomic and metabolomic revealed the effect of shading treatment on cigar tobacco

  2024cites this paper
• Enhancing the Catalytic Activity of Geranylgeranyl Diphosphate Synthase through Ancestral Sequence Reconstruction and Semirational Design.

  2024cites this paper
• Transcriptomic response analysis of ultraviolet mutagenesis combined with high carbon acclimation to promote photosynthetic carbon assimilation in Euglena gracilis

  2024cites this paper
• Development and applications of metabolic models in plant multi-omics research

  2024cites this paper
• Characterization of Two Lycopene Beta-cyclases Reveal Their Essential Roles in Photoprotection in Nicotiana Tabacum

  2024cites this paper
• Characterization of the key aroma compounds in cigar filler tobacco leaves from different production regions

  2024cites this paper
• A Small Subunit of Geranylgeranyl Diphosphate Synthase Functions as an Active Regulator of Carotenoid Synthesis in Nicotiana tabacum

  2023influential citation
• Isolation, expression and functional analysis of GbGGPPS1 gene in Ginkgo biloba

  2023cites this paper
• The high genetic yield of Xinjiang cotton is associated with improvements in boll-leaf system photosynthesis

  2023cites this paper
• Synthesis of Crocin I and Crocin II by Multigene Stacking in Nicotiana benthamiana

  2023cites this paper
• Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway.

  2023cites this paper
• Integrated agronomic, physiological, microstructure, and whole-transcriptome analyses reveal the role of biomass accumulation and quality formation during Se biofortification in alfalfa

  2023cites this paper
• Overexpression of Geranyl Diphosphate Synthase 1 (NnGGPPS1) From Nelumbo nucifera Enhances Carotenoid and Chlorophyll Content and Biomass.

  2023cites this paper
• Overexpression of 1-deoxy-D-xylulose-5-phosphate reductoisomerase enhances the monoterpene content in Litsea cubeba

  2023cites this paper
• The potential roles of carotenoids in enhancing phytoremediation of bisphenol A contaminated soil by promoting plant physiology and modulating rhizobacterial community of tobacco.

  2023cites this paper
• Melatonin-induced MYBs Alleviates Fresh-cut Lotus Root (Nelumbo nucifera Gaertn.) Browning During Storage by Attenuating Flavonoid Biosynthesis and Reactive Oxygen Species (ROS).

  2023cites this paper
• Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

  2023cites this paper
• Development of isopentenyl phosphate kinases and their application in terpenoid biosynthesis.

  2023cites this paper
• Suppression of carotenoid cleavage dioxygenase 1 (NtCCD1) increases carotenoid contents and attenuates reactive oxygen species (ROS) in Tobacco Leaves

  2023influential citation
• Gene rational design: the dawn of crop breeding.

  2022cites this paper
• Inhibition of red chlorophyll catabolite reductase improved chlorophyll and carotenoid synthesis in tobacco

  2022cites this paper
• Integrated eco-physiological, biochemical, and molecular biological analyses of selenium fortification mechanism in alfalfa

  2022cites this paper
• Carotenoids in Drug Discovery and Medicine: Pathways and Molecular Targets Implicated in Human Diseases

  2022cites this paper
• NtDREB-1BL1 Enhances Carotenoid Biosynthesis by Regulating Phytoene Synthase in Nicotiana tabacum

  2022influential citation
• Developmental Differences between Anthers of Diploid and Autotetraploid Rice at Meiosis

  2022cites this paper
• Construction of SHP-GLOX Straw Lignin Degulation System and Its Application Effect in Rice

  2022cites this paper
• Construction of the SHP-GLOX lignin regulation system and its application in rice straw

  2022cites this paper
• Cloning and homologous characterization of geranylgeranyl pyrophosphate synthase (GGPPS) from Withania somnifera revealed alterations in metabolic flux towards gibberellic acid biosynthesis

  2022cites this paper
• Functional characterization and comparison of lycopene epsilon-cyclase genes in Nicotiana tabacum

  2022cites this paper
• Identification and Functional Analysis of Two Novel Genes—Geranylgeranyl Pyrophosphate Synthase Gene ( AlGGPPS ) and Isopentenyl Pyrophosphate Isomerase Gene ( AlIDI )—from Aurantiochytrium limacinum Significantly Enhance De Novo β -Carotene Biosynthesis in Escherichia coli

  year unknowncites this paper