Computational Biology Approaches to Plant Metabolism and Photosynthesis:Applications for Corals in Times of Climate Change and Environmental Stress

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.

Plant Specialized Metabolism:the Easy and the Hard

Although normally termed ＂plant secondary metabolism＂, the phrase ＂plant specialized metabolism＂ has become accepted in recent years, since the boundary between plant primary and secondary metabolism for plant natural products is indistinct （Gang 2005）. The early studies of plant natural products can be traced back thousands of years ago to the utilization of herbs for pharmaceutical and cosmetic purposes.

Plant cytochrome P450 plasticity and evolution

The superfamily of cytochrome P450(CYP)enzymes plays key roles in plant evolution and metabolic diversification.This review provides a status on the CYP Iandscape within green algae and land plants.The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algaespecific clans are recognized.Clan 71,72,and 85 remain the largest CYP clans and include many taxaspecific CYP(sub)families reflecting emergence of linage-specific pathways.Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways.High substrate promiscuity is commonly observed for CYPs from large families,favoring retention of gene duplicates and neofunctionalization,thus seeding acquisition of new functions.Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple exampies of convergent evolution where CYPs have been independently recruited from the same or different CYP families,to adapt to similar environmental challenges or ecological niches.Sometimes only a single or a few mutations are required for functional interconversion.A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database(erda.dk/public/vgrid/PlantP450/).

How plants synthesize coenzyme Q

Coenzyme Q(CoQ)is a conserved redox-active lipid that has a wide distribution across the domains of life.CoQ plays a key role in the oxidative electron transfer chain and serves as a crucial antioxidant in cellular membranes.Our understanding of CoQ biosynthesis in eukaryotes has come mostly from studies of yeast.Recently,significant advances have been made in understanding CoQ biosynthesis in plants.Unique mitochondrial flavin-dependent monooxygenase and benzenoid ring precursor biosynthetic pathways have been discovered,providing new insights into the diversity of CoQ biosynthetic pathways and the evolution of phototrophic eukaryotes.We summarize research progress on CoQ biosynthesis and regulation in plants and recent efforts to increase the CoQ content in plant foods.

Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System

Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the second- ary metabolites in plants may have distinct advantages over microbial production platforms, and thus pro- pose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels： introducing biosynthetic genes, using tran- scription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.

Metabolic Engineering of Tropane Alkaloid Biosynthesis in Plants

Abstract: Over the past decade, the evolving commercial importance of so-called plant secondary metabolites has resulted in a great interest in secondary metabolism and, particularly, in the possibilities to enhance the yield of fine metabolites by means of genetic engineering. Plant alkaloids, which constitute one of the largest groups of natural products, provide many pharmacologically active compounds. Several genes in the tropane alkaloids biosynthesis pathways have been cloned, making the metabolic engineering of these alkaloids possible. The content of the target chemical scopolamine could be significantly increased by various approaches, such as introducing genes encoding the key biosynthetic enzymes or genes encoding regulatory proteins to overcome the specific rate-limiting steps. In addition, antisense genes have been used to block competitive pathways. These investigations have opened up new, promising perspectives for increased production in plants or plant cell culture. Recent achievements have been made in the metabolic engineering of plant tropane alkaloids and some new powerful strategies are reviewed in the present paper.

Plant Synthetic Metabolic Engineering for Enhancing Crop Nutritional Quality

Nutrient deficiencies in crops are a serious threat to human health,especially for populations in poor areas.To overcome this problem,the development of crops with nutrient-enhanced traits is imperative.Biofortification of crops to improve nutritional quality helps combat nutrient deficiencies by increasing the levels of specific nutrient components.Compared with agronomic practices and conventional plant breeding,plant metabolic engineering and synthetic biology strategies are more effective and accurate in synthesizing specific micronutrients,phytonutrients,and/or bioactive components in crops.In this review,we discuss recent progress in the field of plant synthetic metabolic engineering,specifically in terms of research strategies of multigene stacking tools and engineering complex metabolic pathways,with a focus on improving traits related to micronutrients,phytonutrients,and bioactive components.Advances and innovations in plant synthetic metabolic engineering would facilitate the development of nutrient-enriched crops to meet the nutritional needs of humans.

Improving photosynthetic efficiency toward food security:Strategies,advances,and perspectives

Photosynthesis in crops and natural vegetation allows light energy to be converted into chemical energy and thus forms the foundation for almost all terrestrial trophic networks on Earth.The efficiency of photosynthetic energy conversion plays a crucial role in determining the portion of incident solar radiation that can be used to generate plant biomass throughout a growth season.Consequently,alongside the factors such as resource availability,crop management,crop selection,maintenance costs,and intrinsic yield potential,photosynthetic energy use efficiency significantly influences crop yield.Photosynthetic efficiency is relevant to sustainability and food security because it affects water use efficiency,nutrient use efficiency,and land use efficiency.This review focuses specifically on the potential for improvements in photosynthetic efficiency to drive a sustainable increase in crop yields.We discuss bypassing photorespiration,enhancing light use efficiency,harnessing natural variation in photosynthetic parameters for breeding purposes,and adopting new-to-nature approaches that show promise for achieving unprecedented gains in photosynthetic efficiency.

OpNAC1 transcription factor regulates the biosynthesis of the anticancer drug camptothecin by targeting loganic acid O-methyltransferase in Ophiorrhiza pumila

Camptothecin(CPT) is an anticancer pentacyclic quinoline alkaloid widely used to treat cancer patients worldwide. However, the biosynthetic pathway and transcriptional regulation of camptothecin are largely unknown. Ophiorrhiza pumila, the herbaceous plant from the Rubiaceae family, has emerged as a model plant for studying camptothecin biosynthesis and regulation. In this study, a high-quality reference genome of O. pumila with estimated size of ~456.90Mb was reported, and the accumulation level of camptothecin in roots was higher than that in stems and leaves. Based on its spatial distribution in the plant, we examined gene functions and expression by combining genomics with transcriptomic analysis.Two loganic acid O-methyltransferase(OpLAMTs)were identified in strictosidine-producing plant O.pumila, and enzyme catalysis assays showed that OpLAMT1 and not OpLAMT2 could convert loganic acid into loganin. Further knock-out of OpL AMT1expression led to the elimination of loganin and camptothecin accumulation in O. pumila hairy roots.Four key residues were identified in OpLAMT1 protein crucial for the catalytic activity of loganic acid to loganin. By co-expression network, we identified a NAC transcription factor, OpNAC1, as a candidate gene for regulating camptothecin biosynthesis.Transgenic hairy roots and biochemical assays demonstrated that OpNAC1 suppressed OpLAMT1 expression. Here, we reported on two camptothecin metabolic engineering strategies paving the road for industrial-scale production of camptothecin in CPT-producing plants.