Improving photosynthesis through the enhancement of Rubisco carboxylation capacity

2021 ◽  
Author(s):  
Concepción Iñiguez ◽  
Pere Aguiló-Nicolau ◽  
Jeroni Galmés
Keyword(s):  
Active Sites ◽  
Arable Land ◽  
Small Subunit ◽  
Resource Use Efficiency ◽  
Rate Limiting Step ◽  
Promising Target ◽  
Use Efficiency ◽  
Co2 Concentrating Mechanisms ◽  
Near Future ◽  
Rate Limiting

Rising human population, along with the reduction in arable land and the impacts of global change, sets out the need for continuously improving agricultural resource use efficiency and crop yield (CY). Bioengineering approaches for photosynthesis optimization have largely demonstrated the potential for enhancing CY. This review is focused on the improvement of Rubisco functioning, which catalyzes the rate-limiting step of CO2 fixation required for plant growth, but also catalyzes the ribulose-bisphosphate oxygenation initiating the carbon and energy wasteful photorespiration pathway. Rubisco carboxylation capacity can be enhanced by engineering the Rubisco large and/or small subunit genes to improve its catalytic traits, or by engineering the mechanisms that provide enhanced Rubisco expression, activation and/or elevated [CO2] around the active sites to favor carboxylation over oxygenation. Recent advances have been made in the expression, assembly and activation of foreign (either natural or mutant) faster and/or more CO2-specific Rubisco versions. Some components of CO2 concentrating mechanisms (CCMs) from bacteria, algae and C4 plants has been successfully expressed in tobacco and rice. Still, none of the transformed plant lines expressing foreign Rubisco versions and/or simplified CCM components were able to grow faster than wild type plants under present atmospheric [CO2] and optimum conditions. However, the results obtained up to date suggest that it might be achievable in the near future. In addition, photosynthetic and yield improvements have already been observed when manipulating Rubisco quantity and activation degree in crops. Therefore, engineering Rubisco carboxylation capacity continues being a promising target for the improvement in photosynthesis and yield.

scholarly journals Over-expression of the brassinosteroid gene TaDWF4 increases wheat productivity under low and sufficient nitrogen through enhanced carbon assimilation

2021 ◽  
Author(s):  
Matthew John Milner ◽  
Stéphanie M. Swarbreck ◽  
Melanie Craze ◽  
Sarah Bowden ◽  
Howard Griffiths ◽  
...  
Keyword(s):  
Crop Yields ◽  
Agronomic Traits ◽  
Carbon Assimilation ◽  
Fold Increase ◽  
Operating Efficiency ◽  
Over Expression ◽  
Rate Limiting Step ◽  
Marginal Soils ◽  
Use Efficiency ◽  
Rate Limiting

There is a strong pressure to reduce nitrogen (N) fertiliser inputs while maintaining or increasing current cereal crop yields. Brassinosteroids, (BR), are a group of phytohormones essential for plant growth and development, that have been demonstrated to regulate several agronomic traits. DWF4 encodes a cytochrome P450 that catalyses a rate-limiting step in BR synthesis. We show that overexpression of the dominant shoot expressed homoeologue TaDWF4-B in wheat can increase plant productivity by up to 105% under a range of N levels on marginal soils, resulting in increased N use efficiency (NUE). We show that a two to four-fold increase in TaDWF4 transcript levels enhances the responsiveness of genes regulated by N. The productivity increases seen were primarily due to the maintenance of photosystem II operating efficiency and carbon assimilation in plants when grown under limiting N conditions and not an overall increase in photosynthesis capacity. The increased biomass production and yield per plant in TaDWF4 OE lines could be linked to modified carbon partitioning and changes in expression pattern of the growth regulator Target Of Rapamycin, offering a route towards breeding for sustained yield and lower N inputs.

scholarly journals Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Tatiana P Soares da Costa ◽  
Cody J Hall ◽  
Santosh Panjikar ◽  
Jessica A Wyllie ◽  
Rebecca M Christoff ◽  
...  
Keyword(s):  
Herbicidal Activity ◽  
Lysine Biosynthesis ◽  
Proof Of Concept ◽  
Herbicide Resistant ◽  
Modes Of Action ◽  
Rate Limiting Step ◽  
Promising Target ◽  
Chemical Screen ◽  
Germination And Growth ◽  
Rate Limiting

Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides with novel modes of action are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. The first class of plant DHDPS inhibitors with micromolar potency against Arabidopsis thaliana DHDPS were identified using a high throughput chemical screen. We determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. The inhibitors also attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide resistant weeds.

scholarly journals Chemical clustering and visualization applied to macromolecular crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1145-C1145
Author(s):  
Andrew Bruno ◽  
Amanda Ruby ◽  
Joseph Luft ◽  
Thomas Grant ◽  
Jayaraman Seetharaman ◽  
...  
Keyword(s):  
Hierarchical Clustering ◽  
High Throughput ◽  
Active Sites ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Potential Applications ◽  
Crystallization Conditions ◽  
Electron Density Map ◽  
Distance Coefficient ◽  
Rate Limiting

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and the insertion and correct placement of a sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient appears to be robust in this application and coupled with hierarchical clustering and the overlay of crystallization outcome reveals information of biological relevance. While tested with a single example the potential applications appear promising.

What Do We Need from Agriculture?

2012 ◽  
Author(s):  
R. Ford Denison
Keyword(s):  
Food Security ◽  
Environmental Impact ◽  
Crop Yield ◽  
Food Supply ◽  
Resource Use Efficiency ◽  
Scarce Resources ◽  
Use Efficiency ◽  
Negative Environmental Impact ◽  
Near Future

This chapter considers some of the challenges that agriculture is facing now or will face in the near future, including resource-use efficiency and food security. It begins with a discussion of the goals of agriculture, such as improving productivity (yield per acre, to use no more land than necessary), efficiency in the use of scarce resources (to use no more water than necessary, for example), stability over years (to prevent even occasional famines), and sustainability (to maintain all of these benefits over the long term). It then examines the effects of agriculture on everyone, not just farmers, as well as agriculture's underlying long-term problems such as those relating to food supply, food production, and transportation. It also looks at threats to sustainability, particularly those farming practices that lead to long-term decreases in crop yield. Finally, it offers suggestions for limiting the negative environmental impact of agriculture.

scholarly journals Co-operativity in seminal ribonuclease function: binding studies

1987 ◽  
Vol 241 (2) ◽  
pp. 435-440 ◽  
Author(s):  
A Di Donato ◽  
R Piccoli ◽  
G D'Alessio
Keyword(s):  
Active Sites ◽  
Mixed Type ◽  
Equilibrium Dialysis ◽  
Binding Studies ◽  
Rate Limiting Step ◽  
Differential Spectrophotometry ◽  
Limiting Step ◽  
Binding Data ◽  
Hysteretic Effect ◽  
Rate Limiting

Binding of nucleotides to bovine seminal RNAase was studied by differential spectrophotometry and equilibrium dialysis. Cytidine 3′-phosphate, the reaction product of the hydrolytic, rate-limiting step of the reaction, was found to be capable, in contrast to related nucleotides, of discriminating between the two structurally identical active sites of the enzyme. Negative co-operativity, with a ‘half-of-sites’ reactivity, was found at lower concentrations of ligand, whereas at higher concentrations positive co-operativity was detected. These findings exclude that the non-hyperbolic kinetics previously reported for the hydrolytic step of the reaction are due to hysteretic effect. A model of mixed-type co-operativity is proposed for interpreting the binding data.

scholarly journals Simultaneous quantification of depolymerization and mineralization rates by a novel <sup>15</sup>N tracing model

SOIL ◽  
2016 ◽  
Vol 2 (3) ◽  
pp. 433-442 ◽  
Author(s):  
Louise C. Andresen ◽  
Anna-Karin Björsne ◽  
Samuel Bodé ◽  
Leif Klemedtsson ◽  
Pascal Boeckx ◽  
...  
Keyword(s):  
Amino Acids ◽  
Terrestrial Ecosystems ◽  
Organic N ◽  
N Availability ◽  
Simultaneous Quantification ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Use Efficiency ◽  
Soil N Cycle ◽  
Rate Limiting

Abstract. The depolymerization of soil organic matter, such as proteins and (oligo-)peptides, into monomers (e.g. amino acids) is currently considered to be the rate-limiting step for nitrogen (N) availability in terrestrial ecosystems. The mineralization of free amino acids (FAAs), liberated by the depolymerization of peptides, is an important fraction of the total mineralization of organic N. Hence, the accurate assessment of peptide depolymerization and FAA mineralization rates is important in order to gain a better process-based understanding of the soil N cycle. In this paper, we present an extended numerical 15N tracing model Ntrace, which incorporates the FAA pool and related N processes in order to provide a more robust and simultaneous quantification of depolymerization and gross mineralization rates of FAAs and soil organic N. We discuss analytical and numerical approaches for two forest soils, suggest improvements of the experimental work for future studies, and conclude that (i) when about half of all depolymerized peptide N is directly mineralized, FAA mineralization can be as important a rate-limiting step for total gross N mineralization as peptide depolymerization rate; (ii) gross FAA mineralization and FAA immobilization rates can be used to develop FAA use efficiency (NUEFAA), which can reveal microbial N or carbon (C) limitation.

scholarly journals Towards Novel Herbicide Modes of Action by Inhibiting Lysine Biosynthesis in Plants

2021 ◽  
Author(s):  
Tatiana P. Soares da Costa ◽  
Cody J. Hall ◽  
Santosh Panjikar ◽  
Jessica A. Wyllie ◽  
Rebecca M. Christoff ◽  
...  
Keyword(s):  
Herbicidal Activity ◽  
Lysine Biosynthesis ◽  
Proof Of Concept ◽  
Herbicide Resistant ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Promising Target ◽  
Chemical Screen ◽  
Germination And Growth ◽  
Rate Limiting

Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. Using a high throughput chemical screen, we identified the first class of plant DHDPS inhibitors that have micromolar potency against Arabidopsis thaliana DHDPS isoforms. Employing X-ray crystallography, we determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. We also demonstrated that the inhibitors attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide resistant weeds.

scholarly journals Validation of Flory-Huggins model for phenol adsorption by Parthenium hysterophorus in a batch system

2019 ◽  
Vol 2 (2) ◽  
Author(s):  
Zakia Latif1 ◽  
Aliya Fazal2 ◽  
Muhammad Aziz Choudhary1 ◽  
Zahoor Ahmad1 ◽  
Muhammad Aslam Mirza1
Keyword(s):  
Active Sites ◽  
Cost Effective ◽  
Toxic Waste ◽  
Parthenium Hysterophorus ◽  
Phenol Adsorption ◽  
Rate Limiting Step ◽  
Adsorbent Surface ◽  
Ft Ir ◽  
Biomass Dosage ◽  
Rate Limiting

Parthenium hysterophorus weed powder was studied as adsorbent for phenol adsorption from its aqueous standardized solution. The adsorption of pollutant was found improving with an increase of biomass dosage and contact time. The intraparticle diffusion of phenol onto adsorbent surface was identified to be the rate limiting step. Linear form of Flory-Huggins model revealed preeminence to Langmuir, Freundlich, Temkin, and Dubinin-Radushkevich due to highest value of R2. The remediation process was figured out as a physisorption rather than a chemical one based on value of E (0.21KJ/mol). Active sites of sorbent surface identified by FT-IR were oxygen containing functional groups. Recent study proposes cost effective utilization of toxic allergent for treatment of toxic waste.

scholarly journals Effect of the Preparation Method of LaSrCoFeOx Perovskites on the Activity of N2O Decomposition

2021 ◽  
Author(s):  
Nia Richards ◽  
Luke A. Parker ◽  
James H. Carter ◽  
Samuel Pattisson ◽  
David J. Morgan ◽  
...  
Keyword(s):  
Citric Acid ◽  
Active Sites ◽  
Preparation Method ◽  
N2o Decomposition ◽  
Oxygen Species ◽  
Calcination Temperatures ◽  
Highly Active ◽  
Rate Limiting Step ◽  
Enhanced Mobility ◽  
Rate Limiting

AbstractN2O remains a major greenhouse gas and contributor to global warming, therefore developing a catalyst that can decompose N2O at low temperatures is of global importance. We have investigated the use of LaSrCoFeOx perovskites for N2O decomposition and the effect of surface area, A and B site elements, Co–O bond strength, redox capabilities and oxygen mobility have been studied. It was found that by using a citric acid preparation method, perovskites with strong redox capabilities and weak Co–O bonds can be formed at relatively low calcination temperatures (550 °C) resulting in highly active catalysts. The enhanced activity is related to the presence of highly mobile oxygen species. Oxygen recombination on the catalyst surface is understood to be a prominent rate limiting step for N2O decomposition. Here the reduced strength of Co–O bonds and mobile lattice oxygen species suggest that the surface oxygen species have enhanced mobility, aiding recombination, and subsequent regeneration of the active sites. La0.75Sr0.25Co0.81Fe0.19Ox prepared by citric acid method converted 50% of the N2O in the feed (T50) at 448 °C. Graphic Abstract

scholarly journals Waste-Derived Green Nanocatalyst for Biodiesel Production: Kinetic-Mechanism Deduction and Optimization Studies

2021 ◽  
Vol 13 (11) ◽  
pp. 5849
Author(s):  
Chee Yoong Chooi ◽  
Jia Huey Sim ◽  
Shiau Foon Tee ◽  
Zhi Hua Lee
Keyword(s):  
Active Sites ◽  
Reaction Rate ◽  
Surface Reaction ◽  
Pore Diameter ◽  
Preparation Method ◽  
Kinetic Mechanism ◽  
Transesterification Reaction ◽  
Biodiesel Production ◽  
Rate Limiting Step ◽  
Rate Limiting

This research focuses on deducing the kinetic mechanism for biodiesel production catalyzed by a CaO nanocatalyst derived from waste cockle shells via thermal hydration–dehydration treatment. In addition, the CaO nanocatalyst preparation method via thermal hydration–dehydration-related parameters (hydration duration, recalcination temperature, and recalcination duration) was studied and optimized. The transesterification reaction catalyzed by the CaO nanocatalyst followed the Langmuir–Hinshelwood kinetic mechanism with surface reaction as the rate-limiting step. The relatively low activation energy (3786.7 J/mol) for a transesterification reaction offered by the CaO nanocatalyst enhanced the reaction rate to 27.3% FAME yield/hr. The optimal conditions for the thermal hydration–dehydration treatment used to develop the nano CaO catalyst were 6 h of hydration duration, 650 °C of recalcination temperature, and 3 h of recalcination duration. Of biodiesel yield, 94.13% was obtained at a moderate temperature of 60 °C and 3 h reaction time during the transesterification of palm oil catalyzed by the nano-CaO. SEM, BET, and TPD results proved that the CaO nanocatalyst had a large surface area (13.9113 m2/g) and high pore volume (0.0318 cm3/g) that were rich in active sites (1046.46 μmol CO2/g), and the pore diameter (33.17 nm) was accessible to reactants and products.

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