Dr Maxim Kapralov (PI)
I am accepting applications for PhD students, research visits and postdoctoral fellowships. If interested email me: maxim.kapralov@ncl.ac.uk
Current PhD students
2018 cohort
Mathieu Ramon
Project Diatom Recording Using Metabarcoding (DRUM). Main supervisor: Maxim Kapralov; co-supervisor: Edward Haynes (The Food and Environment Research Agency; FERA). Funding: Institute for Agri-Food Research and Innovation (IAFRI).
Diatoms are marine and freshwater unicellular algae which are extremely sensitive to environmental conditions. This sensitivity makes them useful indicators of the quality of aquatic environments. Water Framework Directive includes obligatory surveys of freshwater benthic diatom communities to assess health of the UK rivers. The current survey method uses light microscopy to identify and quantify each species present in samples. However, this method is time consuming, expensive and not suitable for high throughput biomonitoring. Studies proposed another method, DNA barcoding, to identify species using DNA variations from short conservative sequences (barcodes). This method can be combined with the Next Generation Sequencing, that allows the analysis of thousands of sequences simultaneously, to form Metabarcoding. This study aims to unlock the potential of Diatoms DNA Metabarcoding to enable high throughput biomonitoring of rivers in the UK. Furthermore, we will test if the RNA Metabarcoding could be a good indicator of the ecosystems productivity.
Danny Cowan-Turner
Project: The Molecular Evolution of Starch Metabolism in the Guard Cells of CAM Species. Main supervisor: Professor Anne Borland; co-supervisor: Maxim Kapralov. Funding: BBSRC DTP.
Engineering crassulacean acid metabolism (CAM) into C3 crops could be a potential method of significantly improving crop plant WUE (Borland et al., 2014). CAM is an alternate form of photosynthetic metabolism that confers a ~6-fold greater WUE (Borland et al., 2009). That involves the nocturnal fixation of CO2 by phosphoenolpyruvate carboxylate (PEPC) into a C4 acid, which is stored in the vacuole as malic acid until subsequent daytime decarboxylation and re-carboxylation into the Calvin cycle by Ribulose-1,5-bisphosphate carboxylase (RUBISCO). CAM plants are therefore able to shift atmospheric net CO2 uptake to the night, allowing nocturnal stomatal opening, the inverse of C3 and C4 plants, to occur. By moving gas exchange and stomatal opening to the night CAM plants reduced water losses via evapotranspiration. The additional cost of CAM metabolism is almost entirely offset by the advantage of the carbon concentrating effect of malate decarboxylation during the day behind close stomata (Shameer et al., 2018). Allowing CAM metabolism to provide an improved WUE over C3 while not substantially effecting productivity. Implementing CAM in C3 will be a significant feat of engineering in itself, yet there are several significant research questions that need to be addressed before it can be seriously attempted (Borland et al., 2014; Yang et al., 2015). A key question, and the basis of this work, is how stomatal opening is rescheduled to open nocturnally? The rescheduling of CAM guard cell starch degradation is likely orchestrated by a corresponding re-timing of a number of key starch metabolism regulators. This project will investigate this rescheduling of starch metabolism in CAM guard cells and its regulation; and the role of starch metabolism in regulating stomatal aperture. It ultimately aims to identify the enzymes and regulators involved in CAM guard cell starch metabolism.
Osita Williams Nwokeocha
Project: Investigating the role of malate metabolism in stomatal and photosynthetic regulation of Crassulacean Acid Metabolism (CAM). Main supervisor: Professor Anne Borland; co-supervisor: Maxim Kapralov. Funding: Nigerian government.
The recent publication of the Kalanchoe fedstchenkoi genome (Yang et al 2018) the ease of genetic transformation of this species (Hartwell et al, 2016) presents the opportunity to test hypotheses pertaining to the role of malate turnover in modulating stomatal movement and photosynthetic activity in this CAM model plant. This project will use CRISPR-CAS mutants of K. fedstchenkoi, generated by collaborators in the USA, and which have had the expression of both PEPC1 and PEPC2 isogenes knocked down singly and in combination. These plants would be expected to show reduced diel turnover of malate and so can be used to test following hypotheses: 1. The diel opening and closing of CAM stomata are dictated by the day/night turnover of malate. 2. Rubisco activity is modulated by diurnal intracellular CO2 supply in CAM. 3. The degree of leaf succulence is positively correlated with diel malate turnover.
2019 cohort
Wasim Asjid Iqbal
Project: Modelling effects of climate change on photosynthetic enzymes to find solutions for future food and environmental security. Main supervisor: Maxim Kapralov; co-supervisor: Georg Lietz. Funding: NERC.
Photosynthesis, the most important biological process on a planetary scale, is limited under high temperature by the CO2 fixing enzyme, Rubisco, and its catalytic chaperone, Rubisco activase. Rubisco is the most abundant enzyme on a planet with estimates of its global mass ranging from 0.04 to 0.4 Gt, where the upper limit approaching current global mass of humans. And like humans, Rubisco punches above its weight in its ability to change ecosystems. Sage et al. (J Exp Bot 2008) showed that Rubisco and Rubisco activase could be the single principal control over a high thermal sensitivity and hence the future success of black spruce, the predominant primary producer and a major carbon sink in the boreal forests of North America. Despite Rubisco being the key player in both CO2 fixation and the future success of species, very little work has been done to model how its performance will affect future of ecosystems under different climate change scenarios.
The proposed project will combine fields of bio- and environmental informatics using our data on enzyme properties combined with data on protein sequences and structure, species distribution and climate from publicly available databases. The major objective is to model effects of climate change on Rubisco and Rubisco activase performance on the molecular, species, ecosystem, and planetary levels. This PhD project will inform human-assisted evolution of heat tolerance in key species of ecological and agricultural importance, which could mitigate negative effects of climate change, while meeting nutritional and energy demands of a growing world population – key UN sustainable development goals.
Rebecca Louise Moore
Main supervisor: Maxim Kapralov; co-supervisor: Jon Marles-Wright. Funding: EPSRC.
Rubisco is found in all photosynthetic organisms on the planet, from trees to bacteria. There is a large natural variance in kinetic properties between organisms, with some of the best performing variants found in red-algae and cyanobacteria. There are, however, taxonomic incompatibilities that prevent recombinant assembly and function of distant Rubisco variants in plants; researchers recently expressed red-algal Rubisco in tobacco but could not identify any folded and functioning enzyme. Rubisco is a large, multi-subunit protein complex that requires several chaperones for correct assembly and function. The chaperone requirements are not known in many of the understudied taxonomic clades where interesting Rubisco variants are found.
This project is a structural-functional investigation of Rubisco variants and their folding requirements. By assembling Rubisco chimeras and using Chlamydomonas reinhardtii as an expression system, we want to find the minimum requirement for red-algal Rubisco expression in a ‘green’ system. This project will also incorporate working towards finding novel chaperones in certain red-algae and characterize interactions with Rubisco. We hope to provide novel insights that will assist in the efforts to express improved Rubisco variants in globally important crop species.
Rebecca studied Biochemistry at the University of Edinburgh, with a dissertation project in Dr. JP Arulanandam’s lab, looking at protein interactions involved in cell division. She then moved to Munich to work at the Max Planck Institute for Biochemistry where she joined Dr. Naoko Mizuno’s structural biology group investigating cell to cell adhesion. Her final placement before joining us in Newcastle was in Professor Saul Purton’s lab in UCL, where she worked to develop synthetic biology tools to engineer the chloroplast in Chlamydomonas reinhardtii. This PhD project combines all her interests, from structural to synthetic biology!
Iain Hope
Main supervisor: Maxim Kapralov; co-supervisors: Jon Telling, Dana Ofiteru, Gary Caldwell. Funding: EPSRC.
Plant Rubiscos represent ‘the tip of the iceberg’. We propose to investigate a critically understudied part of the ‘submerged iceberg’: Rubiscos from cold adapted aquatic algae and bacteria, which dominate marine and glacial environments in polar regions. Some Rubiscos from psychrophilic (cold loving) organisms could be used to improve photosynthesis in crops because of high selectivity for CO2 and low sensitivity for O2.
Objectives:
1. Find and characterise new Rubiscos from psychrophilic organisms.
2. Achieve heterologous expression of newly found psychrophilic Rubiscos.
3. Investigate the dynamics of engineered bacterial and algal populations grown at pilot laboratory scale.
2020 cohort
Bethan Morris
Main supervisor: Maxim Kapralov; co-supervisors: Martin Edwards and Stephen Chivasa (Durham). Funding: BBSRC.
Humankind faces the unprecedented challenge of meeting the needs of a growing global population projected to hit the 9-10 billion mark by 2050. How to feed the rising population and meet the high-energy demands to sustain economic growth without destroying the environment is a formidable task. Tackling this key global challenge requires new agritech innovations developed from “thinking outside the box”. Photosynthesis stands as an attractive system, which can be targeted for improvements to increase biomass for energy and for food. Our research aims to understand how plants can acclimate to high temperatures through modifications to the basic process of photosynthetic carbon fixation. In translational terms, the research outcomes will provide essential knowledge for engineering better heat tolerance in crops to boost their yield under high temperatures and to mitigate negative effects of hot summers predicted to increase in both duration and frequency due to climate change.
Plants in different biomes across the world have adapted to different temperature regimes, and net photosynthesis can acclimate on a seasonal basis to growth-season temperature, so there is clearly considerable diversity in the sensitivity of plants to increasing temperatures. To study mechanisms of enzymic responses during plant acclimation, we will analyse Rubisco kinetic properties, expression of different copies of rbcS and Rubisco activase genes, changes in Rubisco small subunit composition, and Rubisco posttranslational modifications in plants cultivated under contrasting temperatures.
Emma Riley
Predicting the effects of increasing soil temperatures on beneficial plant symbionts and plant pathogens through Synthetic Biology.
Main supervisor: Ciarán Kelly (Northumbria); co-supervisor: Maxim Kapralov. Funding: One Planet DTP (NERC).
In Anthropocene, human activities impacting the climate and environment are causing unprecedented loss of plant and animal life. Microorganisms play a central role in carbon and nutrient cycling, human health, and agriculture, therefore microbial adaptation to Climate Change is a key consideration (Cavicchioli et al. 2019). Furthermore, the human population is predicted to exceed 9 billion by 2050 and agricultural productivity will struggle to meet new demands. This project aims to study the putative effects of Climate Change on the interaction between important crops and agriculturally important bacterial species; in particular, the impact of increasing soil temperature on the evolution of pathogenic bacteria, which evolve faster than their host plants. A number of genetic approaches will be used to artificially evolve the bacterial species, such as random mutagenesis, the use of synthetic sRNAs and CRISPR/Cas gene editing. It is timely and essential to focus on soil-based bacteria, as soil-borne pathogens are more difficult to treat than those above ground. If time allows, the approaches used in this study will be applied to a beneficial plant symbiont as well. It is hoped that this project and the technology developed can contribute to an environmentally-sustainable and climate-robust future for both humans and plant life.