Engineering new capacities for solar energy utilisation in bacteria
Lead Research Organisation:
University of Sheffield
Department Name: School of Biosciences
Abstract
Photosynthesis captures the power of sunlight to drive the growth of plants on land and single-celled bacteria and plankton in the oceans, underpinning all global food chains and providing the oxygen we breathe. Because our planet Earth is mostly covered in water, the quantity and activity of water based photosynthetic bacteria is stupendous; billions of tonnes of photosynthetic bacteria grow in the oceans every year. These bacteria have to compete with each other for sunlight, and have evolved to live at different depths and environments, even growing in extreme conditions 100 metres or more below the surface. Sunlight is made up of a spectrum of many different colours of light and different bacteria have evolved specialised chemicals called pigments that absorb a particular colour of the spectrum.
Future biotechnological applications of photosynthesis are likely to require multicoloured bacteria containing multiple pigments that can harvest more of the solar spectrum than evolution has demanded of them. That way they could use more solar energy for making chemicals useful for man. Achieving this would mean putting together 'mix and match' combinations of pigments from different bacteria inside one cell. This is now possible because we have been finding out how photosynthetic bacteria make each type of pigment - chlorophylls, bacteriochlorophylls, bilins and carotenoids. They do it by using sets of biological machines called enzymes that work together in a production line called a biosynthetic pathway. We have found that we can create new pigment biosynthesis pathways by combining the genetic codes for enzymes from more than one type of photosynthetic bacterium. This teaches us more about how the natural enzymes and pathways work and being able to build or make something is the ultimate test of whether you understand it.
The first part of this research programme will create new pathways and combinations of pigments in a photosynthetic bacterium. The second part will find out how these new pigment combinations work together to absorb new colours of light from the solar spectrum both inside the cell, and on biomimetic silicon chips. The third part starts the process of converting a bacterial cell such as E. coli, which is colourless and lives by respiring oxygen the way humans do, into a photosynthetic cell. The simple way to do this is by importing a primitive light-powered protein called proteorhodopsin from oceanic bacteria, but we will also begin the more ambitious large-scale genetic engineering of E. coli and similar bacteria so they can make bacteriochlorophyll, bilin and carotenoid pigments. Such cells will have internal solar panels that allow them to use sunlight for the first time. These light-powered cell factories have great potential for future biotechnology and bioenergy applications such as the production of, for example, alcohols, alkanes and novel pharmaceuticals.
In the last part of this research programme we will take something that is already useful, in this case photosynthetic cells that make biodiesel, and use our pigment biosynthesis engineering to make them more efficient at using light to drive biodiesel production. We will go prospecting for new pigment biosynthesis genes, since we have only scratched the surface in terms of the number of pigment pathway genes out there in the oceans. New genes can be found using a machine that sees the colour of cells and plucks valuable single bacteria out of seawater so their DNA can be sequenced to look for new pigment pathways. We hope to use the genes we discover, as well as the genes we already know about, to build new bacteria that can capture and use solar energy. This knowledge is important to us all, not just because capturing and using solar energy fuels life, but it also holds the secret of using cells that one day could give us clean, unlimited energy and valuable chemicals from sunlight.
Future biotechnological applications of photosynthesis are likely to require multicoloured bacteria containing multiple pigments that can harvest more of the solar spectrum than evolution has demanded of them. That way they could use more solar energy for making chemicals useful for man. Achieving this would mean putting together 'mix and match' combinations of pigments from different bacteria inside one cell. This is now possible because we have been finding out how photosynthetic bacteria make each type of pigment - chlorophylls, bacteriochlorophylls, bilins and carotenoids. They do it by using sets of biological machines called enzymes that work together in a production line called a biosynthetic pathway. We have found that we can create new pigment biosynthesis pathways by combining the genetic codes for enzymes from more than one type of photosynthetic bacterium. This teaches us more about how the natural enzymes and pathways work and being able to build or make something is the ultimate test of whether you understand it.
The first part of this research programme will create new pathways and combinations of pigments in a photosynthetic bacterium. The second part will find out how these new pigment combinations work together to absorb new colours of light from the solar spectrum both inside the cell, and on biomimetic silicon chips. The third part starts the process of converting a bacterial cell such as E. coli, which is colourless and lives by respiring oxygen the way humans do, into a photosynthetic cell. The simple way to do this is by importing a primitive light-powered protein called proteorhodopsin from oceanic bacteria, but we will also begin the more ambitious large-scale genetic engineering of E. coli and similar bacteria so they can make bacteriochlorophyll, bilin and carotenoid pigments. Such cells will have internal solar panels that allow them to use sunlight for the first time. These light-powered cell factories have great potential for future biotechnology and bioenergy applications such as the production of, for example, alcohols, alkanes and novel pharmaceuticals.
In the last part of this research programme we will take something that is already useful, in this case photosynthetic cells that make biodiesel, and use our pigment biosynthesis engineering to make them more efficient at using light to drive biodiesel production. We will go prospecting for new pigment biosynthesis genes, since we have only scratched the surface in terms of the number of pigment pathway genes out there in the oceans. New genes can be found using a machine that sees the colour of cells and plucks valuable single bacteria out of seawater so their DNA can be sequenced to look for new pigment pathways. We hope to use the genes we discover, as well as the genes we already know about, to build new bacteria that can capture and use solar energy. This knowledge is important to us all, not just because capturing and using solar energy fuels life, but it also holds the secret of using cells that one day could give us clean, unlimited energy and valuable chemicals from sunlight.
Technical Summary
This sLoLa programme is organised into four interdependent sections. In the first, we will combine chlorophyll (Chl), bacteriochlorophyll (BChl) and carotenoid biosynthesis genes from bacteria and plants to create new pigment pathways tailored that extend the spectral range for absorbing solar energy. The morphology, organisation and performance of altered photosynthetic complexes and membranes comprising these novel pigments will be assessed in the second section using functional, proteomic and state-of-the-art imaging approaches, including electron microscopy, affinity mapping AFM, and super-resolution optical imaging. By applying selection pressure to grow under defined, restricted light regimes we will select engineered strains with improved photosynthetic performance. In the third part of the programme we will compile and then test multigene constructs for biosynthesis of proteorhodopsins, pigments, lipids, assembly factors and photosystem apoproteins. Following co-expression of these gene assemblies in heterotrophic bacteria such as E. coli and Ralstonia eutropha the outcomes will be assessed using simple growth tests, mass spectrometry, atomic force and electron microscopy, and spectroscopy. The fourth part of the programme, to be conducted in parallel with the other sections, proceeds initially by optimising the light-driven production of alkanes in Rhodobacter sphaeroides and Synechocystis, and by establishing an electro-biosynthesis platform for metabolite production in Ralstonia eutropha and Rhodobacter sphaeroides. Then this section builds on the design and construction of new photosynthetic systems in the other sections; proteorhodopsins, engineered pigment biosynthesis and photosystem pathways, augmented by hitherto undiscovered genes, will be used to enhance solar-powered production of metabolites in photosynthetic bacteria and in heterotrophs converted for absorbing and using light.
Planned Impact
Economic impacts
Nanotechnology: Development of nanotechnological tools for imaging and functional measurements of biological samples. AFM, including affinity-mapping, and super-resolution optical microscopy, as well as picosecond lifetime and spectral imaging, will be developed and applied to membranes from plants and bacteria, and to enzymes and surface-attached nanoarrays of membrane protein complexes. AJC will test new optical microscope technologies and develop new applications and data analysis approaches for industrial partner Andor Technology. Bruker Nano Surfaces Division test new developments in probe manufacture in the CNH laboratory.
Separation technologies. We collaborate with Thermofisher on innovative methodologies for separating peptides prior to MS analysis, and with Bruker for mass spectrometry.
Synthetic biology. Dr Pin Yang, CEO of InCelliGEN, a biotechnology company specialising in genome and pathway synthesis, has expressed interest in our programme to construct 'photosynthesis modules' for expression in a variety of bacteria.
High-Throughput Techniques. Development of novel high-throughput screening methods of single colonies of mutant bacterial strains (CNH/WH) will be undertaken in collaboration with BMG LabTech. Utilising next generation fluorescent plate readers which can produce fluorescent spectra will decrease the time taken to screen for new fluorescent pigments or knockouts.
Biofuels, CO2 remediation and Biosensors. WH and CNH will work with Tata Steel, who are looking to cut CO2 emissions by 50% by 2015. Waste CO2 could be used as a carbon source for electrobiosynthesis in R. eutropha or R. sphaeroides.
Societal Impacts
The sLoLa team encompasses molecular genetics and biosynthetic pathway engineering (Huang, Hunter), biochemistry, spectroscopy, structural studies using electron microscopy and atomic force microscopy (Bullough, Hunter, Johnson), mass spectrometry (Dickman), and super-resolution/spectral imaging/lifetime microscopy (Cadby). The multidisciplinary nature of this research project will train young researchers in a wide variety of practical skills, providing an outstanding training environment for PhD students and postdoctoral scientists, working to meet ambitious technical goals and targets.
Communication and engagement with potential beneficiaries
Synthetic biology, food and energy security and the nano-scale world are highly topical in the media, and the work in this application will be communicated by, for example, the Krebs Festival, to be held in November 2015. This three-month, large-scale public engagement and outreach activity will be supported by this sLoLa; Matt Johnson and named PDRA Dr Nathan Adams are part of the steering committee.
Ongoing University outreach activities for younger audiences (Festival of the Mind, Mobile University, Sheffield Science and Engineering Festival, Researchers Night) will be supported by PIs (Reid/Cadby/Johnson), and PDRAs and PhD students will be encouraged to present their research at these events over the course of the sLola.
Nathan Adams is a presenter at national science festivals; in 2013 he undertook 28 science presenter/public engagement activities at the British Science Festival, Bang!, Cheltenham Science Festival, CBBC Live, Edinburgh Festival, TV and Radio with the support of the University and professional bodies, reaching over 2 million people through media appearances and demonstrations of science. NA will continue his science presenting on TV and radio during the sLoLa. PIs and PDRAs will disseminate important findings via press releases and interviews with the broadcast and print media, in collaboration with the office for public engagement.
Nanotechnology: Development of nanotechnological tools for imaging and functional measurements of biological samples. AFM, including affinity-mapping, and super-resolution optical microscopy, as well as picosecond lifetime and spectral imaging, will be developed and applied to membranes from plants and bacteria, and to enzymes and surface-attached nanoarrays of membrane protein complexes. AJC will test new optical microscope technologies and develop new applications and data analysis approaches for industrial partner Andor Technology. Bruker Nano Surfaces Division test new developments in probe manufacture in the CNH laboratory.
Separation technologies. We collaborate with Thermofisher on innovative methodologies for separating peptides prior to MS analysis, and with Bruker for mass spectrometry.
Synthetic biology. Dr Pin Yang, CEO of InCelliGEN, a biotechnology company specialising in genome and pathway synthesis, has expressed interest in our programme to construct 'photosynthesis modules' for expression in a variety of bacteria.
High-Throughput Techniques. Development of novel high-throughput screening methods of single colonies of mutant bacterial strains (CNH/WH) will be undertaken in collaboration with BMG LabTech. Utilising next generation fluorescent plate readers which can produce fluorescent spectra will decrease the time taken to screen for new fluorescent pigments or knockouts.
Biofuels, CO2 remediation and Biosensors. WH and CNH will work with Tata Steel, who are looking to cut CO2 emissions by 50% by 2015. Waste CO2 could be used as a carbon source for electrobiosynthesis in R. eutropha or R. sphaeroides.
Societal Impacts
The sLoLa team encompasses molecular genetics and biosynthetic pathway engineering (Huang, Hunter), biochemistry, spectroscopy, structural studies using electron microscopy and atomic force microscopy (Bullough, Hunter, Johnson), mass spectrometry (Dickman), and super-resolution/spectral imaging/lifetime microscopy (Cadby). The multidisciplinary nature of this research project will train young researchers in a wide variety of practical skills, providing an outstanding training environment for PhD students and postdoctoral scientists, working to meet ambitious technical goals and targets.
Communication and engagement with potential beneficiaries
Synthetic biology, food and energy security and the nano-scale world are highly topical in the media, and the work in this application will be communicated by, for example, the Krebs Festival, to be held in November 2015. This three-month, large-scale public engagement and outreach activity will be supported by this sLoLa; Matt Johnson and named PDRA Dr Nathan Adams are part of the steering committee.
Ongoing University outreach activities for younger audiences (Festival of the Mind, Mobile University, Sheffield Science and Engineering Festival, Researchers Night) will be supported by PIs (Reid/Cadby/Johnson), and PDRAs and PhD students will be encouraged to present their research at these events over the course of the sLola.
Nathan Adams is a presenter at national science festivals; in 2013 he undertook 28 science presenter/public engagement activities at the British Science Festival, Bang!, Cheltenham Science Festival, CBBC Live, Edinburgh Festival, TV and Radio with the support of the University and professional bodies, reaching over 2 million people through media appearances and demonstrations of science. NA will continue his science presenting on TV and radio during the sLoLa. PIs and PDRAs will disseminate important findings via press releases and interviews with the broadcast and print media, in collaboration with the office for public engagement.
Organisations
Publications
Adams NB
(2016)
The catalytic power of magnesium chelatase: a benchmark for the AAA(+) ATPases.
in FEBS letters
Adams NB
(2016)
Nanomechanical and Thermophoretic Analyses of the Nucleotide-Dependent Interactions between the AAA(+) Subunits of Magnesium Chelatase.
in Journal of the American Chemical Society
Adams NBP
(2020)
The active site of magnesium chelatase.
in Nature plants
Adams NBP
(2019)
Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand.
in Scientific reports
Adams PG
(2018)
Correlated fluorescence quenching and topographic mapping of Light-Harvesting Complex II within surface-assembled aggregates and lipid bilayers.
in Biochimica et biophysica acta. Bioenergetics
Barnett SFH
(2017)
Repurposing a photosynthetic antenna protein as a super-resolution microscopy label.
in Scientific reports
Benson SL
(2015)
An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis.
in Nature plants
Bisson C
(2017)
The molecular basis of phosphite and hypophosphite recognition by ABC-transporters.
in Nature communications
Bryant D
(2020)
Biosynthesis of the modified tetrapyrroles-the pigments of life
in Journal of Biological Chemistry
| Description | This sLola programme grant spanned seven years, and over 90 papers were published on the topic of photosynthesis, the process that drives nearly all life on Earth. The sLola programme advanced our understanding of the biosynthesis, organisation and function of photosynthetic membranes, and we developed approaches to modify existing photosystems and to build new photosynthetic systems from scratch. The long term aim is to engineer improved photosynthetic reactions, to absorb more CO2 from the atmosphere and to produce more food. Significant new knowledge generated. • Photosynthesis requires chlorophylls and carotenoid pigments. We found the key parts of the chlorophyll biosynthesis pathway and to prove that we had found all the components we assembled the whole sequence of reactions in the non-pigmented bacterium Escherichia coli, turning the cells green. • We also succeeded in changing the carotenoid pathway so new photosynthetic complexes could be made to harvest new regions of the solar spectrum. • We advanced our knowledge of how photosynthesis works in plants, cyanobacteria and plants, in particular by determining the 3-D structures of the chlorophyll-carotenoid-protein complexes that absorb and use solar energy. • The Blue Waters supercomputer, on the 100-million-atom scale, enabled all the photosynthetic reactions in a simple bacterial cell to be simulated for the first time, paving the way to first-principles modelling of whole living cells. • It was shown that the light activated protein proteorhodopsin extends the viability of bacterial cells and it can convert previously heterotrophic cells to a photosynthetic growth mode. • We tailored a de novo-designed protein for the study of excitonic up- and downconversion, which behaved as an organic semiconductor. • We used Raman microscopy for 'bioprospecting' the oceans to find new bacteria that use solar energy. New or improved research methods or skills developed. • We invented new nanotechnology approaches to assemble photosynthetic energy transfer reactions on silicon and glass surfaces. Coupling such reactions to plasmonic structures has the potential to create new technologies for solar energy capture, quantum computing, quantum communications and photocatalysis. • New methods were developed to measure the interactions between single electron transfer protein molecules. • We developed SimCells - chromosome-free bacterial compartments that can be programmed to manufacture and deliver metabolites, for example potent anticancer drugs against a variety of cancer cell lines. To what extent were the award objectives met? Many of the original objectives were met, but we did not succeed is assembling all the photosynthetic reactions in E. coli, nor did we advance the biofuels part of the grant. On the other hand, we succeeded with many things that could not have been even imagined when the proposal was written in 2014 (eg protein 3D structures, Sim Cells, supercomputing). Important new research questions opened up. Can we create new 'smart' cells, first simulating them in a computer, then designing them for applications in biomanufacturing, healthcare, agriculture, biosensing and bioremediation? Particularly noteworthy new research networks/collaborations/partnerships. This sLola provided a platform for the award of a €7.5M ERC Synergy programme grant (2020-26) to CNH and collaborators Dario Leister (Munich) and Josef Komenda (Trebon, Czech Republic). |
| Exploitation Route | Our papers on synthetic biology - SimCells, large scale computing of living systems, assembly of modified biosynthetic pathways, nanotechnology with biological components, de novo-designed organic semiconductor proteins - could be taken forward for biomanufacturing, biomedicine, bioremediation and biocomputing. For example, one of us (Prof. Wei Huang) has formed a spin-out company, Oxford SimCell Ltd, that uses non-replicating bacterial SimCells to manufacture and deliver metabolites, for example potent anticancer drugs against a variety of cancer cell lines. Our development of de novo-designed proteins has potential for biocompatible excitonic up- or down-converting materials complexed with native or non-native biological systems, which could be harnessed for biomedical applications by converting highly penetrating low-energy light, generating deleterious photochemical reactions to kill tumours, for example. The designed four-helix bindle protein, and derivatives thereof, can additionally be adapted to bind to glass or metallic surfaces, enabling direct patterning of highly thermostable molecular aggregates and the possibility of exploring strong light-matter interactions in well-defined molecular systems. |
| Sectors | Agriculture, Food and Drink,Energy,Environment,Manufacturing, including Industrial Biotechology |
| Description | Economic impacts 1. Nanotechnology: Development of nanotechnological tools for imaging and functional measurements of biological samples. We conducted alpha and beta tests of AFM probes from the Bruker fabrication facility in Santa Barbara, to assess their suitability for high-resolution nanomechanical and topological imaging of biological membranes. The in-kind benefit from our close relationship with Bruker established over many years was worth ~£7500. The feedback we provide directly informs Bruker's probe manufacturing process and promises to enhance the resolution routinely available to other biological users through improved probe sharpness 2. Microscale thermophoresis collaboration with Nanotemper Technologies GmbH The cutting edge technique of microscale thermophoresis has allowed us to rapidly understand the binding kinetics of multiple protein-protein and protein-ligand systems. Dr Nate Adams worked with NanoTemper Technologies GmbH, the developers of the technique, to optimise our experiments for complex multisubunit proteins. This knowledge has been transferred back to the company in the form of talks at their symposiums. Dr Nate Adams was subsequently appointed as Senior Scientist at NanoTemper Technologies. 3. Super-resolution imaging collaboration with SciMeasure Analytical Systems (Georgia, USA) and Cairn Research (Kent, UK) The collection of techniques known under the term "super resolution" won the 2015 Nobel prize in Chemistry for achieving sub-diffraction imaging, and have changed the world of biological imaging. Dr Ashley Cadby collaborated with two companies; SciMeasure Analytical Systems (Georgia, USA) and Cairn Research (Kent, UK), successfully developing and testing on testing a novel camera architecture known as Non Destructive Readout. 4. Separation technologies with ThermoFisher. ThermoFisher has provided benefit to the sLola by providing in-house training to Dr Phil Jackson and Prof Mark Dickman on the operation, maintenance and data analysis associated with the QE HF mass spectrometer. The ongoing collaboration with ThermoFisher (Dr Ken Cook) utilises and develops novel bioseparations interfaced with mass spectrometry for the analysis of peptides and proteins which underpin a number of projects associated with the sLola. 5. Mass spectrometry with Bruker Daltonics. Bruker Daltonics trained Dr Phil Jackson on the installation and operation of APCI source on the maXis UHR TOF. 6. Spin-out company for non-replicating bacterial SimCells to manufacture and deliver metabolites Prof. Wei Huang has formed a spin-out company, Oxford SimCell Ltd, that uses non-replicating bacterial SimCells to manufacture and deliver metabolites, for example potent anticancer drugs against a variety of cancer cell lines. Societal Impacts 1. Training of the next generation of multidisciplinary academic and industrial scientists. The sLoLa team encompassed molecular genetics, biochemistry, spectroscopy, electron microscopy atomic force microscopy, mass spectrometry and super-resolution optical microscopy, providing an outstanding cross-discipline training environment for PhD students and postdoctoral scientists. Society requires scientists with the intellectual ability to produce the innovations that are needed for a successful bio-based economy. The multidisciplinary nature of this research project trained young researchers in a wide variety of practical skills that allow them to think of innovative, cross-discipline solutions to crucial biological problems. As a direct benefit of employment on the sLola programme grant several postdoctoral scientists secured positions in universities, biotechnology companies, and at national science facilities: • Dr Dan Canniffe - Tenure Track Fellow, Institute of Systems, Molecular and Integrative Biology, University of Liverpool • Dr Andrew Hitchcock, Royal Society University Research Fellow, School of Biosciences, University of Sheffield • Dr Nate Adams - Senior Scientist at NanoTemper Technologies Gmbh, Munich • Dr David Swainsbury, Lecturer, School of Biological Sciences, University of East Anglia • Dr Guangyu Chen, Tenure-track Associate Professor, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University • Dr Pu Qian, Research & Development Scientist III at Thermo Fisher Scientific, Eindhoven, Netherlands • Dr David Farmer, PDRA, Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire. • Dr Craig MacGregor-Chatwin, PDRA, Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire. Outreach and science communication (a) Dr. Matt Johnson performed a leadership role (together with Dr Nate Adams) in organising the 2015 KrebsFest Science Festival in Sheffield and series of Outreach events, which was Highly Commended in the Public Engagement and Advocacy category at the Association of Research Managers and Administrators (ARMA) in June 2016. KrebsFest included nine collaborative projects, new arts commissions, an exhibition and events in Sheffield's Winter Garden which included a giant 28 metre inflatable E. coli being unveiled, an exhibition in Western Bank Library, a large-scale public open night, a schools project challenging schoolchildren to make a film about what inspires them about science shown at a dedicated schools night, and three talks by Nobel Prize Winners and a launch. It has a continuing legacy through the University's ITunes service. (b) Dr Nate Adams an sLola PDRA, undertook a wide variety of science outreach activities (see below). Date Activity Venue Type & size of audience Venue 27/08/2015 Presenter Shambala Music and Arts Festival Mixed - 100 Northamptonshire 06/11/2015 Producer KrebsFest Mixed - 450 Sheffield 10/11/2015 Producer KrebsFest Students - 200 Sheffield 13/11/2015 Producer KrebsFest Mixed - 1000+ Sheffield 13/11/2015 On screen KrebsFest NewsRound report Mixed Country wide 06/11/2015 Artist HiddenWorlds exhibit Mixed - 5000+ Sheffield 19/02/2016 Designer SmashFest Children London 19/02/2016 Presenter SmashFest Children - 100 London 11/03/2016 Presenter Discover Night Children - 450 Sheffield 10/06/2015 Presenter Dr Nate's Travelling Rainbow Show Mixed - 450 Cheltenham Dr Nate Adams has also mixed science and art to visualise different interpretations of his biochemical research, particularly on the biosynthesis of chlorophyll: 2018 Festival of the Mind: The Sound of Science, audience of 750. Nate Employed lots of musicians, and the content was played on BBC 6music, is on vinyl CD and the book he wrote for it is being released in May 2022. 2019 Aegis and Metabolon tour went to Hartlepool 2020, Cheltenham Science Festival had to be online during lockdown. The Sound of Science fwas presented online from Nate's home, with thousands of viewers. Nate had another show 'Colourful Science' in which Nate demonstrated chlorophyll fluorescence from his home; there were ~1000 viewers and it featured on BBC news. 2020 Festival of the Mind - Physical Education. Circus science to illustrate Nate's ChlH chlorophyll biosynthesis paper in Nature Plants. Nate employed 4 circus artists during lockdown, with funding from Performing Arts North and the Royal Society of Biology. (c) Fulldome planetarium show, Birth of Planet Earth. Photosynthesis is responsible for providing energy for most life on Earth, and requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We have summarised this process in a movie, the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. New techniques were used to build, simulate, analyze, and visualize the structures shown in the movie, including the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers. https://www.youtube.com/watch?v=cUHxfpPkN6E The subsequent paper by Sener et al (Sener, M., Levy, S., Stone, J.E., Christensen, A.J., Isralewitz, Patterson, R., Borkiewicz, Carpenter, J., Hunter, C.N., Luthey-Schulten, Z and Cox, D (2021) Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. Parallel Computing, 102 Article number 102698) details the public outreach of science made possible by the fulldome planetarium show, Birth of Planet Earth, which introduces the story of life emerging on our planet and, particularly, how it is powered by harvesting the energy of sunlight, i.e., photosynthesis. This visualization is a retelling of the ancient story of "nourishment and growth," but with atomistic accuracy obtained by a decade of experimental and computational research, rendered accessible to children as a result of a multi-year collaboration between biophysicists, visualization scientists, and artists. The relevant papers are: Sener, M., Strümpfer, J, Abhishek, S., Hunter, C.N. and Schulten, K (2016) Overall energy conversion efficiency of a photosynthetic vesicle. eLife; 5:e09541. Singharoy, A., Maffeo, C., Delgado-Magnero, K.H. Swainsbury, D.J.K., Sener, M., Kleinekathöfer, U., Vant, J.E., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D., Stone, J., Phillips, J., Pogorelov, T.V., Mallus, M.I., Chipot, C., Luthey-Schulten, Z., Tieleman, P., Hunter, C.N., Tajkhorshid, E., Aksimentiev, A., and Schulten, K. (2019) Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell 179, 1098-1111.e23. Significant academic impact - new research areas and breakthroughs The funding for a multidisciplinary team of PDRAs allowed us to tackle scientific problems, and to publish research, that would not have been possible with separate research grants. We generated over 90 papers and generated significant new knowledge. • Completion of the pathway of chlorophyll biosynthesis, which greens our planet. • Elucidation of the 3D structures of photosynthetic complexes in phototrophic bacteria • We found all the enzymes that construct arguably the most important molecule on Earth, chlorophyll. Billions of tonnes of this molecule are produced annually, but only until recently did we uncover every single step in the process, assembling the pathway in E coli and turning it green, and in doing so prove we had every enzyme in the pathway. • We used atomic force microscopy to reveal the membrane organization of photosystem complexes in Prochlorococcus, the most abundant phototrophic organism on Earth. A global abundance of 2.9 ± 0.1 × 1027 Prochlorococcus cells in the oceans fix 4 Gigatonnes of carbon per year, which is comparable to the total primary productivity of the world's croplands. • Simulation of photosynthesis on the 100-million-atom scale using the Blue Waters supercomputer • De novo-design of a protein to perform as an organic semiconductor. • We used Raman microscopy for 'bioprospecting' the oceans to find new bacteria that use solar energy. • We invented new nanotechnology approaches to assemble photosynthetic energy transfer reactions on silicon and glass surfaces. Coupling such reactions to plasmonic structures has the potential to create new technologies for solar energy capture, quantum computing, quantum communications and photocatalysis. • New methods were developed to measure the interactions between single electron transfer protein molecules. • We developed SimCells - chromosome-free bacterial compartments that can be programmed to manufacture and deliver metabolites, for example potent anticancer drugs against a variety of cancer cell lines. |
| First Year Of Impact | 2015 |
| Sector | Energy,Manufacturing, including Industrial Biotechology |
| Impact Types | Cultural,Societal,Economic |
| Title | How the O2-dependent Mg-protoporphyrin monomethyl ester cyclase forms the fifth ring of chlorophylls |
| Description | Data-files acquired by reverse phase liquid chromatography coupled online to electrospray-ionisation mass spectrometry (Q Exactive HF, Thermo Scientific).(1) 20200213_PJ_GC_MS1: full-scan MS, 500-700 m/z(2) 20200213_PJ_GC_PRM: product ion scans by parallel reaction monitoring for cyclase substrate MgPME, product DV PChlide a, and catalytic intermediates 131-hydroxy-MgPME and 131-keto-MgPME at m/z 598, 611, 614 and 612 respectively.Thermo RAW files are included in mzML format which is readable by open source applications such as SeeMS (http://proteowizard.sourceforge.net/download.html). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.shef.ac.uk/articles/dataset/How_the_O2-dependent_Mg-protoporphyrin_monomethyl_ester... |
| Title | How the O2-dependent Mg-protoporphyrin monomethyl ester cyclase forms the fifth ring of chlorophylls |
| Description | Data-files acquired by reverse phase liquid chromatography coupled online to electrospray-ionisation mass spectrometry (Q Exactive HF, Thermo Scientific).(1) 20200213_PJ_GC_MS1: full-scan MS, 500-700 m/z(2) 20200213_PJ_GC_PRM: product ion scans by parallel reaction monitoring for cyclase substrate MgPME, product DV PChlide a, and catalytic intermediates 131-hydroxy-MgPME and 131-keto-MgPME at m/z 598, 611, 614 and 612 respectively.Thermo RAW files are included in mzML format which is readable by open source applications such as SeeMS (http://proteowizard.sourceforge.net/download.html). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.shef.ac.uk/articles/dataset/How_the_O2-dependent_Mg-protoporphyrin_monomethyl_ester... |