The Flux Capacitor: How mitochondria modulate metabolic flux and gene expression

Lead Research Organisation: University College London
Department Name: Genetics Evolution and Environment

Abstract

Mitochondria are often called the powerhouses of the cell as they produce nearly all the energy needed for living. Recent research shows that mitochondria do much more than generate energy: they integrate virtually all metabolic inputs and outputs of cells. These inputs and outputs depend on diet, temperature, growth, age and physical demands. If mitochondria cannot match metabolic supply to demand, they signal a stress state to the nucleus resulting in changes in the activity of genes. These changes might ameliorate the stress, or if that fails, tip the cell towards programmed death. Mitochondria can be seen as 'flux capacitors'.

The problem is that mitochondria are uniquely vulnerable to mechanical faults. This is because the vital proteins that carry out respiration are encoded by two different genomes that have a tendency to diverge - genes in the mitochondria mutate nearly 50 times faster than those in the nucleus, and are inherited from the mother only, whereas genes in the nucleus are recombined by sex every generation. These radical differences in inheritance can result in mismatches that affect the performance of mitochondria - the flux capacitor itself becomes faulty, which impacts on both the inputs and outputs of the cell, and its stress state.

Mutations in either the mitochondrial or nuclear genes encoding the proteins involved in respiration can cause catastrophic diseases, and more subtle genetic differences contribute to common conditions such as diabetes, cancer, neurodegeneration and ageing. But the extent to which mismatches between mitochondrial and nuclear genes affect health through the lifecourse is uncertain, as there are hundreds of mitochondria in every cell, and their performance can differ substantially. Animal models show that 'mitonuclear mismatches' really do affect health, for example causing male infertility and altered lifespan. Even when the health effects are too subtle to notice, mitonuclear mismatches can alter the activity of thousands of genes. Because these mismatches are produced every generation, they most likely have substantial health impacts. Until recently, though, this has been nearly impossible to verify.

Our programme of research will analyse how mitonuclear mismatches affect the inputs and outputs of mitochondria, and how these changes impact on gene activity and health. We will use a model organism, the fruitfly Drosophila, in which mitochondrial genes have been deliberately mismatched to the nuclear genome. These flies have known health outcomes such as male infertility, but how their faulty mitochondria cause these defects is unknown; treatments that might improve their health are unknown for the same reasons.

We will address these questions using cutting-edge experimental methods. Specifically, we will measure mitochondrial performance in real time to establish how mitonuclear mismatches alter the function of different tissues over the lifecourse of males and females, and how mitochondrial performance is altered by dietary treatments. We will generate global profiles of metabolite levels, allowing us to relate mitochondrial function to the 'metabolomic profile' of each tissue. Finally, we will use Next Generation Sequencing to measure changes in gene activity in each tissue, with each treatment, in males and females. We will use this information to build a set of mathematical models that map changes in mitochondrial function to shifts in metabolic flux, gene activity and health, allowing us to generalise our conclusions to be valuable for human and animal health.

Our pilot studies show that we can indeed measure real-time changes in mitochondrial performance linked with male infertility. Antioxidant treatments have remarkably different outcomes depending on mitonuclear mismatches, in one case improving male fertility yet causing high (90%) mortality in female flies. We therefore anticipate our findings will have important implications for lifelong health.

Technical Summary

Mitochondria are central to metabolism but vulnerable to dysfunction, as respiratory proteins are encoded by two genomes (nuclear and mitochondrial) with radically different modes and tempi of evolution. Mitonuclear mismatches are produced each generation and can disrupt health, e.g. causing male infertility, altering lifespan and perturbing gene expression. But the incomplete penetrance of mitochondrial conditions means it has proved difficult to establish clear causality from alterations in mitochondrial function to changes in metabolic flux, shifts in gene expression and distinct phenotypes. Drosophila can give unparalleled insights into the consequences of mitonuclear mismatches, as these can be isolated from confounding factors that affect other models. We will therefore use a fly model to elucidate how mitonuclear incompatibilities affect (i) mitochondrial physiology (using high-resolution fluororespirometry on individual fly tissues), (ii) metabolomic profile, and (iii) gene expression (using Next Generation Sequencing) enabling us to (iv) construct predictive metabolic flux models for both males and females. We will use one coadapted control line and two experimental lines in which the mitochondrial genome is mismatched to the nuclear genome, combined with three treatments designed to interfere with signalling between the mitochondria and nucleus. Finally, we will assess how mitochondrial function, metabolomic profile, gene expression and phenotypes evolve over the lifecourse of flies. Our pilot data has already uncovered striking differences in response to the antioxidant NAC, determined by mitonuclear incompatibilities; in one line male fertility improved but 90% of females died; NAC did not affect mortality in other lines. We therefore anticipate that our work will generate fundamental biological knowledge on how mitonuclear variations cause differences in physiology, wellbeing, drug interactions and lifelong susceptibility to disease between individuals.

Planned Impact

Who will benefit from this research?

Our considerations have highlighted seven particular groups of end users that we wish to target through our pathway to impact activities:

1) Investigators and scholars of the evolutionary history of eukaryotes (Academic/Public Sector Researchers e.g. Evolutionary Biologists)
2) Researchers and other stakeholders of eukaryote based biotechnological applications (Academic/Public Sector Researchers, Organisations e.g. Bioprocessing Research Industry Club (BRIC), and Private Sector/Industry)
3) Medical researchers of mitochondrial, metabolic, and ageing related diseases (Academic/Public Sector Researchers, Medical Practitioners)
4) Health policy makers and government bodies interested in increasing general population quality of life through healthy ageing. (Public Sector Health Researchers e.g. NIHR related, Public Sector Health Policy Makers e.g. NIHR, HRA and Department of Health)
5) Regulatory policy makers and regulatory body for treatments impacting on mitochondrial function and metabolism. (Public Sector Regulator e.g. EMA, MHRA)
6) Researchers, producers and distributors of nutritional supplements that may impact health via mitochondrial interventions. (Private Sector Stakeholders e.g. Pharma/Nutritional Supplement developers/producers)
7) Members of the public interested in mitochondria and healthy ageing guidelines. (General Public)

How will they benefit from this research?

Researchers interested in mitonuclear evolution and metabolism will gain insights from our data. Not only will we produce empirical data that with give vital insights into mitochondrial metabolism, but we will merge all the empirical data to produce a flux model. What we will deliver from this grant will be of interest to a wide range of scientists; from evolutionary ecologists to functional biologists.

Biomedical scientists, policy makers and government bodies will be interested in our findings because of their relevance to human complex diseases (the accumulation and impact of mitochondrial mutations), the disruption of adaptive mitonuclear combinations by human migration (the scope for the coevolution of beneficial mitonuclear combinations) and the limits of mitonuclear compatibility. Biomedical researchers and policy makers will rely on such data in order to develop rigorous, but sensitive, management of medical interventions, including mitochondrial replacement therapy and three-parent IVF, and to establish appropriate policies that regulate these applications.

By addressing the role of mitochondrial function in supporting healthy ageing this work could influence not only researchers but also policy makers and clinical practitioners, with consequent impact upon quality of life for the wider public. Moreover, our work will touch upon the effects of mitonuclear genomic incompatibility in determining health outcomes from pharmacological or other medical interventions. This could influence not only those involved in the research, development, and production of such interventions but also those tasked with setting and consequently those adhering to policy on medical and pharmacological regulation.

Finally, our research will be of broad interest to the wider community and school pupils. They have a natural fascination in mitochondrial disease and mitochondrial replacement therapy as a cure. The project findings will be made readily available to the general public and the project team will engage directly with schools, to make sure that the project findings are placed into a broad context of evolution and the life sciences.

Publications

10 25 50
 
Description Still mostly in talks to wide audiences, see specific examples
First Year Of Impact 2019
Sector Education,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural,Societal

 
Description Mitonuclear panel of fruit flies 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Dr Flo Camus has contributed to the Flux Capacitor grant and is now funded by the Leverhulme Trust for a related project on which I am a Co-I. This project involves generating a larger panel of mitonuclear fruitflies, with a wider range of phenotypes. We will be able to implement some of the information from this project into the Flux Capacitor project.
Collaborator Contribution Collaboration using equivalent mitonuclear fly model, with a wider panel but less detailed metabolic analysis then the Flux Capacitor, therefore complementary project funded by the Leverhulme Trust
Impact Just started.
Start Year 2019
 
Description Stalk-eyed fly metabolism in relation to gene drive 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Respirometry on male-female differences in stalk-eyed flies in relation to gene drive
Collaborator Contribution pilot studies of stalk-eyed fly metabolism in relation to Drosophila
Impact None yet
Start Year 2020
 
Description Bedales School, Eckersley Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Major annual lecture that has been going for more than 50 years. Bedales school plus several other local schools including St Swithuns, plus public through local radio station. Interacted with pupils for 2 hrs beforehand and had 1 hr Q&A afterwards
Year(s) Of Engagement Activity 2020
URL https://www.bedales.school/news/award-winning-biochemist-delivers-annual-eckersley-lecture
 
Description Big Biology podcast with Art Woods and Marty Martin 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact podcast on big ideas in biology, in this case on the role of energy flow in structuring evolution
Year(s) Of Engagement Activity 2020
URL https://www.bigbiology.org/season-3#episode49
 
Description Cambridge University Genetics Department seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Seminar, usual Q&A sessions and full-day discussions with faculty and students, including local companies working on ageing (Methuselah).
Invited to give lecture on the role of mitochondria in ageing at a major conference on ageing later this year as a result.
Year(s) Of Engagement Activity 2019
URL https://www.gen.cam.ac.uk/events/genetics-seminar-series-professor-nick-lane
 
Description City of London School, Science Week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk during science week, extended Q&A session afterwards
Year(s) Of Engagement Activity 2020
 
Description Guy Foundation online lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Lecture on the role of fields and quantum tunnelling in biology and especially bioenergetics
Year(s) Of Engagement Activity 2020
URL https://www.theguyfoundation.org/wp-content/uploads/2020/11/GMT20201118-141526_ProfNickLane_1920x108...
 
Description Hans Westerhoff festschrift, Free University of Amsterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Part of a symposium that made a serious effort to influence policy decisions based on systems biology. Dutch media presence and EU policy makers.
Video available of whole symposium (link below); my contribution from around 1:27.
Year(s) Of Engagement Activity 2020
URL https://av-media.vu.nl/mediasite/Play/de9c6bd53a34405fa80c01b39253f4551d
 
Description Highgate School, Science Week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact A talk and Q&A top Highgate School plus other local schools invited.
Year(s) Of Engagement Activity 2020
 
Description How the Light Gets In Festival, Kenwood House, September 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Gave a 45 minute lecture, a 10 minute filmed interview, and took part in a 1-hour debate on the evolution of life. Led to other invitations to give talks including at Highgate school and impacted on unusual audiences, including very positively on Brian Eno who was in the audience.
Year(s) Of Engagement Activity 2019
URL https://iai.tv/video/the-mystery-of-life?utm_source=YouTube&utm_medium=pinnedcomment
 
Description How the Light Gets In winter revel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact How the Light Gets In Wintrer Revel - took part in two online debates with Danniel Dennet, Sara Walker and Gunes Taylor; also gave a standalone public lecture. Took part in more informal discussions after each event with members of the public.
Year(s) Of Engagement Activity 2021
URL https://howthelightgetsin.org/festivals/winter/debates-and-speakers/speakers
 
Description Lecture to Eton College Scientific Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Lecture to the Eton College Scientific Society, including discussion beforehand with members and an extensive Q&A session afterwards
Year(s) Of Engagement Activity 2019
 
Description Migala YouTube channel, transmission especial 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact In-depth podcast interview on Mexican Youtube channel, attracting 30,000 viewers live plus another 10,000 afterwards
Year(s) Of Engagement Activity 2020
URL https://www.youtube.com/watch?v=UrL8Krm-Hls&t=5364s
 
Description Molecular Frontiers lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact 1 hour lecture followed by a 1-hour Q&A session here: https://www.youtube.com/watch?v=GJsUc29yajU&t=2893s
and lots of networking and interactions with school children at the University of Stockholm, see for example here: https://www.youtube.com/watch?v=2oluTiaxB5s
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=Ag6csAska_s&t=723s
 
Description Sheffield University, Animal and Plant Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited by ACCE DTP students in Sheffield as their annual seminar speaker (contributing the the Dept Animal and Plant Sciences seminar series).
Year(s) Of Engagement Activity 2019
URL https://www.sheffield.ac.uk/aps/research/seminar-programme
 
Description St Paul's Girls' School talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact St Paul's Girls' School plus other local schools invited. Lecture plus Q&A session, direct inspiration for girls to enter science
Year(s) Of Engagement Activity 2019
URL https://spgs.org/about/news/professor-nick-lane-visits-st-pauls/
 
Description St Pauls' School, Biomedical Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk to St Paul's School plus local schools invited. Aim to inspire next generation to go into science.
Year(s) Of Engagement Activity 2019
 
Description Student Christmas Crick Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited Christmas lecture for PhD students at the Crick Institute, plus broader audience of other researchers and some public. About 400 attendees. Good Q&A session afterwards followed by discussion at drinks reception.
Year(s) Of Engagement Activity 2020
URL https://www.crick.ac.uk/whats-on/student-christmas-crick-lecture-nick-lane
 
Description Symposium on Synthetic Biology, Bremen University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Online keynote lecture in PhD student symposium
Year(s) Of Engagement Activity 2020
URL https://www.uni-bremen.de/fb2/news/detailansicht/bmb-symposium-2020-synthetic-biology-a-canvas-for-c...
 
Description University of Melbourne Derek Denton Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Several related networking events and smaller seminars, valuable discussion particularly relating to metabolism in cancer
Year(s) Of Engagement Activity 2019
URL https://events.unimelb.edu.au/presenters/9534-professor-nick-lane