Cell cycle control in archaea

Lead Research Organisation: University College London
Department Name: MRC Laboratory of Molecular Cell Biology

Abstract

All life on earth can be divided up into three domains, eubacteria, archaea and eukaryotes (plants, animals, fungi etc). While eubacteria and archaeal cells tend to be small and to be simple in organisation, almost all eukaryote cells are large and share an extraordinarily complex internal architecture. Maintaining this order as cells grow and divide requires an elaborate set of molecular machines. Much of the core "cell division cycle" machinery involved in coordinating cell growth and division in complex eukaryotic cells was identified in pioneering genetic studies in the 1970s by Lee Hartwell and Paul Nurse. This knowledge now underpins much of biomedicine, from cancer, where the control of cell division goes awry, to regenerative medicine.

Until very recently it was not clear how complex eukaryotic cells might have arisen. Now, however, as the result of surveys of different environments to identify the genomes of organisms that can't be cultivated using metagenomic sequencing, it has become clear that many of the machines that function to maintain the dynamic internal organisation of eukaryote cells have their origins in archaea. An improved understanding of the origins of eukaryotes therefore requires a better understanding of archaeal cell biology - more specifically studies in TACK/Loki-family archaea to which we are most closely related.

Currently, far and away the best model system in which to carry out experimental research into our archaeal origins is Sulfolobus (a member of the TACK-family archaea). Importantly, Sulfolobus has a cell division cycle that seems to be ordered in a similar way to the eukaryotic cell cycle. However, little is known about the molecular machinery involved in its regulation. This is both because of the paucity of research in archaea, and the difficulties of doing cell biology in a small extremophile. We aim to change this. As the result of the recent development of Sulfolobus molecular genetics, cheap whole genomic sequencing (enabling mutant genes to be cloned) and the development of super-resolution microscopy (which enables these small cells to be imaged using light) now is the perfect time to use Sulfolobus as an experimental model to determine how the archaea cell division cycle is structured and to identify the molecular machines involved in its regulation. This will enable us to determine for example whether archaea have a cell cycle clock like that found in eukaryotes and checkpoints like those used to couple DNA replication to cell division in eukaryotes.

By doing so we expect to learn much about this understudied domain of life of earth. In addition, we expect this work to give us a better understanding of our origins, and of the function of the eukaryotic cell division cycle, which plays such an important role in human development, homeostasis and disease.

Technical Summary

Advances in metagenomic sequencing have shown that much of the machinery thought to define eukaryotic cell biology (e.g. actin/histones/smallGTPases/ubiquitin) has its origins in archaea. These recent findings helped to establish the case that eukaryotic cells likely arose through the merger of an archaeal host cell, which gave rise to the cytoplasm and nucleus, with a bacterial partner, which gave rise to modern day mitochondria.

Importantly, these striking similarities between the biology of eukaryotic cells and members of the TACK-family archaea extend to the cell cycle. Thus, key events in the eukaryotic cell division cycle, including DNA replication and abscission, are driven by machinery of archaeal origin. Furthermore, work by the late Rolf Bernander and colleagues revealed that the cell cycle in the TACK-family archaeon, Sulfolobus, is structured in a similar way to the eukaryotic cell cycle: origins undergo coordinated firing once per cell cycle, there is a temporal separation of DNA replication and division, and DNA segregation is coupled to the act of cell division. These findings suggest that the eukaryotic cell cycle arose from a primitive archaeal cell cycle.

Despite this, and despite the importance of studying the logic and origins of cell cycle control for our understanding of many aspects of basic human biology (from cancer to stem cell biology), we know next to nothing about the molecular mechanisms that underpin the archaeal cell division cycle. Here, we aim to change this using a combination of molecular genetic approaches, like those used to lay the foundations of our understanding of the eukaryotic cell division cycle in the 1970s, together with super-resolution imaging in Sulfolobus. Through this work we aim to dissect the logic of archaeal cell cycle control in detail and to identify the underlying molecular mechanisms involved. In doing so, we expect to shed light on the structure, function and origins of the eukaryotic cell cycle.

Planned Impact

We expect this research in archaeal cell biology to have a wide-ranging impact on our understanding of archaeal cells, on the evolutionary trajectory that led from an archaeal host to the first eukaryotes, and on our fundamental understanding of the conservation of cell biological systems and protein complexes across the domains of life.

Interdisciplinary academic impact:
To ensure that this work has such an academic impact, we aim to present our results, technical advances and ideas at conferences that span different fields. These will include the BSCB and ASCB (cell biology communities), evolutionary cell biology conferences (Janelia Farm/KITP Santa Barbara), and more specialized archaeal meetings (Cytoskeleton of plant and microbial cells, Gordon conference, to which BB is invited speaker in 2016). We will also aim to publish our results in a timely manner in high-impact open access journals that have a wide readership across disciplines.

Collaboration:
We will simultaneously ensure that this work reaches the larger community through frequent meetings and consultation with our collaborators at UCL (Ricardo Henriques, Finn Werner, Rob De Bruin), in continental Europe (Ann-Christin Lindas and Thijs Ettema) and in the US (Ethan Garner and Grant Jensen).

Exploitation of results and industrial partnership:
Tools developed through our work, such as the live-cell imaging platform for hyperthermophiles, will be made widely available to the community. We will also work with our partner Cherry Biotech to explore the possibility of commercialization, and potential industrial application to other extremophiles of industrial value. To aid skill dissemination, we have already put together a "working with Sulfolobus" protocol book which we have made available to our collaborators.

Training of the workforce:
We are also firmly committed to training postdocs (such as the Researcher Co-Investigator on the project) and graduate students at UCL (currently hosting two funded rotation students from the LMCB and BBSRC LiDo programs) to further expand the scope and potential of this work.

Dissemination, communication and public engagement:
We will strive to bring our results to the larger community through the publication of high impact open access papers, accompanied by reviews to help bridge disciplines. In parallel, we have developed a plan to engage with the larger public through public lectures, online media, school visits and UCL-organized public events. We have also specifically earmarked funds to participate in the Royal Society's Summer Exhibition, a landmark public event in the UK.

In summary, we expect that this research will bring long-term benefits to the UK research community: providing training to a new generation of interdisciplinary cell biologists; opening up new directions in a young field of archaeal cell biology research while placing UK scientists at centre stage, extending this collaborative network to Europe and beyond; bridging the fields of archaeal biology and eukaryotic cell biology; finally, expanding the potential of archaea species as a source for industrial innovation.

Publications

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Laine R (2019) NanoJ: a high-performance open-source super-resolution microscopy toolbox in Journal of Physics D: Applied Physics

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Stoddard PR (2017) Evolution of polymer formation within the actin superfamily. in Molecular biology of the cell

 
Description We have discovered what we think are some of the key regulators of the Saci cell cycle.
We are writing this up as a paper.
At the same time, we have developed live imaging and have seen the first ever Saci cell divisions love at 75°C
Exploitation Route We will be making our sulfolscope available to the community.
Sectors Environment

 
Description Marie Curie postdoc award for Gautam Day
Amount € 200,000 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 01/2017 
End 12/2019
 
Description Wellcome consortium grant to study the archaeal origins of the eukaryotic cytoskeleton
Amount £3,000,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2016 
End 11/2021
 
Title Archaeal genetics comes to the lab 
Description We are now one of the few labs in the world to do molecular genetics in Sulfolobus 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? No  
Impact In Saci we are now able to do i) tranformations ii) gene over-expression iii) dominant negative expression iv) mutagenesis v) CRISPRi 
 
Title Sulfoscope 
Description We have developed the first microscope for imaging extremophiles. We can image 1 micron cells at 75°C 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact This promises to open up archaeal and extremophile cell biology. 
 
Title Tools for cell confinement 
Description Micro-fabricated devices for confining and patterning cells 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact We expect these methods to be broadly useful to study cell shape and mechanics 
 
Description Archaeal origins of eukaryotic cell organisation 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Public 
PI Contribution Am leading a Wellcome collaboration
Collaborator Contribution Am leading a collaboration for Wellcome funding
Impact none yet
Start Year 2015
 
Description Archaeal origins of eukaryotic cell organisation 
Organisation University of Warwick
Country United Kingdom 
Sector Academic/University 
PI Contribution Am leading a Wellcome collaboration
Collaborator Contribution Am leading a collaboration for Wellcome funding
Impact none yet
Start Year 2015
 
Description Jeremy Carlton 
Organisation King's College London
Department Division of Imaging Sciences and Biomedical Engineering
Country Unknown 
Sector Academic/University 
PI Contribution We are discussing the role of ESCRTIII in abscission with Jeremy. We also have a joint PhD student who is working on a related project.
Collaborator Contribution So far its just discussion
Impact The collaboration is interdisciplinary. They are focusing on the biochemistry and we are focusing on the mechanics.
Start Year 2016
 
Description Sonja Albers lab 
Organisation Albert Ludwigs University of Freiburg
Country Germany 
Sector Hospitals 
PI Contribution We have had people exchange
Collaborator Contribution We have had people exchange and are drafting a joint project
Impact none yet
Start Year 2017
 
Description Sulfolobus - AC Lindas 
Organisation Stockholm University
Country Sweden 
Sector Academic/University 
PI Contribution Dr AC Lindas has been helping us to use Sulfolobus as a model system at the MRC LMCB.
Collaborator Contribution They have provided us with advice and reagents.
Impact This has helped us to win two grant awards: The Wellcome collaborative award and a BBSRC grant.
Start Year 2015
 
Description Sulfolobus - UCL 
Organisation University College London
Department MRC Laboratory for Molecular Cell Biology (LMCB)
Country United Kingdom 
Sector Academic/University 
PI Contribution Finn Werner and Rob de Bruin have been working together with us in establishing Sulfolobus as a model system at the LMCB.
Collaborator Contribution They have helped us with protocols and reagents.
Impact We now have Sulfolobus growing!
Start Year 2015
 
Description Wellcome consortium to study achaeal origins of eukaryotic cell organisations 
Organisation Harvard University
Country United States 
Sector Academic/University 
PI Contribution I lead this Wellcome funded consortium that includes: Jan Lowe, Ricardo Henriques, Ann Christin Lindas, Thijs Ettema, Ethan Garner, Mohan Balasubramanian
Collaborator Contribution We are working together
Impact We have published a review, have held meetings, and are developing ideas and projects.
Start Year 2016
 
Description Wellcome consortium to study achaeal origins of eukaryotic cell organisations 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Public 
PI Contribution I lead this Wellcome funded consortium that includes: Jan Lowe, Ricardo Henriques, Ann Christin Lindas, Thijs Ettema, Ethan Garner, Mohan Balasubramanian
Collaborator Contribution We are working together
Impact We have published a review, have held meetings, and are developing ideas and projects.
Start Year 2016
 
Description Wellcome consortium to study achaeal origins of eukaryotic cell organisations 
Organisation Stockholm University
Country Sweden 
Sector Academic/University 
PI Contribution I lead this Wellcome funded consortium that includes: Jan Lowe, Ricardo Henriques, Ann Christin Lindas, Thijs Ettema, Ethan Garner, Mohan Balasubramanian
Collaborator Contribution We are working together
Impact We have published a review, have held meetings, and are developing ideas and projects.
Start Year 2016
 
Description Wellcome consortium to study achaeal origins of eukaryotic cell organisations 
Organisation University of Warwick
Country United Kingdom 
Sector Academic/University 
PI Contribution I lead this Wellcome funded consortium that includes: Jan Lowe, Ricardo Henriques, Ann Christin Lindas, Thijs Ettema, Ethan Garner, Mohan Balasubramanian
Collaborator Contribution We are working together
Impact We have published a review, have held meetings, and are developing ideas and projects.
Start Year 2016
 
Description Wellcome consortium to study achaeal origins of eukaryotic cell organisations 
Organisation Uppsala University
Country Sweden 
Sector Academic/University 
PI Contribution I lead this Wellcome funded consortium that includes: Jan Lowe, Ricardo Henriques, Ann Christin Lindas, Thijs Ettema, Ethan Garner, Mohan Balasubramanian
Collaborator Contribution We are working together
Impact We have published a review, have held meetings, and are developing ideas and projects.
Start Year 2016
 
Description Core staff talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact I gave a talk to all the core staff in the building (secretariat/kitchen staff/receptionist etc).
Year(s) Of Engagement Activity 2019
 
Description EMBO Drosophila polarity meeting with Eli Knust in Ringberg 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I spoke at Eli's meeting
Year(s) Of Engagement Activity 2018
 
Description EMBO Molecular Biology of Archaea meeting Vienna 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I attended the meeting and shared ideas and data
Year(s) Of Engagement Activity 2018
 
Description EMBO meeting on life cycles in Plon Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave chalk talk at meeting on evolutionary life cycles
Year(s) Of Engagement Activity 2018
 
Description Eukaryotic evolution meeting - Royal Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Spoke at workshop
Year(s) Of Engagement Activity 2018
 
Description European Cytoskeletal Forum meeting 2017 - helsinki 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact spoke at cytoskeleton meeting
Year(s) Of Engagement Activity 2017
 
Description Janelia Farm meeting on origins of eukaryotes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave a talk
Year(s) Of Engagement Activity 2018
 
Description Lorenz workshop on evolution of biomolecular networks, Netherlands 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended and spoke at workshop
Year(s) Of Engagement Activity 2018
 
Description Sevilla 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk at the University
Year(s) Of Engagement Activity 2019
 
Description Talk Paris IBPS 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented work to Institute as part of their seminar programme
Year(s) Of Engagement Activity 2018
 
Description Talk at Edinburgh Wellcome cell biology centre 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Was invited seminar speaker
Year(s) Of Engagement Activity 2018
 
Description Talk at XVth UK Archaeal Workshop, Lancaster University. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact described plans to study evolution of cell division
Year(s) Of Engagement Activity 2017
 
Description Talk at the Genetics Department in Cambridge 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was invited by the post-docs
Year(s) Of Engagement Activity 2018
 
Description UK Archaeal annual meeting talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Spoke at annual meeting
Year(s) Of Engagement Activity 2019
 
Description Wellcome consortium meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We had a summer and winter meeting.
This included members from our Wellcome consortium from the US, UK, and Sweden
Year(s) Of Engagement Activity 2018
 
Description Woods Hole 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gave talk and participated in Woods Hole physiology course.
Year(s) Of Engagement Activity 2015