Cell cycle control in archaea

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.

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.

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.