Periodic Reporting for period 5 - CELL-in-CELL (Understanding host cellular systems that drive an endosymbiotic interaction)
Periodo di rendicontazione: 2024-07-01 al 2025-05-31
Endosymbiosis is a phenomenon where one cell lives within another. This interaction can be beneficial for both partners. It can also be negative for one or -at times- both partners. As such, these interactions between cells can be unstable resulting in the interaction breaking down. Sometimes these interactions evolve so the partners become interdependent and inseparable. This can lead to the integration of one cell within the other. In these cases, the two cells have become one and they now have the same evolutionary destiny.
This process is incredibly important for evolution as it changes the characteristics of the interacting cells and creates novel evolutionary trajectories, allowing radical changes in cell function and organismal ecology to occur. This process has been fundamental for the evolution of cellular complexity and, indeed, played a critical role in the evolution of eukaryotes, a process that eventually led to the evolution of plants, fungi, and animals (including humans). There was probably no more important evolutionary transition in the history of life.
We understand very little about how endosymbiotic interactions can arise, and which cellular mechanisms underpin an interaction to allow such systems to become stable. The aim of this project was to develop an experimental system for identifying the cell biology that controls an endosymbiotic interaction, allowing two different species to manifest a long-term and intimate interaction. To do this we focussed on a microbe, a single-cell protist, called Paramecium bursaria, found in most ponds around the world, which can incubate hundreds of photosynthetic green algal microbes within its cell. This is an excellent system for understanding endosymbiotic interactions because the interaction has yet to become an obligate interaction, which means we can experimentally manipulate both partners separately and together. These organisms form an endosymbiotic partnership, exchanging metabolites and providing other functions important for their collective ecology.
The objective of this project was to develop approaches to understand how stable endosymbiotic interactions come to be and use these to identify the cellular systems that control endosymbiosis. Using our new approaches, we identified: the cellular systems that enabled host to recognise their endosymbiotic partners, the proteins that control metabolic trade between host and endosymbiont, the proteins that constitute and control the compartment that hosts the endosymbiotic partner cells, and how both partners can act to punish each other. Importantly, because our approach identified the genes that control this process, we then used phylogenomic analysis to investigate how these genes evolved so we understand the evolutionary changes that underpinned the evolution of an endosymbiotic systems.
This work allows us to compare and contrast different endosymbiotic systems and understand how such interactions can evolve. The work also provides us with the experimental capabilities to modify and perturb these interactions, providing understanding of the cellular and ecological factors that drive these important symbioses.
This process is incredibly important for evolution as it changes the characteristics of the interacting cells and creates novel evolutionary trajectories, allowing radical changes in cell function and organismal ecology to occur. This process has been fundamental for the evolution of cellular complexity and, indeed, played a critical role in the evolution of eukaryotes, a process that eventually led to the evolution of plants, fungi, and animals (including humans). There was probably no more important evolutionary transition in the history of life.
We understand very little about how endosymbiotic interactions can arise, and which cellular mechanisms underpin an interaction to allow such systems to become stable. The aim of this project was to develop an experimental system for identifying the cell biology that controls an endosymbiotic interaction, allowing two different species to manifest a long-term and intimate interaction. To do this we focussed on a microbe, a single-cell protist, called Paramecium bursaria, found in most ponds around the world, which can incubate hundreds of photosynthetic green algal microbes within its cell. This is an excellent system for understanding endosymbiotic interactions because the interaction has yet to become an obligate interaction, which means we can experimentally manipulate both partners separately and together. These organisms form an endosymbiotic partnership, exchanging metabolites and providing other functions important for their collective ecology.
The objective of this project was to develop approaches to understand how stable endosymbiotic interactions come to be and use these to identify the cellular systems that control endosymbiosis. Using our new approaches, we identified: the cellular systems that enabled host to recognise their endosymbiotic partners, the proteins that control metabolic trade between host and endosymbiont, the proteins that constitute and control the compartment that hosts the endosymbiotic partner cells, and how both partners can act to punish each other. Importantly, because our approach identified the genes that control this process, we then used phylogenomic analysis to investigate how these genes evolved so we understand the evolutionary changes that underpinned the evolution of an endosymbiotic systems.
This work allows us to compare and contrast different endosymbiotic systems and understand how such interactions can evolve. The work also provides us with the experimental capabilities to modify and perturb these interactions, providing understanding of the cellular and ecological factors that drive these important symbioses.
To understand which cell functions may control the Paramecium bursaria interaction, we have developed a targeted method for perturbing host function using RNAi. We have combined this work with genome and transcriptome sequencing and detailed bioinformatic analysis to understand the evolution of functional networks relevant to the endosymbiotic interaction. In parallel we have also conducted 3D proteomic analysis so we can understand where each protein is localised relative to the cellular architectures important for host-algal interaction. This work has allowed us to directly study host cellular systems that control an endosymbiotic interaction. Furthermore, these experiments can be conducted on a grand scale and, theoretically, every cellular system can be tested in a similar way. To our knowledge Paramecium bursaria is the first microbial endosymbiosis that is now tractable for reverse genetic manipulation in this manner.
Our work has targeted around 1000 host functions/genes selected from comparisons of functional networks, evolutionary reconstruction of the host proteomes, and identifying proteins that localise to the interface of the host/algal interaction.
This work has demonstrated:
1) Key protein neofunctionalisation events that have led to the evolution of the endomembrane system that controls the host symbiosomes (where symbiotic algae are housed within the host cell).
2) How the host barters amino acids with the algal endosymbionts and how this has been shaped by horizontal gene transfer.
3) An understanding of how the host has modified phagotrophic sensory systems for partner recognition.
4) The importance of phosphate in regulation of the endosymbiotic interaction, and how phosphate trade has been shaped by horizontal gene transfer.
5) The proteome that associates with symbiosomes and lysosomes and how these systems maintain or destroy the endosymbiotic interaction.
6) How the host and endosymbiont interact through RNA in a way that punishes host for large-scale destruction of the algae.
These factors are all important for the stability of the endosymbiotic interactions and therefore provide a model of how such important long-term and stable interactions can arise. Furthermore, they show we can now manipulate the interaction in several different ways, opening up the opportunity to conduct a combination of cell biological and ecological interaction-based experiments in order to fully understand the dynamics of an endosymbiotic cellular interaction both from the perspective of cell function and evolutionary ecology. This objective gained follow up funding from the UK Biotechnology and Biological Sciences Research Council (starting 2024).
All these observations represent individual papers whether published, in review, or in preparation. In concert with these works we have also published a series of protocol development papers and primary sequencing data papers, twinned with submissions of sequence data to public access databases and detailed descriptions of methodology to protocols.io.
Our work has targeted around 1000 host functions/genes selected from comparisons of functional networks, evolutionary reconstruction of the host proteomes, and identifying proteins that localise to the interface of the host/algal interaction.
This work has demonstrated:
1) Key protein neofunctionalisation events that have led to the evolution of the endomembrane system that controls the host symbiosomes (where symbiotic algae are housed within the host cell).
2) How the host barters amino acids with the algal endosymbionts and how this has been shaped by horizontal gene transfer.
3) An understanding of how the host has modified phagotrophic sensory systems for partner recognition.
4) The importance of phosphate in regulation of the endosymbiotic interaction, and how phosphate trade has been shaped by horizontal gene transfer.
5) The proteome that associates with symbiosomes and lysosomes and how these systems maintain or destroy the endosymbiotic interaction.
6) How the host and endosymbiont interact through RNA in a way that punishes host for large-scale destruction of the algae.
These factors are all important for the stability of the endosymbiotic interactions and therefore provide a model of how such important long-term and stable interactions can arise. Furthermore, they show we can now manipulate the interaction in several different ways, opening up the opportunity to conduct a combination of cell biological and ecological interaction-based experiments in order to fully understand the dynamics of an endosymbiotic cellular interaction both from the perspective of cell function and evolutionary ecology. This objective gained follow up funding from the UK Biotechnology and Biological Sciences Research Council (starting 2024).
All these observations represent individual papers whether published, in review, or in preparation. In concert with these works we have also published a series of protocol development papers and primary sequencing data papers, twinned with submissions of sequence data to public access databases and detailed descriptions of methodology to protocols.io.
We believe we have achieved key progress beyond the state of the art in two ways:
i) We have developed a targeted method for perturbing host function so we can identify host cell systems that control the interaction. To our knowledge, Paramecium bursaria is the first microbial endosymbiosis that is now tractable for reverse genetic manipulation on a grand scale, allowing the direct study of any host-encoded cellular systems that control an endosymbiotic interaction.
ii) We have identified multiple different cellular systems: metabolic exchange, cellular recognition, partner punishment, and endomembrane management which we can manipulate to alter the outcome of the interaction in different ways. As part of this work, we have shown the evolutionary processes that have allowed such systems to arrive, demonstrating a role for horizontal gene transfer but an absence of endosymbiotic gene transfer. This has helped to address a long-term debate in the field. Collectively these works will allow us to understand how complex endosymbiotic interactions arise and opens up the possibility of manipulation for bio-production and/or industrial scale carbon fixation.
i) We have developed a targeted method for perturbing host function so we can identify host cell systems that control the interaction. To our knowledge, Paramecium bursaria is the first microbial endosymbiosis that is now tractable for reverse genetic manipulation on a grand scale, allowing the direct study of any host-encoded cellular systems that control an endosymbiotic interaction.
ii) We have identified multiple different cellular systems: metabolic exchange, cellular recognition, partner punishment, and endomembrane management which we can manipulate to alter the outcome of the interaction in different ways. As part of this work, we have shown the evolutionary processes that have allowed such systems to arrive, demonstrating a role for horizontal gene transfer but an absence of endosymbiotic gene transfer. This has helped to address a long-term debate in the field. Collectively these works will allow us to understand how complex endosymbiotic interactions arise and opens up the possibility of manipulation for bio-production and/or industrial scale carbon fixation.