The architecture and evolution of host control in a microbial symbiosis
Lead Research Organisation:
University of Manchester
Department Name: School of Biological Sciences
Abstract
Beneficial symbioses are widespread in nature and underpin the function of both natural and manmade ecosystems. Moreover, by providing the interacting species with new ecological functions, symbiosis represents an important source of innovation and has thus played a crucial role in the evolution of life on Earth. In endosymbiosis, endosymbiont cells live within host cells and, as such, hosts have evolved mechanisms to control these endosymbionts, collectively termed "host control". However, despite decades of study, the molecular mechanisms that hosts use to control their endosymbionts remain poorly understood. In particular, how the architecture of host control systems has evolved to provide hosts with sufficient flexibility to respond to changing conditions whilst also being evolutionarily robust is unknown for any symbiosis.
Experimental studies of these questions in many symbioses are challenging because symbiotic organisms are not easily cultured independently nor typically amenable to genetic manipulation. In this project we overcome these challenges by using an experimentally tractable microbial symbiosis between the single-celled ciliate host Paramecium and the green alga Chlorella for which we have developed tools to "knockdown" the expression of target genes. In this symbiosis, hosts exchange nitrogen compounds derived from heterotrophy for carbohydrates from algal photosynthesis. In previous work we discovered that hosts modulate the number of algal symbionts in response to light intensity to maximise their fitness gains, but how hosts exert this control is not clear. In preliminary experiments for this proposal, we have discovered two putative mechanisms of host control, combining both positive and negative control levers, that hosts appear to use to regulate the number of algal symbionts per host cell. We predict that such multi-layered host control enables more precise regulation of endosymbiont number across environmental gradients whilst also providing a degree of redundancy so that the system has greater evolutionary robustness.
To test these ideas, we will perform "gene knockdown" experiments to disrupt either each individual or both host control mechanisms and measure how this affects host growth, plasticity and fitness. Using cutting edge molecular methods, we will discover how each of the host control mechanisms works through understanding their effect on gene regulation and metabolism in both the host and symbiont. Finally, we will use experimental evolution to discover how the symbiosis recovers from disruption of host control systems, and test whether multiple layers of control enhance evolutionary robustness.
Together these experiments will advance our understanding of the biology of symbioses, helping to solve the long-standing evolutionary puzzle of how and why symbioses evolve. In so doing the research will also provide insight into how symbioses and the important functions they perform can be maintained in natural and man-made ecosystems.
Experimental studies of these questions in many symbioses are challenging because symbiotic organisms are not easily cultured independently nor typically amenable to genetic manipulation. In this project we overcome these challenges by using an experimentally tractable microbial symbiosis between the single-celled ciliate host Paramecium and the green alga Chlorella for which we have developed tools to "knockdown" the expression of target genes. In this symbiosis, hosts exchange nitrogen compounds derived from heterotrophy for carbohydrates from algal photosynthesis. In previous work we discovered that hosts modulate the number of algal symbionts in response to light intensity to maximise their fitness gains, but how hosts exert this control is not clear. In preliminary experiments for this proposal, we have discovered two putative mechanisms of host control, combining both positive and negative control levers, that hosts appear to use to regulate the number of algal symbionts per host cell. We predict that such multi-layered host control enables more precise regulation of endosymbiont number across environmental gradients whilst also providing a degree of redundancy so that the system has greater evolutionary robustness.
To test these ideas, we will perform "gene knockdown" experiments to disrupt either each individual or both host control mechanisms and measure how this affects host growth, plasticity and fitness. Using cutting edge molecular methods, we will discover how each of the host control mechanisms works through understanding their effect on gene regulation and metabolism in both the host and symbiont. Finally, we will use experimental evolution to discover how the symbiosis recovers from disruption of host control systems, and test whether multiple layers of control enhance evolutionary robustness.
Together these experiments will advance our understanding of the biology of symbioses, helping to solve the long-standing evolutionary puzzle of how and why symbioses evolve. In so doing the research will also provide insight into how symbioses and the important functions they perform can be maintained in natural and man-made ecosystems.
Technical Summary
Endosymbiosis is fundamental to the origin of complex life, enabling evolutionary innovation and functional compartmentalization by the merger of once independent lineages into singular units. Endosymbiont cells live inside the cells of their host, and thus hosts have evolved to regulate and control their symbionts, but the underlying molecular mechanisms are not understood. In particular, how the architecture of host control has evolved to provide both ecological flexibility and evolutionary robustness is unknown.
We focus here on two newly discovered putative mechanisms of control that the host Paramecium bursaria (PB) uses to manipulate its Chlorella (CH) endosymbionts. Specifically, we hypothesise that the PB arginine-to-polyamine pathway acts as a provisioning-type positive control lever on endosymbionts, whereas the PB chitin processing pathway acts as a sanction-type negative control lever through endosymbiont digestion. We predict that such an integrated multi-layered host control architecture enables both precise modulation of endosymbionts by hosts (i.e., plasticity) and enhanced evolutionary robustness.
We test these ideas using RNAi knockdown experiments. We will knockdown either the PB arginine-to-polyamine pathway, the PB chitin processing pathway, or both, and measure the effects upon host growth, plasticity and fitness using established methods. In tandem, we will use a combination of photochemistry, RNAseq and LC-MS metabolomic analyses to understand the cellular impacts of disrupting host control on both PB and CH. We will use experimental evolution to understand the longer-term impacts of disrupting single or multiple control mechanisms for the symbiosis and mechanisms of compensatory evolution to mitigate deleterious effects of host control disruption. We will again use multi-omics methods to gain a detailed mechanistic understanding the molecular mechanisms enabling the evolutionary robustness of symbiosis.
We focus here on two newly discovered putative mechanisms of control that the host Paramecium bursaria (PB) uses to manipulate its Chlorella (CH) endosymbionts. Specifically, we hypothesise that the PB arginine-to-polyamine pathway acts as a provisioning-type positive control lever on endosymbionts, whereas the PB chitin processing pathway acts as a sanction-type negative control lever through endosymbiont digestion. We predict that such an integrated multi-layered host control architecture enables both precise modulation of endosymbionts by hosts (i.e., plasticity) and enhanced evolutionary robustness.
We test these ideas using RNAi knockdown experiments. We will knockdown either the PB arginine-to-polyamine pathway, the PB chitin processing pathway, or both, and measure the effects upon host growth, plasticity and fitness using established methods. In tandem, we will use a combination of photochemistry, RNAseq and LC-MS metabolomic analyses to understand the cellular impacts of disrupting host control on both PB and CH. We will use experimental evolution to understand the longer-term impacts of disrupting single or multiple control mechanisms for the symbiosis and mechanisms of compensatory evolution to mitigate deleterious effects of host control disruption. We will again use multi-omics methods to gain a detailed mechanistic understanding the molecular mechanisms enabling the evolutionary robustness of symbiosis.