Skip to main content

The Evolution of the Chlamydiae - an Experimental Approach

Final Report Summary - EVOCHLAMY (The Evolution of the Chlamydiae - an Experimental Approach)

Chlamydiae (e.g. Chlamydia trachomatis) are primarily known as major bacterial pathogens, affecting over 100 Million of people worldwide each year. Yet chlamydiae are also ubiquitous in the environment where they thrive as symbionts in protists. This project employed experimental evolution approaches and state-of-the-art genome-based methods to better understand the biology and evolution of these unique intracellular bacteria.
Using chlamydial symbionts as model system, we have established a framework for carrying out evolution experiments to study evolutionary dynamics and adaptation of obligate intracellular bacteria. This included wet-lab experiments to establish long-term protist cultures and to cryo-preserve evolved populations, sequencing approaches and a bioinformatics workflow to analyze pool sequencing data, and infection assays to investigate fitness of evolved bacterial populations. Long term evolution experiments (LTEE) revealed substitution rates surprisingly similar to those observed for free-living bacteria. A number of mutational hot spots associated with temperature adaptation were identified, and we observed that within a range of 500 generations, the bacterial symbionts became less virulent, driving the symbiosis to a more mutualistic state.
Changes in gene expression likely play a key role during early adaptation. To this end we have established the first transcriptional landscape of a chlamydial symbiont during its entire developmental cycle. We found that Protochlamydia amoebophila shows a biphasic metabolism during infection, which involves energy parasitism and amino acids as carbon source during initial stages and a post-replicative switch to endogenous glucose-based ATP production. This represents a unique adaptation to exploit eukaryotic host cells, which likely contributed to the evolutionary success of this group of microbes.
Phylogenomic and advanced phylogenetic analysis of chlamydial genomes further revealed a massive expansion of eukaryotic-like ubiquitination-related genes, unmatched among bacteria. Gene birth-and-death evolution in concert with genomic drift might be responsible for the evolution of these gene families, which represents a previously undescribed mechanism by which isolated bacterial populations diversify.
Analyzing single-cell amplified chlamydial genomes from marine environments, we discovered chlamydiae that encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection – revealing a hitherto unknown potential of chlamydiae to adapt to different environments.
In the context of our genomic studies, we have also tested a popular hypothesis involving chlamydial symbionts in the emergence of primary photosynthetic eukaryotes by facilitating the interaction of cyanobacteria with their eukaryotic host cells. Yet in our analysis we found no compelling evidence from gene trees that chlamydiae played any role in establishing the primary plastid endosymbiosis.
In summary, genomics and experimental evolution approaches carried out in the context of this project has resulted in a number of original, highly unexpected and exciting findings, which together helped to advance our understanding of the biology and evolution of chlamydiae.