Ancestral sequence reconstruction and functional expression of proteins involved in bacterial magnetosome biogenesis – ANCESMAG

Despite their simple cell architecture, prokaryotes have compartmentalized specific biochemical reactions into specialized and membrane-bounded structures that are similar to eukaryotic organelles. These organelle-like microcompartments are functionally diverse and complex, and uncovering the mechanisms underlying their biogenesis and maintenance is essential to biological research. However, little is known about the different evolutionary steps that led to their emergence and complexification.
Among these prokaryotic organelles, the magnetosome is one of the most complex because its assembly and functioning rely on the invagination of the cytoplasmic membrane and the interaction of many proteins and enzymes to biomineralize magnetic minerals. Compared to other organelles, the magnetic properties of the magnetosome give the opportunity to easily concentrate and observe them in magnetotactic bacteria (MTB) to which they are specific. Moreover, the fact that magnetosome genes are clustered within a large genomic region can facilitate the study of their evolution that remains controversial and unclear.
The known primary function of magnetosomes is to sense the Earth’s geomagnetic field lines to facilitate MTB navigation along the oxic-anoxic transition zone in aquatic sediments. However, which selective advantage arose from the ancestral non-magnetic magnetosome in the first MTB remains unknown. With the diversification of bacteria, MTB species evolved magnetosome chains with different shapes and chemical composition in different genus and phyla. The evolutionary steps that led ancestral magnetosomes to gradually emerge in their current diversity is difficult to assess without prokaryotic fossils. But some phylogenetic methods developed in evolutionary biology may fill this gap and help to resurrect paleo-magnetosomes over geological times. In ANCESMAG, we aim to use such approach to resurrect the ancestral magnetosome structure and chemical composition over magnetosome evolution. Through the heterologous expression of these paleomagnetosome gene clusters in a model MTB species, ANCESMAG will reveal how magnetosome biogenesis evolved and specialized.
For years, our consortium dramatically increased the knowledge on the genetic basis of magnetosome biogenesis and on MTB diversity and phylogenetic distribution. The magnetosome biogenesis relies on a large genomic region involving several dozens of genes among which 9 of them are shared by all MTB. Other magnetosome genes are associated to MTB with specific magnetosome shapes and chemical composition or to specific MTB species that are polyphyletically distributed in the Bacteria domain. In ANCESMAG, we will resolve the genes MTB and magnetosome evolutionary histories to propose a robust ancestral sequence reconstruction (ASR) of paleoproteins and paleo-gene clusters. To increase the accuracy of these evolutionary inferences, the genomes of few additional MTB within the diversity of early-diverging MTB phyla will be sequenced and added to our genome database. After genomic functional annotation, bacteria and magnetosome evolution will be inferred from the concatenation of shared riboproteins and magnetosome proteins.
From these trees, we will model the ancestral sequence and composition of the paleo-magnetosome gene cluster that will then be characterized in vivo. A magnetobacterial model strain specifically engineered for the heterologous expression of the magnetosome gene clusters will be used to resurrect the organelle phenotype evolution. Such an interdisciplinary approach using advanced methods developed in paleogenomics and synthetic biology will give the access to the past biology of organisms, and will in general improve our understanding of the evolutionary mechanisms leading to organelles emergence and complexification.