Molecular Adaptations in Extremely Halophilic Protists

Abstract

Halophiles, organisms adapted to hypersaline habitats, represent unique cases in which to study evolutionary and ecological processes. To overcome the high level of stress in these habitats and to keep cellular components functional, halophiles have developed adaptations like amino acid content bias in proteins exposed to high salt, the use of solutes (organic or inorganic) to maintain high intracellular osmotic strength, and the salt-dependent adjustment of plasma membrane fluidity. Halophilic bacteria and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, very few investigations of halophilic phagotrophic protists, i.e. protozoa, have been conducted and knowledge about their evolution is lacking. The goal of this thesis is to characterize the molecular adaptations of halophilic protozoa, using as the primary model the stramenopile Halocafeteria seosinensis, through transcriptomic and genomic analyses, including a study of gene expression as a function of salinity. Examination of the inferred cytoplasmic proteomes of two halophilic protozoa, H. seosinensis and the heterolobosean Pharyngomonas kirbyi, indicated an increased hydrophilicity compared to the proteomes of marine protists, but an absence of the acidic signature commonly detected in halophilic prokaryotes that accumulate high levels of cytosolic inorganic ions. These results implied levels of intracellular salt in halophilic protozoa higher than in marine protists, but lower than in ‘salt-in’ microbes. Concordantly, genes putatively involved in synthesis and transport of organic osmolytes that could contribute to balance the osmotic equilibrium in H. seosinensis (e.g. hydroxyectoine) were up-regulated at high salt. Other salt-responsive genes were involved in stress response (e.g. chaperones), ion homeostasis (e.g. Na+/H+ transporter), metabolism and transport of lipids (e.g. sterol biosynthetic genes), carbohydrate metabolism (e.g. glycosidases), and signal transduction pathways (e.g. transcription factors). Several potential gene duplication and/or lateral gene transfer events could have favored adaptability to high salt (e.g. involving genes coding for ion transporters and peroxidase). This study proposes that a transition toward high-salt adaptation in halophilic protozoa probably requires a shift in amino acid composition of proteins and alteration of transcriptional programs, leading to modification of cell structure properties like membrane fluidity and increased stress resistance.