Genetics and proteomics of haloarchaea from Deep Lake, Antarctica

• Main Author: Liao, Yan
• Format: Doctoral or Postdoctoral Thesis
• Language: unknown
• Published: UNSW Sydney 2017
• Subjects: Proteomics; Psychrophilic haloarchaea; Genetics; FOS Biological sciences; Cold adaptation; Antarctica; Antarctic; Vestfold; Vestfold Hills; Antarc*
• Online Access: https://dx.doi.org/10.26190/unsworks/3129; http://hdl.handle.net/1959.4/57339

Psychrophilic haloarchaea dominate life in Deep Lake, a monomictic hypersaline lake in the Vestfold Hills of Antarctica. Halorubrum lacusprofundi and Halohasta litchfieldiae represent ~ 10% and ~ 44% of the Deep Lake community, respectively. Their relative abundance has been linked to genomic distinctions including an ability to utilize specific nutrients. A gene transfer system was developed for Hrr. lacusprofundi, the first for any psychrophilic Archaea. A gene knockout was constructed for an acetamidase/formamidase gene, which represents a class of genes not previously experimentally studied in Archaea. Disruption of the gene resulted in the inability of cells to utilize acetamide for growth. By investigating the phylogeny of acetamidases/formamidases in Bacteria and Archaea and the environmental relevance of acetamide, it was concluded that accumulation of acetamide-related pollutants may promote the selection of species harboring acetamidase/formamidase genes. An integrative approach combining microscopy and quantitative proteomics enabled a comprehensive investigation of ecologically relevant mechanisms of growth, survival and speciation of the two species. Specific growth temperatures, substrates and growth phase led to biofilm formation in Hrr. lacusprofundi, with extracellular DNA and quorum sensing linked to biofilm formation. Sucrose metabolism in Hht. litchfieldiae was shown to increase carbohydrate uptake and glycolysis and decrease pyruvate uptake and metabolism, TCA cycle, glycerol metabolism and gluconeogenesis. Both species responded to low temperature by modifying their cell morphology and cell envelope, maintaining osmotic balance and translation initiation, and altering RNA turnover and tRNA modification. Distinctions between the two species included DNA protection and repair strategies and pathways for metabolism of glycerol and pyruvate. Low temperature enhanced the levels of CRISPR Cas proteins and the core gene expression machinery in Hht. litchfieldiae. A novel pathway for PHA granule synthesis was proposed in Hrr. lacusprofundi. Overall, the research identified specific characteristics that may enhance the competitiveness of each species, and therefore represents a strong advance for Antarctic microbial ecology, hypersaline systems, and biology of Archaea. The development of the gene knockout system combines well with the development of proteomic methods, providing a solid basis for future studies of these important lake species.