Characterization of a single TRAM domain RNA-binding protein from the Antarctic methanogen Methanococcoides burtonii

• Main Author: Taha, Taha
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: UNSW, Sydney 2016
• Subjects: RNA-seq; Antarctic microorganism; OB-fold; Ribosomal protein L5; RlmD; RumA; psychrophile; Ace Lake; Antarctic; The Antarctic; Antarc*; Antarctica
• Online Access: http://hdl.handle.net/1959.4/56384; https://unsworks.unsw.edu.au/bitstreams/f5c926e1-6ba9-4d4e-8b0c-dbaa98bd43a2/download; https://doi.org/10.26190/unsworks/19064

Methanococcoides burtonii, a methanogen that was isolated from Ace Lake, Antarctica, has proven to be a useful model for studying the molecular mechanisms of cold adaptation in Archaea. In Ace Lake, M. burtonii only experiences temperatures below 4 degrees and nucleic acid binding proteins have been inferred to play important roles in cold adaptation. In this thesis, the three M. burtonii ctr (cold-responsive TRAM domain) genes (proteins) Mbur_0304, Mbur_0604 and Mbur_1445 are referred to as ctr1 (Ctr1), ctr2 (Ctr2) and ctr3 (Ctr3), respectively. The thesis reports the first experimental studies to assess evolutionary, biophysical and structural properties and unique characteristics related to nucleic acid binding, including specific interactions describing putative roles of Ctr3 in the cell. During purification, E. coli nucleic acids consistently co-purified with recombinant Ctr3. The liberated nucleic acid from proteins was able to be digested with RNase indicating the bound nucleic acid was RNA. The bound RNA was able to be removed by treating the recombinant proteins with mild urea to partially unfold the protein, eluting the protein across a NaCl gradient, and refolding it by dialysis. Purification of recombinant RNA-free proteins allowed thorough assessment of the structure-function-stability relationship of Ctr3. Ctr3 unfolded reversibly with a two-state mechanism (Tm of ~ 50 degrees). The predicted three-dimensional structure of Ctr3 exhibited substantial structural similarities with the TRAM domain of RumA protein (RlmD) from E. coli. The aromatic residues, particularly the four phenylalanine residues of Ctr3 appeared to be surface exposed and in close proximity to each other on the putative RNA-binding surface, similar to the aromatic residues in RumA-TRAM domain, suggesting similar roles in RNA interaction. An on-column in vitro binding assay was used to capture M. burtonii RNA targets of Ctr3, and analysed relative to a complete reconstruction of the M. burtonii transcriptome obtained from total RNA. ...