Single TRAM domain RNA-binding proteins inArchaea: functional insight from Ctr3 from the Antarctic methanogenMethanococcoides burtonii

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TRAM domain proteins present inArchaeaandBacteriahave a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsiveTRAM domain protein3) from the Antarctic archaeonMethanococcoides burtoniithat has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3in vitrowas determined using RNA-seq. Ctr3-boundM. burtoniiRNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins withinArchaeacompared with their apparent absence inBacteria, and scarcity of Csps inArchaeabut prevalence inBacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.

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