Single TRAMdomain RNA‐binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii

• Published in: Environmental Microbiology
• Main Authors: Taha, Siddiqui, K. S., Campanaro, S., Najnin, T., Deshpande, N., Williams, T. J., Aldrich‐Wright, J., Wilkins, M., Curmi, P. M. G., Cavicchioli, R.
• Other Authors: Australian Research Council
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2016
• Subjects: Antarctic; The Antarctic; Antarc*
• Online Access: http://dx.doi.org/10.1111/1462-2920.13229; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1462-2920.13229; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13229; https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1462-2920.13229; https://sfamjournals.onlinelibrary.wiley.com/doi/am-pdf/10.1111/1462-2920.13229

Summary TRAM domain proteins present in A rchaea and Bacteria have a β‐barrel shape with anti‐parallel β‐sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins ( C sps). 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, C tr3 ( c old‐responsive TR AM domain protein 3 ) from the Antarctic archaeon M ethanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid ( RNA ) bound by C tr3 in vitro was determined using RNA ‐seq. C tr3‐bound M . burtonii RNA with a preference for transfer (t) RNA and 5S ribosomal RNA , and a potential binding motif was identified. In t RNA , the motif represented the C loop; a region that is conserved in t RNA from all domains of life and appears to be solvent exposed, potentially providing access for C tr3 to bind. C tr3 and C sps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within A rchaea compared with their apparent absence in B acteria , and scarcity of C sps in A rchaea but prevalence in B acteria , suggests they represent distinct evolutionary lineages of functionally equivalent RNA ‐binding proteins.