title: Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.
abstract: TRAM domain proteins present in Archaea 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 (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-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA 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 within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
authors.lastname: Taha
authors.affiliation: Life Sciences Department, King Fahd University of Petroleum and Minerals, Dhahran, Kingdom of Saudi Arabia.
authors.forename: K S
authors.initials: KS
authors.lastname: Siddiqui
authors.affiliation: Department of Biology, University of Padua, Via U. Bassi 58/B, 35121, Padova, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Campanaro
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: T
authors.initials: T
authors.lastname: Najnin
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: N
authors.initials: N
authors.lastname: Deshpande
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: T J
authors.initials: TJ
authors.lastname: Williams
authors.affiliation: Nanoscale Organization and Dynamic Group, School of Science and Health, Western Sydney University, Penrith, 2560, NSW, Australia.
authors.forename: J
authors.initials: J
authors.lastname: Aldrich-Wright
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Wilkins
authors.affiliation: School of Physics, The University of New South Wales, Sydney, NSW, 2052, Australia. r.cavicchioli@unsw.edu.au.
authors.forename: P M G
authors.initials: PM
authors.lastname: Curmi
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia. p.curmi@unsw.edu.au.
authors.forename: R
authors.initials: R
authors.lastname: Cavicchioli
mesh_terms: D000864:Antarctic Regions; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003080:Cold Temperature; D017019:Methanosarcinaceae / Q000235:genetics*; D019642:RNA, Archaeal / Q000737:chemistry* / Q000378:metabolism; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D019642:RNA, Archaeal; D012341:RNA, Ribosomal, 5S; D016601:RNA-Binding Proteins; D012343:RNA, Transfer