Single TRAMdomain RNA‐binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii
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 i...
Published in: | Environmental Microbiology |
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Main Authors: | , , , , , , , , , |
Other Authors: | |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2016
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Subjects: | |
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: | 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. |
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