Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii
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....
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Online Access: | http://handle.uws.edu.au:8081/1959.7/uws:34285 https://doi.org/10.1111/1462-2920.13229 |
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ftunivwestsyd:oai:researchdirect.westernsydney.edu.au:uws_34285 2023-05-15T13:54:14+02:00 Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii Taha Siddiqui, Khawar Sohail Campanaro, S. Najnin, T. Deshpande, Nandan Williams, Timothy J. Aldrich-Wright, Janice R. (R7187) Wilkins, Marc R. Curmi, Paul M. Cavicchioli, Ricardo Nanoscale (Host institution) 2016 print 15 http://handle.uws.edu.au:8081/1959.7/uws:34285 https://doi.org/10.1111/1462-2920.13229 eng eng U.K., Wiley-Blackwell ARC DP110103232 Environmental Microbiology--1462-2912--1462-2920 Vol. 18 Issue. 9 pp: 2810-2824 http://purl.org/au-research/grants/arc/DP110103232 060504 - Microbial Ecology 970106 - Expanding Knowledge in the Biological Sciences archaebacteria RNA-binding proteins journal article 2016 ftunivwestsyd https://doi.org/10.1111/1462-2920.13229 2020-12-05T17:19:26Z 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. Article in Journal/Newspaper Antarc* Antarctic University of Western Sydney (UWS): Research Direct Antarctic The Antarctic Environmental Microbiology 18 9 2810 2824 |
institution |
Open Polar |
collection |
University of Western Sydney (UWS): Research Direct |
op_collection_id |
ftunivwestsyd |
language |
English |
topic |
060504 - Microbial Ecology 970106 - Expanding Knowledge in the Biological Sciences archaebacteria RNA-binding proteins |
spellingShingle |
060504 - Microbial Ecology 970106 - Expanding Knowledge in the Biological Sciences archaebacteria RNA-binding proteins Taha Siddiqui, Khawar Sohail Campanaro, S. Najnin, T. Deshpande, Nandan Williams, Timothy J. Aldrich-Wright, Janice R. (R7187) Wilkins, Marc R. Curmi, Paul M. Cavicchioli, Ricardo Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
topic_facet |
060504 - Microbial Ecology 970106 - Expanding Knowledge in the Biological Sciences archaebacteria RNA-binding proteins |
description |
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. |
author2 |
Nanoscale (Host institution) |
format |
Article in Journal/Newspaper |
author |
Taha Siddiqui, Khawar Sohail Campanaro, S. Najnin, T. Deshpande, Nandan Williams, Timothy J. Aldrich-Wright, Janice R. (R7187) Wilkins, Marc R. Curmi, Paul M. Cavicchioli, Ricardo |
author_facet |
Taha Siddiqui, Khawar Sohail Campanaro, S. Najnin, T. Deshpande, Nandan Williams, Timothy J. Aldrich-Wright, Janice R. (R7187) Wilkins, Marc R. Curmi, Paul M. Cavicchioli, Ricardo |
author_sort |
Taha |
title |
Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
title_short |
Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
title_full |
Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
title_fullStr |
Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
title_full_unstemmed |
Single TRAM domain RNA-binding proteins in Archaea : functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
title_sort |
single tram domain rna-binding proteins in archaea : functional insight from ctr3 from the antarctic methanogen methanococcoides burtonii |
publisher |
U.K., Wiley-Blackwell |
publishDate |
2016 |
url |
http://handle.uws.edu.au:8081/1959.7/uws:34285 https://doi.org/10.1111/1462-2920.13229 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
ARC DP110103232 Environmental Microbiology--1462-2912--1462-2920 Vol. 18 Issue. 9 pp: 2810-2824 http://purl.org/au-research/grants/arc/DP110103232 |
op_doi |
https://doi.org/10.1111/1462-2920.13229 |
container_title |
Environmental Microbiology |
container_volume |
18 |
container_issue |
9 |
container_start_page |
2810 |
op_container_end_page |
2824 |
_version_ |
1766259933733453824 |