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....
Published in: | Environmental Microbiology |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
John Wiley & Sons
2016
|
Subjects: | |
Online Access: | http://hdl.handle.net/10072/408923 https://doi.org/10.1111/1462-2920.13229 |
id |
ftgriffithuniv:oai:research-repository.griffith.edu.au:10072/408923 |
---|---|
record_format |
openpolar |
spelling |
ftgriffithuniv:oai:research-repository.griffith.edu.au:10072/408923 2023-11-12T04:06:24+01:00 Single TRAM domain RNA-binding proteins in Archaea: Functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii Taha Siddiqui, KS Campanaro, S Najnin, T Deshpande, N Williams, TJ Aldrich‐Wright, J Wilkins, M Curmi, PMG Cavicchioli, R 2016 http://hdl.handle.net/10072/408923 https://doi.org/10.1111/1462-2920.13229 en eng John Wiley & Sons Environmental Microbiology Taha, Siddiqui, KS; Campanaro, S; Najnin, T; Deshpande, N; Williams, TJ; Aldrich‐Wright, J; Wilkins, M; Curmi, PMG; Cavicchioli, R, Single TRAM domain RNA-binding proteins in Archaea: Functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii, Environmental Microbiology, 2016, 18 (9), pp. 2810-2824 http://hdl.handle.net/10072/408923 1462-2912 doi:10.1111/1462-2920.13229 metadata only access Evolutionary biology Microbiology Ecology Journal article 2016 ftgriffithuniv https://doi.org/10.1111/1462-2920.13229 2023-10-16T22:26:18Z 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. No Full Text Article in Journal/Newspaper Antarc* Antarctic Griffith University: Griffith Research Online Antarctic The Antarctic Environmental Microbiology 18 9 2810 2824 |
institution |
Open Polar |
collection |
Griffith University: Griffith Research Online |
op_collection_id |
ftgriffithuniv |
language |
English |
topic |
Evolutionary biology Microbiology Ecology |
spellingShingle |
Evolutionary biology Microbiology Ecology Taha Siddiqui, KS Campanaro, S Najnin, T Deshpande, N Williams, TJ Aldrich‐Wright, J Wilkins, M Curmi, PMG Cavicchioli, R Single TRAM domain RNA-binding proteins in Archaea: Functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii |
topic_facet |
Evolutionary biology Microbiology Ecology |
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. No Full Text |
format |
Article in Journal/Newspaper |
author |
Taha Siddiqui, KS Campanaro, S Najnin, T Deshpande, N Williams, TJ Aldrich‐Wright, J Wilkins, M Curmi, PMG Cavicchioli, R |
author_facet |
Taha Siddiqui, KS Campanaro, S Najnin, T Deshpande, N Williams, TJ Aldrich‐Wright, J Wilkins, M Curmi, PMG Cavicchioli, R |
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 |
John Wiley & Sons |
publishDate |
2016 |
url |
http://hdl.handle.net/10072/408923 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 |
Environmental Microbiology Taha, Siddiqui, KS; Campanaro, S; Najnin, T; Deshpande, N; Williams, TJ; Aldrich‐Wright, J; Wilkins, M; Curmi, PMG; Cavicchioli, R, Single TRAM domain RNA-binding proteins in Archaea: Functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii, Environmental Microbiology, 2016, 18 (9), pp. 2810-2824 http://hdl.handle.net/10072/408923 1462-2912 doi:10.1111/1462-2920.13229 |
op_rights |
metadata only access |
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_ |
1782327489471709184 |