Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii
Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive...
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:112223 2023-05-15T13:48:53+02:00 Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii Saunders, N. F. W. Goodchild, A. Raftery, M. Guilhaus, M. Curmi, P. M. G. Cavicchioli, R. 2005-01-01 https://espace.library.uq.edu.au/view/UQ:112223 eng eng Amer Chemical Soc doi:10.1021/pr049797+ issn:1535-3893 Biochemical Research Methods proteome LC/LC-MS/MS archaea methanogenesis psychrophile CRISPR locus hypothetical proteins conserved gene context Halobacterium Sp Nrc-1 Rna-binding Domain Comparative Genomics Prokaryotic Genomes Genes Pathways Biology Family Classification Identification Journal Article 2005 ftunivqespace https://doi.org/10.1021/pr049797 2020-12-22T02:15:53Z Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive, integrated analysis of the latter proteins using threading, InterProScan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. Functional information was obtained for 55 proteins, providing new insight into the physiology of M. burtonii. Many of the proteins were predicted to be involved in DNA/RNA binding or modification and cell signaling, suggesting a complex, uncharacterized regulatory network controlling cellular processes during growth at low-temperature. Novel enzymatic functions were predicted for several proteins, including a putative candidate gene for the posttranslational modification of the key methanogenesis enzyme coenzyme M methyl reductase. A bacterial-like CRISPR locus was identified as a strong candidate for archaeal-bacterial lateral gene transfer. Gene context analysis proved a valuable augmentation to the other predictive methods in several cases, by revealing conserved gene associations and annotations in other microbial genomes. Our results underscore the importance of addressing the "hypothetical protein problem" for a complete understanding of cell physiology. Article in Journal/Newspaper Antarc* Antarctic The University of Queensland: UQ eSpace Antarctic The Antarctic |
institution |
Open Polar |
collection |
The University of Queensland: UQ eSpace |
op_collection_id |
ftunivqespace |
language |
English |
topic |
Biochemical Research Methods proteome LC/LC-MS/MS archaea methanogenesis psychrophile CRISPR locus hypothetical proteins conserved gene context Halobacterium Sp Nrc-1 Rna-binding Domain Comparative Genomics Prokaryotic Genomes Genes Pathways Biology Family Classification Identification |
spellingShingle |
Biochemical Research Methods proteome LC/LC-MS/MS archaea methanogenesis psychrophile CRISPR locus hypothetical proteins conserved gene context Halobacterium Sp Nrc-1 Rna-binding Domain Comparative Genomics Prokaryotic Genomes Genes Pathways Biology Family Classification Identification Saunders, N. F. W. Goodchild, A. Raftery, M. Guilhaus, M. Curmi, P. M. G. Cavicchioli, R. Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
topic_facet |
Biochemical Research Methods proteome LC/LC-MS/MS archaea methanogenesis psychrophile CRISPR locus hypothetical proteins conserved gene context Halobacterium Sp Nrc-1 Rna-binding Domain Comparative Genomics Prokaryotic Genomes Genes Pathways Biology Family Classification Identification |
description |
Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive, integrated analysis of the latter proteins using threading, InterProScan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. Functional information was obtained for 55 proteins, providing new insight into the physiology of M. burtonii. Many of the proteins were predicted to be involved in DNA/RNA binding or modification and cell signaling, suggesting a complex, uncharacterized regulatory network controlling cellular processes during growth at low-temperature. Novel enzymatic functions were predicted for several proteins, including a putative candidate gene for the posttranslational modification of the key methanogenesis enzyme coenzyme M methyl reductase. A bacterial-like CRISPR locus was identified as a strong candidate for archaeal-bacterial lateral gene transfer. Gene context analysis proved a valuable augmentation to the other predictive methods in several cases, by revealing conserved gene associations and annotations in other microbial genomes. Our results underscore the importance of addressing the "hypothetical protein problem" for a complete understanding of cell physiology. |
format |
Article in Journal/Newspaper |
author |
Saunders, N. F. W. Goodchild, A. Raftery, M. Guilhaus, M. Curmi, P. M. G. Cavicchioli, R. |
author_facet |
Saunders, N. F. W. Goodchild, A. Raftery, M. Guilhaus, M. Curmi, P. M. G. Cavicchioli, R. |
author_sort |
Saunders, N. F. W. |
title |
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
title_short |
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
title_full |
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
title_fullStr |
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
title_full_unstemmed |
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii |
title_sort |
predicted roles for hypothetical proteins in the low-temperature expressed proteome of the antarctic archaeon methanococcoides burtonii |
publisher |
Amer Chemical Soc |
publishDate |
2005 |
url |
https://espace.library.uq.edu.au/view/UQ:112223 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.1021/pr049797+ issn:1535-3893 |
op_doi |
https://doi.org/10.1021/pr049797 |
_version_ |
1766249919378620416 |