Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.

@article{citeulike:2783957, abstract = {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.}, address = {School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia.}, author = {Saunders, N. F. and Goodchild, A. and Raftery, M. and Guilhaus, M. and Curmi, P. M. and Cavicchioli, R. }, citeulike-article-id = {2783957}, doi = {10.1021/pr049797+}, issn = {1535-3893}, journal = {Journal of proteome research}, keywords = {antarctic, archaea, bioinformatics, function, methanococcoides, prediction, protein, psychrophily}, number = {2}, pages = {464--472}, posted-at = {2008-05-11 10:09:25}, priority = {2}, title = {Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.}, url = {http://dx.doi.org/10.1021/pr049797+}, volume = {4}, year = {2005} }

TY - JOUR ID - citeulike:2783957 L3 - citeulike-article-id:2783957 TI - Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. JF - Journal of proteome research VL - 4 IS - 2 SP - 464 EP - 472 AD - School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia. SN - 1535-3893 N2 - 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. KW - antarctic KW - archaea KW - bioinformatics KW - function KW - methanococcoides KW - prediction KW - protein KW - psychrophily AU - Saunders, NF AU - Goodchild, A AU - Raftery, M AU - Guilhaus, M AU - Curmi, PM AU - Cavicchioli, R PY - 2005///r UR - http://dx.doi.org/10.1021/pr049797+ ER -