The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Protein interaction maps for complete genomes based on gene fusion events
Abstract
A large-scale effort to measure, detect and analyse protein-protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.
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“Detection of genuine gene fusion events has been reported long before the first complete genomes became available (110,111), but beyond that point they have been proven instrumental in detecting gene/protein associations with high specificity (112,113).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [113]
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Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Protein-Protein Interaction Detection: Methods and Analysis
Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. S. (2014) · International Journal of Proteomics · doi:10.1155/2014/147648 · Cited by 811
Zinc through the Three Domains of Life
Andreini, C., Banci, L., Bertini, I., & Rosato, A. (2006) · Journal of Proteome Research · doi:10.1021/pr0603699 · Cited by 648
A motif-based profile scanning approach for genome-wide prediction of signaling pathways
Yaffe, M. B., Leparc, G. G., Lai, J., Obata, T., Volinia, S., & Cantley, L. C. (2001) · Nature Biotechnology · doi:10.1038/86737 · Cited by 517
Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes
Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., & Gelfand, M. S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305837200 · Cited by 472
Metadata
- Authors
- Enright, A. J., Iliopoulos, I., Kyrpides, N. C., & Ouzounis, C. A.
- Venue
- Nature
- Published
- 1999-11
- Volume
- 402
- Issue
- 6757
- Pages
- 86-90
- ISSN
- 0028-0836
- 1476-4687
- Cited by
- 818
- References
- 28
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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- Enright, A. J., Iliopoulos, I., Kyrpides, N. C., & Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature. https://doi.org/10.1038/47056
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