Molecular Evolutionary Analysis of Yeast Protein Interaction Network
To understand life as biological system, evolutionary
understanding is indispensable. Protein interactions data are rapidly
accumulating and are suitable for system-level evolutionary analysis.
We have analyzed yeast protein interaction network by both
mathematical and biological approaches. In this poster presentation,
we inferred the evolutionary birth periods of yeast proteins by
reconstructing phylogenetic profile. It has been thought that hub
proteins that have high connection degree are evolutionary old. But
our analysis showed that hub proteins are entirely evolutionary new.
We also examined evolutionary processes of protein complexes. It
showed that member proteins of complexes were tend to have
appeared in the same evolutionary period. Our results suggested that
protein interaction network evolved by modules that form the
functional unit. We also reconstructed standardized phylogenetic trees
and calculated evolutionary rates of yeast proteins. It showed that
there is no obvious correlation between evolutionary rates and
connection degrees of yeast proteins.
[1] U. Guldener, M. Munsterkotter, G. Kastenmuller, N. Strack, J. van
Helden, C. Lemer, et al., "CYGD: the Comprehensive Yeast Genome
Database", Nucleic Acid Research, vol. 33 (Database issue), pp.
D364-D368, Jan, 2005.
[2] L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, et al., "A
protein interaction map of Drosophila melanogaster", Science, vol. 5, no.
302, pp. 1727-1736, Dec, 2003.
[3] S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, et al: "A
map of the interactome network of the metazoan C. elegans", Science, vol.
23, no. 303, pp. 540-543, Jan, 2004.
[4] M. Pellegrini, EM. Marcotte, MJ. Thompson, D. Eisenberg, TO. Yeates.
"Assigning protein functions by comparative genome analysis: protein
phylogenetic profiles", Proceeding of National Academy of Sciences
USA, vol. 96, no. 8, pp. 4285-4288, Apr, 1999.
[5] E. Eisenberg, E.Y. Levanon, "Preferential attachment in the protein
network evolution", Physycal Review Letter, vol. 91, no. 13, pp. 138701,
Sep, 2003.
[6] H. Qin, H.H. Lu, W.B. Wu, W.H. Li, "Evolution of the yeast protein
interaction network", Proceeding of National Academy of Sciences USA,
vol. 100, no. 22, pp. 12820-12824, Oct, 2003.
[7] NCBI Entrez genome database (http://www.ncbi.nlm.nih.gov/entrez/
query.fcgi?db=Genome).
[8] S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman, "Basic local
alignment search tool", Journal of Molecular Biology, vol. 215, no. 3, pp.
403-410, Oct, 1990.
[9] W.R. Pearson, D.J. Lipman, "Improved tools for biological sequence
comparison", Proceeding of National Academy of Sciences USA, vol. 85,
no. 8, pp. 2444-2448, Apr, 1988.
[10] T. Endo, S. Ogishima, H. Tanaka, "Standardized phylogenetic tree: a
reference to discover functional evolution", Journal of Molecular
Evolution, vol. 57 (supplement 1), pp. S174-181, 2003.
[11] J.D. Han, N. Bertin, T. Hao, D.S. Goldberg, G.F. Berriz, L.V. Zhang,
"Evidence for dynamically organized modularity in the yeast
protein-protein interaction network", Nature, vol. 430, no. 6995, pp.
88-93, Jul, 2004.
[1] U. Guldener, M. Munsterkotter, G. Kastenmuller, N. Strack, J. van
Helden, C. Lemer, et al., "CYGD: the Comprehensive Yeast Genome
Database", Nucleic Acid Research, vol. 33 (Database issue), pp.
D364-D368, Jan, 2005.
[2] L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, et al., "A
protein interaction map of Drosophila melanogaster", Science, vol. 5, no.
302, pp. 1727-1736, Dec, 2003.
[3] S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, et al: "A
map of the interactome network of the metazoan C. elegans", Science, vol.
23, no. 303, pp. 540-543, Jan, 2004.
[4] M. Pellegrini, EM. Marcotte, MJ. Thompson, D. Eisenberg, TO. Yeates.
"Assigning protein functions by comparative genome analysis: protein
phylogenetic profiles", Proceeding of National Academy of Sciences
USA, vol. 96, no. 8, pp. 4285-4288, Apr, 1999.
[5] E. Eisenberg, E.Y. Levanon, "Preferential attachment in the protein
network evolution", Physycal Review Letter, vol. 91, no. 13, pp. 138701,
Sep, 2003.
[6] H. Qin, H.H. Lu, W.B. Wu, W.H. Li, "Evolution of the yeast protein
interaction network", Proceeding of National Academy of Sciences USA,
vol. 100, no. 22, pp. 12820-12824, Oct, 2003.
[7] NCBI Entrez genome database (http://www.ncbi.nlm.nih.gov/entrez/
query.fcgi?db=Genome).
[8] S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman, "Basic local
alignment search tool", Journal of Molecular Biology, vol. 215, no. 3, pp.
403-410, Oct, 1990.
[9] W.R. Pearson, D.J. Lipman, "Improved tools for biological sequence
comparison", Proceeding of National Academy of Sciences USA, vol. 85,
no. 8, pp. 2444-2448, Apr, 1988.
[10] T. Endo, S. Ogishima, H. Tanaka, "Standardized phylogenetic tree: a
reference to discover functional evolution", Journal of Molecular
Evolution, vol. 57 (supplement 1), pp. S174-181, 2003.
[11] J.D. Han, N. Bertin, T. Hao, D.S. Goldberg, G.F. Berriz, L.V. Zhang,
"Evidence for dynamically organized modularity in the yeast
protein-protein interaction network", Nature, vol. 430, no. 6995, pp.
88-93, Jul, 2004.
@article{"International Journal of Biological, Life and Agricultural Sciences:63006", author = "Soichi Ogishima and Takeshi Hase and So Nakagawa and Yasuhiro Suzuki and Hiroshi Tanaka", title = "Molecular Evolutionary Analysis of Yeast Protein Interaction Network", abstract = "To understand life as biological system, evolutionary
understanding is indispensable. Protein interactions data are rapidly
accumulating and are suitable for system-level evolutionary analysis.
We have analyzed yeast protein interaction network by both
mathematical and biological approaches. In this poster presentation,
we inferred the evolutionary birth periods of yeast proteins by
reconstructing phylogenetic profile. It has been thought that hub
proteins that have high connection degree are evolutionary old. But
our analysis showed that hub proteins are entirely evolutionary new.
We also examined evolutionary processes of protein complexes. It
showed that member proteins of complexes were tend to have
appeared in the same evolutionary period. Our results suggested that
protein interaction network evolved by modules that form the
functional unit. We also reconstructed standardized phylogenetic trees
and calculated evolutionary rates of yeast proteins. It showed that
there is no obvious correlation between evolutionary rates and
connection degrees of yeast proteins.", keywords = "Protein interaction network, evolution, modularity,
evolutionary rate, connection degrees.", volume = "1", number = "11", pages = "166-4", }