Abstract
Original language | English |
---|---|
Pages (from-to) | 2513-2520 |
Number of pages | 8 |
Journal | Molecular Biology and Evolution |
Volume | 28 |
Issue number | 9 |
DOIs | |
Publication status | Published - 2011 |
Externally published | Yes |
Keywords
- disordered proteins
- microRNA regulation
- phosphorylation
- protein evolution
- protein-protein interaction
- microRNA
- article
- correlation coefficient
- gene control
- human
- molecular evolution
- nonhuman
- protein analysis
- protein phosphorylation
- protein protein interaction
- Amino Acid Substitution
- Animals
- Computational Biology
- Evolution, Molecular
- Gene Expression Regulation
- Genome, Human
- Humans
- Mice
- MicroRNAs
- Protein Conformation
- Protein Folding
- Proteins
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The relationships among MicroRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. / Chen, Chun-Chang; Chuang, Trees-Juen; Li, Wen-Hsiung.
In: Molecular Biology and Evolution, Vol. 28, No. 9, 2011, p. 2513-2520.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - The relationships among MicroRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate
AU - Chen, Chun-Chang
AU - Chuang, Trees-Juen
AU - Li, Wen-Hsiung
N1 - 被引用次數:15 Export Date: 21 March 2016 CODEN: MBEVE 通訊地址: Li, W.-H.; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; 電子郵件: whli@sinica.edu.tw 化學物質/CAS: MicroRNAs; Proteins 參考文獻: Bloom, J.D., Adami, C., Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response (2004) BMC Evol Biol, 4, p. 14; Bossi, A., Lehner, B., Tissue specificity and the human protein interaction network (2009) Mol Syst Biol, 5, p. 260; Brown, C.J., Johnson, A.K., Daughdrill, G.W., Comparing models of evolution for ordered and disordered proteins (2010) Mol Biol Evol, 27, pp. 609-621; Brown, C.J., Takayama, S., Campen, A.M., Vise, P., Marshall, T.W., Oldfield, C.J., Williams, C.J., Keith Dunker, A., Evolutionary rate heterogeneity in proteins with long disordered regions (2002) Journal of Molecular Evolution, 55 (1), pp. 104-110. , DOI 10.1007/s00239-001-2309-6; Chen, F.C., Chen, C.J., Li, W.H., Chuang, T.J., Gene family size conservation is a good indicator of evolutionary rates (2010) Mol Biol Evol, 27, pp. 1750-1758; 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PY - 2011
Y1 - 2011
N2 - Many indicators of protein evolutionary rate have been proposed, but some of them are interrelated. The purpose of this study is to disentangle their correlations. We assess the strength of each indicator by controlling for the other indicators under study. We find that the number of microRNA (miRNA) types that regulate a gene is the strongest rate indicator (a negative correlation), followed by disorder content (the percentage of disordered regions in a protein, a positive correlation); the strength of disorder content as a rate indicator is substantially increased after controlling for the number of miRNA types. By dividing proteins into lowly and highly intrinsically disordered proteins (L-IDPs and H-IDPs), we find that proteins interacting with more H-IDPs tend to evolve more slowly, which largely explains the previous observation of a negative correlation between the number of protein-protein interactions and evolutionary rate. Moreover, all of the indicators examined here, except for the number of miRNA types, have different strengths in L-IDPs and in H-IDPs. Finally, the number of phosphorylation sites is weakly correlated with the number of miRNA types, and its strength as a rate indicator is substantially reduced when other indicators are considered. Our study reveals the relative strength of each rate indicator and increases our understanding of protein evolution. © 2011 The Author.
AB - Many indicators of protein evolutionary rate have been proposed, but some of them are interrelated. The purpose of this study is to disentangle their correlations. We assess the strength of each indicator by controlling for the other indicators under study. We find that the number of microRNA (miRNA) types that regulate a gene is the strongest rate indicator (a negative correlation), followed by disorder content (the percentage of disordered regions in a protein, a positive correlation); the strength of disorder content as a rate indicator is substantially increased after controlling for the number of miRNA types. By dividing proteins into lowly and highly intrinsically disordered proteins (L-IDPs and H-IDPs), we find that proteins interacting with more H-IDPs tend to evolve more slowly, which largely explains the previous observation of a negative correlation between the number of protein-protein interactions and evolutionary rate. Moreover, all of the indicators examined here, except for the number of miRNA types, have different strengths in L-IDPs and in H-IDPs. Finally, the number of phosphorylation sites is weakly correlated with the number of miRNA types, and its strength as a rate indicator is substantially reduced when other indicators are considered. Our study reveals the relative strength of each rate indicator and increases our understanding of protein evolution. © 2011 The Author.
KW - disordered proteins
KW - microRNA regulation
KW - phosphorylation
KW - protein evolution
KW - protein-protein interaction
KW - microRNA
KW - article
KW - correlation coefficient
KW - gene control
KW - human
KW - molecular evolution
KW - nonhuman
KW - protein analysis
KW - protein phosphorylation
KW - protein protein interaction
KW - Amino Acid Substitution
KW - Animals
KW - Computational Biology
KW - Evolution, Molecular
KW - Gene Expression Regulation
KW - Genome, Human
KW - Humans
KW - Mice
KW - MicroRNAs
KW - Protein Conformation
KW - Protein Folding
KW - Proteins
UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-80052183299&origin=inward&txGid=478ad246f281822f6085ebbfc1b90841
UR - https://www.scopus.com/results/citedbyresults.uri?sort=plf-f&cite=2-s2.0-80052183299&src=s&imp=t&sid=9251756b722ba02ce0d6c0962fc3e200&sot=cite&sdt=a&sl=0&origin=recordpage&editSaveSearch=&txGid=39b244d75855d7637e937b94f1c82b47
U2 - 10.1093/molbev/msr068
DO - 10.1093/molbev/msr068
M3 - Article
VL - 28
SP - 2513
EP - 2520
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 9
ER -