A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes

作者: Mehmet Somel , Melissa A. Wilson Sayres , Gregory Jordan , Emilia Huerta-Sanchez , Matteo Fumagalli

DOI: 10.1093/MOLBEV/MST098

关键词: BiologyProteasomeHuman genomeGeneticsBalancing selectionGeneNonsynonymous substitutionGenomePopulationNegative selection

摘要: Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population and comparative data to search for functional processes showing relaxed specifically in the human lineage, whereas remaining evolutionarily other mammals. Consistent with previous studies, find that olfactory receptor genes display such a signature of relaxation humans. Intriguingly, proteasome also show prominent signal human-specific relaxation: multiple subunits, including four members catalytic core particle, contain nonsynonymous sites across Chimpanzee do not similar trend. Human bear no evidence recent positive balancing selection. These results suggest subunits; exact biological causes, however, remain unknown.

参考文章(53)
Aaron Ciechanover, Proteolysis: from the lysosome to ubiquitin and the proteasome. Nature Reviews Molecular Cell Biology. ,vol. 6, pp. 79- 87 ,(2005) , 10.1038/NRM1552
Lydie Combaret, Dominique Dardevet, Isabelle Rieu, Marie-Noëlle Pouch, Daniel Béchet, Daniel Taillandier, Jean Grizard, Didier Attaix, A leucine‐supplemented diet restores the defective postprandial inhibition of proteasome‐dependent proteolysis in aged rat skeletal muscle The Journal of Physiology. ,vol. 569, pp. 489- 499 ,(2005) , 10.1113/JPHYSIOL.2005.098004
Chimpanzee Sequencing and Analysis Consortium Waterson Robert H. waterston@ gs. washington. edu Lander Eric S. lander@ broad. mit. edu Wilson Richard K. rwilson@ watson. wustl. edu, None, Initial sequence of the chimpanzee genome and comparison with the human genome Nature. ,vol. 437, pp. 69- 87 ,(2005) , 10.1038/NATURE04072
N. E. Tawa, I. C. Kettelhut, A. L. Goldberg, Dietary protein deficiency reduces lysosomal and nonlysosomal ATP-dependent proteolysis in muscle. American Journal of Physiology-endocrinology and Metabolism. ,vol. 263, ,(1992) , 10.1152/AJPENDO.1992.263.2.E326
R. Drmanac, A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns, B. G. Kermani, P. Carnevali, I. Nazarenko, G. B. Nilsen, G. Yeung, F. Dahl, A. Fernandez, B. Staker, K. P. Pant, J. Baccash, A. P. Borcherding, A. Brownley, R. Cedeno, L. Chen, D. Chernikoff, A. Cheung, R. Chirita, B. Curson, J. C. Ebert, C. R. Hacker, R. Hartlage, B. Hauser, S. Huang, Y. Jiang, V. Karpinchyk, M. Koenig, C. Kong, T. Landers, C. Le, J. Liu, C. E. McBride, M. Morenzoni, R. E. Morey, K. Mutch, H. Perazich, K. Perry, B. A. Peters, J. Peterson, C. L. Pethiyagoda, K. Pothuraju, C. Richter, A. M. Rosenbaum, S. Roy, J. Shafto, U. Sharanhovich, K. W. Shannon, C. G. Sheppy, M. Sun, J. V. Thakuria, A. Tran, D. Vu, A. W. Zaranek, X. Wu, S. Drmanac, A. R. Oliphant, W. C. Banyai, B. Martin, D. G. Ballinger, G. M. Church, C. A. Reid, Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays Science. ,vol. 327, pp. 78- 81 ,(2010) , 10.1126/SCIENCE.1181498
Katherine S Pollard, Sofie R Salama, Bryan King, Andrew D Kern, Tim Dreszer, Sol Katzman, Adam Siepel, Jakob S Pedersen, Gill Bejerano, Robert Baertsch, Kate R Rosenbloom, Jim Kent, David Haussler, Forces Shaping the Fastest Evolving Regions in the Human Genome PLOS Genetics. ,vol. 2, pp. 1599- 1611 ,(2005) , 10.1371/JOURNAL.PGEN.0020168
Denis Pierron, Nicolás Gutiérrez Cortés, Thierry Letellier, Lawrence I. Grossman, Current relaxation of selection on the human genome: tolerance of deleterious mutations on olfactory receptors. Molecular Phylogenetics and Evolution. ,vol. 66, pp. 558- 564 ,(2013) , 10.1016/J.YMPEV.2012.07.032
Prateek Kumar, Steven Henikoff, Pauline C Ng, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols. ,vol. 4, pp. 1073- 1081 ,(2009) , 10.1038/NPROT.2009.86
David Brawand, Magali Soumillon, Anamaria Necsulea, Philippe Julien, Gábor Csárdi, Patrick Harrigan, Manuela Weier, Angélica Liechti, Ayinuer Aximu-Petri, Martin Kircher, Frank W. Albert, Ulrich Zeller, Philipp Khaitovich, Frank Grützner, Sven Bergmann, Rasmus Nielsen, Svante Pääbo, Henrik Kaessmann, The evolution of gene expression levels in mammalian organs Nature. ,vol. 478, pp. 343- 348 ,(2011) , 10.1038/NATURE10532