Protein evolution in yeast transcription factor subnetworks.
When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associations involving yeast transcription factors (TFs) reveals that TF hubs do not tend to evolve significantly more slowly than TF non-hubs. This result holds for all four major types of TF hubs: interaction hubs, regulatory in-degree and out-degree hubs, as well as co-regulatory hubs that jointly regulate target genes with many TFs. Furthermore, TF regulatory in-degree hubs tend to evolve significantly more quickly than TF non-hubs. Most importantly, the correlations between evolutionary rate (K(A)/K(S)) and degrees for TFs are significantly more positive than those for generic proteins within the same global protein-protein interaction and transcriptional regulatory networks. Compared to generic protein hubs, TF hubs operate at a higher level in the hierarchical structure of cellular networks, and hence experience additional evolutionary forces (relaxed negative selection or positive selection through network rewiring). The striking difference between the evolution of TF hubs and generic protein hubs demonstrates that components within the same global network can be governed by distinct organizational and evolutionary principles.
Wang
Yong
Y
Bioinformatics Program, Boston University, Boston, MA 02215, USA.
Franzosa
Eric A
EA
Zhang
Xiang-Sun
XS
Xia
Yu
Y
D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D025941:Protein Interaction Mapping; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
Science. 2007 Aug 10;317(5839):815-9
17690298
Science. 2005 Feb 4;307(5710):724-7
15692050
Mol Biol Evol. 2007 May;24(5):1113-21
17347158
Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43
16176987
PLoS Biol. 2004 Dec;2(12):e398
15534694
Mol Biol Evol. 2004 Jan;21(1):108-16
14595100
BMC Evol Biol. 2007 Jan 29;7:9
17257443
Genome Biol. 2005;6(12):R103
16356266
Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8
15800036
Genome Biol. 2009;10(4):R35
19358738
Science. 2002 Oct 25;298(5594):799-804
12399584
Science. 2006 Dec 22;314(5807):1938-41
17185604
Nucleic Acids Res. 1998 Jan 1;26(1):73-9
9399804
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D446-51
16381908
Science. 2008 Mar 28;319(5871):1797-9
18369141
Science. 2000 Nov 10;290(5494):1151-5
11073452
Mol Biol Evol. 2000 Jan;17(1):32-43
10666704
Nature. 2004 Sep 16;431(7006):308-12
15372033
Science. 2009 Jan 23;323(5913):498-501
19164747
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
3547335
Cell. 2008 Jun 27;133(7):1135-7
18585345
Nat Rev Genet. 2004 Feb;5(2):101-13
14735121
Mol Biol Evol. 2009 Oct;26(10):2387-95
19597162
Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13532-7
16157877
BMC Evol Biol. 2004 May 27;4:13
15165289
Nucleic Acids Res. 2009 Oct;37(18):5943-58
19661283
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
16381927
BMC Evol Biol. 2003 May 23;3:11
12769820
Mol Biol Evol. 2006 Feb;23(2):327-37
16237209
Genome Biol. 2004;5(2):206
14759249
Nature. 2004 Jun 10;429(6992):661-4
15190353
BMC Evol Biol. 2003 Jan 6;3:1
12515583
Nature. 2006 Sep 28;443(7110):415-20
17006507
BMC Evol Biol. 2003 Oct 02;3:21
14525624
J Evol Biol. 2009 Dec;22(12):2430-7
19878412
Science. 2002 Apr 26;296(5568):750-2
11976460
Science. 2005 Aug 5;309(5736):938-40
16081737
Cell. 2003 Nov 14;115(4):389-99
14622594
Mol Biol Evol. 2006 Sep;23(9):1751-61
16782762
Science. 2006 May 19;312(5776):1054-9
16709784
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17614-9
17101967
Curr Opin Struct Biol. 2004 Jun;14(3):283-91
15193307
Genes Dev. 2006 Feb 15;20(4):435-48
16449570
BMC Evol Biol. 2004 Jun 01;4:14
15171796
Comput Appl Biosci. 1997 Oct;13(5):555-6
9367129
PLoS Comput Biol. 2009 Jun;5(6):e1000413
19521505
Nature. 2007 Sep 6;449(7158):54-61
17805289
Nature. 2004 Jul 1;430(6995):88-93
15190252
Genetics. 2001 Jun;158(2):927-31
11430355
Curr Biol. 2007 Jun 19;17(12):1007-13
17540568
Nature. 2008 Apr 17;452(7189):840-5
18421347
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Nature. 2001 Jun 28;411(6841):1046-9
11429604
J Exp Zool B Mol Dev Evol. 2004 Jul 15;302(4):392-411
15287103
Curr Opin Biotechnol. 2006 Oct;17(5):481-7
16962765
Proc Natl Acad Sci U S A. 2005 May 17;102(20):7203-8
15883364
Nature. 2006 Sep 28;443(7110):401-2
17006502
Mol Cell. 2008 Mar 14;29(5):552-62
18342603
Nat Rev Genet. 2006 May;7(5):337-48
16619049
Nature. 2004 Sep 2;431(7004):99-104
15343339
PLoS Biol. 2008 Feb;6(2):e38
18303948
Genes Dev. 2002 Dec 1;16(23):3017-33
12464632