title: Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves.
abstract: F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle-Saale, Germany.
authors.forename: Aura
authors.initials: A
authors.lastname: Navarro-Quezada
authors.forename: Nadine
authors.initials: N
authors.lastname: Schumann
authors.forename: Marcel
authors.initials: M
authors.lastname: Quint
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019143:Evolution, Molecular; D044783:F-Box Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D017434:Protein Structure, Tertiary
chemical_list: D044783:F-Box Proteins; D010940:Plant Proteins
references.citation: Plant Mol Biol. 2004 Dec;56(6):929-45
references.pmid: 15821991
references.citation: Genome Res. 2006 Aug;16(8):1017-30
references.pmid: 16825662
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: PLoS Biol. 2004 Jul;2(7):E206
references.pmid: 15252449
references.citation: Nature. 2003 Mar 27;422(6930):433-8
references.pmid: 12660784
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Plant Physiol. 2011 Feb;155(2):835-50
references.pmid: 21119043
references.citation: Plant J. 2005 Jul;43(1):153-63
references.pmid: 15960624
references.citation: Nat Rev Genet. 2008 Dec;9(12):951-63
references.pmid: 19002141
references.citation: Genes Dev. 2009 Feb 15;23(4):512-21
references.pmid: 19196655
references.citation: Plant Physiol. 2004 Jul;135(3):1179-97
references.pmid: 15266052
references.citation: Nat Genet. 2007 Sep;39(9):1151-5
references.pmid: 17676040
references.citation: Syst Biol. 2007 Aug;56(4):564-77
references.pmid: 17654362
references.citation: Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6
references.pmid: 18428792
references.citation: Curr Opin Plant Biol. 2007 Dec;10(6):624-32
references.pmid: 17851112
references.citation: Nat Genet. 2005 Sep;37(9):986-90
references.pmid: 16086015
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Mol Biol Evol. 2000 Jan;17(1):32-43
references.pmid: 10666704
references.citation: Plant J. 2009 Dec;60(5):757-70
references.pmid: 19682297
references.citation: Nat Genet. 2005 May;37(5):501-6
references.pmid: 15806101
references.citation: Plant Physiol. 2008 Nov;148(3):1189-200
references.pmid: 18775973
references.citation: Plant Cell. 2009 Dec;21(12):3718-31
references.pmid: 20040540
references.citation: Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11519-24
references.pmid: 12169662
references.citation: J Mol Evol. 1989 Aug;29(2):170-9
references.pmid: 2509717
references.citation: Plant Cell. 2002 Jul;14(7):1469-82
references.pmid: 12119368
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
references.pmid: 16845082
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):835-40
references.pmid: 19126682
references.citation: Sci China Life Sci. 2012 Jun;55(6):497-506
references.pmid: 22744179
references.citation: J Mol Evol. 1995 Dec;41(6):1152-9
references.pmid: 8587111
references.citation: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references.pmid: 22039361
references.citation: BMC Bioinformatics. 2004 Aug 19;5:113
references.pmid: 15318951
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14694-9
references.pmid: 21873230
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references.pmid: 22127870
references.citation: Genome Res. 2003 Feb;13(2):137-44
references.pmid: 12566392
references.citation: Plant Mol Biol. 2006 Mar;60(4):599-615
references.pmid: 16525894
references.citation: Science. 2007 Jul 20;317(5836):338-42
references.pmid: 17641193
references.citation: Bioinformatics. 2006 Jun 15;22(12):1540-2
references.pmid: 16595560
references.citation: PLoS One. 2011 Jan 28;6(1):e16219
references.pmid: 21297981
references.citation: Nucleic Acids Res. 2005 Jan 20;33(2):511-8
references.pmid: 15661851
references.citation: Genomics. 2008 Oct;92(4):246-53
references.pmid: 18620041