Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 3, 2009, Pages 835-840

  Xu, Guixia ^a   Ma, Hong ^b,c   Nei, Masatoshi ^c   Kong, Hongzhi ^a  

^a INSTITUTE OF BOTANY   (China)

^b FUDAN UNIVERSITY   (China)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Birth and death evolution; F box protein; Multigene family; Plant evolution

Indexed keywords

F BOX PROTEIN;

ARABIDOPSIS; ARTICLE; EXON; FRAMESHIFT MUTATION; GENE CLUSTER; GENE DUPLICATION; GENE INTERACTION; GENETIC VARIABILITY; INTRON; MULTIGENE FAMILY; PHYLOGENY; PLANT EVOLUTION; PLANT GENE; PLESIOMORPHY; PRIORITY JOURNAL; PROTEIN DOMAIN; RICE;

AMINO ACID SEQUENCE; ARABIDOPSIS; EVOLUTION, MOLECULAR; F-BOX PROTEINS; ORYZA SATIVA; PHYLOGENY; PLANTS; POPULUS; PROTEIN STRUCTURE, TERTIARY; TANDEM REPEAT SEQUENCES;

ARABIDOPSIS; LILIOPSIDA;

EID: 58849132032     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0812043106     Document Type: Article

References (36)

1. Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121-152.
2. Nei M (2007) The new mutation theory of phenotypic evolution. Proc Natl Acad Sci USA 104:12235-12242.
3. Niimura Y, Nei M (2006) Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J Hum Genet 51:505-517.
4. Nozawa M, Nei M (2007) Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci USA 104:7122-7127.
5. Redon R, et al. (2006) Global variation in copy number in the human genome. Nature 444:444-454.
6. Nozawa M, Kawahara Y, Nei M (2007) Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci USA 104:20421-20426.
7. Nei M, Niimura Y, Nozawa M (2008) The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9:951-963.
8. Smalle J, Vierstra RD (2004) The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol 55:555-590.
9. Hellmann H, Estelle M (2002) Plant development: Regulation by protein degradation. Science 297:793-797.
10. Cardozo T, Pagano M (2004) The SCF ubiquitin ligase: Insights into a molecular machine. Nat Rev Mol Cell Biol 5:739-751.
11. Deshaies RJ (1999) SCF and Cullin/Ring H2-based ubiquitin ligases. Annu Rev Cell Dev Biol 15:435-467.
12. Skp2 SCF ubiquitin ligase complex. Nature 416:703-709.
13. Bai C, Richman R, Elledge SJ (1994) Human cyclin F. EMBO J 13:6087-6098.
14. Kipreos ET, Pagano M (2000) The F-box protein family. Genome Biol 1:REVIEWS3002.
15. Gagne JM, et al. (2002) The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci USA 99:11519-11524.
16. Jain M, et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467-1483.
17. Lechner E, et al. (2006) F-box proteins everywhere. Curr Opin Plant Biol 9:631-638.
18. Wikstrom N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B Biol Sci 268:2211-2220.
19. Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113-1130.
20. Nam J, et al. (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc Natl Acad Sci USA 101:1910-1915.
21. Shiu SH, et al. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16:1220-1234.
22. Kong H, et al. (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J 50:873-885.
23. Rizzon C, Ponger L, Gaut BS (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comp Biol 2:e115.
24. Wang L, et al. (2004) Genome-wide analysis of S-Locus F-box-like genes in Arabidopsis thaliana. Plant Mol Biol 56:929-945.
25. Kim HS, Delaney TP (2002) Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14:1469-1482.
26. Young JM, et al. (2008) Extensive copy-number variation of the human olfactory receptor gene family. Am J Hum Genet 83:228-242.
27. Niimura Y, Nei M (2007) Extensive gains and losses of olfactory receptor genes in Mammalian evolution. PLoS ONE 2:e708.
28. Dharmasiri N, et al. (2005) Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell 9:109-119.
29. Schwager KM, et al. (2007) Characterization of the VIER F-BOX PROTEINE genes from Arabidopsis reveals their importance for plant growth and development. Plant Cell 19:1163-1178.
30. Xu G, Kong H (2007) Duplication and divergence of floral MADS-box genes in grasses: evidence for the generation and modification of novel regulators. J Integr Plant Biol 49:760-768.
31. Vandenbussche M, Theissen G, Van de Peer Y, Gerats T (2003) Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. Nucleic Acids Res 31:4401-4409.
32. Shan H, et al. (2007) Patterns of gene duplication and functional diversification during the evolution of the AP1/SQUA subfamily of plant MADS-box genes. Mol Phylogen Evol 44:26-41.
33. Thomas JH (2006) Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res 16:1017-1030.
34. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
35. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755-763.
36. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.