Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns

Basha, 2006, The N-terminal arm of small heat shock proteins is important for both chaperone activity and substrate specificity, J Biol Chem, 281, 39943, 10.1074/jbc.M607677200

Blanc, 2003, A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome, Genome Res, 13, 137, 10.1101/gr.751803

Blanc, 2004, Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution, Plant Cell, 16, 1679, 10.1105/tpc.021410

Boorstein, 1994, Molecular evolution of the HSP70 multigene family, J Mol Evol, 38, 1, 10.1007/BF00175490

Casneuf, 2006, Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana, Genome Biol, 7, R13, 10.1186/gb-2006-7-2-r13

Caspers, 1995, The expanding small heat-shock protein family, and structure predictions of the conserved “alpha-crystallin domain”, J Mol Evol, 40, 238, 10.1007/BF00163229

de Jong, 1998, Genealogy of the alpha-crystallin-small heat-shock protein superfamily, Int J Biol Macromol, 22, 151, 10.1016/S0141-8130(98)00013-0

Drouin, 2002, Characterization of the gene conversion between the multigene family members of the yeast genome, J Mol Evol, 55, 14, 10.1007/s00239-001-0085-y

Duarte, 2006, Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis, Mol Biol Evol, 23, 469, 10.1093/molbev/msj051

Force, 2005, The origin of subfunctions and modular gene regulation, Genetics, 170, 433, 10.1534/genetics.104.027607

Franck, 2004, Evolutionary diversity of vertebrate small heat shock proteins, J Mol Evol, 59, 792, 10.1007/s00239-004-0013-z

Fu, 2006, Phylogenetic and biochemical studies reveal a potential evolutionary origin of small heat shock proteins of animals from bacterial class A, J Mol Evol, 62, 257, 10.1007/s00239-005-0076-5

Giese, 2005, Evidence for an essential function of the N terminus of a small heat shock protein in vivo, independent of in vitro chaperone activity, Proc Natl Acad Sci USA, 102, 18896, 10.1073/pnas.0506169103

Gil, 2002, Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life, Proc Natl Acad Sci USA, 99, 4454, 10.1073/pnas.062067299

Gil, 2003, The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes, Proc Natl Acad Sci USA, 100, 9388, 10.1073/pnas.1533499100

Goff, 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science, 296, 92, 10.1126/science.1068275

Guan, 2004, Characterization of the genomic structures and selective expression profiles of nine class I small heat shock genes clustered on two chromosomes in rice (Oryza sativa L.), Plant Mol Biol, 56, 795, 10.1007/s11103-004-5182-z

Gupta, 1995, Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationships among animals, plants and fungi species, Mol Biol Evol, 12, 1063

Harberer, 2004, Transcriptional similarities: dissimilarities and conservation of cis-elements in duplicated genes of Arabidopsis, Plant Physiol, 136, 3009, 10.1104/pp.104.046466

Haslbeck, 2005, Some like it hot: the structure and function of small heat-shock proteins, Nat Struct Mol Biol, 12, 842, 10.1038/nsmb993

Haslbeck, 2004, A domain in the N-terminal part of Hsp26 is essential for chaperone function and oligomerization, J Mol Biol, 343, 445, 10.1016/j.jmb.2004.08.048

Hughes, 2005, Gene duplication and the origin of novel proteins, Proc Natl Acad Sci USA, 102, 8791, 10.1073/pnas.0503922102

Kim, 1998, Small heat shock protein of Methanococcus jannaschii, a hyperthermophile, Proc Natl Acad Sci USA, 95, 9129, 10.1073/pnas.95.16.9129

Kotak, 2007, A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis, Plant Cell, 19, 182, 10.1105/tpc.106.048165

Kumar, 2004, MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Brief Bioinform, 5, 150, 10.1093/bib/5.2.150

Lee, 2000, A small heat shock protein cooperates with heat shock protein 70 systems to reactivate a heat-denatured protein, Plant Physiol, 122, 189, 10.1104/pp.122.1.189

Lee, 1995, Structure and in vitro molecular chaperone activity of cytosolic small heat shock proteins from pea, J Biol Chem, 270, 10432, 10.1074/jbc.270.18.10432

Lee, 1997, A small heat shock protein stably binds heat-denatured model substrates and can maintain a substrate in a folding-competent state, EMBO J, 16, 659, 10.1093/emboj/16.3.659

Lenne, 1994, A low molecular mass heat-shock protein is localized to higher plant mitochondria, Plant Physiol, 105, 1255, 10.1104/pp.105.4.1255

Lynch, 2000, The probability of duplicate gene preservation by subfunctionalization, Genetics, 154, 459, 10.1093/genetics/154.1.459

Ma, 2006, Identification and characterization of a stress-inducible and a constitutive small heat-shock protein targeted to the matrix of plant peroxisomes, Plant Physiol, 141, 47, 10.1104/pp.105.073841

Mondragon-Palomino, 2005, Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana, Mol Biol Evol, 22, 2444, 10.1093/molbev/msi241

Nakamoto, 2007, The small heat shock proteins and their clients, Cell Mol Life Sci, 64, 294, 10.1007/s00018-006-6321-2

Narberhaus, 2002, Alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network, Microbiol Mol Biol Rev, 66, 64, 10.1128/MMBR.66.1.64-93.2002

Posada, 2004, Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests, Syst Biol, 53, 793, 10.1080/10635150490522304

Remington, 2004, Contrasting modes of diversification in the Aux/IAA and ARF gene families, Plant Physiol, 135, 1738, 10.1104/pp.104.039669

Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180

Ronquist, 2006, Comment on “Phylogenetic MCMC algorithms are misleading on mixtures of trees”, Science, 312, 367, 10.1126/science.1123622

Sampedro, 2006, Genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ESTs, J Plant Res, 119, 11, 10.1007/s10265-005-0253-z

Sawyer, 1999

Scharf, 2001, The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing alpha-crystallin domains (Acd proteins), Cell Stress Chaperones, 6, 225, 10.1379/1466-1268(2001)006<0225:TEFOAT>2.0.CO;2

Shiu, 2004, Comparative analysis of the receptor-like kinase family in Arabidopsis and rice, Plant Cell, 16, 1220, 10.1105/tpc.020834

Siddique, 2003, Tomato heat stress protein Hsp16.1-CIII represents a member of a new class of nucleocytoplasmic small heat stress proteins in plants, Cell Stress Chaperones, 8, 381, 10.1379/1466-1268(2003)008<0381:THSPHR>2.0.CO;2

Stechmann, 2003, Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90, J Mol Evol, 57, 408, 10.1007/s00239-003-2490-x

Sun, 2005, Small heat shock proteins: molecular structure and chaperone function, Cell Mol Life Sci, 62, 2460, 10.1007/s00018-005-5190-4

Taylor, 2004, Duplication and divergence: the evolution of new genes and old ideas, Annu Rev Genet, 38, 615, 10.1146/annurev.genet.38.072902.092831

Tuskan, 2006, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, 313, 1596, 10.1126/science.1128691

van Montfort, 2001, Crystal structure and assembly of a eukaryotic small heat shock protein, Nat Struct Biol, 8, 1025, 10.1038/nsb722

van Montfort, 2002, Structure and function of the small heat shock protein/alpha-crystallin family of molecular chaperones, Adv Protein Chem, 59, 105, 10.1016/S0065-3233(01)59004-X

Vierling, 1991, The heat shock response in plants, Annu Rev Plant Physiol Plant Mol Biol, 42, 579, 10.1146/annurev.pp.42.060191.003051

Vierling, 1988, A heat shock protein localized to chloroplasts is a member of a eukaryotic superfamily of heat shock proteins, EMBO J, 7, 575, 10.1002/j.1460-2075.1988.tb02849.x

Vision, 2000, The origins of genomic duplications in Arabidopsis, Science, 290, 2114, 10.1126/science.290.5499.2114

Wang, 2004, Roles of plant heat-shock proteins and molecular chaperones in the abiotic stress response, Trends Plant Sci, 9, 244, 10.1016/j.tplants.2004.03.006

Wang, 2006, Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice, BMC Bioinformatics, 7, 447, 10.1186/1471-2105-7-447

Waters, 1995, The molecular evolution of the small heat shock proteins in plants, Genetics, 141, 785, 10.1093/genetics/141.2.785

Waters, 2003, Molecular adaptation and the origin of land plants, Mol Phyl Evol, 29, 456, 10.1016/j.ympev.2003.07.018

Waters, 2007, Evolutionary analysis of the small heat shock proteins in five complete algal genomes, J Mol Evol, 65, 162, 10.1007/s00239-006-0223-7

Waters, 1999, Chloroplast small heat shock proteins: Evidence for atypical evolution of an organelle-localized protein, Proc Natl Acad Sci USA, 96, 14394, 10.1073/pnas.96.25.14394

Waters, 1999, The diversification of plant cytosolic small heat shock proteins preceded the divergence of mosses, Mol Biol Evol, 16, 127, 10.1093/oxfordjournals.molbev.a026033

Waters, 1996, Evolution, structure and function of the small heat shock proteins in plants, J Exp Bot, 47, 325, 10.1093/jxb/47.3.325

Waters, 2003, The genome of Nanoarchaeum equitans: insights into early archaeal evolution, parasitism and the minimal genome, Proc Natl Acad Sci USA, 100, 12984, 10.1073/pnas.1735403100

Yang, 2006, Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication, Plant Physiol, 142, 820, 10.1104/pp.106.083642

Yazaki, 2004, The Rice PIPELINE: a unification tool for plant functional genomics, Nucleic Acids Res, 32, D383, 10.1093/nar/gkh001

Yu, 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. indica), Science, 296, 79, 10.1126/science.1068037

Zhang, 2002, Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana, Mol Biol Evol, 19, 1464, 10.1093/oxfordjournals.molbev.a004209

Zimmermann, 2004, GENEVESTIGATOR Arabidopsis Microarray Database and Analysis Toolbox, Plant Physiol, 136, 2621, 10.1104/pp.104.046367