publication . Other literature type . Article . 2015

The evolution of WRKY transcription factors.

Rinerson, Charles I; Rabara, Roel C; Tripathi, Prateek; Shen, Qingxi J; Rushton, Paul J;
  • Published: 01 Feb 2015
  • Publisher: Springer Science and Business Media LLC
Abstract
Background The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain. Results Only two WRKY genes are present in th...
Subjects
Medical Subject Headings: food and beveragesfungi
free text keywords: Research Article, WRKY transcription factor, Evolution, Lateral gene transfer, Resistance protein, Charophyte, Plant Science, Genome, WRKY protein domain, Whole genome sequencing, Fusion protein, Biology, Horizontal gene transfer, Transcription factor, Gene, Protein domain, Genetics, Botany
42 references, page 1 of 3

Rushton, PJ, Macdonald, H, Huttly, AK, Lazarus, CM, Hooley, R. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol. 1995; 29 (4): 691-702 [OpenAIRE] [PubMed] [DOI]

Yamasaki, K, Kigawa, T, Inoue, M, Tateno, M, Yamasaki, T, Yabuki, T. Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell. 2005; 17 (3): 944-56 [OpenAIRE] [PubMed] [DOI]

Duan, MR, Nan, J, Liang, YH, Mao, P, Lu, L, Li, L. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Res. 2007; 35 (4): 1145-54 [OpenAIRE] [PubMed] [DOI]

Yamasaki, K, Kigawa, T, Watanabe, S, Inoue, M, Yamasaki, T, Seki, M. Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor. J Biol Chem. 2012; 287 (10): 7683-91 [OpenAIRE] [PubMed] [DOI]

Eulgem, T, Rushton, PJ, Robatzek, S, Somssich, IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000; 5 (5): 199-206 [OpenAIRE] [PubMed] [DOI]

Rushton, PJ, Somssich, IE, Ringler, P, Shen, QJ. WRKY transcription factors. Trends Plant Sci. 2010; 15 (5): 247-58 [OpenAIRE] [PubMed] [DOI]

Zhang, Y, Wang, L. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 2005; 5: 1 [OpenAIRE] [PubMed] [DOI]

Rensing, SA, Lang, D, Zimmer, AD, Terry, A, Salamov, A, Shapiro, H. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science. 2008; 319 (5859): 64-9 [OpenAIRE] [PubMed] [DOI]

Banks, JA, Nishiyama, T, Hasebe, M, Bowman, JL, Gribskov, M, dePamphilis, C. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011; 332 (6032): 960-3 [OpenAIRE] [PubMed] [DOI]

Babu, MM, Iyer, LM, Balaji, S, Aravind, L. The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res. 2006; 34 (22): 6505-20 [OpenAIRE] [PubMed] [DOI]

Brand, LH, Fischer, NM, Harter, K, Kohlbacher, O, Wanke, D. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res. 2013; 41 (21): 9764-78 [OpenAIRE] [PubMed] [DOI]

Timme, RE, Bachvaroff, TR, Delwiche, CF. Broad phylogenomic sampling and the sister lineage of land plants. PLoS One. 2012; 7 (1): e29696 [OpenAIRE] [PubMed] [DOI]

Hori, K, Maruyama, F, Fujisawa, T, Togashi, T, Yamamoto, N, Seo, M. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat Commun. 2014; 5: 3978 [OpenAIRE] [PubMed] [DOI]

Edgar, RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32 (5): 1792-7 [OpenAIRE] [PubMed] [DOI]

Tamura, K, Stecher, G, Peterson, D, Filipski, A, Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30 (12): 2725-9 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
Abstract
Background The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain. Results Only two WRKY genes are present in th...
Subjects
Medical Subject Headings: food and beveragesfungi
free text keywords: Research Article, WRKY transcription factor, Evolution, Lateral gene transfer, Resistance protein, Charophyte, Plant Science, Genome, WRKY protein domain, Whole genome sequencing, Fusion protein, Biology, Horizontal gene transfer, Transcription factor, Gene, Protein domain, Genetics, Botany
42 references, page 1 of 3

Rushton, PJ, Macdonald, H, Huttly, AK, Lazarus, CM, Hooley, R. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol. 1995; 29 (4): 691-702 [OpenAIRE] [PubMed] [DOI]

Yamasaki, K, Kigawa, T, Inoue, M, Tateno, M, Yamasaki, T, Yabuki, T. Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell. 2005; 17 (3): 944-56 [OpenAIRE] [PubMed] [DOI]

Duan, MR, Nan, J, Liang, YH, Mao, P, Lu, L, Li, L. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Res. 2007; 35 (4): 1145-54 [OpenAIRE] [PubMed] [DOI]

Yamasaki, K, Kigawa, T, Watanabe, S, Inoue, M, Yamasaki, T, Seki, M. Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor. J Biol Chem. 2012; 287 (10): 7683-91 [OpenAIRE] [PubMed] [DOI]

Eulgem, T, Rushton, PJ, Robatzek, S, Somssich, IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000; 5 (5): 199-206 [OpenAIRE] [PubMed] [DOI]

Rushton, PJ, Somssich, IE, Ringler, P, Shen, QJ. WRKY transcription factors. Trends Plant Sci. 2010; 15 (5): 247-58 [OpenAIRE] [PubMed] [DOI]

Zhang, Y, Wang, L. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 2005; 5: 1 [OpenAIRE] [PubMed] [DOI]

Rensing, SA, Lang, D, Zimmer, AD, Terry, A, Salamov, A, Shapiro, H. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science. 2008; 319 (5859): 64-9 [OpenAIRE] [PubMed] [DOI]

Banks, JA, Nishiyama, T, Hasebe, M, Bowman, JL, Gribskov, M, dePamphilis, C. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011; 332 (6032): 960-3 [OpenAIRE] [PubMed] [DOI]

Babu, MM, Iyer, LM, Balaji, S, Aravind, L. The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res. 2006; 34 (22): 6505-20 [OpenAIRE] [PubMed] [DOI]

Brand, LH, Fischer, NM, Harter, K, Kohlbacher, O, Wanke, D. Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res. 2013; 41 (21): 9764-78 [OpenAIRE] [PubMed] [DOI]

Timme, RE, Bachvaroff, TR, Delwiche, CF. Broad phylogenomic sampling and the sister lineage of land plants. PLoS One. 2012; 7 (1): e29696 [OpenAIRE] [PubMed] [DOI]

Hori, K, Maruyama, F, Fujisawa, T, Togashi, T, Yamamoto, N, Seo, M. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat Commun. 2014; 5: 3978 [OpenAIRE] [PubMed] [DOI]

Edgar, RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32 (5): 1792-7 [OpenAIRE] [PubMed] [DOI]

Tamura, K, Stecher, G, Peterson, D, Filipski, A, Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30 (12): 2725-9 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
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publication . Other literature type . Article . 2015

The evolution of WRKY transcription factors.

Rinerson, Charles I; Rabara, Roel C; Tripathi, Prateek; Shen, Qingxi J; Rushton, Paul J;