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Wheat WCBP1 encodes a putative copper-binding protein involved in stripe rust resistance and inhibition of leaf senescence.

Li X, Liu T, Chen W, Zhong S, Zhang H, Tang Z, Chang Z, Wang L, Zhang M, Li L, Rao H, Ren Z, Luo P - BMC Plant Biol. (2015)

Bottom Line: We cloned a candidate gene encoding wheat copper-binding protein (WCBP1) by amplifying the polymorphic region, and we mapped WCBP1 to a 0.64 cM genetic interval.Brachypodium, rice, and sorghum have genes and genomic regions syntenic to this region.Sequence analysis suggested that the resistant WCBP1 allele might have resulted from a deletion of 36-bp sequence of the wheat genomic sequence, rather than direct transfer from Th. intermedium. qRT-PCR confirmed that WCBP1 expression changes in response to pathogen infection.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. sadoneli@gmail.com.

ABSTRACT

Background: Stripe rust, a highly destructive foliar disease of wheat (Triticum aestivum), causes severe losses, which may be accompanied by reduced photosynthetic activity and accelerated leaf senescence.

Methods: We used suppression subtractive hybridization (SSH) to examine the mechanisms of resistance in the resistant wheat line L693 (Reg. No. GP-972, PI 672538), which was derived from a lineage that includes a wide cross between common and Thinopyrum intermedium. Sequencing of an SSH cDNA library identified 112 expressed sequence tags.

Results: In silico mapping placed one of these tags [GenBank: JK972238] on chromosome 1A. Primers based on [GenBank: JK972238] amplified a polymorphic band, which co-segregated with YrL693. We cloned a candidate gene encoding wheat copper-binding protein (WCBP1) by amplifying the polymorphic region, and we mapped WCBP1 to a 0.64 cM genetic interval. Brachypodium, rice, and sorghum have genes and genomic regions syntenic to this region.

Discussion: Sequence analysis suggested that the resistant WCBP1 allele might have resulted from a deletion of 36-bp sequence of the wheat genomic sequence, rather than direct transfer from Th. intermedium. qRT-PCR confirmed that WCBP1 expression changes in response to pathogen infection.

Conclusions: The unique chromosomal location and expression mode of WCBP1 suggested that WCBP1 is the putative candidate gene of YrL693, which was involved in leaf senescence and photosynthesis related to plant responses to stripe rust infection during the grain-filling stage.

No MeSH data available.


Related in: MedlinePlus

The WCBP1 gene, its putative protein structure, and its phylogenetic tree. a The predicted mRNA structure of WCBP1 is shown above the genomic sequence, including introns (thin lines) and exons (thick lines). ATG represents the methionine start codon, and TGA represents the stop codon. b Coding regions of two heavy metal copper-binding domains in exons 1 and 3. The major differences between the resistance-and susceptibility-associated WCBP1 alleles are a SNP in exon 1 and a 36 bp deletion in exon 4. c Alignment of the amino acid sequences and secondary structures of the proteins putatively encoded by the resistance-and susceptibility-associated alleles of WCBP1. d Phylogenetic tree constructed using the neighbor-joining algorithm in MEGA 5.05 following WCBP1 protein sequence alignment using the CLUSTALW program. Accession numbers for the other heavy metal copper-binding proteins were as follows: EMS53947 (Triticum urartu) (11.37 %), EMT15307 (Aegilops tauschii) (11.37 %), XP_003573974 (Brachypodium distachyon) (11.37 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002465840 (Sorghum bicolor) (6.65 %), AFK36536 (Medicago truncatula) (4.72 %), XP_004497534 (Cicer arietinum) (4.72%), XP_004955283 (Setaria italica) (4.58 %), BAK03814 (Hordeum vulgare subsp. vulgare) (4.15 %), XP_004304460 (Fragaria vesca subsp. vesca) (4.01%), DAA49855 (Zea mays) (3.93 %), NP_195958 (Arabidopsis thaliana) (3.79 %), EOA20845 (Capsella rubella) (3.79 %), XP_004246628 (Solanum lycopersicum) (3.72 %), XP_003542527 (Glycine max) (3.72 %), AFK35929 (Lotus japonicus) (3.72 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002276537 (Vitis vinifera) (3.72%) and AFW90521 (Phaseolus vulgaris) (3.29 %)
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Fig5: The WCBP1 gene, its putative protein structure, and its phylogenetic tree. a The predicted mRNA structure of WCBP1 is shown above the genomic sequence, including introns (thin lines) and exons (thick lines). ATG represents the methionine start codon, and TGA represents the stop codon. b Coding regions of two heavy metal copper-binding domains in exons 1 and 3. The major differences between the resistance-and susceptibility-associated WCBP1 alleles are a SNP in exon 1 and a 36 bp deletion in exon 4. c Alignment of the amino acid sequences and secondary structures of the proteins putatively encoded by the resistance-and susceptibility-associated alleles of WCBP1. d Phylogenetic tree constructed using the neighbor-joining algorithm in MEGA 5.05 following WCBP1 protein sequence alignment using the CLUSTALW program. Accession numbers for the other heavy metal copper-binding proteins were as follows: EMS53947 (Triticum urartu) (11.37 %), EMT15307 (Aegilops tauschii) (11.37 %), XP_003573974 (Brachypodium distachyon) (11.37 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002465840 (Sorghum bicolor) (6.65 %), AFK36536 (Medicago truncatula) (4.72 %), XP_004497534 (Cicer arietinum) (4.72%), XP_004955283 (Setaria italica) (4.58 %), BAK03814 (Hordeum vulgare subsp. vulgare) (4.15 %), XP_004304460 (Fragaria vesca subsp. vesca) (4.01%), DAA49855 (Zea mays) (3.93 %), NP_195958 (Arabidopsis thaliana) (3.79 %), EOA20845 (Capsella rubella) (3.79 %), XP_004246628 (Solanum lycopersicum) (3.72 %), XP_003542527 (Glycine max) (3.72 %), AFK35929 (Lotus japonicus) (3.72 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002276537 (Vitis vinifera) (3.72%) and AFW90521 (Phaseolus vulgaris) (3.29 %)

Mentions: The open reading frame (ORF) (Fig. 5a) of the candidate resistance gene encodes a putative wheat copper binding protein 1 (WCBP1) predicted to contain 346 amino acids in resistant lines (AGS38338) and 358 amino acids in susceptible lines. The SNP in the first exon (Additional file 1: Figure S5) does not change the deduced amino acid sequence. The 36 bp repeated sequence in the fourth exon (Fig. 5b and Additional file 1: Figure S3) caused an addition of 12 amino acids (K K K D K G A G D G G E) in the susceptible line (Fig. 5b) at amino acids 242–253. The deduced amino acid sequence forms a protein containing two predicted copper-binding domains, at amino acids 34–39 (L H C A G C, exon 1), and at amino acids 170–175 (L H C D G C, exon 3) (Fig. 5b). The full-length, deduced WCBP1 protein shows sequence similarity with known heavy metal-binding proteins from diverse species. Phylogenetic analysis indicated that WCBP1 shared the highest similarity with the EMS53947 protein (Fig. 5d), but they did not cluster together.Fig. 5


Wheat WCBP1 encodes a putative copper-binding protein involved in stripe rust resistance and inhibition of leaf senescence.

Li X, Liu T, Chen W, Zhong S, Zhang H, Tang Z, Chang Z, Wang L, Zhang M, Li L, Rao H, Ren Z, Luo P - BMC Plant Biol. (2015)

The WCBP1 gene, its putative protein structure, and its phylogenetic tree. a The predicted mRNA structure of WCBP1 is shown above the genomic sequence, including introns (thin lines) and exons (thick lines). ATG represents the methionine start codon, and TGA represents the stop codon. b Coding regions of two heavy metal copper-binding domains in exons 1 and 3. The major differences between the resistance-and susceptibility-associated WCBP1 alleles are a SNP in exon 1 and a 36 bp deletion in exon 4. c Alignment of the amino acid sequences and secondary structures of the proteins putatively encoded by the resistance-and susceptibility-associated alleles of WCBP1. d Phylogenetic tree constructed using the neighbor-joining algorithm in MEGA 5.05 following WCBP1 protein sequence alignment using the CLUSTALW program. Accession numbers for the other heavy metal copper-binding proteins were as follows: EMS53947 (Triticum urartu) (11.37 %), EMT15307 (Aegilops tauschii) (11.37 %), XP_003573974 (Brachypodium distachyon) (11.37 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002465840 (Sorghum bicolor) (6.65 %), AFK36536 (Medicago truncatula) (4.72 %), XP_004497534 (Cicer arietinum) (4.72%), XP_004955283 (Setaria italica) (4.58 %), BAK03814 (Hordeum vulgare subsp. vulgare) (4.15 %), XP_004304460 (Fragaria vesca subsp. vesca) (4.01%), DAA49855 (Zea mays) (3.93 %), NP_195958 (Arabidopsis thaliana) (3.79 %), EOA20845 (Capsella rubella) (3.79 %), XP_004246628 (Solanum lycopersicum) (3.72 %), XP_003542527 (Glycine max) (3.72 %), AFK35929 (Lotus japonicus) (3.72 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002276537 (Vitis vinifera) (3.72%) and AFW90521 (Phaseolus vulgaris) (3.29 %)
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Related In: Results  -  Collection

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Fig5: The WCBP1 gene, its putative protein structure, and its phylogenetic tree. a The predicted mRNA structure of WCBP1 is shown above the genomic sequence, including introns (thin lines) and exons (thick lines). ATG represents the methionine start codon, and TGA represents the stop codon. b Coding regions of two heavy metal copper-binding domains in exons 1 and 3. The major differences between the resistance-and susceptibility-associated WCBP1 alleles are a SNP in exon 1 and a 36 bp deletion in exon 4. c Alignment of the amino acid sequences and secondary structures of the proteins putatively encoded by the resistance-and susceptibility-associated alleles of WCBP1. d Phylogenetic tree constructed using the neighbor-joining algorithm in MEGA 5.05 following WCBP1 protein sequence alignment using the CLUSTALW program. Accession numbers for the other heavy metal copper-binding proteins were as follows: EMS53947 (Triticum urartu) (11.37 %), EMT15307 (Aegilops tauschii) (11.37 %), XP_003573974 (Brachypodium distachyon) (11.37 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002465840 (Sorghum bicolor) (6.65 %), AFK36536 (Medicago truncatula) (4.72 %), XP_004497534 (Cicer arietinum) (4.72%), XP_004955283 (Setaria italica) (4.58 %), BAK03814 (Hordeum vulgare subsp. vulgare) (4.15 %), XP_004304460 (Fragaria vesca subsp. vesca) (4.01%), DAA49855 (Zea mays) (3.93 %), NP_195958 (Arabidopsis thaliana) (3.79 %), EOA20845 (Capsella rubella) (3.79 %), XP_004246628 (Solanum lycopersicum) (3.72 %), XP_003542527 (Glycine max) (3.72 %), AFK35929 (Lotus japonicus) (3.72 %), EAY78671 (Oryza sativa indica group) (3.72%), XP_002276537 (Vitis vinifera) (3.72%) and AFW90521 (Phaseolus vulgaris) (3.29 %)
Mentions: The open reading frame (ORF) (Fig. 5a) of the candidate resistance gene encodes a putative wheat copper binding protein 1 (WCBP1) predicted to contain 346 amino acids in resistant lines (AGS38338) and 358 amino acids in susceptible lines. The SNP in the first exon (Additional file 1: Figure S5) does not change the deduced amino acid sequence. The 36 bp repeated sequence in the fourth exon (Fig. 5b and Additional file 1: Figure S3) caused an addition of 12 amino acids (K K K D K G A G D G G E) in the susceptible line (Fig. 5b) at amino acids 242–253. The deduced amino acid sequence forms a protein containing two predicted copper-binding domains, at amino acids 34–39 (L H C A G C, exon 1), and at amino acids 170–175 (L H C D G C, exon 3) (Fig. 5b). The full-length, deduced WCBP1 protein shows sequence similarity with known heavy metal-binding proteins from diverse species. Phylogenetic analysis indicated that WCBP1 shared the highest similarity with the EMS53947 protein (Fig. 5d), but they did not cluster together.Fig. 5

Bottom Line: We cloned a candidate gene encoding wheat copper-binding protein (WCBP1) by amplifying the polymorphic region, and we mapped WCBP1 to a 0.64 cM genetic interval.Brachypodium, rice, and sorghum have genes and genomic regions syntenic to this region.Sequence analysis suggested that the resistant WCBP1 allele might have resulted from a deletion of 36-bp sequence of the wheat genomic sequence, rather than direct transfer from Th. intermedium. qRT-PCR confirmed that WCBP1 expression changes in response to pathogen infection.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China. sadoneli@gmail.com.

ABSTRACT

Background: Stripe rust, a highly destructive foliar disease of wheat (Triticum aestivum), causes severe losses, which may be accompanied by reduced photosynthetic activity and accelerated leaf senescence.

Methods: We used suppression subtractive hybridization (SSH) to examine the mechanisms of resistance in the resistant wheat line L693 (Reg. No. GP-972, PI 672538), which was derived from a lineage that includes a wide cross between common and Thinopyrum intermedium. Sequencing of an SSH cDNA library identified 112 expressed sequence tags.

Results: In silico mapping placed one of these tags [GenBank: JK972238] on chromosome 1A. Primers based on [GenBank: JK972238] amplified a polymorphic band, which co-segregated with YrL693. We cloned a candidate gene encoding wheat copper-binding protein (WCBP1) by amplifying the polymorphic region, and we mapped WCBP1 to a 0.64 cM genetic interval. Brachypodium, rice, and sorghum have genes and genomic regions syntenic to this region.

Discussion: Sequence analysis suggested that the resistant WCBP1 allele might have resulted from a deletion of 36-bp sequence of the wheat genomic sequence, rather than direct transfer from Th. intermedium. qRT-PCR confirmed that WCBP1 expression changes in response to pathogen infection.

Conclusions: The unique chromosomal location and expression mode of WCBP1 suggested that WCBP1 is the putative candidate gene of YrL693, which was involved in leaf senescence and photosynthesis related to plant responses to stripe rust infection during the grain-filling stage.

No MeSH data available.


Related in: MedlinePlus