The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wi...The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.展开更多
Kiwifruit is an important fruit crop that is highly sensitive to environmental stresses,such as drought,heat,cold,water logging and phytopathogens.Therefore it is indispensable to identify stress-responsive candidate ...Kiwifruit is an important fruit crop that is highly sensitive to environmental stresses,such as drought,heat,cold,water logging and phytopathogens.Therefore it is indispensable to identify stress-responsive candidate genes in kiwifruit cultivars for the stress resistance improvement.Here we report the isolation and characterization of a novel kiwifruit R1R2R3-MYB homolog(AcMYB3R)whose expression was induced by drought,salinity and cold stress.In vitro assays showed that AcMYB3R is a nuclear protein with transcriptional activation activity by binding to the cis-element of the kiwifruit orthologue of G2/M phase-specific gene KNOLLE.The Arabidopsis transgenic plants overexpressing AcMYB3R showed drastically enhanced tolerance to drought and salt stress.The expressions of stress-responsive genes such as RD29A,RD29B,COR15A and RD22 were prominently up-regulated by ectopic expression of Ac MYB3R.Our study provides a valuable piece of information for functional genomics studies of kiwifruit and molecular breeding in improving stress tolerance for crop production.展开更多
R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2 R3-MYB genes were identified from six Rosaceae species, includin...R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2 R3-MYB genes were identified from six Rosaceae species, including 105 in woodland strawberry(Fragaria vesca), 173 in European pear(Pyrus communis), 219 in apple(Malus domestica), 121 in peach(Prunus persica), 121 in Chinese rose(Rosa chinensis), and 99 in black raspberry(Rubus occidentalis). All R2 R3-MYB genes in the six Rosaceae species were clustered into 51 species-specific duplicated clades with 109 genes and 50 lineage-specific duplicated clades with 242 genes according to phylogenetic analysis. R2 R3-MYB genes were distributed on all chromosomes in each of the six species, with a small amount of tandem duplication events. The proportion of tandem repeat genes ranged from 0 to 25.1%. The R2 R3-MYB protein was conserved in a clade and likely to share similar functions. The distribution of Ks showed the duplication times of R2 R3-MYB genes in six Rosaceae species. Furthermore, most of the R2 R3-MYB genes had Ka/Ks values less than 1, which indicated they were driven by purifying selection during the evolutionary processes. The GO term enrichment analysis revealed that R2 R3-MYB genes in strawberry and black raspberry were more divergent than in other Rosaceae species. Analysis of transcriptomes of 42 different tissues and development stages of woodland strawberry showed that high expression levels of R2 R3-MYB suggested that the R2 R3-MYB genes in strawberry played a key role in growth and development of both vegetative tissues and fruits. The strawberry R2 R3-MYB genes in sub-group of S1, S2, S11, S20, and S22 had high expression levels both in young leaves(YL) and old leaves(OL) strawberry tissues under drought treatments.展开更多
Based on the transcriptome of Rosa rugosa, one anthocyanin-promoting R2R3-MYB gene, RrMYB10.1 (Accession Nos:MH717244), was cloned from the petals of Rosa rugosa ‘Zizhi’. Sequence analysis results showed that RrMYB1...Based on the transcriptome of Rosa rugosa, one anthocyanin-promoting R2R3-MYB gene, RrMYB10.1 (Accession Nos:MH717244), was cloned from the petals of Rosa rugosa ‘Zizhi’. Sequence analysis results showed that RrMYB10.1 had a full length opening reading frame of 747bp, encoding 249 amino acids. Sequence analysis revealed that RrMYB10.1 contained the conserved R2R3-MYB domain, two atypical anthocyanin-promoting motifs and a conserved amino acid signature for the interaction with bHLH protein. The results of phylogenic tree revealed that RrMYB10.1 showed high homology with other anthocyanin-promoting proteins in Rosacea, and sharing the highest identity (98.39%) with RhMYB10. RT-PCR results showed that RrMYB10.1 was mainly expressed in petals among various tissues and expressed significantly higher in petals in bud stage than in opening period. To sum up, these results showed that RrMYN10.1 may play a key role in regulating anthocyanin concentration, thus providing a certain foundation on regulating flower color formation in Rosa rugosa.展开更多
Anthocyanin is one of water-soluble natural pigments widely existing in flowers, fruits, stems, leaves and seeds of plants, and it is the major factor conferring pink or red to the petals of Rosa rugose. MYB TFs play ...Anthocyanin is one of water-soluble natural pigments widely existing in flowers, fruits, stems, leaves and seeds of plants, and it is the major factor conferring pink or red to the petals of Rosa rugose. MYB TFs play an important role in the anthocyanin synthesis in plants. This work aimed to clone the MYB gene related to anthocyanin synthesis in the petals of Rosa rugose, and explore the relationship between them to lay a good foundation for gene engineering improvement of R. rugose. Based on the transcriptional data, a full-length cDNA sequence of MYB Gene, RrMYB113 (GenBank accession Nos MG720012), was cloned at the first time from the petals of Rosa rugose “Zi zhi” with RT-PCR and RACE methods. The full-length cDNA is 885 bp with an open reading frame of 654 bp, encoding 216 amino acids. The derived RrMYB113 protein has a molecular weight of 25,297.64 Da, a calculated pI of 9.61, a R2R3-MYB domain and bHLH binding domain, and it also has the signature motifs ((A/S/G)NDV and KPRPR(T/S)), thus belonging to Sg6 R2R3-MYB subfamily. In the secondary structure of RrMYB113 protein, there is 37.04% α-helix, 39.81% random coil, 14.81% extended peptide chain, and 8.33% β-corner. There is no transmembrane domain and no signal peptide cleavage site, seventeen Ser phosphorylation sites, fifteen Thr phosphorylation sites, four Tyr phosphorylation sites, and no O-glycosylation sites. The expression of RrMYB113 increased with the color deepening in petals, and it expressed at a higher level in petals than in other tissues of R. rugose “Zi zhi”. These results are meaningful to reveal that RrMYB113 might be an important regulator in anthocyanin biosynthesis and coloration in the petals of R. rugose.展开更多
R2R3-MYB transcription factor plays an important role in plant anthocyanin synthesis. Based on the transcriptional database of Rosa rugosa, one MYB transcription factor related to floral color, RrMYB6, was cloned. By ...R2R3-MYB transcription factor plays an important role in plant anthocyanin synthesis. Based on the transcriptional database of Rosa rugosa, one MYB transcription factor related to floral color, RrMYB6, was cloned. By using bioinformatics analysis method, cloning MYB gene and analyzing its function in anthocyanin biosynthesis regulation, we hope to lay a solid foundation for new color variety breeding of R. rugosa. Using the R. rugosa “Zi zhi” as the material, we obtained the total length of cDNA of RrMYB6 by RT-PCR and RACE. By analyzing its bioinformatics, we found that the formula of the protein was C1491H2368N452O470S17, molecular weight was 34690.97 Da, the theoretical pI was 8.74. In addition, it belonged to unstable protein with an unstable index at 50.59, and it was also a hydrophilic protein with the total average hydrophobic index at -0.847. In the secondary structure of RrMYB6 protein, the Alpha helix accounted for 32.35%, random coil was 47.39%, extended strand was 11.11%, and beta turn was 9.15%. The sequence analysis showed that RrMYB6 had a typical R2R3-MYB domain and bHLH binding domain, and it also had an N1, C1, C2 inhibitory motif, belonging to the Sg4 subfamily MYB protein. What’s more, evolutionary analysis indicated that the RrMYB6 protein was closely related with the MYB protein in Rosacea family, while it was far from those in other families. The expression analysis showed that RrMYB6 protein decreased with the color of petals deeping, and its expression was the lowest in the petals while the highest in stamens. According to the above results, it was speculated that RrMYB6 was involved in regulating the anthocyanin synthesis of R. rugosa, which belonged to negative regulatory mechanism.展开更多
Objective To detect the relationship between the polymorphism of the glycogen-targeting regulatory subunit of the skeletal muscle glycogen-associated protein phosphatase 1 (PPP1R3) gene and type 2 diabetes by case-con...Objective To detect the relationship between the polymorphism of the glycogen-targeting regulatory subunit of the skeletal muscle glycogen-associated protein phosphatase 1 (PPP1R3) gene and type 2 diabetes by case-control study. Methods We genotyped the PPP1R3 gene Asp905Tyr polymorphism and a common 3'-untranslated region AT (AU)-rich element (ARE) polymorphism in 101 type 2 diabetic patients and 101controls by oligonucleotide ligation assay (OLA) and polyacrylamide gel elecrophoresis, respectively. Results Subjects with Tyr/Tyr genotypes whose body mass index (BMI)<25 were used as the reference group. Those whose BMI25 with Asp905 had a 3.66-fold increase (95% CI: 1.48-9.06, P=0.005) in type 2 diabetes risk. No association was found between 3'UTR ARE polymorphism and type 2 diabetes mellitus (OR=1.15; 95% CI: 0.62-2.14, P=0.65). Conclusion A joint effect between the Asp905 and BMI increases the risk of type 2 diabetes, and Asp905Tyr and ARE polymorphism of PPP1R3 gene are not the major diabetogenic gene variants in Chinese population.展开更多
基金supported by the National Natural Science Foundation of China(31372362)
文摘The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.
基金financially supported by the National Natural Science Foundation of China (31471157 and 31700266)
文摘Kiwifruit is an important fruit crop that is highly sensitive to environmental stresses,such as drought,heat,cold,water logging and phytopathogens.Therefore it is indispensable to identify stress-responsive candidate genes in kiwifruit cultivars for the stress resistance improvement.Here we report the isolation and characterization of a novel kiwifruit R1R2R3-MYB homolog(AcMYB3R)whose expression was induced by drought,salinity and cold stress.In vitro assays showed that AcMYB3R is a nuclear protein with transcriptional activation activity by binding to the cis-element of the kiwifruit orthologue of G2/M phase-specific gene KNOLLE.The Arabidopsis transgenic plants overexpressing AcMYB3R showed drastically enhanced tolerance to drought and salt stress.The expressions of stress-responsive genes such as RD29A,RD29B,COR15A and RD22 were prominently up-regulated by ectopic expression of Ac MYB3R.Our study provides a valuable piece of information for functional genomics studies of kiwifruit and molecular breeding in improving stress tolerance for crop production.
基金supported by the Fundamental Research Funds for the Central Universities, China (SYSB201804)partly supported by the open funds of the State Key Laboratory of Crop Genetics and Germplasm Enhancement, China (ZW201813)
文摘R2R3-MYB gene family play important roles in plants development, metabolism, and responses to various biotic and abiotic stresses. In this study, 838 R2 R3-MYB genes were identified from six Rosaceae species, including 105 in woodland strawberry(Fragaria vesca), 173 in European pear(Pyrus communis), 219 in apple(Malus domestica), 121 in peach(Prunus persica), 121 in Chinese rose(Rosa chinensis), and 99 in black raspberry(Rubus occidentalis). All R2 R3-MYB genes in the six Rosaceae species were clustered into 51 species-specific duplicated clades with 109 genes and 50 lineage-specific duplicated clades with 242 genes according to phylogenetic analysis. R2 R3-MYB genes were distributed on all chromosomes in each of the six species, with a small amount of tandem duplication events. The proportion of tandem repeat genes ranged from 0 to 25.1%. The R2 R3-MYB protein was conserved in a clade and likely to share similar functions. The distribution of Ks showed the duplication times of R2 R3-MYB genes in six Rosaceae species. Furthermore, most of the R2 R3-MYB genes had Ka/Ks values less than 1, which indicated they were driven by purifying selection during the evolutionary processes. The GO term enrichment analysis revealed that R2 R3-MYB genes in strawberry and black raspberry were more divergent than in other Rosaceae species. Analysis of transcriptomes of 42 different tissues and development stages of woodland strawberry showed that high expression levels of R2 R3-MYB suggested that the R2 R3-MYB genes in strawberry played a key role in growth and development of both vegetative tissues and fruits. The strawberry R2 R3-MYB genes in sub-group of S1, S2, S11, S20, and S22 had high expression levels both in young leaves(YL) and old leaves(OL) strawberry tissues under drought treatments.
文摘Based on the transcriptome of Rosa rugosa, one anthocyanin-promoting R2R3-MYB gene, RrMYB10.1 (Accession Nos:MH717244), was cloned from the petals of Rosa rugosa ‘Zizhi’. Sequence analysis results showed that RrMYB10.1 had a full length opening reading frame of 747bp, encoding 249 amino acids. Sequence analysis revealed that RrMYB10.1 contained the conserved R2R3-MYB domain, two atypical anthocyanin-promoting motifs and a conserved amino acid signature for the interaction with bHLH protein. The results of phylogenic tree revealed that RrMYB10.1 showed high homology with other anthocyanin-promoting proteins in Rosacea, and sharing the highest identity (98.39%) with RhMYB10. RT-PCR results showed that RrMYB10.1 was mainly expressed in petals among various tissues and expressed significantly higher in petals in bud stage than in opening period. To sum up, these results showed that RrMYN10.1 may play a key role in regulating anthocyanin concentration, thus providing a certain foundation on regulating flower color formation in Rosa rugosa.
文摘Anthocyanin is one of water-soluble natural pigments widely existing in flowers, fruits, stems, leaves and seeds of plants, and it is the major factor conferring pink or red to the petals of Rosa rugose. MYB TFs play an important role in the anthocyanin synthesis in plants. This work aimed to clone the MYB gene related to anthocyanin synthesis in the petals of Rosa rugose, and explore the relationship between them to lay a good foundation for gene engineering improvement of R. rugose. Based on the transcriptional data, a full-length cDNA sequence of MYB Gene, RrMYB113 (GenBank accession Nos MG720012), was cloned at the first time from the petals of Rosa rugose “Zi zhi” with RT-PCR and RACE methods. The full-length cDNA is 885 bp with an open reading frame of 654 bp, encoding 216 amino acids. The derived RrMYB113 protein has a molecular weight of 25,297.64 Da, a calculated pI of 9.61, a R2R3-MYB domain and bHLH binding domain, and it also has the signature motifs ((A/S/G)NDV and KPRPR(T/S)), thus belonging to Sg6 R2R3-MYB subfamily. In the secondary structure of RrMYB113 protein, there is 37.04% α-helix, 39.81% random coil, 14.81% extended peptide chain, and 8.33% β-corner. There is no transmembrane domain and no signal peptide cleavage site, seventeen Ser phosphorylation sites, fifteen Thr phosphorylation sites, four Tyr phosphorylation sites, and no O-glycosylation sites. The expression of RrMYB113 increased with the color deepening in petals, and it expressed at a higher level in petals than in other tissues of R. rugose “Zi zhi”. These results are meaningful to reveal that RrMYB113 might be an important regulator in anthocyanin biosynthesis and coloration in the petals of R. rugose.
文摘R2R3-MYB transcription factor plays an important role in plant anthocyanin synthesis. Based on the transcriptional database of Rosa rugosa, one MYB transcription factor related to floral color, RrMYB6, was cloned. By using bioinformatics analysis method, cloning MYB gene and analyzing its function in anthocyanin biosynthesis regulation, we hope to lay a solid foundation for new color variety breeding of R. rugosa. Using the R. rugosa “Zi zhi” as the material, we obtained the total length of cDNA of RrMYB6 by RT-PCR and RACE. By analyzing its bioinformatics, we found that the formula of the protein was C1491H2368N452O470S17, molecular weight was 34690.97 Da, the theoretical pI was 8.74. In addition, it belonged to unstable protein with an unstable index at 50.59, and it was also a hydrophilic protein with the total average hydrophobic index at -0.847. In the secondary structure of RrMYB6 protein, the Alpha helix accounted for 32.35%, random coil was 47.39%, extended strand was 11.11%, and beta turn was 9.15%. The sequence analysis showed that RrMYB6 had a typical R2R3-MYB domain and bHLH binding domain, and it also had an N1, C1, C2 inhibitory motif, belonging to the Sg4 subfamily MYB protein. What’s more, evolutionary analysis indicated that the RrMYB6 protein was closely related with the MYB protein in Rosacea family, while it was far from those in other families. The expression analysis showed that RrMYB6 protein decreased with the color of petals deeping, and its expression was the lowest in the petals while the highest in stamens. According to the above results, it was speculated that RrMYB6 was involved in regulating the anthocyanin synthesis of R. rugosa, which belonged to negative regulatory mechanism.
文摘Objective To detect the relationship between the polymorphism of the glycogen-targeting regulatory subunit of the skeletal muscle glycogen-associated protein phosphatase 1 (PPP1R3) gene and type 2 diabetes by case-control study. Methods We genotyped the PPP1R3 gene Asp905Tyr polymorphism and a common 3'-untranslated region AT (AU)-rich element (ARE) polymorphism in 101 type 2 diabetic patients and 101controls by oligonucleotide ligation assay (OLA) and polyacrylamide gel elecrophoresis, respectively. Results Subjects with Tyr/Tyr genotypes whose body mass index (BMI)<25 were used as the reference group. Those whose BMI25 with Asp905 had a 3.66-fold increase (95% CI: 1.48-9.06, P=0.005) in type 2 diabetes risk. No association was found between 3'UTR ARE polymorphism and type 2 diabetes mellitus (OR=1.15; 95% CI: 0.62-2.14, P=0.65). Conclusion A joint effect between the Asp905 and BMI increases the risk of type 2 diabetes, and Asp905Tyr and ARE polymorphism of PPP1R3 gene are not the major diabetogenic gene variants in Chinese population.
文摘【目的】从澳洲坚果(Macadamia integrifolia)叶片中克隆MYB1转录因子基因(MiMYB1)并进行生物信息学分析,为揭示R2R3-MYB家族转录因子成员在澳洲坚果中的抗逆作用机制提供参考依据。【方法】利用PCR从澳洲坚果品种桂热一号叶片中克隆MiMYB1基因,采用ProtParam、TMHMM Server v.2.0和SMART:Main page等在线分析软件对MiMYB1蛋白进行生物信息学分析,运用DNAMAN 7.0进行蛋白氨基酸多序列比对分析,并从NCBI中选取126个拟南芥R2R3-MYB家族成员,以Geneious Pro v4.8.4中的邻接法(Neighbor-joining,NJ)构建系统发育进化树。【结果】从澳洲坚果品种桂热一号叶片中克隆获得的MiMYB1基因序列全长1205 bp,包含1062 bp的开放阅读框(ORF),共编码353个氨基酸,GenBank登录号为MN254975。MiMYB1蛋白具有2个SANT保守结构域,属于R2R3-MYB家族,是无跨膜结构、无信号肽且定位于细胞核的不稳定亲水性蛋白。MiMYB1氨基酸序列(MN254975)与荷花NnMYB39氨基酸序列(XP010277911.1)的亲缘关系最近,相似性为71.81%;与哥伦比亚锦葵HuMYB102-like(XP021293847.1)、榴莲DzMYB102-like(XP022777375.1)、木薯MeMYB102-like(XP021596793.1)和高山栎QsMYB102-like(XP023877052.1)的MYB氨基酸序列相似性分别为67.47%、68.63%、64.44%和67.28%。MiMYB1蛋白与126个拟南芥R2R3-MYB家族成员的系统发育进化分析结果显示,MiMYB1与AtMYB41的亲缘关系最近,与AtMYB41、AtMYB74和AtMYB102同属于S11亚族,具有相似的生物学功能,即与植物抗逆性功能相关。【结论】MiMYB1是典型的植物R2R3-MYB转录因子,在澳洲坚果的抗逆反应中发挥作用。
