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
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
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
BACKGROUNDChronic neutrophilic leukemia (CNL) is a rare bone marrow proliferative tumorand a heterogeneous disorder. In 2016, the World Health Organization includedactivating mutations in the CSF3R gene as one of the ...BACKGROUNDChronic neutrophilic leukemia (CNL) is a rare bone marrow proliferative tumorand a heterogeneous disorder. In 2016, the World Health Organization includedactivating mutations in the CSF3R gene as one of the diagnostic criteria, withCSF3R T618I being the most common mutation. The disease is often accompaniedby splenomegaly, but no developmental abnormalities and significant reticularfibrosis, and no Ph chromosome and BCR-ABL fusion gene. So, it is difficult todiagnose at the first presentation in the absence of classical symptoms. Herein wedescribe a rare CNL patient without splenomegaly whose initial diagnostic cluewas neutrophilic hyperactivity.CASE SUMMARYThe patient is an 80-year-old Han Chinese man who presented with one month offatigue and fatigue aggravation in the last half of the month. He had nosplenomegaly, but had persistent hypofibrinogenemia, obvious skin bleeding, andhemoptysis, and required repeated infusion of fibrinogen therapy. After manyrelevant laboratory examinations, histopathological examination, and sequencinganalysis, the patient was finally diagnosed with CNL [CSF3R T618I positive:c.1853C>T (p.T618I) and c.2514T>A (p.C838)].CONCLUSIONThe physical examination and blood test for tumor-related genes are insufficientto establish a diagnosis of CNL. Splenomegaly is not that important, buthyperplasia of interstitial neutrophil system and activating mutations in CSF3Rare important clues to CNL diagnosis.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
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
Colony-stimulating factor 3 receptor(CSF3R)mutations have been identified in a variety of myeloid disorders.Although CSF3R point mutations(eg,T618I)are emerging as key players in chronic neutrophilic leukemia/atypical...Colony-stimulating factor 3 receptor(CSF3R)mutations have been identified in a variety of myeloid disorders.Although CSF3R point mutations(eg,T618I)are emerging as key players in chronic neutrophilic leukemia/atypical chronic myelogenous leukemia,the significance of rarer CSF3R mutations is unknown.Here,we report a 32-year-old female who was diagnosed as Philadelphia chromosome-positive acute lymphoblastic leukemia(Ph^(+)ALL)with the CSF3R M696T mutation and was undergone unrelated donor hematopoietic stem cell transplantation.The patient achieved complete remission with chemotherapy in combination with tyrosine kinase inhibitor(TKI)and long-term survival by unrelated donor transplantation.Meanwhile,we performed a series of experiments using murine interleukin 3(IL-3)-dependent Ba/F3 cell line to evaluate the transforming capacity of the CSF3R M696T mutation.We confirmed the presence of a CSF3R M696T germline mutation in this patient which was inherited from her mother.The in vitro experiment results showed that the CSF3R M696T mutation contributes marginally to the tumor transformation of Ba/F3 cells,indicating that CSF3R M696T mutation was neutral in tumor transformation ability.We concluded that TKI is effective in patients with the CSF3R M696T mutation in Ph+ALL and donors with CSF3R M696T mutation might still be selected as the candidate for transplantation.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BACKGROUNDChronic neutrophilic leukemia (CNL) is a rare bone marrow proliferative tumorand a heterogeneous disorder. In 2016, the World Health Organization includedactivating mutations in the CSF3R gene as one of the diagnostic criteria, withCSF3R T618I being the most common mutation. The disease is often accompaniedby splenomegaly, but no developmental abnormalities and significant reticularfibrosis, and no Ph chromosome and BCR-ABL fusion gene. So, it is difficult todiagnose at the first presentation in the absence of classical symptoms. Herein wedescribe a rare CNL patient without splenomegaly whose initial diagnostic cluewas neutrophilic hyperactivity.CASE SUMMARYThe patient is an 80-year-old Han Chinese man who presented with one month offatigue and fatigue aggravation in the last half of the month. He had nosplenomegaly, but had persistent hypofibrinogenemia, obvious skin bleeding, andhemoptysis, and required repeated infusion of fibrinogen therapy. After manyrelevant laboratory examinations, histopathological examination, and sequencinganalysis, the patient was finally diagnosed with CNL [CSF3R T618I positive:c.1853C>T (p.T618I) and c.2514T>A (p.C838)].CONCLUSIONThe physical examination and blood test for tumor-related genes are insufficientto establish a diagnosis of CNL. Splenomegaly is not that important, buthyperplasia of interstitial neutrophil system and activating mutations in CSF3Rare important clues to CNL diagnosis.
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.
基金This work was supported by funds from the Ministry of Science and Technology of China(2018YFA0107801 and 2017YFA0103402)the National Natural Science Foundation of China(82070192,81770105,81770155,and 81670171).
文摘Colony-stimulating factor 3 receptor(CSF3R)mutations have been identified in a variety of myeloid disorders.Although CSF3R point mutations(eg,T618I)are emerging as key players in chronic neutrophilic leukemia/atypical chronic myelogenous leukemia,the significance of rarer CSF3R mutations is unknown.Here,we report a 32-year-old female who was diagnosed as Philadelphia chromosome-positive acute lymphoblastic leukemia(Ph^(+)ALL)with the CSF3R M696T mutation and was undergone unrelated donor hematopoietic stem cell transplantation.The patient achieved complete remission with chemotherapy in combination with tyrosine kinase inhibitor(TKI)and long-term survival by unrelated donor transplantation.Meanwhile,we performed a series of experiments using murine interleukin 3(IL-3)-dependent Ba/F3 cell line to evaluate the transforming capacity of the CSF3R M696T mutation.We confirmed the presence of a CSF3R M696T germline mutation in this patient which was inherited from her mother.The in vitro experiment results showed that the CSF3R M696T mutation contributes marginally to the tumor transformation of Ba/F3 cells,indicating that CSF3R M696T mutation was neutral in tumor transformation ability.We concluded that TKI is effective in patients with the CSF3R M696T mutation in Ph+ALL and donors with CSF3R M696T mutation might still be selected as the candidate for transplantation.
基金the Natural Science Foundation of China (31000307)the Outstanding Young Scientist Foundation of Shandong Province (BS2010NY004)+1 种基金the Open Project of State Key Laboratory of Crop Biology of Shandong Agricultural University (2010KF03)the Strengthening Project of Ludong University Subject Building
