Protein disulphide isomerase (PDI) is an oxidoreductase enzyme abundant in the endoplasmic reticulum (ER). In plants, PDIs have been shown to assist the folding and deposition of seed storage proteins during the bioge...Protein disulphide isomerase (PDI) is an oxidoreductase enzyme abundant in the endoplasmic reticulum (ER). In plants, PDIs have been shown to assist the folding and deposition of seed storage proteins during the biogenesis of protein bodies in the endosperm. Cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv. Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species were reported in our previous publications. Promoter sequences of three homoeologous genes encoding typical PDI, located on chromosome group 4 of bread wheat, and PDI promoter sequence analysis of Triticum urartu, Aegilops speltoides and Aegilops tauschii had also been reported previously. In this study, we report the isolation and sequencing of a ~700 bp region, comprising ~600 bp of the putative promoter region and 88 bp of the first exon of the typical PDI gene, in five accessions each from Triticum urartu (AA), Aegilops speltoides (BB) and Aegilops tauschii (DD). Sequence analysis indicated large variation among sequences belonging to the different genomes, while close similarity was found within each species and with the corresponding homoeologous PDI sequences of Triticum aestivum cv. CS (AABBDD) resulting in an overall high conservation of the sequence conferring endosperm-specific expression.展开更多
Objective:To understand the cause for the differences between potentially mild Southeast Asian and the more pathogenic ZIKV in South America.Methods:A comparative genomic analysis was performed to determine putative c...Objective:To understand the cause for the differences between potentially mild Southeast Asian and the more pathogenic ZIKV in South America.Methods:A comparative genomic analysis was performed to determine putative causations stemming from ZIKV.Results:Phylogcnctic analyses integrating geographical and time factors revealed that Southeast Asian ZIKV might not be the direct source of South American outbreaks as previously speculated.Amino acid residues unique to South American ZIKV isolates at the envelope,pr and NS1 proteins are listed and shown in the structural context.These unique residues on external viral proteins are not found in Southeast Asian ZIKV and could be responsible for the ongoing outbreak either via an intrinsic property of the virus or interactions with human immunity.Only a selected few primer/probe sets currently in clinical use were identified of being capable of detecting ZIKV strains worldwide.The envelope proteins of dengue virus(DENV) and ZIKV also showed a remarkable degree of similarity especially at the surface residues.Conclusions:findings that may help explain the cross-reactivity of DENV antibodies to ZIKV.Thus,major caveats must be exercised in using existing diagnostic tools for ZIKV.展开更多
C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immuni- ties. The globular (gC1q) domain similar with C1q was also found in many non-complement ...C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immuni- ties. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse func- tions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through compre- hensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-con- taining (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q do- main. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.展开更多
Domain insertions and deletions lead to variations in the domain architectures of the proteins from their common ancestor. In this work, we investigated four groups of the RhoGEF-containing proteins from different org...Domain insertions and deletions lead to variations in the domain architectures of the proteins from their common ancestor. In this work, we investigated four groups of the RhoGEF-containing proteins from different organisms with domain archi- tectures RhoGEF-PH-SH3, SH3-RhoGEF-PH, RhoGEF-PH, and SH3-RhoGEF defined in the Pfam database. The phylogenetic trees were constructed using each individual domain and/or the combinations of all the domains. The phyloge- netic analysis suggests that RhoGEF-PH-SH3 and SH3-RhoGEF-PH might have evolved from RhoGEF-PH through the insertion of SH3 independently, while SH3- RhoGEF of proteins in fruit fly might have evolved from SH3-RhoGEF-PH by the degeneration of PH domain.展开更多
文摘Protein disulphide isomerase (PDI) is an oxidoreductase enzyme abundant in the endoplasmic reticulum (ER). In plants, PDIs have been shown to assist the folding and deposition of seed storage proteins during the biogenesis of protein bodies in the endosperm. Cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv. Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species were reported in our previous publications. Promoter sequences of three homoeologous genes encoding typical PDI, located on chromosome group 4 of bread wheat, and PDI promoter sequence analysis of Triticum urartu, Aegilops speltoides and Aegilops tauschii had also been reported previously. In this study, we report the isolation and sequencing of a ~700 bp region, comprising ~600 bp of the putative promoter region and 88 bp of the first exon of the typical PDI gene, in five accessions each from Triticum urartu (AA), Aegilops speltoides (BB) and Aegilops tauschii (DD). Sequence analysis indicated large variation among sequences belonging to the different genomes, while close similarity was found within each species and with the corresponding homoeologous PDI sequences of Triticum aestivum cv. CS (AABBDD) resulting in an overall high conservation of the sequence conferring endosperm-specific expression.
基金supported by Thailand Research Fund-Mahidol University(RSA5880062)by the Office of the Higher Education Commission and Mahidol University under the National Research Universities Initiativesupported by the Royal Golden Jubilee Ph.D.Program (Grant No.PHD/0204/2552)
文摘Objective:To understand the cause for the differences between potentially mild Southeast Asian and the more pathogenic ZIKV in South America.Methods:A comparative genomic analysis was performed to determine putative causations stemming from ZIKV.Results:Phylogcnctic analyses integrating geographical and time factors revealed that Southeast Asian ZIKV might not be the direct source of South American outbreaks as previously speculated.Amino acid residues unique to South American ZIKV isolates at the envelope,pr and NS1 proteins are listed and shown in the structural context.These unique residues on external viral proteins are not found in Southeast Asian ZIKV and could be responsible for the ongoing outbreak either via an intrinsic property of the virus or interactions with human immunity.Only a selected few primer/probe sets currently in clinical use were identified of being capable of detecting ZIKV strains worldwide.The envelope proteins of dengue virus(DENV) and ZIKV also showed a remarkable degree of similarity especially at the surface residues.Conclusions:findings that may help explain the cross-reactivity of DENV antibodies to ZIKV.Thus,major caveats must be exercised in using existing diagnostic tools for ZIKV.
基金Acknowledgements This work was supported by the National Major Basic Research Program （No. 2004CB117401）；by the National Natural Science Foundation of China （No. 90408013）.
文摘C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immuni- ties. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse func- tions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through compre- hensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-con- taining (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q do- main. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.
基金We thank anonymous reviewers for their helpful comments.This work was supported by the National High-Tech Research and Development Program of China(Grant No.2003AA231030)the Excellent Young Teachers Program of the Ministry of Education of China(2003),and Beijing Normal University.
文摘Domain insertions and deletions lead to variations in the domain architectures of the proteins from their common ancestor. In this work, we investigated four groups of the RhoGEF-containing proteins from different organisms with domain archi- tectures RhoGEF-PH-SH3, SH3-RhoGEF-PH, RhoGEF-PH, and SH3-RhoGEF defined in the Pfam database. The phylogenetic trees were constructed using each individual domain and/or the combinations of all the domains. The phyloge- netic analysis suggests that RhoGEF-PH-SH3 and SH3-RhoGEF-PH might have evolved from RhoGEF-PH through the insertion of SH3 independently, while SH3- RhoGEF of proteins in fruit fly might have evolved from SH3-RhoGEF-PH by the degeneration of PH domain.
