A novel method based on discrete wavelet transform （DWT） and cross-covariance for revealing the evolution of species at different spatial resolutions is presented. The trypsin proteins of different species are chose...A novel method based on discrete wavelet transform （DWT） and cross-covariance for revealing the evolution of species at different spatial resolutions is presented. The trypsin proteins of different species are chosen as an example to describe the evolution relationship according to the evolution vectors by using this method. The results indicated that this method is a promising approach to reveal species evolution at different spatial resolutions.展开更多
Plants have evolved a large number of transcription factors（TF）, which are enriched among duplicate genes,highlighting their roles in complex regulatory networks. The APETALA2/EREBP-like genes constitute a large pla...Plants have evolved a large number of transcription factors（TF）, which are enriched among duplicate genes,highlighting their roles in complex regulatory networks. The APETALA2/EREBP-like genes constitute a large plant TF family and participate in development and stress responses. To probe the conservation and divergence of AP2/EREBP genes,we analyzed the duplication patterns of this family in Brassicaceae and identified interacting proteins of representative Arabidopsis AP2/EREBP proteins. We found that many AP2/EREBP duplicates generated early in Brassicaceae history were quickly lost, but many others were retained in all tested Brassicaceae species, suggesting early functional divergence followed by persistent conservation. In addition,the sequences of the AP2 domain and exon numbers were highly conserved in rosids. Furthermore, we used 16 A.thaliana AP2/EREBP proteins as baits in yeast screens and identified 1,970 potential AP2/EREBP-interacting proteins,with a small subset of interactions verified in planta. Many AP2 genes also exhibit reduced expression in an antherdefective mutant, providing a possible link to developmental regulation. The putative AP2-interacting proteins participate in many functions in development and stress responses,including photomorphogenesis, flower development, pathogenesis, drought and cold responses, abscisic acid and auxin signaling. Our results present the AP2/EREBP evolution patterns in Brassicaceae, and support a proposed interaction network of AP2/EREBP proteins and their putative interacting proteins for further study.展开更多
Macromolecular assemblies such as protein complexes and protein/RNA condensates are involved in most fundamental cellular processes.The arrangement of subunits within these nano-assemblies is critical for their biolog...Macromolecular assemblies such as protein complexes and protein/RNA condensates are involved in most fundamental cellular processes.The arrangement of subunits within these nano-assemblies is critical for their biological function and is determined by the topology of physical contacts within and between the subunits forming the complex.Describing the spatial arrangement of these interactions is of central importance to understand their functional and stability consequences.In this concept article,we propose a circuit topology-based formalism to define the topology of a complex consisting of linear polymeric chains with interand intrachain interactions.We apply our method to a system of model polymer chains as well as protein assemblies.We show that circuit topology can categorize different forms of chain assemblies.Our multi-chain circuit topology should aid analysis and predictions of mechanistic and evolutionary principles in the design of macromolecular assemblies.展开更多
基金We thank the National Natural Science Foundation of China(Project No.29975033)the Education Office Program of Jiangxi province([2005]242)for financial support
文摘A novel method based on discrete wavelet transform （DWT） and cross-covariance for revealing the evolution of species at different spatial resolutions is presented. The trypsin proteins of different species are chosen as an example to describe the evolution relationship according to the evolution vectors by using this method. The results indicated that this method is a promising approach to reveal species evolution at different spatial resolutions.
基金financial support from the National Natural Science Foundation of China (91131007)funds from Fudan University
文摘Plants have evolved a large number of transcription factors（TF）, which are enriched among duplicate genes,highlighting their roles in complex regulatory networks. The APETALA2/EREBP-like genes constitute a large plant TF family and participate in development and stress responses. To probe the conservation and divergence of AP2/EREBP genes,we analyzed the duplication patterns of this family in Brassicaceae and identified interacting proteins of representative Arabidopsis AP2/EREBP proteins. We found that many AP2/EREBP duplicates generated early in Brassicaceae history were quickly lost, but many others were retained in all tested Brassicaceae species, suggesting early functional divergence followed by persistent conservation. In addition,the sequences of the AP2 domain and exon numbers were highly conserved in rosids. Furthermore, we used 16 A.thaliana AP2/EREBP proteins as baits in yeast screens and identified 1,970 potential AP2/EREBP-interacting proteins,with a small subset of interactions verified in planta. Many AP2 genes also exhibit reduced expression in an antherdefective mutant, providing a possible link to developmental regulation. The putative AP2-interacting proteins participate in many functions in development and stress responses,including photomorphogenesis, flower development, pathogenesis, drought and cold responses, abscisic acid and auxin signaling. Our results present the AP2/EREBP evolution patterns in Brassicaceae, and support a proposed interaction network of AP2/EREBP proteins and their putative interacting proteins for further study.
文摘Macromolecular assemblies such as protein complexes and protein/RNA condensates are involved in most fundamental cellular processes.The arrangement of subunits within these nano-assemblies is critical for their biological function and is determined by the topology of physical contacts within and between the subunits forming the complex.Describing the spatial arrangement of these interactions is of central importance to understand their functional and stability consequences.In this concept article,we propose a circuit topology-based formalism to define the topology of a complex consisting of linear polymeric chains with interand intrachain interactions.We apply our method to a system of model polymer chains as well as protein assemblies.We show that circuit topology can categorize different forms of chain assemblies.Our multi-chain circuit topology should aid analysis and predictions of mechanistic and evolutionary principles in the design of macromolecular assemblies.
