Tyrosinase （Ty） is a common enzyme found in many different animal groups. In our previous study, genome sequencing revealed that the Ty family is expanded in the Pacific oyster （Crassostrea gigas）. Here, we examin...Tyrosinase （Ty） is a common enzyme found in many different animal groups. In our previous study, genome sequencing revealed that the Ty family is expanded in the Pacific oyster （Crassostrea gigas）. Here, we examine the larger number of Ty family members in the Pacific oyster by high-level structure prediction to obtain more information about their function and evolution, especially the unknown role in biomineralization. We verified 12 Ty gene sequences from Crassostrea gigas genome and Pinctadafucata martensii transcriptome. By using phylogenetic analysis of these Tys with functionally known Tys from other molluscan species, eight subgroups were identified （CgTy_sl, CgTy s2, MolTy sl, MolTy-s2, MolTy-s3, PinTy-s 1, PinTy-s2 and PviTy）. Structural data and surface pockets of the dinuclear copper center in the eight subgroups of molluscan Ty were obtained using the latest versions of prediction online servers. Structural comparison with other Ty proteins from the protein databank revealed functionally important residues （HA1, HA2, HA3, HB1, HB2, HB3, Z l-Z9） and their location within these protein structures. The structural and chemical features of these pockets which may related to the substrate binding showed considerable variability among mollusks, which undoubtedly defines Ty substrate binding. Finally, we discuss the potential driving forces of Ty family evolution in mollusks. Based on these observations, we conclude that the Ty family has rapidly evolved as a consequence of substrate adaptation in mollusks.展开更多
Thousands of proteins undergo arginine methylation,a widespread post-translational modification catalyzed by several protein arginine methyltransferases(PRMTs).However,global understanding of their biological function...Thousands of proteins undergo arginine methylation,a widespread post-translational modification catalyzed by several protein arginine methyltransferases(PRMTs).However,global understanding of their biological functions is limited due to the lack of a complete picture of the catalytic network for each PRMT.Here,we systematically identified interacting proteins for all human PRMTs and demonstrated their functional importance in mRNA splicing and translation.We demonstrated significant overlapping of interactomes of human PRMTs with the known methylarginine-containing proteins.Different PRMTs are functionally redundant with a high degree of overlap in their substrates and high similarities between their putative methylation motifs.Importantly,RNA-binding proteins involved in regulating RNA splicing and translation contain highly enriched arginine methylation regions.Moreover,inhibition of PRMTs globally alternates alternative splicing(AS)and suppresses translation.In particular,ribosomal proteins are extensively modified with methylarginine,and mutations in their methylation sites suppress ribosome assembly,translation,and eventually cell growth.Collectively,our study provides a global view of different PRMT networks and uncovers critical functions of arginine methylation in regulating mRNA splicing and translation.展开更多
The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tR...The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAu^t gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the mo- nophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were （（Gymnophiona （Caudata, Anura））. Based on the phylogenetic trees, type 1 was recognized as the ancestral type for am- phibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaning- ful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family展开更多
Chloroplasts are organelles found in plant cells that conduct photosynthesis. The subchloroplast locations of proteins are correlated with their functions. With the availability of a great number of protein data, it i...Chloroplasts are organelles found in plant cells that conduct photosynthesis. The subchloroplast locations of proteins are correlated with their functions. With the availability of a great number of protein data, it is highly desired to develop a com- putational method to predict the subchloroplast locations of chloroplast proteins. In this study, we proposed a novel method to predict subchloroplast locations of proteins using tripeptide compositions. It first used the binomial distribution to optimize the feature sets. Then the support vector machine was selected to perform the prediction of subchloroplast locations of proteins. The proposed method was tested on a reliable and rigorous dataset including 259 chloroplast proteins with sequence identity ≤ 25%. In the jack-knife cross-validation, 92.21% envelope proteins, 93.20% thylakoid mem- brane, 52.63% thylakoid lumen and 85.00% stroma can be correctly identified. The overall accuracy achieves 88.03% which is higher than that of other models. Based on this method, a predictor called ChloPred has been built and can be freely available from http：//cobi.uestc.edu.cn/people/hlin/tools/ChloPred/. The predictor will provide important information for theoretical and experimental research of chloroplast proteins.展开更多
基金Supported by the National Natural Science Foundation of China(No.31530079)the Western Pacifi c Ocean System:Structure,Dynamics and Consequences(No.XDA11000000)+1 种基金the Technological Innovation Project(No.2015ASKJ02-03,fi nancially supported by Qingdao National Laboratory for Marine Science and Technology)the Earmarked Fund for Modern Agro-Industry Technology Research System(No.CARS-48)
文摘Tyrosinase （Ty） is a common enzyme found in many different animal groups. In our previous study, genome sequencing revealed that the Ty family is expanded in the Pacific oyster （Crassostrea gigas）. Here, we examine the larger number of Ty family members in the Pacific oyster by high-level structure prediction to obtain more information about their function and evolution, especially the unknown role in biomineralization. We verified 12 Ty gene sequences from Crassostrea gigas genome and Pinctadafucata martensii transcriptome. By using phylogenetic analysis of these Tys with functionally known Tys from other molluscan species, eight subgroups were identified （CgTy_sl, CgTy s2, MolTy sl, MolTy-s2, MolTy-s3, PinTy-s 1, PinTy-s2 and PviTy）. Structural data and surface pockets of the dinuclear copper center in the eight subgroups of molluscan Ty were obtained using the latest versions of prediction online servers. Structural comparison with other Ty proteins from the protein databank revealed functionally important residues （HA1, HA2, HA3, HB1, HB2, HB3, Z l-Z9） and their location within these protein structures. The structural and chemical features of these pockets which may related to the substrate binding showed considerable variability among mollusks, which undoubtedly defines Ty substrate binding. Finally, we discuss the potential driving forces of Ty family evolution in mollusks. Based on these observations, we conclude that the Ty family has rapidly evolved as a consequence of substrate adaptation in mollusks.
基金This work was supported by the National Natural Science Foundation of China(31730110,31661143031,91940303,and 91753135)the Science and Technology Commission of Shanghai Municipality grant(17JC1404900,18XD1404400,and 20ZR1467300)a Joint Research grant with State Key Laboratory of Microbial Metabolism,School of Life Science and Biotechnology,Shanghai Jiao Tong University(MMLKF16-11).
文摘Thousands of proteins undergo arginine methylation,a widespread post-translational modification catalyzed by several protein arginine methyltransferases(PRMTs).However,global understanding of their biological functions is limited due to the lack of a complete picture of the catalytic network for each PRMT.Here,we systematically identified interacting proteins for all human PRMTs and demonstrated their functional importance in mRNA splicing and translation.We demonstrated significant overlapping of interactomes of human PRMTs with the known methylarginine-containing proteins.Different PRMTs are functionally redundant with a high degree of overlap in their substrates and high similarities between their putative methylation motifs.Importantly,RNA-binding proteins involved in regulating RNA splicing and translation contain highly enriched arginine methylation regions.Moreover,inhibition of PRMTs globally alternates alternative splicing(AS)and suppresses translation.In particular,ribosomal proteins are extensively modified with methylarginine,and mutations in their methylation sites suppress ribosome assembly,translation,and eventually cell growth.Collectively,our study provides a global view of different PRMT networks and uncovers critical functions of arginine methylation in regulating mRNA splicing and translation.
文摘The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAu^t gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the mo- nophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were （（Gymnophiona （Caudata, Anura））. Based on the phylogenetic trees, type 1 was recognized as the ancestral type for am- phibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaning- ful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family
文摘Chloroplasts are organelles found in plant cells that conduct photosynthesis. The subchloroplast locations of proteins are correlated with their functions. With the availability of a great number of protein data, it is highly desired to develop a com- putational method to predict the subchloroplast locations of chloroplast proteins. In this study, we proposed a novel method to predict subchloroplast locations of proteins using tripeptide compositions. It first used the binomial distribution to optimize the feature sets. Then the support vector machine was selected to perform the prediction of subchloroplast locations of proteins. The proposed method was tested on a reliable and rigorous dataset including 259 chloroplast proteins with sequence identity ≤ 25%. In the jack-knife cross-validation, 92.21% envelope proteins, 93.20% thylakoid mem- brane, 52.63% thylakoid lumen and 85.00% stroma can be correctly identified. The overall accuracy achieves 88.03% which is higher than that of other models. Based on this method, a predictor called ChloPred has been built and can be freely available from http：//cobi.uestc.edu.cn/people/hlin/tools/ChloPred/. The predictor will provide important information for theoretical and experimental research of chloroplast proteins.
