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Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum

Journal of Integrative Plant Biology 2023年第10期65卷 2320-2335页

作者： Dake Zhao Ya Zhang Huanxing Ren Yana Shi Ding Dong Zonghang Li Guanghong Cui Yong Shen Zongmin Mou Edward JKennelly Luqi Huang Jue Ruan Suiyun Chen Diqiu Yu Yupeng Cun School of Ecology and Environmental Science Yunnan UniversityKunming 650500China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000China Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders Pediatric Research InstituteMinistry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400014China Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Faculty of Life Science and Technology Kunming University of Science and TechnologyKunming 650500China National Resource Center for Chinese Materia Medica Chinese Academy of Chinese Medical SciencesBeijing 100700China College of Agriculture and Biotechnology Yunnan Agricultural UniversityKunming 650201China Department of Biological Sciences Lehman CollegeCity University of New YorkBronx 10468New YorkUSA Graduate Center City University of New YorkBronx 10468New YorkUSA State Key Laboratory for Conservation and Utilization of Bio‐resources in Yunnan Yunnan UniversityKunming 650500China

Diterpenoid alkaloids(DAs) have been often utilized in clinical practice due to their analgesic and anti-infammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains *** this study, we successfully assembled a highquality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum(***)(5.76 Gb). An A. vilmorinianumspecific whole-genome duplication event was discovered using comparative genomic analysis,which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in *** as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.

关键词： Aconitum vilmorinianum acute toxicity biosynthetic pathway diterpenoid alkaloid evolutionary origin genome assembly

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Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

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The Innovation 2021年第4期2卷 43-55页

作者： Ke-Jia Shan Changshuo Wei Yu Wang Qing Huan Wenfeng Qian State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in *** the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a ***,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular *** find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular *** novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation ***,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into ***,our findings provide data-driven support for the natural origin of SARS-CoV-2.

关键词： SARS-CoV-2 molecular spectrum de novo mutations mutational signature evolutionary origin mRNA mutation

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Cloning and Sequence Analysis of lef-3 Gene from Pieris rapae Granulovirus

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Agricultural Sciences in China 2010年第5期9卷 681-689页

作者： MENG Xiang-kun GONG Cheng-liang XUE Ren-yu CAO Guang-li ZHU Yue-xiong Medical College of Soochow University Suzhou 215123 P.R.China

To better understand the origination and evolution of lef-3 gene from baculovirus genome and determine the relationships between various viruses at molecular level, late expression factor 3 gene （lef-3） fragments of Pieris rapae granulovirus were obtained through conventional PCR method and sequenced after cloned into T-vector. Then, bioinformatics analysis on lef-3 gene and its encoding sequences were conducted by using bid-softs. Four mutations were appeared in the ORF of cloned lef-3 gene, which did not alter the characteristics of amino acids. It was inferred that PiraGV LEF-3 protein contained 399 amino acids, the molecular weight of which was 3.99 kD. Prediction of the LEF-3 advanced structure and homology comparison between other LEF-3 from various baculoviruses showed that the lef-3 gene might encode the single-stranded DNA-binding protein. The result of BLAST revealed that the lef-3 gene only existed in Lepidoptera host for the baculovirus genome, and the evolution analysis illustrated that lef-3 gene could be divided into 3 groups including one granulovirus （GV） group and 2 nucleopolyhedrovirus （NPV） groups. The selection pressure analysis of GV lef-3 gene coding region showed that the majority of lef-3 genes performed negative selection, while the Ka/Ks differed from different lef-3 gene, to some extent, which also performed positive selection. The origination analysis revealed that lef-3 gene of baculovirus might derive from bacteria. The lef-3 gene of PiraGV was cloned successfully and the possible patterns of origination and evolution were speculated through bioinformatics analysis.

关键词： Pieris rapae granulovirus late expression factor 3 (LEF-3) single-stranded DNA-binding protein (SSB) evolutionary origin

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Cloning,Sequencing of F and HN Genes and Molecular Characteristics of Goose Paramyxovirus BZ02 Isolate

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Animal Husbandry and Feed Science 2009年第6期1卷 24-26,41页

作者： XIAO Yue-qiang YANG Chun-fu GUAN YU WU Xin-ming LIU Ji-san SHEN Zhi-qiang Shandong Binzhou Animal Science&Veterinary Medicine Academy Binzhou 256600 China Shandong Lvdu Bio-science&Technology Co. Ltd Binzhou 256600 China

[ Objective] The aim of this study was to clone and sequence F and HN genes of the isolated goose paramyxovirus and thus further investigate on its pathogenesis and evolutionary origins. [ Method] According to the published F and HN gene sequences of Avian Paramyxovirus Typelat home and abroad, two pairs of primers （ FF, FR; HNF, HNR） were designed by DNAstar software, and Fand HNgenes were also amplified by PCR. The PCR products were recovered and ligated to T vector, while the positive clones were identified by ampicillin plate screening and PCR. After bacteria shaking, the plasmid was extracted and sent to Shanghai Sangon for sequencing. The sequences were compared with the sequences in GenBank, and the phylogenetic tree was drawn by DNAstar software. Meanwhile, the phylogenetic analysis of amino acid residues was also studied. [Result] The ORF of Fgene was 1 662 bp encoding 553 amino acids, and its cleavage site was 112R-R-Q-K-R-F117, which was consistent with the characteristics of virulent strains. 101-bit and 121-bit amino acid residues were K （Lys） and D （Asp）. The ORF of HN gene was 1 716 bp encoding 571 amino acids. The homology of HN sequence in 29 strains of goose paramyxovirus to YG97 was the highest, accounting for 99.6%. Analysis of glycosylation sites revealed that glycosylation site of BZ02 strain at 538 -540aa disappeared. The phylogenetic tree drawn by HN genes was highly consistent with that drawn by Fgenes. Compared with the homology of F and HN nucleotide sequence of the published typelgoose paramyxovirus in China, BZ02, JG97, HG97 and YG97 were divided into the same sub-group, and the nucleotide and amino acid sequences homologies were highest between BZ02 and YG97 strain. E Condusionl BZ02, JG97, HG97 and YG97 have the same evolutionary origin or all originate from YG97.

关键词： Paramyxovirus BZ02 strain evolutionary origin

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The discovery of the mini-protease:Seryl Histidine Dipeptide

The discovery of the mini-protease:Seryl Histidine Dipeptide

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中国化学会第26届学术年会化学生物分会场

作者： Xiao-xia Liu, Yan Liu, Ming-Kun Lin, Yu-fen Zhao* The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005

Our previous researches showed that Seryl-Histidine dipeptide (Ser-His) could cleave proteins such as bovine serum albumen (BSA) [1] and green fluorescence protein (GFP) [4] over wide ranges of pH and temperature, as well as DNA [1], with a hydrolysis mechanism. Therefore, Ser-His is the shortest peptide with the hydrolysis cleavage activity on protein, and its function is similar to serine protease. Recently, the discovery of extended substrate specificity of opossum chymase illuminated the origin of mast cell chymases [5, 6]. So, to investigate the function of Ser-His further might provide more information to understand the function group evolution for the origin of serine protease. In this paper, high resolution mass spectrometry was applied to study the cleavage sites of Seryl-Histidine dipeptide (Ser-His) on two different proteins, namely green fluorescence proteins (xm18) and cyclophilin A. It was found that the two different protein, were both cleaved by Ser-His into small polypeptide fragments. Through comparison of the cleavage activity of Ser-His and Protease K, it means that the hydrolysis activity of Ser-His is about one thirty thousandths of that of Protease K. Although Ser-His possesses non-specificity cleavage activity on the primary sequence of substrate proteins, but, amino acid residue, F, is the more favorite cleavage site (Fig. 1 and Fig. 2), which is similar to the natural serine protease, chymotrypsin. Therefore, the smallest peptide, Ser-His dipeptdie, was named the as mini-protease. It implied that Ser-His is probably the origin of serine proteases.

关键词： Ser-His diepetide mini-protease cleavage selectivity evolutionary origin

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