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Simple Summary: The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is indigenous to the United States and has become a significant invasive agricultural pest in China. In this study, we identified and cloned one trehalase gene (LoTRE1) encoding a soluble protein in L. oryzophilus and compared the relative expression levels of LoTRE1 in different tissues. The purified LoTRE1 protein was obtained using a prokaryotic expression system, and its enzymatic properties were explored. Amino acid sequence homology modeling of LoTRE1 and molecular docking between the LoTRE1 protein and substrate trehalose were simulated, which further provided a theoretical basis for revealing the role of LoTRE1 in the degradation mechanism of trehalose. In addition, the LoTRE1 double-stranded RNA (dsRNA) was synthesized in vitro, and its RNAi effect in L. oryzophilus was detected via feeding. The results suggested that LoTRE1 played a vital role in L. oryzophilus development, which could be useful for providing information for insect pest control in the future. Trehalase is the only enzyme known for the irreversible splitting of trehalose and plays a major role in insect growth and development. In this report, we describe a basic study of the trehalase gene fragment encoding a soluble trehalase from Lissorhoptrus oryzophilus (LoTRE1). Sequence alignment and phylogenetic analysis suggested that LoTRE1 was similar to some known insect trehalases and belongs to the Coleoptera trehalase group. Additionally, LoTRE1 was expressed mainly in the fat body. Purified protein was obtained using heterologous expression of LoTRE1 in Escherichia coli, and the recombinant protein exhibited the ability to decompose trehalose. Enzyme–substrate docking indicated the potential involvement of other residues in the catalytic activity, in addition to Asp 333. Moreover, feeding of adults on LoTRE1 dsRNA silenced the transcription of LoTRE1 and thereby reduced the activity of trehalase and increased the trehalose content; it also led to a 12% death rate. This study reveals essential molecular features of trehalase and offers insights into the structural aspects of this enzyme, which might be related to its function. Taken together, the findings demonstrate that LoTRE1 is indispensable for adults of this pest and provide a new target for the control of L. oryzophilus. [ABSTRACT FROM AUTHOR]

A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence about its activity on the virus. It is of high significance to develop a drug that can combat the virus effectively to save valuable human lives. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods such as deep learning to develop drugs that can combat such a disease effectively since 2019-nCoV is highly homologous to SARS-CoV. In the present work, we first collected virus RNA sequences of 18 patients reported to have 2019-nCoV from the public domain database, translated the RNA into protein sequences, and performed multiple sequence alignment. After a careful literature survey and sequence analysis, 3C-like protease is considered to be a major therapeutic target and we built a protein 3D model of 3C-like protease using homology modeling. Relying on the structural model, we used a pipeline to perform large scale virtual screening by using a deep learning based method to accurately rank/identify protein–ligand interacting pairs developed recently in our group. Our model identified potential drugs for 2019-nCoV 3C-like protease by performing drug screening against four chemical compound databases (Chimdiv, Targetmol-Approved_Drug_Library, Targetmol-Natural_Compound_Library, and Targetmol-Bioactive_Compound_Library) and a database of tripeptides. Through this paper, we provided the list of possible chemical ligands (Meglumine, Vidarabine, Adenosine, d-Sorbitol, d-Mannitol, Sodium_gluconate, Ganciclovir and Chlorobutanol) and peptide drugs (combination of isoleucine, lysine and proline) from the databases to guide the experimental scientists and validate the molecules which can combat the virus in a shorter time. [ABSTRACT FROM AUTHOR]

In the metabolic glycosylation grid of steviol glycosides, UGT76G1 was shown to catalyze at least eight different glucosylation steps, including the formation of rebaudioside B (Reb B) and rebaudioside A (Reb A) (Olsson et al., 2016). In this study, the accumulation of steviolbioside, Reb B, stevioside (ST) and Reb A in more than 140 samples of stevia leaves collected from different regions in China were analyzed by high-performance liquid chromatography (HPLC), and five genotypes, 'N01-N05', with significantly different levels of the abovementioned glycosides were discovered. Mutations in the UGT76G1 gene cloned from cDNAs from these five genotypes were identified, and the functions of the recombinant UGT76G1 variants were ascertained by adding steviolbioside and ST substrates. In addition, homology modeling and molecular docking were used to elucidate the functional differences between variants and UGT76G1. Comparing the sequences of the five variants ' N01-N05 ' with UGT76G1 (AY345974.1) revealed that base substitutions were not observed in ' N01 '. By contrast, ' N02 ' exhibited 9 single nucleotide polymorphisms (SNPs) and 9 associated amino acid substitutions or insertions with notable variations in the protein structure; however, an enzyme assay showed similar functionalities between the variant and UGT76G1. In ' N03 ', 49 SNPs and 29 associated amino acid substitutions or insertions were identified and shown to induce significant variations in the protein structure, especially in the binding pocket, resulting in the lack of functionality of this variant in the enzyme assay. These results were in agreement with the docking profiles. Moreover, a nonsense mutation of p.1090T > G in ' N04 ' and an insertion of a 68 base fragment in ' N05 ' were found, and both produced a premature protein without any catalytic activity. Therefore, UGT76G1 , which is vital to the content of main steviol glycosides, should be a key gene marker for the molecular breeding of Stevia rebaudiana. Our investigations also revealed the location and orientation of active groups of the receptors and donors in the UGT76G1 enzyme, which play key roles in determining whether the enzyme has any enzymatic activity. Image 1 • Five stevia genotypes with significantly different concentration of steviol glycosides were found by a broad screening. • Five variants of UGT76G1 were finally detected and three of them were discovered for the first time. • Insertion of a fragment containing 68 bases in the UGT76G1 leds to production of premature protein. • UGT76G1 should be a key marker gene for molecular breeding of S. rebaudiana. • The location and orientation of active groups of receptor and donor play a key role to the enzyme activity of UGT76G1. [ABSTRACT FROM AUTHOR]

Abstract Noroviruses are the primary cause of non-bacterial acute gastroenteritis worldwide, and GII.8 belongs to a non-epidemic genotype with a limited understanding currently. In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the "4+1+1" application strategy with newly designed primer sets, the genome of one GII.8 strain GZ2017-L601 from China was firstly sequenced that comprised 7476 nucleotides. The homology of the new genome and the previous only GII.8 genome reached 93.8% identity at the nucleotide level, but only 10, 6, 7 amino acid mutations occurred in three ORFs. When compared the new strain with other GII reference strains, p22 and P2 were calculated as the variable encoding regions, and NTPase, VPg, 3CL, RdRp and S were shown as the conserved ones. We then reconstructed the evolutionary process of the GII.8 genotype using other available sequences in GenBank. Based on the partial N/C region, all GII.8 strains could be subdivided chronologically into four clusters, which spans 1967–1994, 1997–2005, 2003–2009, and 2007–2017, respectively. Moreover, differences of capsid P proteins between GII.8 strains and the epidemic GII.4 strain VA387 were also compared. There existed 147/310 distinct amino acid sites in the alignment, including two insertion and three deletion mutations. Distribution of antigen epitopes of two GII.8 variants was comparable, but the numbers of antigenic sites of GII.8 strains were less than that of VA387. In summary, the first GII.8 genome from China was assembled and extensively characterized, and a time-order evolutionary process of this genotype was identified with a static pattern of antigenic variations. Highlights • The first GII.8 norovirus genome sequence from China was obtained and analyzed. • GII.8 could be chronologically divided into four clusters based on the N/C region. • The numbers of antigenic sites of GII.8 strains were less than that of GII.4 VA387. • No obvious changes in epitope distribution were found between different GII.8 strains. [ABSTRACT FROM AUTHOR]

Noroviruses are still the primary cause of non-bacterial acute gastroenteritis worldwide. Recently, a novel GII.17 norovirus variant emerged and caused an infection peak in the cold season of 2014/2015 in some Asian countries, including China. In this study, in order to understand the evolutionary advantage of the novel variant, complete genomic sequences of GII.17 NoV strains from South China were comprehensively analyzed. Pairwise alignments of new GII.17 genomes with representative sequences of each GII genotype were performed. Inconsistent homology was observed between different protein-encoding regions, of which VPg (NS5) and P2 were found to be the most conserved and variable ones, respectively. The differences between new sequences and other reported GII.17 genomes were also compared, and 84 mismatched nucleotides were found, resulting in 15 amino acid changes. Then, all capsid sequences of different GII.17 NoV variants were collected for multiple alignments, and a total of 87 spots were identified during their evolution process. Homology modeling of capsid proteins of four GII.17 variants was carried out based on comparison with GII.4 VA387 strain, and structural differences were mainly embodied in five extended loops. Furthermore, positions of potential conformational epitope regions of new GII.17 variants were found more similar or adjacent to those of GII.4 rather than those of the former GII.17 variants. In summary, nine GII.17 strains from South China were extensively characterized based on their complete genomes, and a different distribution pattern of epitope residues was predicted on the new GII.17 variant capsid from that of the former ones. [ABSTRACT FROM AUTHOR]

Norovirus is an important pathogen which accounts for majority of the viral related acute gastroenteritis. Recently, a variant of genotype GII.17 was reported to be predominant over GII.4 and accounted for several acute gastroenteritis outbreaks in Asia. In the current study, the full genome of a norovirus strain ZHITHC-12 isolated during this outbreak period in China was identified and characterized. The viral genome was 7557 nucleotides in length and a phylogenetic analysis based on full length genome sequences indicated that ZHITHC-12 belonged to GII.17 genotype. A further phylogenetic analysis based on all available polymerase and capsid sequences showed that ZHITHC-12 was in Cluster III on both phylogenetic trees and grouped with other strains also isolated during 2013 to 2015. Moreover, homology modeling analysis based on GII norovirus capsid 5BSX template revealed that substitutions, mutations, and more importantly, deletions and insertions, occurred at or near the putative epitopes and histo-blood group antigen (HBGA) binding sites in its protruding P2 domain, which might confer new antigenic or biological properties for this novel variant. In summary, the first full genome and capsid protein structure of a novel norovirus GII.17 variant isolated in China was extensively characterized. The data would be helpful not only for the epidemiology study, but also for the diagnostic tool development and effective vaccine design in the future. [ABSTRACT FROM AUTHOR]

Noroviruses (NoVs) are the primary cause of non-bacterial acute gastroenteritis worldwide. Most NoV infections are caused by GII.4, but GII.6 is also an important genotype with a long-term persistence in human populations. In this study, the complete genome sequence of a NoV strain GZ2010-L96 isolated in China was identified and analyzed phylogenetically. The viral genome comprised 7550 nucleotides, and its phylogenetic analysis revealed that the strain belonged to GII.6 genotype. All reported GII.6 NoV capsid protein sequences were also collected for comparative analysis, and GZ2010-L96 was clustered into GII.6-b with other 8 strains. Meanwhile, it was found that 53 spots on viral capsid showed subcluster specificity according to multiple alignments. Moreover, homologous modeling of GZ2010-L96 based on comparison with GII.4 VA387 strain showed a different antigen distribution pattern. In summary, the genome of the GII.6 strain GZ2010-L96 detected in China was extensively characterized, and phylogenetic analyses of GII.6 NoVs based on the capsid proteins may reveal a different evolution process from the predominant genotype GII.4. [ABSTRACT FROM AUTHOR]

Abstract: In this study, an effective Escherichia coli expression system was used to study the role of residues in the antitumor-analgesic peptide from Chinese scorpion Buthus martensii Karsch (BmKAGAP). To evaluate the extent to which residues of the toxin core contribute to its analgesic activity, nine mutants of BmKAGAP were obtained by PCR. Using site-directed mutagenesis, all of these residues were individually substituted by one amino acid. These were then subjected to a circular dichroism analysis, and an analgesic activity assay in mice. This study represents a thorough mapping and elucidation of the epitopes that underlie the molecular basis of the analgesic activity. The three-dimensional structure of BmKAGAP was established by homology modeling. Our results revealed large mutant-dependent differences that indicated important roles for the studied residues. With our ongoing efforts for establishing the structure and analgesic activity relationship of BmKAGAP, we have succeeded in pinpointing which residues are important for the analgesic activity. [Copyright &y& Elsevier]

UDP-glycosyltransferases (UGTs) are an important and functionally diverse family of enzymes involved in secondary metabolite biosynthesis. Coumarin is one of the most common skeletons of natural products with candidate pharmacological activities. However, to date, many reported GTs from plants mainly recognized flavonoids as sugar acceptors. Only limited GTs could catalyze the glycosylation of coumarins. In this study, a new UGT was cloned from Cistanche tubulosa, a valuable traditional tonic Chinese herb, which is abundant with diverse glycosides such as phenylethanoid glycosides, lignan glycosides, and iridoid glycosides. Sequence alignment and phylogenetic analysis showed that CtUGT1 is phylogenetically distant from most of the reported flavonoid UGTs and adjacent to phenylpropanoid UGTs. Extensive in vitro enzyme assays found that although CtUGT1 was not involved in the biosynthesis of bioactive glycosides in C. tubulosa, it could catalyze the glucosylation of coumarins umbelliferone 1, esculetine 2, and hymecromone 3 in considerable yield. The glycosylated products were identified by comparison with the reference standards or NMR spectroscopy, and the results indicated that CtUGT1 can regiospecifically catalyze the glucosylation of hydroxyl coumarins at the C7-OH position. The key residues that determined CtUGT1's activity were further discussed based on homology modeling and molecular docking analyses. Combined with site-directed mutagenesis results, it was found that H19 played an irreplaceable role as the crucial catalysis basis. CtUGT1 could be used in the enzymatic preparation of bioactive coumarin glycosides., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Storage mites, such as Tyrophagus putrescentiae, are an important source of allergens that cause allergic diseases in humans. It has previously been indicated that T. putrescentiae has a high sensitization rate as an allergen in some Asian and European countries. Identifying and cloning the allergens in this species may enable improved diagnostic and therapeutic approaches. The aim of the present study was to clone and sequence the T. putrescentiae group 13 allergen (Tyr p 13) isolated from storage mites in China, to use bioinformatics tools to model its biophysical characteristics and to induce protein expression to test its IgE-binding activity. The full-length cDNA comprised 486 bp and was predicted to include a signal peptide of 22 amino acids. Its secondary structure was shown to comprise an α-helix (10.79%), extended strand (33.81%) and random coils (55.40%). Using homology modeling, the present study constructed a reasonable tertiary structure of Tyr p 13. Linear Bcell epitopes at amino acids 47-53, 70-76, 81-86, 101-105 and 112120 were predicted. Three discontinuous B-cell epitopes were also predicted: i) 47, 48, 49, 50, 51, 52, 53, 70, 71, 72 and 73; ii) 91, 92, 93, 94, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121 and 138; and iii) 74, 76, 79, 81, 82, 83, 84, 86, 101, 102, 103, 104 and 105. SDS-PAGE identified a specific band at the predicted molecular weight of the recombinant Tyr p 13 (rTyr p 13), demonstrating its successful expression. The rTyr p 13 bound to IgE in the serum of 13.2% (5/38) of patients allergic to T. putrescentiae, according to ELISA. The successful cloning of Tyr p 13 and basic bioinformatics analysis of the protein provided a foundation for the further study of this allergen with regards to the diagnosis and treatment of patients allergic to storage mites. These results provided a theoretical basis for the design of rTyr p 13 with modified B-cell epitopes. [ABSTRACT FROM AUTHOR]

In this study, a more detailed genetic characterization of the VP1 capsid protein of uncommon norovirus (NoV) GII.14 strains reported previously in Japan and China was performed using sequence analyses and homology modeling technique. The result of genetic comparison with the M7 prototype strain of GII.14 revealed that 10 amino acid mutations were observed at the same positions across the P2 and P1-2 subdomains in both Japanese and Chinese strains. By the homology modeling of the P domain, 7 out of these 10 mutations were predicted to be located on the surface-exposed P2 and P1-2 subdomains. All GII.14 strains had an altered RGD-like motif (RGT → KGT). While the Chinese strains contained 5 random amino acid changes in the S domain and the P2 subdomain, these changes were not detected in the Japanese strains. In addition, the histo-blood group antigen (HBGA)-binding interfaces remain identical to those of the previously determined GII.4 structure (VA387), suggesting the conservation of HBGA binding profile within the GII genogroup. Taken together, this report provides supportive structural data that antigenic drifts that occurred mostly in the P2 and P1-2 subdomains might be sufficient to generate new mutants, thus permitting the GII.14 virus to escape the host pre-existing immunity. These results also suggest the need for comparing the evolutionary profiles and structural models of rare NoV genotypes to an insight into NoV evolution., (© 2013 Wiley Periodicals, Inc.)