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Arabidopsis thaliana NOP10 is required for gametophyte formation

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Journal of Integrative Plant Biology 2018年第8期60卷 723-736页

作者： Lin-Xiao Li Hong-Ze Liao Li-Xi Jiang Qing Tan De Ye Xue-Qin Zhang state key laboratory of Plant Physiology and Biochemistry College of Biological Sciences China Agricultural University state key laboratory of non-food biomass Energy and enzyme technology National Engineering Research Center for Non-Food Biorefinery and Guangxi Key Laboratory of Biorefinery Guangxi Academy of Sciences College of Agriculture & Biotechnology Zhejiang University

The female gametophyte is crucial for sexual reproduction of higher plants, yet little is known about the molecular mechanisms underlying its development. Here, we report that Arabidopsis thaliana NOP10 （AtNOP10） is required for female gametophyte formation. AtNOP10 was expressed predominantly in the seedling and reproductive tissues, including anthers, pollen grains, and ovules. Mutations in AtNOP10 interrupted mitosis of the functional megaspore during early development and prevented polar nuclear fusion in the embryo sacs. AtNOP10 shares a high level of amino acid sequence similarity with Saccharornycescerevisiae （yeast） NOPIo （ScNOP1o）, an important compo- nent of the H/ACA small nucleolar ribonucleoprotein particles （H/ACA snoRNPs） implicated in 18S rRNA synthe- sis and rRNA pseudouridylation. Heterologous expression of ScNOP10 complemented the mutant phenotype of Atnop10. Thus, AtNOPIo influences functional megaspore mitosis and polar nuclear fusion during gametophyte formation in Arabidopsis.

关键词： Figure Arabidopsis thaliana NOP10 is required for gametophyte formation

Mechanism and Application of enzyme Treatment on Wool

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Journal of Donghua University(English Edition) 2011年第2期28卷 226-232页

作者：程文红周启澄袁琴华 state key laboratory of non-food biomass and enzyme technology Guangxi Academy of Sciences College of Textiles Donghua University College of Chemistry Chemical Engineering and Biotechnology Donghua University

Protease treatments on wool have its inherent defect in shrink-proofing because protease will decompose wool through cell membrane complex （CMC）. In order to solve this problem, mechanism of enzyme treatments on wool was adequately analyzed and possible enzyme applications were discussed. The mechanism of enzyme treatment on wool was analyzed through weight loss, strength, scanning electron microscopy （SEM）, electrophoresis, sodium dodecyl sulfate polyacrylamide gel electrophoresis （ SDS- PAGE）, and amino acids composition. Based on the results, a possible novel multifunetional enzyme treatment on wool to achieve shrink-resistance was proposed. In order to shorten enzyme treatment time, the rate of proteolysis of wool was investigated. Considering the specificity of proteases, wool composition, and structure of dyes, a better enzyme pretreatment before dyeing to get better dyeabflity and lower dyeing temperature was discussed.

关键词： enzyme treatments wool mechanism and application dyeability

Safety assessment of a novel marine multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 according to phenotype and whole genome-sequencing analysis

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food Science and Human Wellness 2024年第4期13卷 2048-2059页

作者： Xueyan Mo Mengcheng Zhou Yanmei Li Lili Yu Huashang Bai Peihong Shen Xing Zhou Haojun Zhu Huijie Sun Ru Bu Chengjian Jiang state key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Science and TechnologyGuangxi UniversityNanning 530004China National Engineering Research Center for non-food Biorefinery State Key Laboratory of Non-Food Biomass and Enzyme TechnologyGuangxi Research Center for Biological Science and TechnologyGuangxi Academy of SciencesNanning 530007China Guangxi key laboratory for Green Processing of Sugar Resources College of Biological and Chemical EngineeringGuangxi University of Science and TechnologyLiuzhou 545006China

The application of microorganisms as probiotics is limited due to lack of safety ***,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove *** safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing *** showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely *** morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were *** hyphae and phospholipase were *** one retroelement(Tad1-65_BG)was *** biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined ***6 had no resistance to common antifungal *** enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were *** toxicity test with mice demonstrated that GXDK6 is ***6 has a good reproduction ability in the simulation gastrointestinal ***6 also has a strong antioxidant ability,β-glucosidase,and inulinase *** sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.

关键词： Meyerozyma guilliermondii Safety assessment Probiotics Marine mangrove microorganisms Whole-genome sequencing analysis

Prediction of Mutations in H7 Hemagglutinins from Influenza A Virus

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Journal of Biomedical Science and Engineering 2020年第8期13卷 175-186页

作者： Shaomin Yan Guang Wu National Engineering Research Center for non-food Biorefinery State Key Laboratory of Non-Food Biomass and Enzyme Technology Guangxi Biomass Engineering Technology Research Center Guangxi Key Laboratory of Bio-Refinery Nanning China

Influenza A viruses have led several pandemics and epidemics in human history. H7 subtype influenza mainly infects avian but also humans occasionally. Since the outbreak of H7N9 subtype influenza occurred in China in 2013, this virus is still circulating in domestic poultry and leading several waves of influenza. To prevent influenza, vaccination is an important strategy. However, influenza virus evolves constantly, but unpredictably. If we would have a one-to-one cause-mutation relationship, the mutation prediction would be possible. However, many external causes, which led to the mutations in the past, might not leave any trace due to the change in environments, whereas the current virus might not be subject to the historically external causes because of evolution. Furthermore, the protein should have the internal causes, which might be quite unclear and difficult to quantify, to engineer mutations. Indeed, various forces twist proteins into 3-demensional structures, whereas any perturbation could lead to a mutation. Of various internal causes for mutation, randomness in protein primary structure should play an important role in mutation. Over years, we have developed three methods to quantify the randomness within a protein primary structure;thus we build a relationship between cause, which is randomness in primary structure, and mutations, which are occurrence and non-occurrence of mutation. In this way, the cause-mutation relationship becomes the problem of classification, which can be solved using logistic regression and neural network. In this study, we apply this model to predict 1) the mutation positions in H7 hemagglutinins from influenza A virus and 2) the would-be-mutated amino-acids at predicted positions with the amino-acid mutating probability. The results show suitability and predictability in such modelling, and pave the way for further development.

关键词： Hemagglutinin Influenza Mutation Neural Network Prediction Randomness

Progress of studies in enzyme engineering and rational design based on protein structures

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Progress of studies in enzyme engineering and rational desig...

Correlation of Combined Characters of Amino Acid and Whole Protein with Success Rate of Crystallization of <i>Lactobacillus</i>Proteins

The Ninth National Symposium on enzyme Engineering

作者： Qi-Shi Du Ri-Bo Huang Guangxi Academy of Sciences State Key Laboratory of Non-food Biomass and Enzyme Technology

The 3D structures of biological macromolecules（proteins,RNA,and DNA）are determined by the molecular interactions forces between the structural ***,the biological functions of biological molecules are determined by the structures of *** addition to the three known interaction forces（hydrogen-bond interaction,electrostatic interaction,and van de Waals interaction）,there are several unconventional molecular interaction forces,such as cation-πinteractions,polar hydrogen-π（Hp-π）interactions,π-πstocking interactions,and coordinate interactions,which are less familiar to many *** the 20 natural amino acids 11 of them are involved in the polar hydrogen-π*** DAN and RNA the four nucleic acid components（adenine,guanine,cytosine,and thymine）possess aromatic rings and polar hydrogen atoms,which are the Hp-πinteraction acceptors and *** peptide bond units of protein backbones are also the Hp-πinteraction *** chemical method CCSD/6-311+G（d,p）+H-Bq is used in the study of Hp-π*** the polar hydrogen atom of a peptide unit perpendicularly points to theπ-plane of other peptide bond units,remarkable Hp-πinteraction *** Hp-πinteractions are distance and orientation dependent,and point-to-plane interaction,acting in a broad *** potential energy surface scanning calculations are performed on the quasiπ-plane of peptide bond unit,and around the torsion anglesΦandψbetween two connected peptide *** protein backbones the Hp-πinteraction energies are in the range from-13 to-22kj/mol,close to the hydrogen bond energies（-24 kj/mol）.The potential energy surface scanning for torsion anglesΦandψidentified four loop structural conformations,in which four different Hp-πinteraction types（H-π-l,H-π-2,H-π-3,H-π-4）maintain the shapes of *** physical nature and properties of Hp-πinteractions may provide useful concepts that are helpful for better understanding to the protein folding patterns,and to dev

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Journal of Biomedical Science and Engineering 2019年第4期12卷 245-256页

作者： Shaomin Yan Guang Wu state key laboratory of non-food biomass enzyme technology National Engineering Research Center for Non-Food Biorefinery Guangxi Key Laboratory of Biorefinery Guangxi Academy of Sciences Nanning China

Crystallization of proteins is a very delicate process, which is influenced by many known and unknown factors. Of tested factors, many factors are exclusively related to individual amino-acid characters such as molecular weight or protein characters such as protein length. It is considered necessary to test factors that combine both individual amino-acid characters and protein characters with respect to success rate of crystallization. In this study, two combined characters characterizing individual amino-acid character and protein character, amino acid distribution probability and future composition, were used to correlate the success rate of crystallization of proteins from Lactobacillus via modeling. The results obtained from logistic regression and neural network were compared against the results obtained from each of 533 individual amino-acid characters. This study demonstrated that the combined characters are involved in crystallization process and should be taken into account for predicting the success rate of crystallization process.

关键词： Amino Acid Character Distribution Probability Future Composition Lactobacillus Protein Crystallization

Uptake of Polycyclic Aromatic Hydrocarbons across Bacterial Membrane

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Advances in Microbiology 2020年第7期10卷 331-348页

作者： Shaomin Yan Guang Wu state key laboratory of non-food biomass and enzyme technology National Engineering Research Center for Non-Food Biorefinery Guangxi Key Laboratory of Biorefinery Guangxi Academy of Sciences Nanning China

Polycyclic aromatic hydrocarbons (PAHs) are important pollutants, whose biodegradation and bioremediation with microorganisms are the promising ways to clean environments and reduce their exposure to humans. Although the transportation of PAHs across bacterial membrane is the first step forwards their biodegradation, it receives less attention. In this mini-review, we explore which transport system for uptake of carbon sources can serve for uptake of PAHs in bacteria, and try to uncover some patterns in their transport mechanisms. Collectively, 1) the major carbohydrate transport system, PTS, is unlikely to take PAHs because PAHs lack a hydroxy group for phosphorylation but aromatic acids are good candidates;2) PAHs could probably go through H+ symporters, especially the low-molecular-weight PAHs, which are partially dissolvable in water;3) it is unlikely that PAHs can produce chemiosmotic ion gradients to go through uniporters;and 4) antiporters could serve as transporters to transport PAHs across bacterial membrane only after the metabolism of PAHs generates extra H+ inside cell. Accordingly, the basic mechanism for uptake of PAHs is whether they can donate H+ in order to generate an electrochemical proton gradient to go through symporters.

关键词： Bacteria Polycyclic Aromatic Hydrocarbon Transport Mechanisms

2-Dimensional HP Foldings of Dermaseptin-J2

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Engineering（科研） 2013年第10期5卷 78-84页

Although the hydrophobic-polar (HP) model is a simple model to study protein folding, it is an approximation to the real-life case. Dermaseptin is a subfamily of frog skin active peptide family, which has various antimicrobial activities, and dermaseptin-J2 is a newly found peptide composed of 26 amino acids. In this study, the 2-dimensional HP model was used to analyze the foldings of dermaseptin-J2 and its nine mutants, which were converted to different HP sequences according to the normalized amino acid hydrophobicity index with respect to pH levels and the conversion of glycine as hydrophobic or polar, and each has 847,288,609,443 possible foldings. The results show that the foldings with minimal energy have different native states, which are chiral and can be numerically distinguished and ranked according to the normalized amino acid hydrophobicity index. The nine mutants of dermaseptin-J2 do not affect the minimal energy but affect their native states at pH 7. The results demonstrate that two pH levels and conversion of glycine as hydrophobic or polar affect the native state and minimal energy, suggesting these are two ways to modify dermaseptin-J2.

关键词： Dermaseptin Folding Configuration HP Model Hydrophobicity Index Minimal Energy Native state

Adaptation in polymerase basic protein 1 family from influenza A virus to climate change

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Health 2012年第10期4卷 968-973页

Global climate changes affect the functioning of ecosystems, in particular host-pathogen interactions, with major consequences in health ecology, however, it is less addressed how the change in global temperature affects the protein family of influenza virus. In this study, we studied the adaptation of polymerase basic protein 1 (PB1) family from influenza A virus to temperature change. 3841 PB1 proteins sampled from 1956-2011 were quantified by the amino-acid pair predictability and then compared their general changes with the temperature changes (Had-CRUT3v and CRUTEM4v data sets) of corresponding years on a 5? by 5? grid-box basis. Also, point-to-point comparisons were conducted from 1956 to 1998 in all and different species. The results showed that both changes in the temperature and unpredictable portion of PB1 proteins had similar trends from 1956 to 2011, which provides the evidence of virus adaptation at protein level to climate change.

关键词： Adaptation Evolution Influenza A Virus Polymerase Basic Protein 1 Temperature Change