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Building Quantitative Gene Regulatory Mechanism in Quorum Sensing in Pseudomonas aeruginosaUsing Transcriptomic Data

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Journal of Biomedical Science and Engineering 2020年第2期13卷 13-35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

A large amount of transcriptomic data provides opportunities 1) to verify the gene regulatory mechanism, which is usually obtained from a single experiment, at population level;2) to uncover the gene regulatory mechanism at population level;and 3) to build a quantitatively gene regulatory mechanism. One of the best studied regulatory mechanisms in bacteria is the quorum sensing (QS), which plays an important role in regulation of bacteria population behaviors such as antibiotic production, biofilm formation, bioluminescence, competence, conjugation, motility and sporulation. Pseudomonas aeruginosa is a Gram-negative bacterium causing diseases in plants, animals, humans, and its biofilm and drug-resistance become great concerns in clinics. P. aeruginosa has three QS systems including a specific one for Pseudomonas. In this study, the transcriptomic data of P. aeruginosa were combined from 104 publications and QS gene expressions were analyzed under different experimental conditions. The results demonstrate the quantitatively regulatory mechanisms of QS genes at population level including 1) to rank and group QS-related genes according to their activity;2) to quantitatively define the role of a single global regulator;3) to find out the probability that a global regulator impacts QS genes and the probability that a QS gene responds to global regulators;and 4) to search for overlapped genes under four types of experimental conditions. These results provide integrative information on understanding the regulation of QS genes at population level.

关键词： Gene Quantitative Regulatory Mechanism Pseudomonas aeruginosa Quorum Sensing Transcriptomic Analysis

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Elaboration of Simplest Folding Structures in 2-Dimensional Lattice with Delta-Hemolysin and Its Variants in HP Model

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Journal of Biomedical Science and Engineering 2019年第5期12卷 293-309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

Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.

关键词： Folding Structure Delta-Hemolysin HP Model Hydrophobicity Index Lattice Minimal Energy Native state

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The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales

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Plant Communications 2024年第10期5卷 166-179页

作者： Xiaoyang Han Jingyi Zhao Hong Zhou Xuan Zhou Zixin Deng Zhenhua Liu Yi Yu Department of Gastroenterology Zhongnan Hospital of Wuhan UniversityHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseSchool of Pharmaceutical SciencesWuhan UniversityWuhan 430071China Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China state key laboratory of non-food biomass and enzyme technology Guangxi Academy of SciencesNanning 530007China

Certain plant species within the Apiales order accumulate triterpenoid saponins that feature a distinctive glucose-glucose-rhamnose(G-G-R)sugar chain attached at the C-28 position of the pentacyclic triterpene *** recently,the genomic basis underlying the biosynthesis and evolution of this sugar chain has remained *** this study,we identified two novel glycoside glycosyltransferases(GGTs)that can sequentially install the sugar chain’s second D-glucose and third L-rhamnose during the biosynthesis of asiaticoside and madecassoside,two representative G-G-R sugar chain-containing triterpenoid saponins produced by Centella *** assays revealed the remarkable substrate promiscuity of the two GGTs and the key residues crucial for sugar-donor selectivity of the glucosyltransferase and *** further identified syntenic tandem gene duplicates of the two GGTs in the Apiaceae and Araliaceae families,suggesting a well-conserved genomic basis underlying sugar chain assembly that likely has evolved in the early ancestors of the Apiales ***,expression patterns of the two GGTs in pierced leaves of *** were found to be correlated with the production of asiaticoside and madecassoside,implying their involvement in host defense against herbivores and *** work sheds light on the biosynthesis and evolution of complex saponin sugars,paving the way for future engineering of diverse bioactive triterpenoids with unique glycoforms.

关键词： triterpenoid saponin glycoside glycosyltransferases biosynthesis asiaticoside madecassoside Centella asiatica

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Cross-linkedα-amylase aggregates on Fe3O4 magnetic nanoparticles modified with polydopamine/polyethyleneimine for efficient hydrolysis of starch

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Particuology 2024年第7期90卷 98-105页

作者： Jiandong Cui Xiuming Tang Qingqing Ma Yuyan Chang Qunli Zhang Shiru Jia state key laboratory of food Nutrition and Safety Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin 300457China key laboratory of biomass Chemical Engineering of Ministry of Education Zhejiang UniversityHangzhou 310027China

In this workα-amylase was immobilized on magnetic Fe3O4 nanoparticles with polyethylenimine(PEI)/polydopamine(PDA)coating or 3-aminopropyl triethoxysilane(APTES)for the first time via adsorption–precipitation–*** with the freeα-amylase,the resultant magnetic cross-linkedα-amylase aggregates(PEI/PDA-M-CLEAs and N-M-CLEAs)exhibited excellent thermal and storage stability as well as pH *** storage at 25°C for 60 days,freeα-amylase only retained 60%of its initial activity,while PEI/PDA-M-CLEAs and N-M-CLEAs retained 80%and 78%of their initial activities,***,N-M-CLEAs and PEI/PDA-M-CLEAs showed good *** 6 repeated uses,PEI/PDA-M-CLEAs and N-M-CLEAs still maintained 65%and 62%of their initial activities,***,PEI/PDA-M-CLEAs and N-M-CLEAs exhibited higher starch hydrolysis efficiency than freeα-*** maximum dextrose equivalent(DE)values of starch hydrolysis by PEI/PDA-M-CLEAs and N-M-CLEAs reached 29.24%and 28.79%within 90 min,***,the maximum DE values of starch hydrolysis by the freeα-amylase was only 27.89%even in 150 *** magnetic cross-linkedα-amylase aggregates could be introduced as effective biocatalyst for industrial applications in production of maltose syrups.

关键词： α-amylase Magnetic nanoparticles Functional modification Magnetic cross-linked enzyme aggregates Hydrolysis of starch

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Predicting pH Optimum for Activity of Beta-Glucosidases

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Journal of Biomedical Science and Engineering 2019年第7期12卷 354-367页

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

The working conditions for enzymatic reaction are elegant, but not many optimal conditions are documented in literatures. For newly mutated and newly found enzymes, the optimal working conditions can only be extrapolated from our previous experience. Therefore a question raised here is whether we can use the knowledge on enzyme structure to predict the optimal working conditions. Although working conditions for enzymes can be easily measured in experiments, the predictions of working conditions for enzymes are still important because they can minimize the experimental cost and time. In this study, we develop a 20-1 feedforward backpropagation neural network with information on amino acid sequence to predict the pH optimum for the activity of beta-glucosidase, because this enzyme has drawn much attention for its role in bio-fuel industries. Among 25 features of amino acids being screened, the results show that 11 features can be used as predictors in this model and the amino-acid distribution probability is the best in predicting the pH optimum for the activity of beta-glucosidases. Our study paves the way for predicting the optimal working conditions of enzymes based on the amino-acid features.

关键词： Beta-Glucosidase enzyme pH Optimum Prediction

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Spontaneous Unfolding and Refolding of Plantaricin α-Helix in Molecular Dynamics Simulation

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Computational Molecular Bioscience 2019年第1期9卷 27-39页

Antimicrobial peptides are promising therapeutic agents in view of increasing resistance to conventional antibiotics. Antimicrobial peptides usually fold in α-helical, β-sheet, and extended/random-coil structures. The α-helical antimicrobial peptides are often unstructured in aqueous solution but become structured on bacterial membrane. The α-helical structure allows the partitioning into bacterial membrane. Therefore it is important to understand the mechanism of unfolding and refolding of α-helical structure in antimicrobial peptides. It is not very easy to obverse and study the process of unfolding and refolding of α-helical antimicrobial peptides because of their rapidity. Therefore, molecular simulation provides a way to observe and explain this phenomenon. Plantaricin A is a 26 amino-acid antimicrobial pheromone peptide and can spontaneously unfold and refold under physiological condition. This study demonstrated the unfolding and refolding of plantaricin A by means of molecular simulation, and its mechanism was discussed with its implication to the Levinthal paradox.

关键词： Alpha-Helix Antimicrobial Peptides Protein Folding Plantaricin A

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Correlating Combined Features of Amino Acid and Protein with Crystallization Propensity of Proteins from Mycobacterium tuberculosis

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Journal of Biomedical Science and Engineering 2019年第9期12卷 427-442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 Key Laboratory of Bio-Refinery Guangxi Biomass Engineering Technology Research Center Guangxi Academy of Sciences Nanning China

Since a decade ago, both protein and amino acid features have been correlated with crystallization propensity of proteins in order to develop methods to predict whether a protein can be crystallized. In this continuing study, each of three features combining features of amino acid and protein, was correlated with the crystallization propensity of proteins from Mycobacterium tuberculosis using logistic and neural network models. The results showed that two combined features, amino acid distribution probability and future composition, had good predictions on whether a protein would be crystallized in comparison with the predictions obtained from each of 531 amino acid features. The results obtained from the third combined feature, amino acid pair predictability, demonstrated the trend of crystallization propensity in proteins from Mycobacterium tuberculosis.

关键词： Protein Feature Mycobacterium tuberculosis Protein Crystallization

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Predictors for Predicting Temperature Optimum in Beta-Glucosidases

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Journal of Biomedical Science and Engineering 2019年第8期12卷 414-426页

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

This is the continuation of our studies on beta-glucosidase, which plays an important role in biological processes and recently strong interests focus on their potential role in biofeul production. In order to develop simple methods to predict the optimal working condition for beta-glucosidase, we used a 20-1 feedforward backpropagation neural network to screen possible predictors to predict the temperature optimum of beta-glucosidase from 25 amino-acid properties related to the primary structure of beta-glucosidases. The results show that the normalized polarizability index and amino-acid distribution probability can predict the temperature optimum of beta-glucosidase, which highlights a cost-effective way to predict various enzymatic parameters of beta-glucosidase.

关键词： Beta-Glucosidase enzyme Temperature Optimum Prediction

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Do We Ignore Tobacco’s Positive Ecological Role Too Long?

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Natural Science 2020年第5期12卷 273-280页

Definitely, tobacco is one of the most troubling plants in this planet because of its harmful effects on humans. Therefore, tobacco plantation declines continuously in the world. For such a plant, do we need to eliminate tobacco entirely from the surface of the earth? Perhaps, humans might have ignored the tobacco’s positive role in environment and ecology, especially in the heavily industrialized environments, for too long. Because the human activity generates more and more nitrogen oxides (NOx) in atmosphere, which not only cause imbalance in the global nitrogen cycle but also lead to haze, smog, acid rain, PM2.5, and eventually impact on environment and human health. Unfortunately the current technologies do not provide an efficient way to remove NOx from atmosphere. However, it is only tobacco can remove NOx from atmosphere. Perhaps, we should blame us, humans who use tobacco unwisely, rather than blame tobacco in nature. Anyways, the ability of tobacco to remove NO2 from atmosphere should not be ignored.

关键词： Air Pollution Nitrogen Oxides PM2.5 Phytoremediation Tobacco

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Prediction of Crystallization Propensity of Proteins from Bacillus haloduranUsing Various Amino Acid and Protein Features

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Journal of Biomedical Science and Engineering 2019年第12期12卷 487-499页

Correct prediction of propensity of crystallization of proteins is important for cost- and time-saving in determination of 3-demensional structures because one can focus to crystallize the proteins whose propensity is high through predictions instead of choosing proteins randomly. However, so far this job has yet to accomplish although huge efforts have been made over years, because it is still extremely hard to find an intrinsic feature in a protein to directly relate to the propensity of crystallization of the given protein. Despite of this difficulty, efforts are never stopped in testing of known features in amino acids and proteins versus the propensity of crystallization of proteins from various sources. In this study, the comparison of the features, which were developed by us, with the features from well-known resource for the prediction of propensity of crystallization of proteins from Bacillus haloduran was conducted. In particular, the propensity of crystallization of proteins is considered as a yes-no event, so 185 crystallized proteins and 270 uncrystallized proteins from B. haloduran were classified as yes-no events. Each of 540 amino-acid features including the features developed by us was coupled with these yes-no events using logistic regression and neural network. The results once again demonstrated that the predictions using the features developed by us are relatively better than the predictions using any of 540 amino-acid features.

关键词： Protein Feature Bacillus haloduran Protein Crystallization

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