Science Letters:EHPred: an SVM-based method for epoxide hydrolases recognition and classification

A two-layer method based on support vector machines (SVMs) has been developed to distinguish epoxide hydrolases (EHs) from other enzymes and to classify its subfamilies using its primary protein sequences. SVM classifiers were built using three different feature vectors extracted from the primary sequence of EHs: the amino acid composition (AAC), the dipeptide composition (DPC), and the pseudo-amino acid composition (PAAC). Validated by 5-fold cross tests, the first layer SVM clas- sifier can differentiate EHs and non-EHs with an accuracy of 94.2% and has a Matthew’s correlation coefficient (MCC) of 0.84. Using 2-fold cross validation, PAAC-based second layer SVM can further classify EH subfamilies with an overall accuracy of 90.7% and MCC of 0.87 as compared to AAC (80.0%) and DPC (84.9%). A program called EHPred has also been developed to assist readers to recognize EHs and to classify their subfamilies using primary protein sequences with greater accuracy.

OBSERVATION ON REGIONAL DIFFERENCES OF SOME DEHYDROGENASES AND HYDROLASES IN RAT EPIDIDYMIS

The epididymal epithelia, by secretion, fluid reabsorption and transition, provide a favorable environment for sperm maturation. We observed, with histochemical method, the regional differences of four hydrolases and five dehydrogenases in caput, corpus and cauda of rat epididymis

Duplication and Combination of P-Loop Containing Nucleotide Triphosphate Hydrolases Superfamily

In a genome the set of proteins are formed by duplication and combination of domain superfamilies. P-loop containing nucleotide triphosphate （NTP） hydrolases superfamily is massively duplicated and has the most different partner superfamilies among archaea, bacteria and eukarya, Here, we study the distributions of duplication and combination of p-loop containing NTP hydrolases superfamily in 169 completed genomes. When the total number of domains in a genome is larger, duplication and combination partners of p-loop conraining NTP hydrolases are more. This phenomenon is more obvious in metazoa. The distributions of abundance and corn bination of partners relate to the functions of the protein. Those distributions in metazoa are very different from those in other kingdoms because of complexity of metazoa. Finally the relationship between duplication and combination of p-loop containing NTP hydrolases superfamily in different genomes is described. It fits a power law.

Isolation and Identification of an Acidophilic Fungus and Analysis on the Secreted Glycoside Hydrolases

[Objective] This study aimed to isolate an acidophilic fungus and analyze the acidophilic enzymes secreted by this fungus. [Method] A heterotrophic fungus was isolated from the leaching solution of a uranium ore in Jiangxi Province using oligotrophic acid selective medium （pH 2.5）, and was named RBS-6. This strain was then identified according to its colony morphology and molecular indicator rDNA-ITS. Finally, the glycoside hydrolases secreted by RBS-6 were analyzed. [Result] This fungus RBS-6 was acidophilic, and grew best at pH4.0. Its rDNA-ITS sequence shared the highest homology （98%） with that of Phialophora sp. CGMCC 3329 （GU 082377）. So it was identified as a fungus of Phialophora sp., and was temporarily named as Phialophora sp. RBS-6. It can produce six glycoside hydrolases, in cluding α-galactosidase glucosidase, β-glucosidase, β-mannanase and β-glucanase. All the enzymes were acidophilic, for which the optimum reaction pH was 3.0-4.0. Among them, β-glucanase exhibited the highest activity at pH 3.5 and 50 ℃; in addition, it was heat-stable as 58% of the enzyme activity was remained after incubation at 50 ℃ for 60 min. [Conclusion] The isolated fungus which was identified as an acidophilic member of Phialophora sp., was a new strain producing acidophilic enzymes. This study supplied new data for the research on Phialophora fungi.

Bacterial UDP-Glucose Hydrolases and P2 Receptor-Mediated Responses to Infection: A Commentary

UDP-glucose hydrolases are a group of relatively little known membrane-bound or periplasmic enzymes found in Salmonella enterica and E. coli. UDP-glucose is an agonist for a specific P2 receptor (P2Y14) found on epithelial cells and cells associated with innate immunity. It is also recognised as a ‘danger signal’. Cells respond to mechanical damage by releasing UDP-glucose which activates P2Y14 to trigger an innate immune response;it is postulated that a similar response to bacterial infection may be protective against infection. However, the UDP-glucose hydrolases may constitute virulence factors able to abrogate this response by degradation of the released UDP-glucose.

Machine learning meets enzyme engineering: examples in the design of polyethylene terephthalate hydrolases

The trend of employing machine learning methods has been increasing to develop promising biocatalysts.Leveraging the experimental findings and simulation data,these methods facilitate enzyme engineering and even the design of new-to-nature enzymes.This review focuses on the application of machine learning methods in the engineering of polyethylene terephthalate(PET)hydrolases,enzymes that have the potential to help address plastic pollution.We introduce an overview of machine learning workflows,useful methods and tools for protein design and engineering,and discuss the recent progress of machine learning-aided PET hydrolase engineering and de novo design of PET hydrolases.Finally,as machine learning in enzyme engineering is still evolving,we foresee that advancements in computational power and quality data resources will considerably increase the use of data-driven approaches in enzyme engineering in the coming decades.

Microplastics affect activity and spatial distribution of C,N, and P hydrolases in rice rhizosphere

Microplastics provide a new ecological niche for microorganisms,and the accumulation levels of microplastics(MPs)in terrestrial ecosystems are higher than those in marine ecosystems.Here,we applied the zymography to investigate how MPs–polyethylene[PE],and polyvinyl chloride[PVC])at two levels(0.01%and 1%soil weight)impacted the spatial distribution of soil hydrolases,nutrient availability,and rice growth in paddy soil.MPs increased the above-ground biomass by 13.0%–15.5%and decreased the below-ground biomass by 8.0%–15.1%.Addition of 0.01%and 1%MPs reduced soil NH4+content by 18.3%–63.2%and 52.2%–80.2%,respectively.The average activities of N-and P-hydrolases increased by 0.8%–4.8%and 1.9%–6.3%with addition of MPs,respectively.The nutrient uptake by rice plants and the enzyme activities in hotspots increased with MP content in soil.The accumulation of MPs in paddy soil could provide an ecological niche that facilitates microbial survival,alters the spatial distribution of soil hydrolases,and decreases nutrient availability.

New possibility for PET plastic recycling by a tailored hydrolytic enzyme

Plastic waste puts a huge burden on the ecosystem due to the current lack of mature recycling technology.Poly(ethylene terephthalate)(PET)is one of the most produced plastics in the world.Enzymatic decomposition holds the promise of recovering monomers from PET plastic,and the monomers can be used to regenerate new PET products.However,there are still limitations in the activity and thermal stability of the existing PET hydrolases.The recent study by Lu et al.introduced a novel PET hydrolase via machine learning-aided engineering.The obtained PET hydrolase showed excellent activity and thermal stability in the hydrolysis of PET and is capable of directly degrading large amounts of postconsumer PET products.This approach provides an effective method for recycling PET waste and is expected to improve the current state of plastic pollution worldwide.

Influence of gut microbiome composition on effect variations of anti-cholesterol treatment among individual mice

This study investigated if the variation in the effect of anti-cholesterol(AC)treatment on individual mice are related to gut microbiome composition.The bile salt hydrolase(BSH)activity of 23 commercial fermented milk products was examined to select a fermented milk product for AC treatment.Mice were fed to different diets for 6 weeks:high-fat(60%of total calories from fat;D1),high-dietary fibre(20%cellulose;D2),and low-fat(17.2%of total calories from fat;D3)diets to change their gut microbiomes.Subsequently,faecal microbiome was transplanted(FMT)into mice treated with high cholesterol diet contained 2%cholesterol,followed by AC or non-AC(sterile tap water,STW)treatments.Control groups with normal(NC)and highcholesterol diets(PC)were prepared for both AC and STW treatment.All experimental groups were subjected to serum and liver cholesterol,cholesterol metabolism-related(CMR)gene expression,and intestinal microbiome analyses.D3-FMT mice showed the most significant enhancements in cholesterol ratio and decreased hepatic cholesterol levels with AC treatment.Moreover,upregulation of the Cyp7a1 gene expression was observed in this group.Furthermore,the intestinal microbiome analysis indicated higher abundances of BSH-producing Eubacterium,Bifidobacterium,and Parabacteroides in the D3-FMT+AC group compare to others,potentially contributing to increased bile acid synthesis.

Exploring the bioactive compounds of Feiduqing formula for the prevention and management of COVID-19 through network pharmacology and molecular docking

Background:To explore the effective chemical constituents of Feiduqing formula for prevention and treatment of coronavirus disease 2019(COVID-19).Methods:The compounds and action targets of twelve herbal medicines in Feiduqing formula were collected via Traditional Chinese Medicine Systems Pharmacology Database and Analytic Platform.The genes corresponding to the targets were queried through the UniProt database.The“herbal medicine-ingredient-target”network was established by Cytoscape software.The Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed by Database for Annotation,Visualization and Integrated Discovery.Molecular docking was used to analyze the binding force of core active compounds of Feiduqing formula with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and angiotensin converting enzyme II(ACE2).Results:The“herbal medicine-ingredient-target”network included 434 nodes and 1948 edges,including 222 components such as quercetin,kaempferol,luteolin,etc.The key targets are PTGS2,HSP90AA1,PTGS1,ESR1,AR,NOS2,etc.Gene Ontology function enrichment analysis revealed 2530 items,including RNA polymerase II-specific,response to oxidative stress,transcription factor activity,etc.Kyoto Encyclopedia of Genes and Genomes pathway enrichment screened 169 signal pathways,including Human cytomegalovirus infection,Kaposi sarcoma-associated herpesvirus infection,Hepatitis B,Hepatitis C,IL-17,TNF,etc.The results of molecular docking showed that quercetin,luteolin,β-sitosterol,stigmasterol and other core active compounds have a certain degree of affinity with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2.Conclusion:The active compounds of Feiduqing formula may have a therapeutic effect on COVID-19 pneumonia through the action on PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2,and regulating many signaling pathways.

Analysis on Tissue-specific Expression of Dp XTH1 and Dp XTH2 Genes in Dahlia

[Objective] This study aimed to investigate the functions and related mechanisms of xyloglucan Endotransglycosylase/hydrolases （XTHs） during the growth and development of dahlia. [Method] Using /3-actin as the reference gene, the rela- tive transcription levels of DpXTH1 and DpXTH2 genes in roots, stems, leaves and petals of dahlia were analyzed by real-time RT-PCR. [Result] The DpXTH1 and DpXTH2 were not expressed in the roots, but expressed abundantly in the petals of dahlia. There were little expressions in the stems and leaves of dahlia. [Conclusion] The DpXTH1 and DpXTH2 were petal-specific genes and closely related to the growth and development of petals in dahlia.

Distribution of Soil Enzyme Activities and Microbial Biomass Along a Latitudinal Gradient in Farmlands of Songliao Plain,Northeast China

Soil enzymes activities and microbial biomass have an important influence on nutrient cycling. The spatial distribution of soil enzymes activities and microbial biomass were examined along a latitudinal gradient in farmlands of Songliao Plain, Northeast China to assess the impact of climatic changes along the latitudinal transect on nutrient cycling in agroecosystems. Top soils （0-20 cm depth） were sampled in fields at 7 locations from north （Hallun） to south （Dashiqiao） in the end of October 2005 after maize harvest. The contents of total C, N, and P, C/N, available N, and available P increased with the latitude. The activities of invertase and acid phosphatase, microbial biomass （MB） C and N, and MBC/MBN were significantly correlated with latitude （P 〈 0.05, r^2 = 0.198, 0.635, 0.558, 0.211 and 0.317, respectively）, that is, increasing with the latitude. Significant positive correlations （P 〈 0.05） were observed between invertase activity and the total N and available P, and between acid phosphatase activity and the total C, C/N, available N, total P and available P. The urease, acid phosphatase, and dehydrogenase activities were significantly correlated with the soil pH and electrical conductivity （EC） （P 〈 0.05）. MBC and MBN were positively correlated with the total C, C/N, and available P （P 〈 0.05）. The MBC/MBN ratio was positively correlated with the total C, total N, C/N, and available N （P 〈 0.05）. The spatial distribution of soil enzyme activities and microbial biomass resulted from the changes in soil properties such as soil organic matter, soil pH, and EC, partially owing to variations in temperature and rainfall along the latitudinal gradient.

hOGG1 Ser326Cys polymorphism modifies the significance of the environmental risk factor for colon cancer

AIM:To determine the association of hOGG1 (8-oxoguanine glycosylase I,OGG1) polymorphism of Ser326Cys substitution with colon cancer risk and possible interaction with known environmental risk factors. METHODS:A case-control study with 125 colon cancer cases and 247 controls was conducted, RESULTS:There was no major difference in Ser326Cys genotype distribution between cases and controls.The meat intake tended to increase the odds ratio for colon cancer with an OR of 1.72 (95 % confidence interval;CI=1.12-2.76). Such tendency was more prominent in Cys/Cys carriers (OR=4.31,95 % CI=1.64-11.48),but meat intake was not a significant risk factor for colon cancer in Ser/Ser or Ser/ Cys carriers.The OR for colon cancer was elevated with marginal significance in smokers who were Cys/Cys carriers (OR=2.75,95 % CI=1.07-7.53) but not in Ser/Ser or Ser/ Cys carriers. CONCLUSION:These results suggest that the hOGG1 Ser326Cys polymorphism is probably not a major contributor to individual colon cancer susceptibility overall,but the Cys/ Cys genotype may alter the impact of some environmental factors on colon cancer development.

Arylsulfatase,β-galactosidase and lysozyme in gastric cancer cells and its relationship to invasion

IM To study the distribution of arylsulfatase, βgalactosidase and lysozyme in gastric cancer cells, and its relationship to differentiation and invasion of gastric cancer cells.METHODS Histochemical, immunohistochemical and ruthenium red (RR) electrocytochemical technique for three types of hydrolases and proteoglycans in pericancerous matrix in 33 cases of gastric cancer were observed under light and electron microscopy.RESULTS The expression intensities of arylsulfatase, βglactosidase and lysozyme in mucinous cell carcinomas were more intensive than those in welldifferentiated and poorlydifferentiated adenocarcinomas (P<005-001). The fibrous tissues smooth muscle and proteoglycans close to the cancer cells were degraded. They were found in the region far from the cancer cells. Expression of three enzymes mentioned above was low in adenocarcinoma cells, and fibrous tissues and RR granules were present and intact near the welldifferentiated and poorly differentiated adenocarcinoma cells.CONCLUSION Mucinous cell carcinoma may release various hydrolases into extracellular matrix, inducing degradation of pericancerous matrix and facilitating cancer cell invasion and metastasis..

CYP1A1,CYP2E1 and EPHX1 polymorphisms in sporadic colorectal neoplasms

AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) were enrolled in the study. The variables analyzed were age, gender, tobacco and alcohol consumption, and clinical and histopathological tumor parameters. The CYP1A1 *2A, CYP1A1 *2C CYP2E1 *5B and CYP2E1 *6 polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). The EPHX1 Tyr113 His, EPHX1 His139 Arg and CYP1A1 *2C polymorphisms were detected by real-time PCR. Chisquared test and binary logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the Haploview program, version 2.05.RESULTS Age over 6 2 years was a risk factor for SCRC development(OR = 7.54, 95%CI: 4.94-11.50, P < 0.01). Male individuals were less susceptible to SCRC(OR = 0.55, 95%CI: 0.35-0.85, P < 0.01). The CYP2E1*5B polymorphism was associated with SCRC in the codominant(heterozygous genotype: OR = 2.66, 95%CI: 1.64-4.32, P < 0.01), dominant(OR = 2.82, 95%CI: 1.74-4.55, P < 0.01), overdominant(OR = 2.58, 95%CI: 1.59-4.19, P < 0.01), and log-additive models(OR = 2.84, 95%CI: 1.78-4.52, P < 0.01). The CYP2E1*6 polymorphism was associated with an increased SCRC risk in codominant(heterozygous genotype: OR = 2.81, 95%CI: 1.84-4.28, P < 0.01; homozygous polymorphic : OR = 7. 3 2, 9 5 % C I : 1.85-28.96, P < 0.01), dominant(OR = 2.97, 95%CI: 1.97-4.50, P < 0.01), recessive(OR = 5.26, 95%CI: 1.35-20.50, P = 0.016), overdominant(OR = 2.64, 95%CI: 1.74-4.01, P < 0.01), and log-additive models(OR = 2.78, 95%CI: 1.91-4.06, P < 0.01). The haplotype formed by the minor alleles of the CYP2E1*5B(C) and CYP2E1*6(A) polymorphisms was associated with SCRC(P = 0.002). However, the CYP1A1 *2A, CYP1A1 *2C, EPHX1 Tyr113 His and EPHX1 His139 Arg polymorphisms were not associated with SCRC.CONCLUSION In conclusion, the results demonstrated that CYP2E1*5B and CYP2E1*6 minor alleles play a role in the development of SCRC.

EPHX1 A415G基因多态性与胃肠道肿瘤易感性的Meta分析

目的：探讨微粒体环氧化物水解酶（ EPHX1） A415G基因多态性与胃肠道肿瘤易感性的关系。方法计算机检索PubMed、EMBASE、CBM、维普、万方及中国知网数据库，检索时间截至2013年5月，收集关于EPHX1 A415G基因多态性与胃肠道肿瘤易感性的研究。由2名评价者按照纳入和排除标准独立选择文献、提取资料、评价质量。采用STATA 11.0软件进行Meta分析，计算合并OR值及其95％CI并行敏感性分析和发表偏倚的评估。结果最终纳入18篇文献，包括5852例胃肠道肿瘤患者和8710例对照人群。纳入的结果在GG vs． AA、GA vs． AA、GG/GA vs． AA和GG vs． GA/AA基因型的比较模型中均无异质性。各遗传模型Meta分析结果显示，EPHX1 A415G基因多态性与胃肠道肿瘤遗传易感性的关联性无统计学意义[GG vs． AA：OR＝1.063，95％CI：0.888～1.273；GA vs． AA： OR＝0.935，95％CI：0.867～1.009；GG/GA vs． AA： OR＝0.948，95％CI：0.882～1.020；GG vs． GA/AA：OR＝1.091，95％CI：0.913～1.304]。结论 EPHX1 A415G基因多态性与胃肠道肿瘤易感性之间无明显相关性。

血管紧张素Ⅰ转换酶与职业性肺疾患

血管紧张素Ⅰ转换酶(Angiotensin-I-Converting enzyme,ACE),系统名称:肽基-二肽水解酶(peptidyl dipeptide hydrolase,EC3.4.15.1)。1954年 Skeggs 等发现用马血浆配制的肾素基质中有能使血管紧张素Ⅰ(AT-Ⅰ)转换为 AT-Ⅱ的酶存在,1956年用硫酸铵分离马血浆得到 ACE 精品。1967—1969年,Ng,Bakhle 等发现从 AT-Ⅰ到 AT-Ⅱ的转换主要是在肺内进行,肺内

Hydrolytic Enzyme Inhibitors and Necrotic Reactions in Potato Leaves Reduce Reproductive Success of Colorado Potato Beetle

In field and laboratory conditions the reproductive potential （survival at different stages of development） of the Colorado potato beetle has been measured, the dependence of the parameters of insects fertility on varietal features of the feed has been investigated, the food activity of the representatives of insects from four areas of the Southern Urals has been measured, the intensity and time of hypersensitivity reactions on potato leaves has been defined. In laboratory experiments, the level of activity of hydrolytic enzymes in insects and the level of activity of these enzymes inhibitors in the leaves of three potato varieties differing in their resistance to the Colorado potato beetle have been determined. The results show that the insects-representatives of different samples have different food activity in relation to different potato varieties. High mortality rates were revealed at feeding with leaves of potato of the Bashkir variety characterized by a high level of hydrolases inhibitors and relatively rapid development of necrotic reactions after the appearance of eggs laying on the leaves. We suppose that the neerogenetic barrier appearing in the form of necrosis is the major cause of the fetal mortality of insects. The level of the content of inhibitors inactivating larvae digestive enzymes affects the survival of insects at postembryonic stages. The speed of the necrosis emergence, the level of activity of digestive enzymes inhibitors in potato can be considered as criteria for the selection of breeding material for resistance to the Colorado potato beetle.