Zhou P

References (18)

Title : SPG21, a potential oncogene targeted by miR-128-3p, amplifies HBx-induced carcinogenesis and chemoresistance via activation of TRPM7-mediated JNK pathway in hepatocellular carcinoma - Zhou_2024_Cell.Oncol.(Dordr)__
Author(s) : Zhou P , Yao W , Liu L , Yan Q , Chen X , Wei X , Ding S , Lv Z , Zhu F
Ref : Cell Oncol (Dordr) , : , 2024
Abstract : PURPOSE: Chronic hepatitis B virus (HBV) infection is the primary risk factor for the malignant progression of hepatocellular carcinoma (HCC). It has been reported that HBV X protein (HBx) possesses oncogenic properties, promoting hepatocarcinogenesis and chemoresistance. However, the detailed molecular mechanisms are not fully understood. Here, we aim to investigate the effects of miR-128-3p/SPG21 axis on HBx-induced hepatocarcinogenesis and chemoresistance. METHODS: The expression of SPG21 in HCC was determined using bioinformatics analysis, quantitative real-time PCR (qRT-PCR), western blotting, and immunohistochemistry (IHC). The roles of SPG21 in HCC were elucidated through a series of in vitro and in vivo experiments, including real-time cellular analysis (RTCA), matrigel invasion assay, and xenograft mouse model. Pharmacologic treatment and flow cytometry were performed to demonstrate the potential mechanism of SPG21 in HCC. RESULTS: SPG21 expression was elevated in HCC tissues compared to adjacent non-tumor tissues (NTs). Moreover, higher SPG21 expression correlated with poor overall survival. Functional assays revealed that SPG21 fostered HCC tumorigenesis and invasion. MiR-128-3p, which targeted SPG21, was downregulated in HCC tissues. Subsequent analyses showed that HBx amplified TRPM7-mediated calcium influx via miR-128-3p/SPG21, thereby activating the c-Jun N-terminal kinase (JNK) pathway. Furthermore, HBx inhibited doxorubicin-induced apoptosis by engaging the JNK pathway through miR-128-3p/SPG21. CONCLUSION: The study suggested that SPG21, targeted by miR-128-3p, might be involved in enhancing HBx-induced carcinogenesis and doxorubicin resistance in HCC via the TRPM7/Ca(2+)/JNK signaling pathway. This insight suggested that SPG21 could be recognized as a potential oncogene, offering a novel perspective on its role as a prognostic factor and a therapeutic target in the context of HCC.
ESTHER : Zhou_2024_Cell.Oncol.(Dordr)__
PubMedSearch : Zhou_2024_Cell.Oncol.(Dordr)__
PubMedID: 38753154
Gene_locus related to this paper: human-SPG21

Title : Effects of natural products on functional constipation: analysis of active ingredient and mechanism - Zhou_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__
Author(s) : Zhou P , Wang X , Sun M , Yan S
Ref : Naunyn Schmiedebergs Arch Pharmacol , : , 2023
Abstract : Constipation is a prevalent clinical ailment of the gastrointestinal system, yet its pathogenesis remains ambiguous. Despite the availability of numerous treatment modalities, they are insufficient in resolving the issue for patients. This work conducted a comprehensive review of the existing literature pertaining to the utilization of natural products for the treatment of constipation, with a focus on the efficacy of natural products in treating constipation, and to provide a comprehensive summary of their underlying mechanisms of action. Upon conducting a thorough review of the extant literature, we found that natural products can effectively treat constipation as modern synthetic drugs and compounded drugs with acetylcholinesterase (AChE) effects, rich in fiber and mucus, and the effects of increasing the tension of the ileum and gastrointestinal tract muscle, mediating signaling pathways, cytokine, excitability of the smooth muscle of the gastrointestinal tract, and regulating the homeostasis of intestinal flora. However, there is a wide variety of natural products, and there are still relatively few studies; the composition of natural products is complex, and the mechanism of action of natural products cannot be clarified. In the future, we need to further improve the detailed mechanism of natural products for the treatment of constipation.
ESTHER : Zhou_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__
PubMedSearch : Zhou_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__
PubMedID: 37870581

Title : Bio-interaction of nano and bulk lanthanum and ytterbium oxides in soil system: Biochemical, genetic, and histopathological effects on Eisenia fetida - Adeel_2021_J.Hazard.Mater_415_125574
Author(s) : Adeel M , Shakoor N , Hussain T , Azeem I , Zhou P , Zhang P , Hao Y , Rinklebe J , Rui Y
Ref : J Hazard Mater , 415 :125574 , 2021
Abstract : The massive application of rare earth elements (REEs) in electronic industries cause their inevitable release into the environment; however, its effects on soil biota remain largely unaddressed. We investigated the E. fetida detoxification potential of nano and bulk La(2)O(3) and Yb(2)O(3) and their potential impact on biochemical and genetic markers at 50, 100, 200, 500 and 1000 mg kg(-1) concentration. We found that earthworms bioremediate 3-15% La(2)O(3) and Yb(2)O(3) contaminated soil at low and medium levels, while this potential was limited at higher levels. Nano and bulk La(2)O(3) and Yb(2)O(3) treatment induced neurotoxicity in earthworm by inhibiting acetylcholinesterase by 49-65% and 22-36% at 500 and 1000 mg kg(-1), respectively. Nano La(2)O(3) proved to be highly detrimental, mainly through oxidative stress and subsequent failure of antioxidant system. Nano La(2)O(3) and Yb(2)O(3) at 100 mg kg(-1) significantly down-regulated the expression of annetocin mRNA in the parental and progeny earthworms by 50% and 20%, which is crucial for earthworm reproduction. Similarly, expression level of heat shock protein 70 (HSP70) and metallothionein was significantly upregulated in both generations at medium exposure level. Histological observations showed that nano REEs at 200 mg kg(-1) induced drastic changes in the intestinal epithelium and typhlosole of E. fetida. To date, our results enhance the understanding of interaction between REEs and earthworms.
ESTHER : Adeel_2021_J.Hazard.Mater_415_125574
PubMedSearch : Adeel_2021_J.Hazard.Mater_415_125574
PubMedID: 33756203

Title : CA10 and CA11 negatively regulate neuronal activity-dependent growth of gliomas - Tao_2019_Mol.Oncol_13_1018
Author(s) : Tao B , Ling Y , Zhang Y , Li S , Zhou P , Wang X , Li B , Jun Z , Zhang W , Xu C , Shi J , Wang L
Ref : Mol Oncol , 13 :1018 , 2019
Abstract : Recent studies have revealed that neurons can promote glioma growth through activity-dependent secretion of neurotrophins, especially neuroligin-3. It has therefore been suggested that blocking neuron-derived neurotrophins may serve as a therapeutic intervention for gliomas. Carbonic anhydrase-related proteins 11 and 10 (CA11 and CA10) are secreted synaptic proteins which function as neurexin ligands, and the gene-encoding CA11 is part of a gene signature associated with radiotherapy and prognosis in gliomas. We therefore hypothesized that CA11/CA10 might participate in the neuronal activity-dependent regulation of glioma growth. In this study, we report that CA11 secreted by depolarized cultured neurons within conditioned medium (CM) inhibited the growth of glioma cell lines. CM from depolarized neurons inhibited CA11 expression in glioma cell lines via the Akt signaling pathway. Consistently, CA11 expression was also reduced in clinical glioma samples and negatively associated with high histological grade. Low CA11 expression of gliomas was associated with short survival in four independent datasets [repository of brain neoplasia data (REMBRANDT), The Cancer Genome Atlas (TCGA) lower grade glioma (LGG), GSE4271, and GSE42669]. CA11 knockdown promoted cell growth, clone formation, and migration; inhibited apoptosis; and increased tumor size in xenografted nude mice. Similarly, CA10 and CA10 secreted by depolarized cultured neurons also inhibited the growth of glioma cell lines. Low CA10 expression was associated with short survival in REMBRANDT, TCGA LGG, and GEO GSE4271 datasets. Our results suggest that CA11 and CA10 negatively regulate neuronal activity-dependent glioma growth and inhibit glioma aggression. Thus, CA11/CA10 may represent a potential therapeutic target for the treatment of gliomas.
ESTHER : Tao_2019_Mol.Oncol_13_1018
PubMedSearch : Tao_2019_Mol.Oncol_13_1018
PubMedID: 30636076

Title : One-step orientated immobilization of nanobodies and its application for immunoglobulin purification - Fu_2019_J.Chromatogr.A_1603_15
Author(s) : Fu J , Li J , Wang W , Wu H , Zhou P , Li Y , He Q , Tu Z
Ref : Journal of Chromatography A , 1603 :15 , 2019
Abstract : Affinity chromatography technologies play an important role in the purification of antibodies. To prepare affinity materials, prior isolation and purification of affinity ligands are required before coupling onto solid supports, which is quite expensive and laborious in large-scale applications. In this study, a one-step approach which circumvents the ligand purification procedures was developed to fabricate affinity gel for purifying immunoglobulin G (IgG). A self-labeling tag, haloalkane dehalogenase, was fused to the C-terminal of an anti-Fc variable domain of the heavy chain of the heavy-chain antibody (AFV) which was isolated in previous work. The AFV binds to various sources of IgG and is highly thermal stable. The fusion protein, namely HAFV, was expressed in Escherichia coli as a soluble protein. The binding affinity of HAFV to the Fc region of IgG was characterized and compared with the untagged anti-Fc nanobody. Next, the HAFV was immobilized directly from the crude cell lysate of isopropylthio-beta-D-galactoside (IPTG) induced E. coli. The effects of NaCl concentrations and pH on the capacity of the HAFV resin were investigated. In addition, the one-step coupled HAFV resin was compared with the AFV resin and commercial resins (Protein A and Protein G) by evaluating the static capacity and stability. Though the Protein A (8.34+/-0.37mg/ml) and Protein G (9.19+/-0.28mg/ml) showed higher static capacity, the static capacity of HAFV resin (8.21+/-0.30mg/ml) was better than that of the untagged AFV gel (6.48+/-0.56mg/ml). The recovery results calculated for the reusability and stability show that there is no significant difference between the results obtained for the HAFV gel with those of the untagged AFV gel and commercial Protein A and G. After stored at 37 for 7 days and recycled 10 times, the static capacity of HAFV gel remains above 78%. Our strategy is site-specific, cost-effective, reproducible, and has the potential to dramatically cut down the costs of affinity materials for IgG purification.
ESTHER : Fu_2019_J.Chromatogr.A_1603_15
PubMedSearch : Fu_2019_J.Chromatogr.A_1603_15
PubMedID: 31213362
Gene_locus related to this paper: xanau-halo1

Title : Single intranasal immunization with chimpanzee adenovirus-based vaccine induces sustained and protective immunity against MERS-CoV infection - Jia_2019_Emerg.Microbes.Infect_8_760
Author(s) : Jia W , Channappanavar R , Zhang C , Li M , Zhou H , Zhang S , Zhou P , Xu J , Shan S , Shi X , Wang X , Zhao J , Zhou D , Perlman S , Zhang L
Ref : Emerg Microbes Infect , 8 :760 , 2019
Abstract : The recently identified Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes severe and fatal acute respiratory illness in humans. However, no approved prophylactic and therapeutic interventions are currently available. The MERS-CoV envelope spike protein serves as a crucial target for neutralizing antibodies and vaccine development, as it plays a critical role in mediating viral entry through interactions with the cellular receptor, dipeptidyl peptidase 4 (DPP4). Here, we constructed a recombinant rare serotype of the chimpanzee adenovirus 68 (AdC68) that expresses full-length MERS-CoV S protein (AdC68-S). Single intranasal immunization with AdC68-S induced robust and sustained neutralizing antibody and T cell responses in BALB/c mice. In a human DPP4 knock-in (hDPP4-KI) mouse model, it completely protected against lethal challenge with a mouse-adapted MERS-CoV (MERS-CoV-MA). Passive transfer of immune sera to naive hDPP4-KI mice also provided survival advantages from lethal MERS-CoV-MA challenge. Analysis of sera absorption and isolated monoclonal antibodies from immunized mice demonstrated that the potent and broad neutralizing activity was largely attributed to antibodies targeting the receptor binding domain (RBD) of the S protein. These results show that AdC68-S can induce protective immune responses in mice and represent a promising candidate for further development against MERS-CoV infection in both dromedaries and humans.
ESTHER : Jia_2019_Emerg.Microbes.Infect_8_760
PubMedSearch : Jia_2019_Emerg.Microbes.Infect_8_760
PubMedID: 31130102

Title : Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein - Zhang_2018_Cell.Rep_24_441
Author(s) : Zhang S , Zhou P , Wang P , Li Y , Jiang L , Jia W , Wang H , Fan A , Wang D , Shi X , Fang X , Hammel M , Wang S , Wang X , Zhang L
Ref : Cell Rep , 24 :441 , 2018
Abstract : The major mechanism of antibody-mediated neutralization of the Middle East respiratory syndrome coronavirus (MERS-CoV) involves competition with the cellular receptor dipeptidyl peptidase 4 (DPP4) for binding to the receptor-binding domain (RBD) of the spike (S) glycoprotein. Here, we report a unique epitope and unusual neutralizing mechanism of the isolated human antibody MERS-4. Structurally, MERS-4 approached the RBD from the outside of the RBD-DPP4 binding interface. Such binding resulted in the folding of the beta5-beta6 loop toward a shallow groove on the RBD interface critical for accommodating DPP4. The key residues for binding are identified through site-directed mutagenesis. Structural modeling revealed that MERS-4 binds to RBD only in the "up" position in the S trimer. Furthermore, MERS-4 demonstrated synergy with several reported antibodies. These results indicate that MERS-4 neutralizes MERS-CoV by indirect rather than direct competition with DPP4. This mechanism provides a valuable addition for the combined use of antibodies against MERS-CoV infection.
ESTHER : Zhang_2018_Cell.Rep_24_441
PubMedSearch : Zhang_2018_Cell.Rep_24_441
PubMedID: 29996104

Title : Mice lacking lipid droplet-associated hydrolase, a gene linked to human prostate cancer, have normal cholesterol ester metabolism - Kory_2017_J.Lipid.Res_58_226
Author(s) : Kory N , Grond S , Kamat SS , Li Z , Krahmer N , Chitraju C , Zhou P , Frohlich F , Semova I , Ejsing C , Zechner R , Cravatt BF , Farese RV, Jr. , Walther TC
Ref : J Lipid Res , 58 :226 , 2017
Abstract : Variations in the gene LDAH (C2ORF43), which encodes lipid droplet-associated hydrolase (LDAH), are among few loci associated with human prostate cancer. Homologs of LDAH have been identified as proteins of lipid droplets (LDs). LDs are cellular organelles that store neutral lipids, such as triacylglycerols and sterol esters, as precursors for membrane components and as reservoirs of metabolic energy. LDAH is reported to hydrolyze cholesterol esters and to be important in macrophage cholesterol ester metabolism. Here, we confirm that LDAH is localized to LDs in several model systems. We generated a murine model in which Ldah is disrupted but found no evidence for a major function of LDAH in cholesterol ester or triacylglycerol metabolism in vivo, nor a role in energy or glucose metabolism. Our data suggest that LDAH is not a major cholesterol ester hydrolase, and an alternative metabolic function may be responsible for its possible effect on development of prostate cancer.
ESTHER : Kory_2017_J.Lipid.Res_58_226
PubMedSearch : Kory_2017_J.Lipid.Res_58_226
PubMedID: 27836991
Gene_locus related to this paper: human-LDAH , mouse-Ldah

Title : Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data - Matthews_2015_G3.(Bethesda)_5_1721
Author(s) : Matthews BB , Dos Santos G , Crosby MA , Emmert DB , St Pierre SE , Gramates LS , Zhou P , Schroeder AJ , Falls K , Strelets V , Russo SM , Gelbart WM
Ref : G3 (Bethesda) , 5 :1721 , 2015
Abstract : We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15-18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.
ESTHER : Matthews_2015_G3.(Bethesda)_5_1721
PubMedSearch : Matthews_2015_G3.(Bethesda)_5_1721
PubMedID: 26109357
Gene_locus related to this paper: drome-CG11309

Title : Gene Model Annotations for Drosophila melanogaster: The Rule-Benders - Crosby_2015_G3.(Bethesda)_5_1737
Author(s) : Crosby MA , Gramates LS , Dos Santos G , Matthews BB , St Pierre SE , Zhou P , Schroeder AJ , Falls K , Emmert DB , Russo SM , Gelbart WM
Ref : G3 (Bethesda) , 5 :1737 , 2015
Abstract : In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.
ESTHER : Crosby_2015_G3.(Bethesda)_5_1737
PubMedSearch : Crosby_2015_G3.(Bethesda)_5_1737
PubMedID: 26109356
Gene_locus related to this paper: drome-CG11309

Title : Residue Asn277 Affects the Stability and Substrate Specificity of the SMG1 Lipase from Malassezia globosa - Lan_2015_Int.J.Mol.Sci_16_7273
Author(s) : Lan D , Wang Q , Xu J , Zhou P , Yang B , Wang Y
Ref : Int J Mol Sci , 16 :7273 , 2015
Abstract : Thermostability and substrate specificity are important characteristics of enzymes for industrial application, which can be improved by protein engineering. SMG1 lipase from Malassezia globosa is a mono- and diacylglycerol lipase (MDL) that shows activity toward mono- and diacylglycerols, but no activity toward triacylglycerols. SMG1 lipase is considered a potential biocatalyst applied in oil/fat modification and its crystal structure revealed that an interesting residue-Asn277 may contribute to stabilize loop 273-278 and the 3104 helix which are important to enzyme characterization. In this study, to explore its role in affecting the stability and catalytic activity, mutagenesis of N277 with Asp (D), Val (V), Leu (L) and Phe (F) was conducted. Circular dichroism (CD) spectral analysis and half-life measurement showed that the N277D mutant has better thermostability. The melting temperature and half-life of the N277D mutant were 56.6 degrees C and 187 min, respectively, while that was 54.6 degrees C and 121 min for SMG1 wild type (WT). Biochemical characterization of SMG1 mutants were carried out to test whether catalytic properties were affected by mutagenesis. N277D had similar enzymatic properties as SMG1 WT, but N277F showed a different substrate selectivity profile as compared to other SMG1 mutants. Analysis of the SMG1 3D model suggested that N277D formed a salt bridge via its negative charged carboxyl group with a positively charged guanidino group of R227, which might contribute to confer N277D higher temperature stability. These findings not only provide some clues to understand the molecular basis of the lipase structure/function relationship but also lay the framework for engineering suitable MDL lipases for industrial applications.
ESTHER : Lan_2015_Int.J.Mol.Sci_16_7273
PubMedSearch : Lan_2015_Int.J.Mol.Sci_16_7273
PubMedID: 25837472
Gene_locus related to this paper: malgo-a8puy1

Title : Conversion of a Mono- and Diacylglycerol Lipase into a Triacylglycerol Lipase by Protein Engineering - Lan_2015_Chembiochem_16_1431
Author(s) : Lan D , Popowicz GM , Pavlidis IV , Zhou P , Bornscheuer UT , Wang Y
Ref : Chembiochem , 16 :1431 , 2015
Abstract : Despite the fact that most lipases are believed to be active against triacylglycerides, there is a small group of lipases that are active only on mono- and diacylglycerides. The reason for this difference in substrate scope is not clear. We tried to identify the reasons for this in the lipase from Malassezia globosa. By protein engineering, and with only one mutation, we managed to convert this enzyme into a typical triacylglycerol lipase (the wild-type lipase does not accept triacylglycerides). The variant Q282L accepts a broad spectrum of triacylglycerides, although the catalytic behavior is altered to some extent. From in silico analysis it seems that specific hydrophobic interactions are key to the altered substrate specificity.
ESTHER : Lan_2015_Chembiochem_16_1431
PubMedSearch : Lan_2015_Chembiochem_16_1431
PubMedID: 25955297
Gene_locus related to this paper: malgo-a8puy1

Title : Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A - Tian_2014_J.Mol.Model_20_2257
Author(s) : Tian F , Yang C , Wang C , Guo T , Zhou P
Ref : J Mol Model , 20 :2257 , 2014
Abstract : Use of point mutagenesis technique to improve protein thermostability is a routine strategy in the protein engineering community and directed evolution approach has been widely utilized to fulfill this. However, directed evolution often does not assure a minimalist design for obtaining a desired property in proteins, and other traditional methods such as error-prone PCR and iterative saturation mutagenesis are also too time-consuming and expensive to carry out a systemic search for protein mutation space. In the current study, we performed mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A (LipA) using a virtual scanning strategy. In the procedure, a new characterization method was proposed to describe structural variations upon protein residue mutation, and the generated descriptors were then statistically correlated with protein thermostability change associated with the mutation based on a large panel of structure-solved, melting temperature-known protein mutation data. As a result, linear and nonlinear quantitative structure-thermostability relationship (QSTR) models were built and their statistical quality was verified rigorously through internal cross-validation and external blind test. It is suggested that the nonlinear support vector machine (SVM) performed much better than linear partial least squares (PLS) regression in correlating protein structure and thermostability information. Thus, the SVM model was employed to systematically scan the complete mutation profile of LipA protein, resulting in a 181x19 matrix that characterizes the change in theoretical thermostability of LipA due to the mutation of wild-type residue at each of the 181 sequence sites to other 19 amino acid types. From the profile most mutations were predicted to (i) destabilize LipA structure and (ii) address modest effect on LipA thermostability. Satisfactorily, several known thermostable mutations such as G80V, G111D, M134D, and N161Y were identified properly and, expectedly, a number of mutations including L55Y, A75V, and S162P that have never been reported previously were inferred as hotspot mutations that have high potential to enhance LipA thermostability. The structural basis and energetic property of the five promising mutations were further examined in detail using atomistic molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann/surface area (MM-PB/SA) analysis, revealing intensive nonbonded interaction networks created by these mutations.
ESTHER : Tian_2014_J.Mol.Model_20_2257
PubMedSearch : Tian_2014_J.Mol.Model_20_2257
PubMedID: 24827611

Title : Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei - Zhou_2014_BMC.Genomics_15_294
Author(s) : Zhou P , Zhang G , Chen S , Jiang Z , Tang Y , Henrissat B , Yan Q , Yang S , Chen CF , Zhang B , Du Z
Ref : BMC Genomics , 15 :294 , 2014
Abstract : BACKGROUND: The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically.
RESULTS: Here, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed.
CONCLUSIONS: The genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.
ESTHER : Zhou_2014_BMC.Genomics_15_294
PubMedSearch : Zhou_2014_BMC.Genomics_15_294
PubMedID: 24746234

Title : Comparative analysis of bat genomes provides insight into the evolution of flight and immunity - Zhang_2013_Science_339_456
Author(s) : Zhang G , Cowled C , Shi Z , Huang Z , Bishop-Lilly KA , Fang X , Wynne JW , Xiong Z , Baker ML , Zhao W , Tachedjian M , Zhu Y , Zhou P , Jiang X , Ng J , Yang L , Wu L , Xiao J , Feng Y , Chen Y , Sun X , Zhang Y , Marsh GA , Crameri G , Broder CC , Frey KG , Wang LF , Wang J
Ref : Science , 339 :456 , 2013
Abstract : Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor kappaB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.
ESTHER : Zhang_2013_Science_339_456
PubMedSearch : Zhang_2013_Science_339_456
PubMedID: 23258410
Gene_locus related to this paper: myods-l5mij9 , pteal-l5k8f5 , pteal-l5kjy3 , pteal-l5k6f0 , pteal-l5kxe2 , myods-l5m0a8 , myods-l5lvb4 , pteal-l5k7h7 , myods-l5lm42 , pteal-l5jz73 , pteal-l5kvh1.1 , pteal-l5kvh1.2 , pteal-l5kw21 , myods-l5lug5 , pteal-l5kv18 , myods-l5lbf8 , pteal-l5kwh0 , myods-l5lfh8 , myods-l5lfr7 , myods-l5lu20 , pteal-l5jzi4 , pteal-l5kib7 , pteal-l5kyq5 , myods-l5lf36 , myods-l5lnh7 , myods-l5lu25 , pteal-l5k0u1 , pteal-l5k2g6 , pteal-l5l3r3 , myods-l5mdx5 , pteal-l5k220 , myolu-g1pdp2 , pteal-l5l5n3 , pteal-l5k1s7 , myolu-g1nth4 , pteal-l5l7w7 , pteal-l5l537 , myods-l5lwe4 , pteal-l5klr9 , pteal-l5k670 , pteal-l5jr94 , pteal-l5kvb4 , myolu-g1q4e3 , pteal-l5jrl1

Title : A low molecular mass cutinase of Thielavia terrestris efficiently hydrolyzes poly(esters) - Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
Author(s) : Yang S , Xu H , Yan Q , Liu Y , Zhou P , Jiang Z
Ref : J Ind Microbiol Biotechnol , 40 :217 , 2013
Abstract : A low molecular mass cutinase (designated TtcutA) from Thielavia terrestris was purified and biochemically characterized. The thermophilic fungus T. terrestris CAU709 secreted a highly active cutinase (90.4 U ml(-1)) in fermentation broth containing wheat bran as the carbon source. The cutinase was purified 19-fold with a recovery yield of 4.8 %. The molecular mass of the purified TtcutA was determined as 25.3 and 22.8 kDa using SDS-PAGE and gel filtration, respectively. TtcutA displayed optimal activity at pH 4.0 and 50 degrees C. It was highly stable up to 65 degrees C and in the broad pH range 2.5-10.5. Extreme stability in high concentrations (80 %, v/v) of solvents such as methanol, ethanol, acetone, acetonitrile, isopropanol, and dimethyl sulfoxide was observed for the enzyme. The K (m) values for this enzyme towards p-nitrophenyl (pNP) acetate, pNP butyrate, and pNP caproate were 7.7, 1.0, and 0.52 mM, respectively. TtcutA was able to efficiently degrade various ester polymers, including cutin, polyethylene terephthalate (PET), polycaprolactone (PCL), and poly(butylene succinate) (PBS) at hydrolytic rates of 3 mumol h(-1) mg(-1) protein, 1.1 mg h(-1) mg(-1) protein, 203.6 mg h(-1) mg(-1) protein, and 56.4 mg h(-1) mg(-1) protein, respectively. Because of these unique biochemical properties, TtcutA of T. terrestris may be useful in various industrial applications in the future.
ESTHER : Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
PubMedSearch : Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
PubMedID: 23271406

Title : The Medicago genome provides insight into the evolution of rhizobial symbioses - Young_2011_Nature_480_520
Author(s) : Young ND , Debelle F , Oldroyd GE , Geurts R , Cannon SB , Udvardi MK , Benedito VA , Mayer KF , Gouzy J , Schoof H , Van de Peer Y , Proost S , Cook DR , Meyers BC , Spannagl M , Cheung F , De Mita S , Krishnakumar V , Gundlach H , Zhou S , Mudge J , Bharti AK , Murray JD , Naoumkina MA , Rosen B , Silverstein KA , Tang H , Rombauts S , Zhao PX , Zhou P , Barbe V , Bardou P , Bechner M , Bellec A , Berger A , Berges H , Bidwell S , Bisseling T , Choisne N , Couloux A , Denny R , Deshpande S , Dai X , Doyle JJ , Dudez AM , Farmer AD , Fouteau S , Franken C , Gibelin C , Gish J , Goldstein S , Gonzalez AJ , Green PJ , Hallab A , Hartog M , Hua A , Humphray SJ , Jeong DH , Jing Y , Jocker A , Kenton SM , Kim DJ , Klee K , Lai H , Lang C , Lin S , Macmil SL , Magdelenat G , Matthews L , McCorrison J , Monaghan EL , Mun JH , Najar FZ , Nicholson C , Noirot C , O'Bleness M , Paule CR , Poulain J , Prion F , Qin B , Qu C , Retzel EF , Riddle C , Sallet E , Samain S , Samson N , Sanders I , Saurat O , Scarpelli C , Schiex T , Segurens B , Severin AJ , Sherrier DJ , Shi R , Sims S , Singer SR , Sinharoy S , Sterck L , Viollet A , Wang BB , Wang K , Wang M , Wang X , Warfsmann J , Weissenbach J , White DD , White JD , Wiley GB , Wincker P , Xing Y , Yang L , Yao Z , Ying F , Zhai J , Zhou L , Zuber A , Denarie J , Dixon RA , May GD , Schwartz DC , Rogers J , Quetier F , Town CD , Roe BA
Ref : Nature , 480 :520 , 2011
Abstract : Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
ESTHER : Young_2011_Nature_480_520
PubMedSearch : Young_2011_Nature_480_520
PubMedID: 22089132
Gene_locus related to this paper: medtr-b7fki4 , medtr-b7fmi1 , medtr-g7itl1 , medtr-g7iu67 , medtr-g7izm0 , medtr-g7j641 , medtr-g7jtf8 , medtr-g7jtg2 , medtr-g7jtg4 , medtr-g7kem3 , medtr-g7kml3 , medtr-g7ksx5 , medtr-g7leb3 , medtr-q1s5d8 , medtr-q1s9m3 , medtr-q1t171 , medtr-g7k9e1 , medtr-g7k9e3 , medtr-g7k9e5 , medtr-g7k9e8 , medtr-g7k9e9 , medtr-g7lbp2 , medtr-g7lch3 , medtr-g7ib94 , medtr-g7ljk8 , medtr-g7i6w5 , medtr-g7kvg4 , medtr-g7iam1 , medtr-g7iam3 , medtr-g7l754 , medtr-g7jr41 , medtr-g7l4f5 , medtr-g7l755 , medtr-a0a072vyl4 , medtr-g7jwk8 , medtr-a0a072vhg0 , medtr-a0a072vrv9 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-g7ie19 , medtr-g7kst7 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

Title : Integrating In Silico and In vitro approaches to dissect the stereoselectivity of Bacillus subtilis lipase A toward ketoprofen vinyl ester - Ni_2011_Chem.Biol.Drug.Des_78_301
Author(s) : Ni Z , Zhou P , Jin X , Lin XF
Ref : Chemical Biology Drug Des , 78 :301 , 2011
Abstract : The asymmetric catalysis, as the character of enzyme, attracts increasing attention from the scientific and industrial communities. In this study, the Bacillus subtilis lipase A, as a model enzyme, is studied systematically to dissect its stereoselectivity toward (rac)-ketoprofen vinyl ester using a combination scheme of molecular docking and quantum mechanical/molecular mechanical (QM/MM) analysis. In this procedure, the rational orientation of the two enantiomers of ketoprofen vinyl ester is obtained with the AutoDock performing, and then, the steric contacts between the enzyme and substrate in the docking outputs are examined visually at the atomic level with a small-probe technique. Subsequently, the binding energies of the enzyme-substrate complexes are calculated using an ONIOM (Our own N-layered Integrated Molecular Orbital + Molecular mechanics)-based QM/MM protocol. The results obtained from the theoretical studies show that the B. subtilis lipase A prefer to hydrolyze the (R )-ketoprofen vinyl ester when compared to its (S )-enantiomer, with a relatively high E (stereoselectivity) value of 31.28 charactering its enantioselectivity. Furthermore, to verify the conclusions from the computational analysis, the B. subtilis lipase A gene is cloned to overexpress the recombinant B. subtilis lipase A, and its stereoselectivity was determined. Satisfactorily, the experimental results are in well agreement with the theoretical predictions because the (R )-ketoprofen vinyl ester is found as the preferring enantiomer of the B. subtilis lipase A, with experimentally measured E value of 36.7. We therefore expect that this in silico-in vitro hybrid approach can provide a new and effective avenue to predict the catalytic activity of and to investigate the molecular mechanism of enzyme-mediated asymmetric catalysis and help in understanding the enzymatic process and in rational enzyme design.
ESTHER : Ni_2011_Chem.Biol.Drug.Des_78_301
PubMedSearch : Ni_2011_Chem.Biol.Drug.Des_78_301
PubMedID: 21477088
Gene_locus related to this paper: bacsu-lip