Lin M

References (27)

Title : Mix-and-Read Nanobody-Based Sandwich Homogeneous Split-Luciferase Assay for the Rapid Detection of Human Soluble Epoxide Hydrolase - He_2023_Anal.Chem__
Author(s) : He Q , McCoy MR , Yang H , Lin M , Cui X , Zhao S , Morisseau C , Li D , Hammock BD
Ref : Analytical Chemistry , : , 2023
Abstract : The soluble epoxide hydrolase (sEH) is possibly both a marker for and target of numerous diseases. Herein, we describe a homogeneous mix-and-read assay for the detection of human sEH based on using split-luciferase detection coupled with anti-sEH nanobodies. Selective anti-sEH nanobodies were individually fused with NanoLuc Binary Technology (NanoBiT), which consists of a large and small portion of NanoLuc (LgBiT and SmBiT, respectively). Different orientations of the LgBiT and SmBiT-nanobody fusions were expressed and investigated for their ability to reform the active NanoLuc in the presence of the sEH. After optimization, the linear range of the assay could reach 3 orders of magnitude with a limit of detection (LOD) of 1.4 ng/mL. The assay has a high sensitivity to human sEH and reached a similar detection limit to our previously reported conventional nanobody-based ELISA. The procedure of the assay was faster (30 min total) and easy to operate, providing a more flexible and simple way to monitor human sEH levels in biological samples. In general, the immunoassay proposed here offers a more efficient detection and quantification approach that can be easily adapted to numerous macromolecules.
ESTHER : He_2023_Anal.Chem__
PubMedSearch : He_2023_Anal.Chem__
PubMedID: 36972550

Title : TPPU Downregulates Oxidative Stress Damage and Induces BDNF Expression in PC-12 Cells - Wu_2022_Comput.Math.Methods.Med_2022_7083022
Author(s) : Wu Q , Lin M , Wu P , Zhao C , Yang S , Yu H , Xian W , Song J
Ref : Comput Math Methods Med , 2022 :7083022 , 2022
Abstract : OBJECTIVE: Ischemia-reperfusion is an ongoing clinical challenge that can lead to a series of pathological changes including oxidative stress. The inhibition of soluble epoxide hydrolase inhibitor (sEH) by 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea (TPPU) results in an anti-inflammatory, cardioprotective, and blood vessel growth-promoting effects. Therefore, this study focused on the protective effect of TPPU on a rat pheochromocytoma (PC-12) cell oxidative stress model induced by H(2)O(2). METHODS: CCK-8 and Hoechst 33342 were used to evaluate cell apoptosis and western blot to detect the apoptotic proteins and brain-derived neurotrophic factor (BDNF) expression. RESULT: The incubation with 100 microM, 50 microM, and 25 microM TPPU significantly increased PC-12 cell viability. Epoxyeicosatrienoic acid (EET) pretreatment also protected PC-12 cells from oxidative stress. In addition, TPPU reduced caspase-3 and Bax expression and induced Bcl-2 expression, and EETs exerted the same effect on caspase-3 expression as TPPU. A positive relationship was found between TPPU or EET incubation and BDNF expression. CONCLUSION: These results revealed that TPPU reduced PC-12 cell oxidative stress injury induced by H(2)O(2) and promoted BDNF expression.
ESTHER : Wu_2022_Comput.Math.Methods.Med_2022_7083022
PubMedSearch : Wu_2022_Comput.Math.Methods.Med_2022_7083022
PubMedID: 35872930

Title : Molecular mechanism of LIP05 derived from Monascus purpureus YJX-8 for synthesizing fatty acid ethyl esters under aqueous phase - Zhao_2022_Front.Microbiol_13_1107104
Author(s) : Zhao J , Xu Y , Lu H , Zhao D , Zheng J , Lin M , Liang X , Ding Z , Dong W , Yang M , Li W , Zhang C , Sun B , Li X
Ref : Front Microbiol , 13 :1107104 , 2022
Abstract : Fatty acid ethyl esters are important flavor chemicals in strong-flavor Baijiu. Monascus purpureus YJX-8 is recognized as an important microorganism for ester synthesis in the fermentation process. Enzyme LIP05 from YJX-8 can efficiently catalyze the synthesis of fatty acid ethyl esters under aqueous phase, but the key catalytic sites affecting esterification were unclear. The present work combined homology modeling, molecular dynamics simulation, molecular docking and site-directed mutation to analyze the catalytic mechanism of LIP05. Protein structure modeling indicated LIP05 belonged to alpha/beta fold hydrolase, contained a lid domain and a core catalytic pocket with conserved catalytic triad Ser150-His215-Asp202, and the oxyanion hole composed of Gly73 and Thr74. Ile30 and Leu37 of the lid domain were found to affect substrate specificity. The Pi-bond stacking between Tyr116 and Tyr149 played an important role in stabilizing the catalytic active center of LIP05. Tyr116 and Ile204 determined the substrate spectrum by composing the substrate-entrance channel. Residues Leu83, Ile204, Ile211 and Leu216 were involved in forming the hydrophobic substrate-binding pocket through steric hindrance and hydrophobic interaction. The catalytic mechanism for esterification in aqueous phase of LIP05 was proposed and provided a reference for clarifying the synthesis of fatty acid ethyl esters during the fermentation process of strong-flavor Baijiu.
ESTHER : Zhao_2022_Front.Microbiol_13_1107104
PubMedSearch : Zhao_2022_Front.Microbiol_13_1107104
PubMedID: 36713181

Title : Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics - Lai_2022_Front.Microbiol_13_1113705
Author(s) : Lai J , Huang H , Lin M , Xu Y , Li X , Sun B
Ref : Front Microbiol , 13 :1113705 , 2022
Abstract : Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to alpha/beta-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the alpha/beta hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.
ESTHER : Lai_2022_Front.Microbiol_13_1113705
PubMedSearch : Lai_2022_Front.Microbiol_13_1113705
PubMedID: 36713200

Title : Pharmacokinetic Approach to Combat the Synthetic Cannabinoid PB-22 - Lin_2021_ACS.Chem.Neurosci__
Author(s) : Lin M , Ellis B , Eubanks LM , Janda KD
Ref : ACS Chem Neurosci , : , 2021
Abstract : Synthetic cannabinoids are part of a group of drugs called new psychoactive substances. Most of these cannabinoids are unregulated, and there are no therapeutic treatments for their addictive properties or reversing a potential overdose. Vaccination and catalytic antibodies strategies were investigated to assess their ability to blunt the psychoactive properties of the cannabinoid PB-22. To complement these antibody concentric investigations, we also disclose the discovery of the enzymatic degradation of this cannabinoid. Serum factors including albumin and carboxylesterase were found to catalyze the hydrolysis of PB-22. Affinity, kinetics, animal behavior, and biodistribution studies were utilized to evaluate the efficiency of these pharmacokinetic approaches. Our findings suggest simple antibody binding as the most efficacious means for altering PB-22's effect on the brain. Catalytic approaches only translated to esterases being capable of PB-22's degradation with a catalytic antibody approach providing no proclivity for PB-22's hydrolysis. Pharmacokinetic approaches provide a powerful strategy for treating substance abuse disorders and overdose for drugs where no therapeutic is available.
ESTHER : Lin_2021_ACS.Chem.Neurosci__
PubMedSearch : Lin_2021_ACS.Chem.Neurosci__
PubMedID: 34254505

Title : Chemical Constituents from the Wild Atractylodes macrocephala Koidz and Acetylcholinesterase Inhibitory Activity Evaluation as Well as Molecular Docking Study - Zhu_2021_Molecules_26_
Author(s) : Zhu Q , Lin M , Zhuo W , Li Y
Ref : Molecules , 26 : , 2021
Abstract : Screening the lead compounds which could interact both with PAS and CAS of acetylcholinesterase (AChE) is an important trend in finding innovative drugs for Alzheimer's disease (AD). In this paper, four sesquiterpenes, i.e., atractylenolide III (1), atractylenolide IV (2), 3-acetyl-atractylon (3) and beta-eudesmol (4), were obtained from the wild Atractylode macrocephala grown in Qimen for the first time. Their structures were elucidated mainly by NMR spectroscopy. To screen the potential dual site inhibitors of AChE, the compounds 1, 2, 3, as well as a novel and rare bisesquiterpenoid lactone, biatractylenolide II (5), which was also obtained from the tilted plant in our previous investigation, were evaluated their AChE inhibitory activities by using Ellman's colorimetric method. The results showed that biatractylenolide II displayed moderate inhibitory activity (IC(50) = 19.61 +/- 1.11 microg/mL) on AChE. A further molecular docking study revealed that biatractylenolide II can interact with both the peripheral anionic site (PAS) and the catalytic active site (CAS) of AChE. These data suggest that biatractylenolide II can be considered a new lead compound to research and develop more potential dual site inhibitors of AChE.
ESTHER : Zhu_2021_Molecules_26_
PubMedSearch : Zhu_2021_Molecules_26_
PubMedID: 34885880

Title : Chemical composition and larvicidal activity against Aedes mosquitoes of essential oils from Arisaema fargesii - Huang_2020_Pest.Manag.Sci_76_534
Author(s) : Huang Y , Lin M , Jia M , Hu J , Zhu L
Ref : Pest Manag Sci , 76 :534 , 2020
Abstract : BACKGROUND: Dengue fever is caused by the spread of dengue virus by Aedes mosquito vectors. Currently, the most effective way to control dengue is by preventing mosquitoes from spreading the disease. Arisaema fargesii is a Chinese herbal medicine commonly used to repel mosquitoes. In our laboratory, anti-mosquito chemical components were extracted from A. fargesii, and the effects of these substances on mosquito larvae were examined. RESULTS: In total, 48 compounds corresponding to 98.79% of the total oil were identified and the major compounds identified were linalool (12.38%), carvacrol (8.27%), eugenol (5.21%), and beta-selinene (5.36%). Essential oil had larvicidal activity against Ae. aegypti and Ae. albopictus with LC50 values of 40.49 mg/L, 47.01 mg/L, respectively. The LC50 values of carvacrol, eugenol, linalool and beta-selinene were 32.78, 56.34, 70.56, 136.03 mg/L against Ae. aegypti larvae, and 39.08, 52.07, 82.34, 151.74 mg/L, respectively, against Ae. albopictus larvae. Biochemical assays of Aedes larvae showed that the activities of acetylcholinesterase (AChE), monooxygenases (MO), glutathione-S-transferase (GST), p-Nitrophenyl acetate (p-NPA) esterase, alpha-esterase and beta-esterase were significantly affected by carvacrol. Essential oil induced the detoxification mechanism for the action of GST and MO. CONCLUSION: The result indicates that essential oil of A. fargesii and its isolated constituent have good inhibitory effects on the defense enzymes of Aedes mosquito larvae. A. fargesii essential oil can be used to control Aedes mosquito larvae to prevent the spread of dengue fever. (c) 2019 Society of Chemical Industry.
ESTHER : Huang_2020_Pest.Manag.Sci_76_534
PubMedSearch : Huang_2020_Pest.Manag.Sci_76_534
PubMedID: 31270930

Title : Fascaplysin Derivatives Are Potent Multitarget Agents against Alzheimer's Disease: in Vitro and in Vivo Evidence - Pan_2019_ACS.Chem.Neurosci_10_4741
Author(s) : Pan H , Qiu H , Zhang K , Zhang P , Liang W , Yang M , Mou C , Lin M , He M , Xiao X , Zhang D , Wang H , Liu F , Li Y , Jin H , Yan X , Liang H , Cui W
Ref : ACS Chem Neurosci , 10 :4741 , 2019
Abstract : Alzheimer's disease (AD) is characterized by progressive neurodegeneration and impaired cognitive functions. Fascaplysin is a beta-carboline alkaloid isolated from marine sponge Fascaplysinopsis bergquist in 1988. Previous studies have shown that fascaplysin might act on acetylcholinesterase and beta-amyloid (Abeta) to produce anti-AD properties. In this study, a series of fascaplysin derivatives were synthesized. The cholinesterase inhibition activities, the neuronal protective effects, and the toxicities of these compounds were evaluated in vitro. Compounds 2a and 2b, the two most powerful compounds in vitro, were further selected to evaluate their cognitive-enhancing effects in animals. Both 2a and 2b could ameliorate cognitive dysfunction induced by scopolamine or Abeta oligomers without affecting locomotor functions in mice. We also found that 2a and 2b could prevent cholinergic dysfunctions, decrease pro-inflammatory cytokine expression, and inhibit Abeta-induced tau hyperphosphorylation in vivo. Most importantly, pharmacodynamics studies suggested that 2b could penetrate the blood-brain barrier and be retained in the central nervous system. All these results suggested that fascaplysin derivatives are potent multitarget agents against AD and might be clinical useful for AD treatment.
ESTHER : Pan_2019_ACS.Chem.Neurosci_10_4741
PubMedSearch : Pan_2019_ACS.Chem.Neurosci_10_4741
PubMedID: 31639294

Title : 9-Methylfascaplysin Is a More Potent Abeta Aggregation Inhibitor than the Marine-Derived Alkaloid, Fascaplysin, and Produces Nanomolar Neuroprotective Effects in SH-SY5Y Cells - Sun_2019_Mar.Drugs_17_
Author(s) : Sun Q , Liu F , Sang J , Lin M , Ma J , Xiao X , Yan S , Naman CB , Wang N , He S , Yan X , Cui W , Liang H
Ref : Mar Drugs , 17 : , 2019
Abstract : beta-Amyloid (Abeta) is regarded as an important pathogenic target for Alzheimer's disease (AD), the most prevalent neurodegenerative disease. Abeta can assemble into oligomers and fibrils, and produce neurotoxicity. Therefore, Abeta aggregation inhibitors may have anti-AD therapeutic efficacies. It was found, here, that the marine-derived alkaloid, fascaplysin, inhibits Abeta fibrillization in vitro. Moreover, the new analogue, 9-methylfascaplysin, was designed and synthesized from 5-methyltryptamine. Interestingly, 9-methylfascaplysin is a more potent inhibitor of Abeta fibril formation than fascaplysin. Incubation of 9-methylfascaplysin with Abeta directly reduced Abeta oligomer formation. Molecular dynamics simulations revealed that 9-methylfascaplysin might interact with negatively charged residues of Abeta42 with polar binding energy. Hydrogen bonds and pi(-)pi interactions between the key amino acid residues of Abeta42 and 9-methylfascaplysin were also suggested. Most importantly, compared with the typical Abeta oligomer, Abeta modified by nanomolar 9-methylfascaplysin produced less neuronal toxicity in SH-SY5Y cells. 9-Methylfascaplysin appears to be one of the most potent marine-derived compounds that produces anti-Abeta neuroprotective effects. Given previous reports that fascaplysin inhibits acetylcholinesterase and induces P-glycoprotein, the current study results suggest that fascaplysin derivatives can be developed as novel anti-AD drugs that possibly act via inhibition of Abeta aggregation along with other target mechanisms.
ESTHER : Sun_2019_Mar.Drugs_17_
PubMedSearch : Sun_2019_Mar.Drugs_17_
PubMedID: 30781608

Title : The Associations between Paraoxonase 1 L55M\/Q192R Genetic Polymorphisms and the Susceptibilities of Diabetic Macroangiopathy and Diabetic Microangiopathy: A Meta-Analysis - Wu_2018_Diabetes.Ther_9_1669
Author(s) : Wu C , Wu D , Lin M , Zhong Y
Ref : Diabetes Ther , 9 :1669 , 2018
Abstract : INTRODUCTION: Plenty of studies have focused on the associations of paraoxonase 1 Q192R and L55M genetic polymorphisms with diabetic macroangiopathy and microangiopathy susceptibility, but these associations remain controversial. Therefore, this meta-analysis was conducted to demonstrate these relationships. METHODS: Relevant studies published in English or Chinese were identified in PubMed, Embase, Wanfang Database, and CNKI by applying specific inclusion and exclusion criteria. Statistical analyses were performed using the STATA 12.0 statistical software. RESULTS: 25 Case-control studies were included in the meta-analyses: six on the association between paraoxonase 1 L55M genetic polymorphism and diabetic macroangiopathy risk, nine on the association between L55M and diabetic microangiopathy risk, 12 on the association between Q192R and diabetic macroangiopathy risk, and 12 on the association between Q192R and diabetic microangiopathy risk. Paraoxonase 1 L55M genetic polymorphism was significantly associated with diabetic microangiopathy susceptibility in the dominant model [odds ratio (OR) 0.53, 95% confidence interval (CI) 0.33-0.83, P = 0.006], the homozygous model (OR 0.37, 95% CI 0.16-0.86, P = 0.021), the allelic contrast model (OR 0.62, 95% CI 0.43-0.90, P = 0.011), the recessive model (OR 12.04, 95% CI 8.02-18.06, P = 0.000), and the heterozygous model (OR 0.57, 95% CI 0.38-0.85, P = 0.006), but L55M was not significantly associated with macroangiopathy susceptibility. Paraoxonase 1 Q192R genetic polymorphism was significantly associated with diabetic macroangiopathy susceptibility in the homozygous model (OR 1.88, 95% CI 1.06-3.32, P = 0.030), the allelic contrast model (OR 1.31, 95% CI 1.02-1.69, P = 0.038), and the recessive model (OR 1.55, 95% CI 1.11-2.16, P = 0.010), but not in the dominant and heterozygous models. Meanwhile, there was no significant association between paraoxonase 1 Q192R genetic polymorphism and diabetic microangiopathy susceptibility. CONCLUSION: Paraoxonase 1 L55M and Q192R genetic polymorphisms play important roles in diabetic macroangiopathy and microangiopathy susceptibility. Further well-designed studies based on large samples are needed to confirm these results.
ESTHER : Wu_2018_Diabetes.Ther_9_1669
PubMedSearch : Wu_2018_Diabetes.Ther_9_1669
PubMedID: 29987647

Title : The Apostasia genome and the evolution of orchids - Zhang_2017_Nature_549_379
Author(s) : Zhang GQ , Liu KW , Li Z , Lohaus R , Hsiao YY , Niu SC , Wang JY , Lin YC , Xu Q , Chen LJ , Yoshida K , Fujiwara S , Wang ZW , Zhang YQ , Mitsuda N , Wang M , Liu GH , Pecoraro L , Huang HX , Xiao XJ , Lin M , Wu XY , Wu WL , Chen YY , Chang SB , Sakamoto S , Ohme-Takagi M , Yagi M , Zeng SJ , Shen CY , Yeh CM , Luo YB , Tsai WC , Van de Peer Y , Liu ZJ
Ref : Nature , 549 :379 , 2017
Abstract : Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
ESTHER : Zhang_2017_Nature_549_379
PubMedSearch : Zhang_2017_Nature_549_379
PubMedID: 28902843
Gene_locus related to this paper: 9aspa-a0a2i0b2l6 , 9aspa-a0a2i0w093 , 9aspa-a0a2i0asr1 , 9aspa-a0a2i0vyy1 , 9aspa-a0a2i0a218 , 9aspa-a0a2i0x5j6 , 9aspa-a0a2i0aji0 , 9aspa-a0a2i0a3k8 , 9aspa-a0a2i0win6 , 9aspa-a0a2i0vg82 , 9aspa-a0a2h9zyy3

Title : The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution - Zhang_2016_Sci.Rep_6_19029
Author(s) : Zhang GQ , Xu Q , Bian C , Tsai WC , Yeh CM , Liu KW , Yoshida K , Zhang LS , Chang SB , Chen F , Shi Y , Su YY , Zhang YQ , Chen LJ , Yin Y , Lin M , Huang H , Deng H , Wang ZW , Zhu SL , Zhao X , Deng C , Niu SC , Huang J , Wang M , Liu GH , Yang HJ , Xiao XJ , Hsiao YY , Wu WL , Chen YY , Mitsuda N , Ohme-Takagi M , Luo YB , Van de Peer Y , Liu ZJ
Ref : Sci Rep , 6 :19029 , 2016
Abstract : Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.
ESTHER : Zhang_2016_Sci.Rep_6_19029
PubMedSearch : Zhang_2016_Sci.Rep_6_19029
PubMedID: 26754549
Gene_locus related to this paper: 9aspa-a0a2i0w093 , 9aspa-a0a2i0vyy1 , 9aspa-a0a2i0x5j6 , 9aspa-a0a2i0win6 , 9aspa-a0a2i0vg82

Title : Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora - Zhang_2016_Sci.Rep_6_23122
Author(s) : Zhang L , Zhou Z , Guo Q , Fokkens L , Miskei M , Pocsi I , Zhang W , Chen M , Wang L , Sun Y , Donzelli BG , Gibson DM , Nelson DR , Luo JG , Rep M , Liu H , Yang S , Wang J , Krasnoff SB , Xu Y , Molnar I , Lin M
Ref : Sci Rep , 6 :23122 , 2016
Abstract : Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle.
ESTHER : Zhang_2016_Sci.Rep_6_23122
PubMedSearch : Zhang_2016_Sci.Rep_6_23122
PubMedID: 26975455
Gene_locus related to this paper: 9hypo-a0a151ga75 , 9hypo-a0a151gbh5 , 9hypo-a0a151gd50 , 9hypo-a0a151ggb9 , 9hypo-a0a151gjd5 , 9hypo-a0a151gtv2 , 9hypo-a0a151gxh2 , 9hypo-a0a151gaw8 , 9hypo-a0a151gia2

Title : Simultaneous enantioselective determination of isocarbophos and its main metabolite isocarbophos oxon in rice, soil, and water by chiral liquid chromatography and tandem mass spectrometry - Yao_2015_J.Sep.Sci_38_1663
Author(s) : Yao Z , Lin M , Xu M , Wang T , Ping X , Wu S , Wang Q , Zhang H
Ref : J Sep Sci , 38 :1663 , 2015
Abstract : An efficient enantioselective method for the simultaneous determination of isocarbophos and its main metabolite isocarbophos oxon in rice, soil, and water was developed using liquid chromatography with tandem mass spectrometry. The enantioseparation was performed on a Chiralpak AD-3R column at 30 degrees C using gradient elution. Target compounds were extracted from soil and rice using acetonitrile with omission of a clean-up procedure, while a C18 solid-phase extraction column was used for water samples. Quantification was achieved using matrix-matched calibration. The overall mean recoveries for isocarbophos and isocarbophos oxon enantiomers from the five matrices were 89.7-103 and 90.1-98.7%, with relative standard deviations of 2.1-5.4 and 2.5-4.7%, respectively. Moreover, the absolute configurations of isocarbophos oxon enantiomers were determined by liquid chromatography with tandem mass spectrometry through incubation of each isocarbophos enantiomer in soil, the first eluting enantiomer being confirmed as (R)-(-)-isocarbophos oxon. The proposed method was applied to real soil samples and satisfactory results were obtained.
ESTHER : Yao_2015_J.Sep.Sci_38_1663
PubMedSearch : Yao_2015_J.Sep.Sci_38_1663
PubMedID: 25755196

Title : Systematic Review and Meta-Analysis of the Relationship between EPHX1 Polymorphisms and the Risk of Head and Neck Cancer - Chen_2015_PLoS.One_10_e0123347
Author(s) : Chen H , Ge L , Sui Q , Lin M
Ref : PLoS ONE , 10 :e0123347 , 2015
Abstract : AIM: To evaluate the association between the EPHX1 Tyr113His and His139Arg polymorphisms in the EPHX1 gene and the risk of head and neck cancer. MATERIALS AND
METHODS: Studies on the association of EPHX1 Tyr113His and His139Arg polymorphisms with HNC performed up until June 1st, 2014, were identified using a predefined search strategy. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the strength of these associations.
RESULTS: In this meta-analysis, 10 case-control studies, which included 9 studies of Tyr113His (1890 cases and 1894 controls) and 10 studies of His139Arg polymorphisms (1982 cases and 2024 controls), were considered eligible for inclusion. Overall, the pooled results indicated that the EPHX1 Tyr113His polymorphism was significantly associated with increased HNC risk (Tyr/His vs. Tyr/Tyr, OR = 1.26, 95%1.02-1.57;His/His+ Tyr/His vs. Tyr/Tyr, OR = 1.29, 95% I = 1.03-1.61). However, no significant association was found between the His139Arg polymorphism and HNC risk. In the subgroup analysis, a statistically significant association between the EPHX1 Tyr113His polymorphism and HNC was observed in population-based case-control studies (PCC), which involved less than 500 participants and genotype frequencies in HWE. This association showed minimal heterogeneity after excluding studies that were determined to contribute to heterogeneity. After categorizing the studies by publication time, a sensitivity analysis and cumulative meta-analysis of the two associations were conducted, and the results of the two analyses were consistent. CONCLUSION: Our meta-analysis suggests that EPHX1 Tyr113His polymorphism may be a risk factor for HNC, while the EPHX1 His139Arg polymorphism has no association with HNC risk.
ESTHER : Chen_2015_PLoS.One_10_e0123347
PubMedSearch : Chen_2015_PLoS.One_10_e0123347
PubMedID: 25923690

Title : Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China - Teng_2015_PLoS.One_10_e0122254
Author(s) : Teng C , Zhou Z , Molnar I , Li X , Tang R , Chen M , Wang L , Su S , Zhang W , Lin M
Ref : PLoS ONE , 10 :e0122254 , 2015
Abstract : A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5-42 degreesC with an optimum of 30 degreesC, and at pH 7.0-11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1omega7c/C16:1omega6c or C16:1omega6c/C16:1omega7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
ESTHER : Teng_2015_PLoS.One_10_e0122254
PubMedSearch : Teng_2015_PLoS.One_10_e0122254
PubMedID: 25830331
Gene_locus related to this paper: 9sphi-a0a0b8t8i3 , 9sphi-a0a0b8t3y0

Title : Characterization of the biosynthetic genes for 10,11-dehydrocurvularin, a heat shock response-modulating anticancer fungal polyketide from Aspergillus terreus - Xu_2013_Appl.Environ.Microbiol_79_2038
Author(s) : Xu Y , Espinosa-Artiles P , Schubert V , Xu YM , Zhang W , Lin M , Gunatilaka AA , Sussmuth R , Molnar I
Ref : Applied Environmental Microbiology , 79 :2038 , 2013
Abstract : 10,11-Dehydrocurvularin is a prevalent fungal phytotoxin with heat shock response and immune-modulatory activities. It features a dihydroxyphenylacetic acid lactone polyketide framework with structural similarities to resorcylic acid lactones like radicicol or zearalenone. A genomic locus was identified from the dehydrocurvularin producer strain Aspergillus terreus AH-02-30-F7 to reveal genes encoding a pair of iterative polyketide synthases (A. terreus CURS1 [AtCURS1] and AtCURS2) that are predicted to collaborate in the biosynthesis of 10,11-dehydrocurvularin. Additional genes in this locus encode putative proteins that may be involved in the export of the compound from the cell and in the transcriptional regulation of the cluster. 10,11-Dehydrocurvularin biosynthesis was reconstituted in Saccharomyces cerevisiae by heterologous expression of the polyketide synthases. Bioinformatic analysis of the highly reducing polyketide synthase AtCURS1 and the nonreducing polyketide synthase AtCURS2 highlights crucial biosynthetic programming differences compared to similar synthases involved in resorcylic acid lactone biosynthesis. These differences lead to the synthesis of a predicted tetraketide starter unit that forms part of the 12-membered lactone ring of dehydrocurvularin, as opposed to the penta- or hexaketide starters in the 14-membered rings of resorcylic acid lactones. Tetraketide N-acetylcysteamine thioester analogues of the starter unit were shown to support the biosynthesis of dehydrocurvularin and its analogues, with yeast expressing AtCURS2 alone. Differential programming of the product template domain of the nonreducing polyketide synthase AtCURS2 results in an aldol condensation with a different regiospecificity than that of resorcylic acid lactones, yielding the dihydroxyphenylacetic acid scaffold characterized by an S-type cyclization pattern atypical for fungal polyketides.
ESTHER : Xu_2013_Appl.Environ.Microbiol_79_2038
PubMedSearch : Xu_2013_Appl.Environ.Microbiol_79_2038
PubMedID: 23335766
Gene_locus related to this paper: aspte-curs2

Title : Rational reprogramming of fungal polyketide first-ring cyclization - Xu_2013_Proc.Natl.Acad.Sci.U.S.A_110_5398
Author(s) : Xu Y , Zhou T , Zhou Z , Su S , Roberts SA , Montfort WR , Zeng J , Chen M , Zhang W , Lin M , Zhan J , Molnar I
Ref : Proc Natl Acad Sci U S A , 110 :5398 , 2013
Abstract : Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-beta-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the dihydroxyphenylacetic acid lactone dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal vs. bacterial folding mode difference is portable on creating hybrid enzymes, and we structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first-ring cyclizations will facilitate efforts to the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides.
ESTHER : Xu_2013_Proc.Natl.Acad.Sci.U.S.A_110_5398
PubMedSearch : Xu_2013_Proc.Natl.Acad.Sci.U.S.A_110_5398
PubMedID: 23509261
Gene_locus related to this paper: aspte-curs2 , floch-rads2

Title : A New Anti-acetylcholinesterase alpha-Pyrone Meroterpene, Arigsugacin I, from Mangrove Endophytic Fungus Penicillium sp. sk5GW1L of Kandelia candel - Huang_2013_Planta.Med_79_1572
Author(s) : Huang X , Sun X , Ding B , Lin M , Liu L , Huang H , She Z
Ref : Planta Med , 79 :1572 , 2013
Abstract : Arigsugacin I (1), a new alpha-pyrone meroterpene, along with two known compounds, arigsugacins F (2) and territrem B (3), were isolated from the mangrove endophytic fungus Penicillium sp. sk5GW1L from Kandelia candel. Their structures were identified through mass spectrometry and NMR experiments, and the absolute configuration of compound 1 was further confirmed by low-temperature (100 K) single crystal X-ray diffraction with Cu Kalpha radiation. The absolute configuration of compound 2 was first reported by using X-ray copper radiation. Compounds 1-3 showed inhibitory activities against acetylcholinesterase with IC50 values of 0.64 +/- 0.08 microM, 0.37 +/- 0.11 microM, and 7.03 +/- 0.20 nM, respectively.
ESTHER : Huang_2013_Planta.Med_79_1572
PubMedSearch : Huang_2013_Planta.Med_79_1572
PubMedID: 24081685

Title : Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations - Yuan_2012_PLoS.One_7_e34458
Author(s) : Yuan M , Chen M , Zhang W , Lu W , Wang J , Yang M , Zhao P , Tang R , Li X , Hao Y , Zhou Z , Zhan Y , Yu H , Teng C , Yan Y , Ping S , Wang Y , Lin M
Ref : PLoS ONE , 7 :e34458 , 2012
Abstract : The desert is an excellent model for studying evolution under extreme environments. We present here the complete genome and ultraviolet (UV) radiation-induced transcriptome of Deinococcus gobiensis I-0, which was isolated from the cold Gobi desert and shows higher tolerance to gamma radiation and UV light than all other known microorganisms. Nearly half of the genes in the genome encode proteins of unknown function, suggesting that the extreme resistance phenotype may be attributed to unknown genes and pathways. D. gobiensis also contains a surprisingly large number of horizontally acquired genes and predicted mobile elements of different classes, which is indicative of adaptation to extreme environments through genomic plasticity. High-resolution RNA-Seq transcriptome analyses indicated that 30 regulatory proteins, including several well-known regulators and uncharacterized protein kinases, and 13 noncoding RNAs were induced immediately after UV irradiation. Particularly interesting is the UV irradiation induction of the phrB and recB genes involved in photoreactivation and recombinational repair, respectively. These proteins likely include key players in the immediate global transcriptional response to UV irradiation. Our results help to explain the exceptional ability of D. gobiensis to withstand environmental extremes of the Gobi desert, and highlight the metabolic features of this organism that have biotechnological potential.
ESTHER : Yuan_2012_PLoS.One_7_e34458
PubMedSearch : Yuan_2012_PLoS.One_7_e34458
PubMedID: 22470573
Gene_locus related to this paper: deigi-h8gtt4 , deigi-h8h0j9

Title : Genome sequence of Acinetobacter calcoaceticus PHEA-2, isolated from industry wastewater - Zhan_2011_J.Bacteriol_193_2672
Author(s) : Zhan Y , Yan Y , Zhang W , Yu H , Chen M , Lu W , Ping S , Peng Z , Yuan M , Zhou Z , Elmerich C , Lin M
Ref : Journal of Bacteriology , 193 :2672 , 2011
Abstract : Genome analysis of Acinetobacter calcoaceticus PHEA-2 was undertaken because of the importance of this bacterium for bioremediation of phenol-polluted water and because of the close phylogenetic relationship of this species with the human pathogen Acinetobacter baumannii. To our knowledge, this is the first strain of A. calcoaceticus whose genome has been sequenced.
ESTHER : Zhan_2011_J.Bacteriol_193_2672
PubMedSearch : Zhan_2011_J.Bacteriol_193_2672
PubMedID: 21441526
Gene_locus related to this paper: aciad-q6fc40 , aciba-d0c992 , aciba-q76hj1 , acibt-a3m5r6 , acibt-a3m5t3 , acibt-a3m5x2 , acica-d0ryi9 , acica-d0ryx6 , acicp-f0kgu1 , acicp-f0kh68 , acicp-f0khy0 , acicp-f0kj61 , aciba-w3svn7 , aciba-a0a009wzt4

Title : Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20 - Hauser_2011_J.Bacteriol_193_4268
Author(s) : Hauser LJ , Land ML , Brown SD , Larimer F , Keller KL , Rapp-Giles BJ , Price MN , Lin M , Bruce DC , Detter JC , Tapia R , Han CS , Goodwin LA , Cheng JF , Pitluck S , Copeland A , Lucas S , Nolan M , Lapidus AL , Palumbo AV , Wall JD
Ref : Journal of Bacteriology , 193 :4268 , 2011
Abstract : Desulfovibrio alaskensis G20 (formerly Desulfovibrio desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.
ESTHER : Hauser_2011_J.Bacteriol_193_4268
PubMedSearch : Hauser_2011_J.Bacteriol_193_4268
PubMedID: 21685289
Gene_locus related to this paper: desag-q310n6

Title : Complete genome sequence of the nitrogen-fixing and rhizosphere-associated bacterium Pseudomonas stutzeri strain DSM4166 - Yu_2011_J.Bacteriol_193_3422
Author(s) : Yu H , Yuan M , Lu W , Yang J , Dai S , Li Q , Yang Z , Dong J , Sun L , Deng Z , Zhang W , Chen M , Ping S , Han Y , Zhan Y , Yan Y , Jin Q , Lin M
Ref : Journal of Bacteriology , 193 :3422 , 2011
Abstract : We present here the analysis of the whole-genome sequence of Pseudomonas stutzeri strain DSM4166, a diazotrophic isolate from the rhizosphere of a Sorghum nutans cultivar. To our knowledge, this is the second genome to be sequenced for P. stutzeri. The availability and analysis of the genome provide insight into the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in interactions with host plants.
ESTHER : Yu_2011_J.Bacteriol_193_3422
PubMedSearch : Yu_2011_J.Bacteriol_193_3422
PubMedID: 21515765
Gene_locus related to this paper: pseu5-a4vfn0 , pseu5-a4vj02 , pseu5-a4vrl9 , pseut-f8h720 , pseu5-a4vkl7 , pseu5-a4vgd4 , pseu5-a4vr33

Title : Post-synthetic modification of plant cell walls by expression of microbial hydrolases in the apoplast - Pogorelko_2011_Plant.Mol.Biol_77_433
Author(s) : Pogorelko G , Fursova O , Lin M , Pyle E , Jass J , Zabotina OA
Ref : Plant Mol Biol , 77 :433 , 2011
Abstract : The systematic creation of defined cell wall modifications in the model plant Arabidopsis thaliana by expression of microbial hydrolases with known specific activities is a promising approach to examine the impacts of cell wall composition and structure on both plant fitness and cell wall recalcitrance. Moreover, this approach allows the direct evaluation in living plants of hydrolase specificity, which can differ from in vitro specificity. To express genes encoding microbial hydrolases in A. thaliana, and target the hydrolases to the apoplast compartment, we constructed an expression cassette composed of the Cauliflower Mosaic Virus 35S RNA promoter, the A. thaliana beta-expansin signal peptide, and the fluorescent marker protein YFP. Using this construct we successfully introduced into Colombia-0 plants three Aspergillus nidulans hydrolases, beta-xylosidase/alpha-arabinosidase, feruloyl esterase, acetylxylan esterase, and a Xanthomonas oryzae putative a-L: -arabinofuranosidase. Fusion with YFP permitted quick and easy screening of transformants, detection of apoplastic localization, and protein size confirmation. Compared to wild-type Col-0, all transgenic lines showed a significant increase in the corresponding hydrolytic activity in the apoplast and changes in cell wall composition. Examination of hydrolytic activity in the transgenic plants also showed, for the first time, that the X. oryzae gene indeed encoded an enzyme with alpha-L: -arabinofuranosidase activity. None of the transgenic plants showed a visible phenotype; however, the induced compositional changes increased the degradability of biomass from plants expressing feruloyl esterase and beta-xylosidase/alpha-arabinosidase. Our results demonstrate the viability of creating a set of transgenic A. thaliana plants with modified cell walls to use as a toolset for investigation of how cell wall composition contributes to recalcitrance and affects plant fitness.
ESTHER : Pogorelko_2011_Plant.Mol.Biol_77_433
PubMedSearch : Pogorelko_2011_Plant.Mol.Biol_77_433
PubMedID: 21910026

Title : Sequence analysis of pKF3-70 in Klebsiella pneumoniae: probable origin from R100-like plasmid of Escherichia coli - Yi_2010_PLoS.One_5_e8601
Author(s) : Yi H , Xi Y , Liu J , Wang J , Wu J , Xu T , Chen W , Chen B , Lin M , Wang H , Zhou M , Li J , Xu Z , Jin S , Bao Q
Ref : PLoS ONE , 5 :e8601 , 2010
Abstract : BACKGROUND: Klebsiella pneumoniae is a clinically significant species of bacterium which causes a variety of diseases. Clinical treatment of this bacterial infection is greatly hindered by the emergence of multidrug-resistant strains. The resistance is largely due to the acquisition of plasmids carrying drug-resistant as well as pathogenic genes, and its conjugal transfer facilitates the spread of resistant phenotypes. METHODOLOGY/PRINCIPAL FINDINGS: The 70,057 bp plasmid pKF3-70, commonly found in Klebsiella pneumoniae, is composed of five main functional modules, including regions involved in replication, partition, conjugation, transfer leading, and variable regions. This plasmid is more similar to several Escherichia coli plasmids than any previously reported K. pneumoniae plasmids and pKF3-70 like plasmids share a common and conserved backbone sequence. The replication system of the pKF3-70 is 100% identical to that of RepFII plasmid R100 from E. coli. A beta-lactamase gene ctx-m-14 with its surrounding insertion elements (ISEcp1, truncated IS903 and a 20 bp inverted repeat sequence) may compose an active transposon which is directly bordered by two putative target repeats "ATTAC." CONCLUSIONS/SIGNIFICANCE: The K. pneumoniae plasmid pKF3-70 carries an extended-spectrum beta-lactamase gene, ctx-m-14. The conjugative characteristic makes it a widespread plasmid among genetically relevant genera which poses significant threat to public health.
ESTHER : Yi_2010_PLoS.One_5_e8601
PubMedSearch : Yi_2010_PLoS.One_5_e8601
PubMedID: 20066042

Title : Analysis of complete genome sequence of Neorickettsia risticii: causative agent of Potomac horse fever - Lin_2009_Nucleic.Acids.Res_37_6076
Author(s) : Lin M , Zhang C , Gibson K , Rikihisa Y
Ref : Nucleic Acids Research , 37 :6076 , 2009
Abstract : Neorickettsia risticii is an obligate intracellular bacterium of the trematodes and mammals. Horses develop Potomac horse fever (PHF) when they ingest aquatic insects containing encysted N. risticii-infected trematodes. The complete genome sequence of N. risticii Illinois consists of a single circular chromosome of 879 977 bp and encodes 38 RNA species and 898 proteins. Although N. risticii has limited ability to synthesize amino acids and lacks many metabolic pathways, it is capable of making major vitamins, cofactors and nucleotides. Comparison with its closely related human pathogen N. sennetsu showed that 758 (88.2%) of protein-coding genes are conserved between N. risticii and N. sennetsu. Four-way comparison of genes among N. risticii and other Anaplasmataceae showed that most genes are either shared among Anaplasmataceae (525 orthologs that generally associated with housekeeping functions), or specific to each genome (>200 genes that are mostly hypothetical proteins). Genes potentially involved in the pathogenesis of N. risticii were identified, including those encoding putative outer membrane proteins, two-component systems and a type IV secretion system (T4SS). The bipolar localization of T4SS pilus protein VirB2 on the bacterial surface was demonstrated for the first time in obligate intracellular bacteria. These data provide insights toward genomic potential of N. risticii and intracellular parasitism, and facilitate our understanding of PHF pathogenesis.
ESTHER : Lin_2009_Nucleic.Acids.Res_37_6076
PubMedSearch : Lin_2009_Nucleic.Acids.Res_37_6076
PubMedID: 19661282
Gene_locus related to this paper: neori-c6v4w3 , neori-c6v608

Title : Comparative genomics of emerging human ehrlichiosis agents - Dunning Hotopp_2006_PLoS.Genet_2_e21
Author(s) : Dunning Hotopp JC , Lin M , Madupu R , Crabtree J , Angiuoli SV , Eisen JA , Seshadri R , Ren Q , Wu M , Utterback TR , Smith S , Lewis M , Khouri H , Zhang C , Niu H , Lin Q , Ohashi N , Zhi N , Nelson W , Brinkac LM , Dodson RJ , Rosovitz MJ , Sundaram J , Daugherty SC , Davidsen T , Durkin AS , Gwinn M , Haft DH , Selengut JD , Sullivan SA , Zafar N , Zhou L , Benahmed F , Forberger H , Halpin R , Mulligan S , Robinson J , White O , Rikihisa Y , Tettelin H
Ref : PLoS Genet , 2 :e21 , 2006
Abstract : Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
ESTHER : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedSearch : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedID: 16482227
Gene_locus related to this paper: anapz-q2gj80 , anapz-q2gle9 , anapz-q2glf0 , anapz-q2gln7 , ehrch-q40iu0 , ehrch-q40jj7 , ehrcr-q2gfq9 , neosm-q2gcq8 , neosm-q2gdf2 , neosm-q2gcn8 , anapz-q2gk48 , ehrcr-q2ggj6