美国大陆外来入侵物种斑马纹贻贝(Dreissena polymorpha)潜在生境预测模型

防止外来生物入侵造成危害的重要手段是阻止可能造成入侵的物种进入适合其生存的地区.论文以1864个美国外来入侵物种斑马纹贻贝定点发生数据和开放式基础地理信息数据库Daymet的34个环境变量为主要信息源,采用逻辑斯蒂回归(LR)、分类与回归树模型(CART)、基于规则的遗传算法(GARP)、最大熵法(Maxent)4种途径,建立美国大陆部分潜在生境预测模型,从接受者运行特征曲线下面积(AUC)、Pearson相关系数、Kappa值3个方面来检验模型预测精度,在此基础上分析斑马纹贻贝的空间分布规律及其环境影响因素.研究结果表明:在3个评价指标中,4个生态位模型预测精度均达到优良水平,其中Maxent在物种现实生境模拟、主要生态环境因子筛选、环境因子对物种生境影响的定量描述方面都表现出了优越的性能;距水源距离、海拔高度、降水频率、太阳辐射是影响物种空间分布的主要环境因子.论文提出的研究方法对中国外来入侵物种生境预测具有较强的借鉴意义,研究结果对中国海洋外来入侵物种沙筛贝的预测与防治,具有一定的指导作用.     

ERK1/2 achieves sustained activation by stimulating MAPK phosphatase-1 degradation via the ubiquitin-proteasome pathway

Sustained extracellular signal-regulated kinase 1/2 (ERK1/2) activation does not always correlate with its upstream Ras-Raf-mitogen-activated protein kinase kinase 1/2 (MKK1/2) signal cascade in cancer cells, and the mechanism remains elusive. Here we report a novel mechanism by which sustained ERK1/2 activation is established. We demonstrate that Pb(II), a carcinogenic metal, persistently induces ERK1/2 activity in CL3 human lung cancer cells and that Ras-Raf-MKK1/2 signaling cannot fully account for such activation. It is intriguing that Pb(II) treatment reduces mitogen-activated protein kinase phosphatase 1 (MKP-1) protein levels in time- and dose-dependent manners, which correlates with sustained ERK1/2 activation, and that Pb(II) also induces mRNA and de novo protein synthesis of MKP-1. In Pb(II)-treated cells, MKP-1 is polyubiquitinated, and proteasome inhibitors markedly alleviate the ubiquitination and degradation of MKP-1. Inhibiting the Pb(II)-induced ERK1/2 activation by PD98059 greatly suppresses MKP-1 ubiquitination and degradation. It is remarkable that constitutive activation of MKK1/2 triggers endogenous MKP-1 ubiquitination and degradation in various mammalian cell lines. Furthermore, expression of functional MKP-1 decreases ERK1/2 activation and the c-Fos protein level and enhances cytotoxicity under Pb(II) exposure. Taken together, these results demonstrate that activated ERK1/2 can trigger MKP-1 degradation via the ubiquitin-proteasome pathway, thus facilitating long-term activation of ERK1/2 against cytotoxicity.     

ESR Study of Interfacial Hydration Layers of Polypeptides in Water-Filled Nanochannels and in Vitrified Bulk Solvents

There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1∼7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ∼0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ∼2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.     

Cooperation of ERK and SCFSkp2 for MKP-1 destruction provides a positive feedback regulation of proliferating signaling

The dual-specificity MAPK phosphatase MKP-1/CL100/DUSP1 is an inducible nuclear protein controlled by p44/42 MAPK (ERK1/2) in a negative feedback mechanism to inhibit kinase activity. Here, we report on the molecular basis for a novel positive feedback mechanism to sustain ERK activation by triggering MKP-1 proteolysis. Active ERK2 docking to the DEF motif (FXFP, residues 339-342) of N-terminally truncated MKP-1 in vitro initiated phosphorylation at the Ser(296)/Ser(323) domain, which was not affected by substituting Ala for Ser at Ser(359)/Ser(364). The DEF and Ser(296)/Ser(323) sites were essential for ubiquitin-mediated MKP-1 proteolysis stimulated by MKK1-ERK signaling in H293 cells, whereas the N-terminal domain and Ser(359)/Ser(364) sites were dispensable. ERK activation by serum increased the endogenous level of ubiquitinated phospho-Ser(296) MKP-1 and the degradation of MKP-1. Intriguingly, active ERK-promoted phospho-Ser(296) MKP-1 bound to SCF(Skp2) ubiquitin ligase in vivo and in vitro. Forced expression of Skp2 enhanced MKP-1 polyubiquitination and proteolysis upon ERK activation, whereas depletion of endogenous Skp2 suppressed such events. The kinetics of ERK signaling stimulated by serum correlated with the endogenous MKP-1 degradation rate in a Skp2-dependent manner. Thus, MKP-1 proteolysis can be achieved via ERK and SCF(Skp2) cooperation, thereby sustaining ERK activation.     

Cloning and overexpression of the ascorbate peroxidase gene from the yam (Dioscorea alata) enhances chilling and flood tolerance in transgenic Arabidopsis

Journal of Plant Research - Minghuai 1 (MH1) is a yam (Dioscorea alata) cultivar with high tolerance to flooding but sensitivity to chilling. MH1 responded differently to chilling and flooding...     

The role of cardiolipin in promoting the membrane pore-forming activity of BAX oligomers

BCL-2-associated X (BAX) protein acts as a gatekeeper in regulating mitochondria-dependent apoptosis. Under cellular stress, BAX becomes activated and transforms into a lethal oligomer that causes mitochondrial outer membrane permeabilization (MOMP). Previous studies have identified several structural features of the membrane-associated BAX oligomer; they include the formation of the BH3-in-groove dimer, the collapse of the helical hairpin α5–α6, and the membrane insertion of α9 helix. However, it remains unclear as to the role of lipid environment in determining the conformation and the pore-forming activity of the BAX oligomers. Here we study molecular details of the membrane-associated BAX in various lipid environments using fluorescence and ESR techniques. We identify the inactive versus active forms of membrane-associated BAX, only the latter of which can induce stable and large membrane pores that are sufficient in size to pass apoptogenic factors. We reveal that the presence of CL is crucial to promoting the association between BAX dimers, hence the active oligomers. Without the presence of CL, BAX dimers assemble into an inactive oligomer that lacks the ability to form stable pores in the membrane. This study suggests an important role of CL in determining the formation of active BAX oligomers.     

Determination of Interspin Distance Distributions by cw-ESR Is a Single Linear Inverse Problem

Cw-ESR distance measurement method is extremely valuable for studying the dynamics-function relationship of biomolecules. However, extracting distance distributions from experiments has been a highly technique-demanding procedure. It has never been conclusively identified, to our knowledge, that the problems involved in the analysis are ill posed and are best solved using Tikhonov regularization. We treat the problems from a novel point of view. First of all, we identify the equations involved and uncover that they are actually two linear first-kind Fredholm integral equations. They can be combined into one single linear inverse problem and solved in a Tikhonov regularization procedure. The improvement with our new treatment is significant. Our approach is a direct and reliable mathematical method capable of providing an unambiguous solution to the ill-posed problem. It need not perform nonlinear least-squares fitting to infer a solution from noise-contaminated data and, accordingly, substantially reduces the computation time and the difficulty of analysis. Numerical tests and experimental data of polyproline II peptides with variant spin-labeled sites are provided to demonstrate our approach. The high resolution of the distance distributions obtainable with our new approach enables a detailed insight into the flexibility of dynamic structure and the identification of conformational species in solution state.     

Stepwise activation of the pro-apoptotic protein Bid at mitochondrial membranes

Caspase-8-cleaved Bid (cBid) associates with mitochondria and promotes the activation of BAX, leading to mitochondria outer membrane permeabilization (MOMP) and apoptosis. However, current structural models of cBid are largely based on studies using membrane vesicles and detergent micelles. Here we employ spin-label ESR and site-directed PEGylation methods to identify conformations of cBid at real mitochondrial membranes, revealing stepwise mechanisms in the activation process. Upon the binding of cBid to mitochondria, its structure is reorganized to expose the BH3 domain while leaving the structural integrity only slightly altered. The mitochondria-bound cBid is in association with Mtch2 and it remains in the primed state until interacting with BAX. The interaction subsequently triggers the fragmentation of cBid, causes large conformational changes, and promotes BAX-mediated MOMP. Our results reveal structural differences of cBid between mitochondria and other lipid-like environments and, moreover, highlight the role of the membrane binding in modifying cBid structure and assisting the inactive-to-active transition in function.Subject terms: Biophysical chemistry, Structural biology