Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins (PMPs)

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli.The cells of living organisms contain different types of membranes performing uniquely specific functions that are largely dictated by their protein compositions. Membrane proteome typically contains integral membrane proteins (IMPs)¹ with one or more transmembrane domains (TM) and peripheral membrane proteins (PMPs) without TM. PMPs usually interact with IMPs and function together as protein complexes, as typically demonstrated by the peripheral subunits of the membrane protein complexes such as photosystem (PS) I, PSII, the F₁F₀-ATP synthase, and ABC type transporters (1–6). Identification of the PMPs is important for the understanding of the underlying mechanism of various membrane related functions, and could help to discover novel functionally important membrane protein complexes.Large-scale identification of PMPs were typically performed by identification of the total proteins from the isolated whole membranes from which PMPs were predicted by the absence of TM using topology prediction software such as TMHMM (7), or by identification of the proteins extracted from the intact whole membranes with chaotropic reagents such as high concentration salts, urea, or high pH solution (8–13). These methods can identify some non-TM containing proteins uniquely from the membrane fraction. However, in most cases the majority of the non-TM containing proteins identified with such methods can also be identified from the soluble fraction that is expected to consist of mainly cytoplasmic proteins. Therefore, it is necessary to evaluate whether the non-TM containing proteins identified from the membranes are true PMPs or just some carry-over contaminant from the soluble fraction during sample fractionation. Unfortunately, the high throughput method to perform such an evaluation is still lacking, and such a method is a pressing need considering the ever-increasing number of identified proteins from a single proteomic study.The unicellular photosynthetic cyanobacterium Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis) is an ideal organism for studies in membrane proteomics. Synechocystis is the first cyanobacterium with a completely sequenced genome and contains large numbers of membrane structures (12–14). The organism can naturally take up foreign DNA from environment and integrate it into its genome through homologous recombination, making it simple to perform target mutagenesis for the validation of functional significance of proteins screened from high throughput approaches. The autotrophic growth ability allows Synechocystis to emerge as a potential cost-effective cell factory for producing clean and renewable biofuels to deal with the world-wide crisis of energy shortage and environmental pollution (15–18). Functional proteomics have great potential in the identification of novel target proteins and for discovering and optimizing novel protein networks for the generation of biofuel-producing strains with higher efficiency and less cost.We separated Synechocystis whole cell lysates into membrane and soluble fractions, and identified the proteins in each fraction with unprecedented coverage using high-resolution MS. We present a novel method and its rationale for evaluating the tightness of membrane association for all non-TM containing proteins identified in both fractions. This built a foundation for the large-scale identification of bona fide peripheral membrane proteins, particularly for the hypothetical and unknown proteins that are not known to be physically or functionally associated with the membranes.     

长期淹水对河竹鞭根养分化学计量特征的影响

以长期淹水环境下能生长更新的河竹为材料,调查测定了人工喷灌供水(CK)、淹水6个月(TR)的河竹一年生竹鞭的根生物量和主要养分元素含量,分析长期淹水对河竹鞭根养分化学计量特征的影响,为河竹在水湿地和消落带植被恢复中的应用提供理论依据。结果显示:(1)与CK相比,TR处理下的河竹土中根的N、P、Mg和Ca含量显著降低,Fe含量显著升高,且N、K和Ca含量显著低于TR处理下水中根的含量,而Fe含量显著高于水中根。(2)TR处理的河竹土中根的C/N、C/P、C/K和P/K较CK显著升高,且C/K、N/K和P/K显著高于TR处理的水中根。(3)TR处理的河竹水中根的C-N、C-P、N-P均呈极显著正相关关系,土中根的C-P、C-K、P-K均呈极显著正相关关系;CK河竹土中根的C-P、C-K呈极显著正相关关系,且N-P显著相关;从相关系数看,TR处理下土中根的C-N、N-P和N-K相关性减弱,C-P、C-K和P-K相关性增强,而C-N、C-P、N-P和N-K相关性较水中根减弱,C-K和P-K相关性较水中根增强。(4)TR处理下鞭根生物量和C、N、P、K、Mg、Ca积累量较CK分别显著降低19.46%、42.04%、36.55%、41.39%、60.06%和38.46%,而Fe积累量显著升高,为CK的5.5倍;TR处理下土中根养分积累量显著高于水中根。研究表明,长期淹水虽阻碍了河竹鞭根的养分平衡吸收,但能够提高养分利用效率,并且土中根和水中根具有克隆分工特征,水中根主要起到氧气吸收应对缺氧环境胁迫的功能,是河竹适应长期淹水环境的重要生态对策。     

Vernalophrys algivore gen. nov., sp. nov. (Rhizaria: Cercozoa: Vampyrellida), a New Algal Predator Isolated from Outdoor Mass Culture of Scenedesmus dimorphus

Microbial contamination is the main cause of loss of biomass yield in microalgal cultures, especially under outdoor environmental conditions. Little is known about the identities of microbial contaminants in outdoor mass algal cultures. In this study, a new genus and species of vampyrellid amoeba, Vernalophrys algivore, is described from cultures of Scenedesmus dimorphus in open raceway ponds and outdoor flat-panel photobioreactors. This vampyrellid amoeba was a significant grazer of Scenedesmus and was frequently associated with a very rapid decline in algal numbers. We report on the morphology, subcellular structure, feeding behavior, molecular phylogeny, and life cycle. The new amoeba resembles Leptophrys in the shape of trophozoites and pseudopodia and in the mechanism of feeding (mainly by engulfment). It possesses two distinctive regions in helix E10_1 (nucleotides 117 to 119, CAA) and E23_1 (nucleotides 522 and 523, AG) of the 18S rRNA gene. It did not form a monophyletic group with Leptophrys in molecular phylogenetic trees. We establish a new genus, Vernalophrys, with the type species Vernalophrys algivore. The occurrence, impact of the amoeba on mass culture of S. dimorphus, and means to reduce vampyrellid amoeba contamination in Scenedesmus cultures are addressed. The information obtained from this study will be useful for developing an early warning system and control measures for preventing or treating this contaminant in microalgal mass cultures.     

Hypoglycemic activities of A- and B-type procyanidin oligomer-rich extracts from different Cinnamon barks

Procyanidin oligomers in Cinnamon are thought to be responsible for the biological activity in the treatment of diabetes mellitus (DM). To clarify types of procyanidin oligomers in different Cinnamon species and investigate their different effects, the present study investigated procyanidin oligomers in polyphenolic oligomer-rich extracts of three Cinnamon samples by LC-MS methods, and their hypoglycemic activities were detected in vivo and in vitro. The results showed that two of the three samples from Cinnamomum cassia were rich in B-type procyanidin oligomers, and the other sample was rich in A-type procyanidin oligomers. The Cinnamon extracts were administered at doses of 200 and 300 mg/kg body wt. in high-fat diet-fed and low-dose streptozotocin (STZ)-induced diabetic mice for 14 days. The results showed that blood glucose concentrations were significantly decreased in all Cinnamon extract groups compared with the control group (p < 0.05). Administration of the Cinnamon extracts significantly increased the consumption of extracellular glucose in insulin-resistant HepG2 cells and normal HepG2 cells compared with the control group. These results suggest that both A- and B-type procyanidin oligomers in different Cinnamon species have hypoglycemic activities and may improve insulin sensitivity in type 2 DM.     

火烧对黔中喀斯特山地马尾松林土壤理化性质的影响

在黔中喀斯特山地马尾松人工次生林内取样分析火烧和对照样地间土壤理化指标的变化,研究了火烧对林地土壤理化性质的影响。结果表明马尾松火烧林地表层土壤毛管孔隙度和总孔隙度升高、最大持水量和最小持水量增加,土壤密度和非毛管孔隙度降低、土壤质量含水量和体积含水量减少;土壤有机质、全N量、全P量、全K量,水解N量、有效P量、速效K量、交换性盐基量和pH值增大,阳离子交换量降低。林火对马尾松林地土壤主要理化指标影响的趋势为或表层土壤影响率大于剖面影响率、或表层土壤影响率小于剖面影响率,不同指标在土壤剖面的变化趋势或增加、或降低,对数或幂函数拟合曲线均达相关显著性水平。火烧和对照样地间的表层土壤理化指标变化主要反映了林火影响,近岩层土壤理化指标变化主要是成土母质在空间上的分异,也受生物的影响。乔木层植株死亡率同表层土壤最大持水量、最小持水量、有机质量和全N量的正相关性显著,同土壤密度的负相关性显著;灌木层植株死亡率同表层土壤密度正相关性显著,同毛管孔隙度、总孔隙度、质量含水量、最大持水量、最小持水量、有机质量、全N量、全P量和速效K量的负相关性达显著或极显著水平;灌木层生物损失量同表层土壤密度和有机质量正相关显著,同速效K量的负相关性显著,枯物层生物损失量同pH值的正相关性显著。火烧马尾松林分平均胸径同表层土壤密度正相关性显著,同毛管孔隙度、总孔隙度、质量含水量、最大持水量、最小持水量和有机质量的负相关性显著。     

LEF-1表达与肿瘤进程研究进展

淋巴增强因子-1(lymphoid enhancer factor-1,LEF-1)属于高迁移组分(HMG)家族,它与TCRα的增强子相互作用形成特定的构象,从而与其它因子结合共同调节基因的表达。LEF-1作为核内的转录因子介导Wnt信号通路,对细胞的增殖、分化和凋亡起重要作用。近年来,研究显示许多肿瘤的发生与Wnt信号通路的异常有关,而LEF-1在肿瘤的发生发展侵润过程中起重要作用。同时,LEF-1是一个多启动子基因,编码产生致瘤的全长形式的LEF-1和对Wnt信号通路起负向调控作用的截短形式的LEF-1。研究结果表明,肿瘤的发生发展与LEF/TCF各亚型的比例有关。因此,研究LEF-1的结构、功能以及其在细胞增殖、细胞存活、肿瘤的发生发展过程中的作用意义重大。该文就LEF-1的表达以及与肿瘤的关系作一综述。     

Factors Affecting the Mixotrophic Flagellate Poterioochromonas malhamensis Grazing on Chlorella Cells

Grazing behaviour between protozoa and phytoplankton exists widely in planktonic ecosystems. Poterioochromonas malhamensis is a well‐known and widespread mixotrophic flagellate, which is recognized to play an important role within marine and freshwater planktonic ecosystems and regarded as the greatest contamination threat for mass algal cultures of Chlorella. In this study, a comprehensive range of factors, including morphological characters, biochemical compositions, and specific growth rate of ten species or strains of Chlorella, were evaluated for their effect on the feeding ability of P. malhamensis, which was assessed by two parameters: the clearance rate of P. malhamensis on Chlorella spp. and the specific growth rate of P. malhamensis. The results showed that the clearance rate of P. malhamensis was negatively correlated with cell wall thickness and specific growth rate of Chlorella spp., while the specific growth rate of P. malhamensis was positively correlated with carbohydrate percentage and C/N ratio and negatively correlated with protein, lipid percentage, and nitrogen mass. In conclusion, the factors influencing feeding selectivity include not only the morphological character and chemical composition of Chlorella, but also its population dynamics. Our study provides useful insights into the key factors that affect the feeding selectivity of P. malhamensis and provides basic and constructive data to help in screening for grazing‐resistant microalgae.     

茂兰喀斯特区68种典型植物叶片化学计量特征

研究茂兰喀斯特区不同功能(类)群植物叶片的养分含量及化学计量特征,揭示其在时间和空间尺度上的变化规律,阐明碳(C)、氮(N)、磷(P)、钾(K)等养分含量与C∶N∶P间的相互关系,探讨N∶P对该区域植物生长的指示作用,以期能够更深入的了解其养分利用状况及适生性,为喀斯特森林的稳定性及维持机制提供理论依据。以茂兰喀斯特区68种典型植物为研究对象,分别测定不同生长阶段植物叶片的C、N、P和K含量,并计算其化学计量比。结果表明:研究区68种植物分属40科62属;其叶片C、N、P和K含量的几何平均值分别为445.87 g/kg、17.32 g/kg、1.35 g/kg和9.86 g/kg,C∶N的算术平均值为26.93,C∶P、C∶K、N∶P、N∶K和P∶K的几何平均值分别为330.93、45.22、12.85、1.76和0.137;C与N呈极显著负相关,N与P、K以及P与K均呈极显著正相关,N与C∶P和C∶K、P与C∶N、C∶K和N∶K以及K与C∶N、C∶P和N∶P均呈极显著负相关,且它们之间均具有二次函数、指数函数或幂函数的非线性耦合关系;从变异程度来看,C含量为弱变异,N、P、K含量及各元素的化学计量比则均属中等变异或强变异。从植物不同生活型来比较,各生长阶段的C含量均表现为灌木乔木草本,N、P和K含量均为草本灌木乔木,各元素的化学计量比则均为乔木灌木草本。从植物不同系统发育来分析,各生长阶段蕨类植物的N、P、K含量均要高于种子植物,而各元素的化学计量比则正好相反。从不同生长阶段来看,各功能(类)群植物生长期(或生长盛期)的养分含量均要高于落叶期(或生长末期);乔木、灌木和草本等不同生活型植物落叶期的C∶P、C∶K、N∶P和N∶K均要高于生长期;蕨类植物各元素的化学计量比不同生长阶段间差异都不显著;而种子植物的C∶P、C∶K、N∶P和N∶K则均表现为落叶期生长期。对比我国其他地区及全国和全球尺度上的研究结果,该区域植物的生长发育易受N和P素的双重限制,但又因功能(类)群及生长阶段的不同其受限的养分元素也存在一定差异,体现了对高度异质的喀斯特生境不同的适应策略;而植物体内较高的K含量则可能是提高其自身抗性、适应恶劣环境的重要因素。减少人为干扰、加之适当的保护,在植物生长期配以适量的N素添加,有利于其更好的生长发育,有助于提高喀斯特森林生态系统的稳定性和抗干扰性。研究结果揭示了喀斯特森林植物的适生机制,对喀斯特森林的保护具有重要的指导意义。