Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.     

诺卡氏菌形放线菌β-甘露聚糖酶的水解特性

诺卡氏菌形放线菌（Nocardioform actinomycetes）NA3-540产生的β-甘露聚糖酶（ManNA）能不同程度地水解槐豆胶、瓜胶、田菁胶和魔芋胶等甘露多聚糖为组分的植物胶,生成系列甘露寡糖;该酶只轻微地水解香豆胶,不能水解β-甘露聚糖、黄原胶、海藻胶;ManNA对槐豆胶、瓜胶和魔芋胶多糖的Km值和Vmax分别为1．75、6．13、3．9mg／mL和2485、1303、853μmol／（min／mg）,表明槐豆胶是该酶的理想水解底物。ManNA水解几种植物胶的明显差异,表明甘露聚糖的糖链组成和空间结构明显地影响着β-甘露聚糖酶的水解活性。     

PKCdelta-mediated IRS-1 Ser24 phosphorylation negatively regulates IRS-1 function

The IRS-1 PH and PTB domains are essential for insulin-stimulated IRS-1 Tyr phosphorylation and insulin signaling, while Ser/Thr phosphorylation of IRS-1 disrupts these signaling events. To investigate consensus PKC phosphorylation sites in the PH-PTB domains of human IRS-1, we changed Ser24, Ser58, and Thr191 to Ala (3A) or Glu (3E), to block or mimic phosphorylation, respectively. The 3A mutant abrogated the inhibitory effect of PKCdelta on insulin-stimulated IRS-1 Tyr phosphorylation, while reductions in insulin-stimulated IRS-1 Tyr phosphorylation, cellular proliferation, and Akt activation were observed with the 3E mutant. When single Glu mutants were tested, the Ser24 to Glu mutant had the greatest inhibitory effect on insulin-stimulated IRS-1 Tyr phosphorylation. PKCdelta-mediated IRS-1 Ser24 phosphorylation was confirmed in cells with PKCdelta catalytic domain mutants and by an RNAi method. Mechanistic studies revealed that IRS-1 with Ala and Glu point mutations at Ser24 impaired phosphatidylinositol-4,5-bisphosphate binding. In summary, our data are consistent with the hypothesis that Ser24 is a negative regulatory phosphorylation site in IRS-1.     

The role of the N-terminal domain of chloroplast targeting peptides in organellar protein import and miss-sorting

We have analysed 385 mitochondrial and 567 chloroplastic signal sequences of proteins found in the organellar proteomes of Arabidopsis thaliana. Despite overall similarities, the first 16 residues of transit peptides differ remarkably. To test the hypothesis that the N-terminally truncated transit peptides would redirect chloroplastic precursor proteins to mitochondria, we studied import of the N-terminal deletion mutants of ELIP, PetC and Lhcb2.1. The results show that the deletion mutants were neither imported into chloroplasts nor miss-targeted to mitochondria in vitro and in vivo, showing that the entire transit peptide is necessary for correct targeting as well as miss-sorting.     

A phylogenetic analysis of sleep architecture in mammals: the integration of anatomy, physiology, and ecology

Among mammalian species, the time spent in the two main "architectural" states of sleep--slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep--varies greatly. Previous comparative studies of sleep architecture found that larger mammals, those with bigger brains, and those with higher absolute basal metabolic rates (BMR) tended to engage in less SWS and REM sleep. Species experiencing a greater risk of predation also exhibited less SWS and REM sleep. In all cases, however, these studies lacked a formal phylogenetic and theoretical framework and used mainly correlational analyses. Using independent contrasts and an updated data set, we extended existing approaches with path analysis to examine the integrated influence of anatomy, physiology, and ecology on sleep architecture. Path model structure was determined by nonmutually exclusive hypotheses for the function of sleep. We found that species with higher relative BMRs engage in less SWS, whereas species with larger relative brain masses engage in more REM sleep. REM sleep was the only sleep variable strongly influenced by predation risk; mammals sleeping in riskier environments engage in less REM sleep. Overall, we found support for some hypotheses for the function of sleep, such as facilitating memory consolidation or learning, but not others, such as energy conservation.     

Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1

NADP-dependent methylene-H(4)MPT dehydrogenase, MtdA, from Methylobacterium extorquens AM1 catalyzes the dehydrogenation of methylene-tetrahydromethanopterin and methylene-tetrahydrofolate with NADP(+) as cosubstrate. The X-ray structure of MtdA with and without NADP bound was established at 1.9 A resolution. The enzyme is present as a homotrimer. The alpha,beta fold of the monomer is related to that of methylene-H(4)F dehydrogenases, suggesting a common evolutionary origin. The position of the active site is located within a large crevice built up by the two domains of one subunit and one domain of a second subunit. Methylene-H(4)MPT could be modeled into the cleft, and crucial active site residues such as Phe18, Lys256, His260, and Thr102 were identified. The molecular basis of the different substrate specificities and different catalytic demands of MtdA compared to methylene-H(4)F dehydrogenases are discussed.     

东亚飞蝗羧酸酯酶基因的克隆和原核表达

羧酸酯酶是昆虫体内重要的代谢解毒酶系,其主要功能是水解和结合内源性和外源性含有酯键的有毒物质,减缓其到达靶标部位的时间。东亚飞蝗Locusta migratoria manilensis(Meyen)是我国重要的农业害虫,对其羧酸酯酶基因克隆和表达有助于深入探索杀虫剂代谢毒理机制。本研究首先对羧酸酯酶基因(CarE4)进行了克隆,并将其插入到pCold TF DNA Vector中,在大肠杆菌中进行了原核表达,最后用疏水层析和离子交换层析方法对目的蛋白进行了纯化。本文成功建立了羧酸酯酶蛋白原核表达和纯化技术体系,为进一步研究东亚飞蝗羧酸酯酶的生理功能、结构特点和作用原理提供了基础资料。     

Recent progress in research on insect histone deacetylases (HDACs)

组蛋白乙酰化修饰是一种重要的蛋白质翻译后修饰方式,由组蛋白乙酰基转移酶HATs和组蛋白去乙酰化酶HDACs共同调节.昆虫HDACs蛋白家族根据其同源性和结构的不同共分为4类,各昆虫物种之间既具有较高的保守同源性,同时也表现出一定的物种特异性.HDACs主要参与昆虫的胚胎发育、体节形成、寿命和神经行为等方面的调节.本文从HDACs蛋白的种类、系统发育、生理功能等方面展开,介绍了近年来国内外昆虫HDACs领域的最新研究进展,以期对研究昆虫表型可塑性调节机制以及探索新的害虫防治方法提供借鉴.