Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. They are endowed with important physiological functions but until now only few of them have been studied. Here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. Sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxification, in sulfide-dependent respiration and photosynthesis, and in heavy metal tolerance. It may also play a crucial role in mammals, including humans, because sulfide acts as a neurotransmitter in these organisms. We isolated and purified sulfide:quinone oxidoreductase from the native membranes of the hyperthermophilic bacterium Aquifex aeolicus. We studied the pure and solubilized enzyme by denaturing and non-denaturing polyacrylamide electrophoresis, size-exclusion chromatography, cross-linking, analytical ultracentrifugation, visible and ultraviolet spectroscopy, mass spectrometry and electron microscopy. Additionally, we report the characterization of its enzymatic activity before and after crystallization. Finally, we discuss the crystallization of sulfide:quinone oxidoreductase in respect to its membrane topology and we propose a classification of monotopic membrane protein crystal lattices. Our data support and complement an earlier description of the three-dimensional structure of A. aeolicus sulfide:quinone oxidoreductase (M. Marcia, U. Ermler, G. Peng, H. Michel, Proc Natl Acad Sci USA, 106 (2009) 9625-9630) and may serve as a reference for further studies on monotopic membrane proteins. (C) 2010 Elsevier B.V. All rights reserved.

Characterization and cloning of a novel phospholipase A(2) from the venom of Trimeresurus jerdonii snake

A phospholipase A(2) (PLA(2)) called jerdoxin, was isolated from Trimeresurus jerdonni snake venom and partially characterized. The protein was purified by three chromatographic steps. SDS-polyacrylamide gel electrophoresis in the presence or absence of dithiothreitol showed that it had a molecular mass of 15 kDa. Jerdoxin had an enzymatic activity of 39.4 mumol/min/mg towards egg yolk phosphatidyl choline (PC). It induced edema in the footpads of mice. In addition, jerdoxin exhibited indirect hemolytic activity. About 97% hemolysis was observed when 2 mug/ml enzyme was incubated for 90 min in the presence of PC and Ca2+. No detectable hemolysis was noticed when PC was not added. Ca2+ was necessary for jerdoxin to exert its hemolytic activity, since only 52% hemolysis was seen when Ca2+ was absent in the reaction mixture. Furthermore, jerdoxin inhibited ADP induced rabbit platelet aggregation and the inhibition was dose dependent with an IC50 of 1.0 muM. The complete amino acid sequence of jerdoxin deduced from cDNA sequence shared high homology with other snake venom PLA(2)s, especially the D49 PLA(2)s. Also, the residues concerned to Ca2+ binding were conserved. This is the first report of cDNA sequence of T jerdonii venom PLA(2). (C) 2002 Elsevier Science Ltd. All rights reserved.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

草甘膦的土壤酶效应研究

为了探讨当今世界使用量最大的除草剂——草甘膦的土壤环境效应,本文采用室内模拟方法,较为系统地研究了我国4类土壤:褐土、黄绵土、风沙土和红壤,共11个土样中4种主要酶类(脲酶、转化酶、磷酸酶以及脱氢酶)活性与草甘膦间的关系,计算并得到了能够表征土壤轻度污染的生态剂量值ED10。结果表明:非缓冲液法较好地反映了土壤酶的实际情况;草甘膦总体上激活土壤脲酶、转化酶和脱氢酶活性,最大增幅分别为190%、1372%和42%;抑制磷酸酶活性,最大幅度为35%;磷酸酶与草甘膦间为完全抑制作用机理;激活脱氢酶活性揭示出草甘膦导致了土壤中微生物活性增强,从侧面反映出草甘膦是一种毒性较低的农药。计算获得4类供试土壤褐土、黄绵土、风沙土和红壤ED10值分别为168.3、438.5、35.1和141.4mg·kg-1;在一定程度上用土壤酶活性比生物来表征土壤污染程度更敏感。土壤性质对草甘膦的毒性有重要影响。

A switch-on mechanism to activate maize ribosome-inactivating protein for targeting HIV-infected cells

Maize ribosome-inactivating protein (RIP) is a plant toxin that inactivates eukaryotic ribosomes by depurinating a specific adenine residue at the a-sarcin/ricin loop of 28S rRNA. Maize RIP is first produced as a proenzyme with a 25-amino acid internal inactivation region on the protein surface. During germination, proteolytic removal of this internal inactivation region generates the active heterodimeric maize RIP with full N-glycosidase activity. This naturally occurring switch-on mechanism provides an opportunity for targeting the cytotoxin to pathogen-infected cells. Here, we report the addition of HIV-1 protease recognition sequences to the internal inactivation region and the activation of the maize RIP variants by HIV-1 protease in vitro and in HIV-infected cells. Among the variants generated, two were cleaved efficiently by HIV-1 protease. The HIV-1 protease-activated variants showed enhanced N-glycosidase activity in vivo as compared to their un-activated counterparts. They also possessed potent inhibitory effect on p24 antigen production in human T cells infected by two HIV-1 strains. This switch-on strategy for activating the enzymatic activity of maize RIP in target cells provides a platform for combating pathogens with a specific protease.

燕沟流域退耕地土壤有机碳、全氮和酶活性对植被恢复过程的响应

本文以黄土高原丘陵区陕北延安燕沟流域为例,研究了退耕地土壤有机碳、全氮和酶活性对植被恢复过程的响应。结果表明,随植被恢复年限的增加,植被盖度、多度和物种数均呈现先增加后减少然后又增加的趋势。同当年对照农地相比,随着植被恢复年限的增加,表层(0~20 cm)土壤有机碳、全氮、蔗糖酶、脲酶和碱性磷酸酶活性均明显增加,过氧化氢酶活性随植被恢复年限的增加变化不明显。同对照农地相比,表层土壤有机碳、全氮、蔗糖酶、脲酶和碱性磷酸酶活性分别增加了35%~184.6%、5.7%~157.4%、89.6%~566%、32.9%~331.2%和0.18%~184.8%。表层土壤有机碳和脲酶活性对植被恢复的响应是在植被恢复初期(0~8年),随植被恢复年限的增加而增加,植被恢复8~29年期间,随植被恢复年限的增加而减少,而植被恢复29 a以后,又随植被恢复年限的增加而增加。而表层土壤全氮、蔗糖酶和碱性磷酸酶活性对植被恢复的响应是在植被恢复初期(0~16年),随植被恢复年限的增加而增加,植被恢复16~29年期间,随植被恢复年限的增加而减少,植被恢复29 a以后,又随植被恢复年限的增加而增加。表层土壤蔗糖酶、脲酶和碱性磷酸酶活性与有机碳...

黄土塬区果园套种对土壤微生物及酶活性的影响

研究了黄土塬区塬面不同套种作物的幼树苹果园土壤微生物的分布和酶活性。结果表明，果园土壤中微生物的分布在果树行与套种行中是不均匀的，细菌和真菌多为果树行多于套种行；土壤的过氧化氢酶，蔗糖酶，脲酶以及中性磷酸酶活性在套种小麦的果园中以套作行高于果树行，而套种烤烟则使脲酶和中性磷酸酶活性有所降低。套种豆类有利于土壤肥力的均衡发展。

pH-dependent protein conformational changes in albumin : gold nanoparticle bioconjugates: A spectroscopic study

The conformational changes of bovine serum albumin (BSA) in the albumin:gold nanoparticle bioconjugates were investigated in detail by various spectroscopic techniques including UV-vis absorption, fluorescence, circular dichroism, and Fourier transform infrared spectroscopies. Our studies suggested that albumin in the bioconjugates that was prepared by the common adsorption method underwent substantial conformational changes at both secondary and tertiary structure levels. BSA was found to adopt a more flexible conformational state on the boundary surface of gold nanoparticles as a result of the conformational changes in the bioconjugates. The conformational changes at pH 3.8, 7.0, and 9.0, which corresponded to different isomeric forms of albumin, were investigated, respectively, to probe the pH effect on the conformational changes of BSA in the bioconjugates. The results showed that the pH of the medium influenced the changes greatly and that fluorescence and circular dichroism studies further indicated that the changes were larger at higher pH.

Electrochemistry of glucose oxidase immobilized on the carbon nanotube wrapped by polyelectrolyte

A more stably dispersing of multi-wall carbon nanotube composite (noted as PDDA-MWNT), which was obtained by wrapping the MWNT with poly (diallydimethylammonium) chloride (PDDA), was used for the immobilization of glucose oxidase (GOD) and its bioelectrochemical studies. The morphologies and structures of the PDDA-MWNT composite were characterized by environment-canning electron microscopy (ESEM) and X-ray photoelectron spectroscopy (XPS). Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry were used to feature the GOD adsorbed onto the electrode modified by PDDA-MWNT composite. The immobilized GOD at the PDDA-MWNT films exhibited a pair of well-defined nearly reversible redox peaks and a fast heterogeneous electron transfer rate with the rate constant (k(s)) of 2.76 s(-1). In addition, GOD immobilized in this way retained its bioelectrocatalytic activity for the oxidation of glucose. The method of immobilizing GOD without any additional cross-linking agents presented here is easy and facile, which provides a model for other redox enzymes and proteins.

稀土铽离子对辣根过氧化物酶活力指数的影响

The effect of Tb3+ ion on the Activity Index (RZ=A403/A275) of HRP was investigated by a combination of ultraviolet-visible, FT-infrared and X-ray photoelectron spectroscopic techniques. It was found that Tb3+ ion could bond to the O and/or N group of the amides in the polypeptide chains of HRP, leading to a decrease in the enzymatic activity index of HRP.

Preparation and properties of a selenium-containing catalytic antibody as type I deiodinase mimic

Conversion of thyroxine (T-4) to 3,5,3'-triiodothyronine is an essential first step in controlling thyroid hormone action. Type I deiodinase (DI) can catalyze the conversion to produce the bulk of serum 3,5,3'-triiodothyronine. Acting as a mimic of DI, a selenium-containing catalytic antibody (Se-4C5) prepared by converting the serine residues of monoclonal antibody 4C5 raised against T4 into selenocysteines, can catalyze the deiodination of T4 with dithiothreitol (DTT) as cosubstrate. The mimic enzyme Se-4C5 exhibited a much greater deiodinase activity than model compound ebselen and another selenium-containing antibody Se-Hp4 against GSH. The coupling of selenocysteine with the combining pocket of antibody 4C5 endowed Se-4C5 with enzymatic activity. To probe the catalytic mechanism of the catalytic antibody, detailed kinetic studies were carried out in this paper. Investigations into the deiodinative reaction revealed the relationship between the initial velocity and substrate concentration. The characteristic parallel Dalziel plots demonstrated that Se-4C5-catalyzed reaction mechanism was ping-pong one, involving at least one covalent enzyme intermediate. The kinetic properties of the catalytic antibody were similar to those of DI, with K-m values for T-4 and DTT of approximately 0.8 muM and 1.8 muM, respectively, and a V-m value of 270 pmol per mg of protein per min. The activity could be sensitively inhibited by 6-propyl-2-thiouracil (PTU) with a K-i value of similar to 120 muM at 2.0 muM T-4 concentration. The PTU inhibition was progressively alleviated with the increasing concentration of added DTT, revealing that PTU was a competitive inhibitor for DTT.

Sequence analysis and functional study of thymidylate synthase from zebrafish, Danio rerio

The thymidylate synthase (TS), an important target for many anticancer drugs, has been cloned from different species. But the cDNA property and function of TS in zebrafish are not well documented. In order to use zebrafish as an animal model for screening novel anticancer agents, we isolated TS cDNA from zebrafish and compared its sequence with those from other species. The open reading frame (ORF) of zebrafish TS cDNA sequence was 954 nucleotides, encoding a 318-amino acid protein with a calculated molecular mass of 36.15 kDa. The deduced amino acid sequence of zebrafish TS was similar to those from other organisms, including rat, mouse and humans. The zebrafish TS protein was expressed in Escherichia coli and purified to homogeneity. The purified zebrafish TS showed maximal activity at 28 degrees C with similar K-m value to human TS. Western immunoblot assay confirmed that TS was expressed in all the developmental stages of zebrafish with a high level of expression at the 1-4 cell stages. To study the function of TS in zebrafish embryo development, a short hairpin RNA (shRNA) expression vector, pSilencer 4.1-CMV/TS, was constructed which targeted the protein-coding region of zebrafish TS mRNA. Significant change in the development of tail and epiboly was found in zebrafish embryos microinjected pSilencer4.1-CMV/TS siRNA expression vector.

Effects of photoperiod on growth, mortality and digestive enzymes in miiuy croaker larvae and juveniles

The growth, mortality and digestive enzymes (trypsin, amylase and lipase) in miiuy croaker Miichthys miiuy larvae and juveniles (2-53 dph) were investigated at four photoperiods: 24L:OD), 18L:6D, 12L:12D and OL:24D. Larvae could not feed at OL:24D and did not survive up to 7 dph. In the 24L:OD, 18L:6D, 12L:12D groups, photoperiod had not significant effects on the growth of the rniiuy croaker younger than 20 dph. However, their total length and specific growth rate (SGR) were significantly larger at 18L:6D and 24L:OD than 12L:12D after 20 dph. Photoperiod also affected the mortality of the first feeding larvae (5 dph). being apparently higher in 5 dph larvae at OL:24D (60%) than at other photopenods (20-27%), but no significant differences in mortality were found among other photoperiods. High mortality of the miiuy croaker in 12L:12D, 18L:6D and 24 L:OD groups mainly occurred from 5 (20-27%) to 11 dph (11-16%) and tended to decrease gradually from 15 dph onwards. Digestive enzymes activities in the rniiuy croaker larvae and juveniles had a similar change trend with age at all photoperiods. They underwent drastic changes with age. The specific activity of lipase was significantly higher at 18L:6D and 24L:0D than 12L:12D, but there were no significant differences in specific activities of either trypsin or amylase among photoperiods. With regard to the total length, SGR, survival and digestive enzyme activities, our findings suggested that the optimal light regime for the culture of miiuy croaker during the early life stage was 18L:6D. (C) 2008 Elsevier B.V. All rights reserved.