Five Entry Points of the Mitochondrially Encoded Subunits in Mammalian Complex I Assembly

Complex I (CI) is the largest enzyme of the mammalian mitochondrial respiratory chain. The biogenesis of the complex is a very complex process due to its large size and number of subunits (45 subunits). The situation is further complicated due to the fact that its subunits have a double genomic origin, as seven of them are encoded by the mitochondrial DNA. Understanding of the assembly process and characterization of the involved factors has advanced very much in the last years. However, until now, a key part of the process, that is, how and at which step the mitochondrially encoded CI subunits (ND subunits) are incorporated in the CI assembly process, was not known. Analyses of several mouse cell lines mutated for three ND subunits allowed us to determine the importance of each one for complex assembly/stability and that there are five different steps within the assembly pathway in which some mitochondrially encoded CI subunit is incorporated.Complex I (CI) (NADH-ubiquinone oxidoreductase; EC 1.6.5.3) is one of the main electron entry points in the mitochondrial respiratory electron transport chain catalyzing the oxidation of NADH to reduce ubiquinone to ubiquinol (31, 39, 40), contributing to the proton motive force to synthesize ATP by the process called oxidative phosphorylation (OXPHOS).CI assembly is a difficult problem to address due to the large size of the complex and its dual genomic nature, as 7 out of its 45 subunits are encoded by the mitochondrial DNA (mtDNA) (10, 11). Until very recently, mammalian CI assembly was explained using two different and apparently contradictory models. One model was proposed by following the time course of formation of CI intermediates in human cells in culture once mitochondrial protein synthesis had recovered after its inhibition by doxycycline (36). Based on these observations, human CI was proposed to be assembled through two different modules corresponding to the membrane and peripheral arms. The other model was proposed after analysis of a cohort of four CI-deficient patients in which seven putative assembly intermediates containing a combination of both peripheral- and membrane arm subunits were identified. Thus, an assembly pathway in which the peripheral- and membrane arm subassemblies came together before the completion of each of the arms was proposed (4). However, the most recent studies have refined the previous models and propose an overlapping view of the process. One study, by green fluorescent protein (GFP) tagging of the NDUFS3 subunit, identified six peripheral-arm intermediates. The second and third smaller NDUFS3-containing subassemblies were accumulated and could not advance into higher-molecular-mass species when mitochondrial protein synthesis was inhibited, thus determining the entry point of the mitochondrially encoded subunits in the CI assembly pathway (37). The most recent study analyzed the incorporation of the mitochondrial subunits in a time course to the fully assembled CI and, on the other hand, the incorporation of the nuclear subunits by importing them into isolated mitochondria (24). Although these two models differ in the order in which some subunits are incorporated, they agree on the general human CI assembly pathway, which takes place via evolutionarily conserved modular subassemblies (14, 25, 28, 37).However, the specific entry points of all the mtDNA-encoded CI subunits (ND subunits) in the CI assembly pathway and their roles in the stability of the complex remained to be clarified. Structural studies related to mutations in the ND subunits in pathological cases have given some hints as to the importance of each of them for CI assembly/stability. In this case, defects in specific ND subunits do not have the same effect: ND1, ND4, and ND6 seem to be fundamental to CI assembly, while ND3 and ND5 are important for its activity but not for assembly. On the other hand, mutations in ND2 alter CI assembly, with abnormal intermediate accumulation (19).In this article, we present new insights into the roles of the ND subunits by using mouse cells deficient for ND4, ND6, and a combination of ND6 and ND5. This study has allowed us to propose the five different entry points by which the mtDNA-encoded subunits are sequentially incorporated into the CI assembly pathway, completing the current view of the process. We conclude that ND4 and ND6 are required for the proper function and assembly of CI, although at different degrees due to their different entry points and roles in the CI assembly pathway.     

Assembly of the Paraflagellar Rod and the Flagellum Attachment Zone Complex During the Trypanosoma brucei Cell Cycle

Trypanosomes possess a single flagellum that is attached to their cell body via the flagellum attachment zone (FAZ). The FAZ is composed of two structures: a cytoplasmic filament complex and four microtubules situated next to it. There is a complex transmembrane crosslinking of this FAZ to the paraflagellar rod (PFR) and axoneme within the flagellum. We have partially purified the FAZ complex and have produced monoclonal antibodies both against the FAZ and the paraflagellar rod. The two antibodies against the FAZ (L3B2 and L6B3) recognise the cytoplasmic filament in immunofluorescence and in immunoelectron microscopy. On western blot, they detect a doublet of high molecular weight (M(r) 200,000). Two anti-PFR antibodies (L13D6 and L8C4) recognise the paraflagellar rod in immunofluorescence, but show a difference on Western blot: L13D6 recognises both major PFR proteins, whereas L8C4 is specific for only one of them. Using these new antibodies we have shown that although the growth of both cytoplasmic FAZ filament and external PFR are related, their growth initiates at different time points during the cell cycle and the two structures elongate at distinct rates.     

Long-Term Administration of Valacyclovir Reduces the Number of Epstein-Barr Virus (EBV)-Infected B Cells but Not the Number of EBV DNA Copies per B Cell in Healthy Volunteers

Epstein-Barr virus (EBV) establishes a latent infection in B cells in the blood, and the latent EBV load in healthy individuals is generally stable over time, maintaining a “set point.” It is unknown if the EBV load changes after long-term antiviral therapy in healthy individuals. We treated volunteers with either valacyclovir (valaciclovir) or no antiviral therapy for 1 year and measured the amount of EBV DNA in B cells every 3 months with a novel, highly sensitive assay. The number of EBV-infected B cells decreased in subjects receiving valacyclovir (half-life of 11 months; P = 0.02) but not in controls (half-life of 31 years; P = 0.86). The difference in the slopes of the lines for the number of EBV-infected B cells over time for the valacyclovir group versus the control group approached significance (P = 0.054). In contrast, the number of EBV DNA copies per B cell remained unchanged in both groups (P = 0.62 and P = 0.92 for the control and valacyclovir groups, respectively). Valacyclovir reduces the frequency of EBV-infected B cells when administered over a long period and, in theory, might allow eradication of EBV from the body if reinfection does not occur.Primary infection with Epstein-Barr virus (EBV) is frequently asymptomatic in infants and children, but infection of adolescents and young adults can result in infectious mononucleosis. EBV is associated with several malignancies, including Burkitt''s lymphoma, nasopharyngeal carcinoma, Hodgkin''s disease, and lymphoproliferative disease, in immunocompromised and immunocompetent persons (6, 20).In healthy EBV-seropositive persons, about 1 to 10 in 10⁵ peripheral B cells are infected with EBV (14). The virus establishes latency in memory B cells. The level of the latent EBV load in healthy individuals remains stable over time, maintaining a “set point” for each individual (19). It is uncertain how this “set point” is maintained, but the latent EBV load is thought to reflect a balance between removal of EBV-infected cells due to the half-life of memory B cells and reinfection of new memory B cells during virus reactivation. The EBV genome replicates when B cells latently infected with EBV divide using the host DNA polymerase, which is not sensitive to the action of acyclovir. However, when the virus reactivates in latently infected B cells, EBV replicates using the viral DNA polymerase, which is inhibited by the phosphorylated form of acyclovir. Therefore, blocking production of new virus with acyclovir should decrease the latent EBV load at a rate equivalent to the half-life of memory B cells. Patients with zoster who were treated with oral acyclovir for 28 days showed no reduction in the EBV load in the blood, despite complete inhibition of EBV shedding in the saliva (23). These results suggested that antiviral therapy for longer than 28 days is necessary to detect a reduction in the EBV load in the blood.In this study, we administered either valacyclovir (valaciclovir) (which is absorbed more effectively than acyclovir and metabolized to acyclovir) or no antiviral to healthy volunteers for 12 months and measured the level of EBV DNA in the blood every 3 months.     

EBV Latent Membrane Protein 1 Activates Akt,NFκB,and Stat3 in B Cell Lymphomas

Latent membrane protein 1 (LMP1) is the major oncoprotein of Epstein-Barr virus (EBV). In transgenic mice, LMP1 promotes increased lymphoma development by 12 mo of age. This study reveals that lymphoma develops in B-1a lymphocytes, a population that is associated with transformation in older mice. The lymphoma cells have deregulated cell cycle markers, and inhibitors of Akt, NFκB, and Stat3 block the enhanced viability of LMP1 transgenic lymphocytes and lymphoma cells in vitro. Lymphoma cells are independent of IL4/Stat6 signaling for survival and proliferation, but have constitutively activated Stat3 signaling. These same targets are also deregulated in wild-type B-1a lymphomas that arise spontaneously through age predisposition. These results suggest that Akt, NFκB, and Stat3 pathways may serve as effective targets in the treatment of EBV-associated B cell lymphomas.     

Architecture and Assembly of the Bacillus subtilis Spore Coat

Bacillus spores are encased in a multilayer, proteinaceous self-assembled coat structure that assists in protecting the bacterial genome from stresses and consists of at least 70 proteins. The elucidation of Bacillus spore coat assembly, architecture, and function is critical to determining mechanisms of spore pathogenesis, environmental resistance, immune response, and physicochemical properties. Recently, genetic, biochemical and microscopy methods have provided new insight into spore coat architecture, assembly, structure and function. However, detailed spore coat architecture and assembly, comprehensive understanding of the proteomic composition of coat layers, and specific roles of coat proteins in coat assembly and their precise localization within the coat remain in question. In this study, atomic force microscopy was used to probe the coat structure of Bacillus subtilis wild type and cotA, cotB, safA, cotH, cotO, cotE, gerE, and cotE gerE spores. This approach provided high-resolution visualization of the various spore coat structures, new insight into the function of specific coat proteins, and enabled the development of a detailed model of spore coat architecture. This model is consistent with a recently reported four-layer coat assembly and further adds several coat layers not reported previously. The coat is organized starting from the outside into an outermost amorphous (crust) layer, a rodlet layer, a honeycomb layer, a fibrous layer, a layer of “nanodot” particles, a multilayer assembly, and finally the undercoat/basement layer. We propose that the assembly of the previously unreported fibrous layer, which we link to the darkly stained outer coat seen by electron microscopy, and the nanodot layer are cotH- and cotE- dependent and cotE-specific respectively. We further propose that the inner coat multilayer structure is crystalline with its apparent two-dimensional (2D) nuclei being the first example of a non-mineral 2D nucleation crystallization pattern in a biological organism.     

脂筏在病毒感染中的作用

脂筏是细胞膜上富含鞘脂和胆固醇的微区结构,广泛分布于细胞的膜系统.脂筏中含有诸多信号分子和免疫受体,在细胞的生命活动中扮演非常重要的角色.更为重要的是,脂筏为细胞表面发生的蛋白质-蛋白质和蛋白质-脂类分子间的相互作用提供了平台.研究表明,很多病毒可以利用细胞膜表面的脂筏结构介导其侵入宿主细胞,一些病毒可以借助脂筏结构完成病毒颗粒的组装和出芽.本文将综述不同类型的病毒如SV40、HIV等借助脂筏完成入侵以及流感病毒等利用脂筏完成组装和出芽的证据及机理,并概述目前研究病毒与脂筏相互作用的方法及存在的问题.深入研究脂筏在病毒感染中的作用,将有助于对病毒与宿主细胞的相互作用的理解,从而可能发现新的、有效的对抗病毒的方法。     

Understanding How the Complex Molecular Architecture of Mannan-degrading Hydrolases Contributes to Plant Cell Wall Degradation

Microbial degradation of plant cell walls is a central component of the carbon cycle and is of increasing importance in environmentally significant industries. Plant cell wall-degrading enzymes have a complex molecular architecture consisting of catalytic modules and, frequently, multiple non-catalytic carbohydrate binding modules (CBMs). It is currently unclear whether the specificities of the CBMs or the topology of the catalytic modules are the primary drivers for the specificity of these enzymes against plant cell walls. Here, we have evaluated the relationship between CBM specificity and their capacity to enhance the activity of GH5 and GH26 mannanases and CE2 esterases against intact plant cell walls. The data show that cellulose and mannan binding CBMs have the greatest impact on the removal of mannan from tobacco and Physcomitrella cell walls, respectively. Although the action of the GH5 mannanase was independent of the context of mannan in tobacco cell walls, a significant proportion of the polysaccharide was inaccessible to the GH26 enzyme. The recalcitrant mannan, however, was fully accessible to the GH26 mannanase appended to a cellulose binding CBM. Although CE2 esterases display similar specificities against acetylated substrates in vitro, only CjCE2C was active against acetylated mannan in Physcomitrella. Appending a mannan binding CBM27 to CjCE2C potentiated its activity against Physcomitrella walls, whereas a xylan binding CBM reduced the capacity of esterases to deacetylate xylan in tobacco walls. This work provides insight into the biological significance for the complex array of hydrolytic enzymes expressed by plant cell wall-degrading microorganisms.     

Architecture of Peptide Assembly in Liposome

Abstract

Two chains of amphiphilic α-helical dodecapeptides were connected to a cyclic octapeptide in a parallel or antiparallel arrangement. Conformation, orientation, and association of the dodeca-peptide chains in the presence of dimyristoylphosphatidylcholine (DMPC) liposome were studied. The peptides were easily incorporated into the bilayer membrane. CD measurements revealed that the dodecapeptides took a distorted a-helix conformation due to intramolecular association. Fluorescence quenching measurement of a probe connected to each terminal region of the dodecapeptides revealed that the dodecapeptide chain was located on the membrane surface with a parallel orientation to the surface. Thermal denaturation of the helical structure was suppressed by connecting the two dodecapeptide chains to the cyclic peptide. These experimental results indicate that a supersecondary structure composed of associated α-helices was constructed on the surface of DMPC liposome by using a cyclic peptide as a template.     

EBV阳性胃癌细胞系与阴性胃癌细胞系全基因组表达谱差异比较

目的：探讨EB病毒阳性胃癌细胞系与EB 病毒阴性胃癌细胞系全基因组表达谱的差异。方法：利用Agilent 人类全基因组 表达谱芯片技术在3 种EB病毒阳性胃癌细胞系和3 种EB 病毒阴性胃癌细胞系中筛选EB病毒相关胃癌肿瘤相关基因。选取6 条差异表达基因,应用实时荧光定量PCR验证芯片结果的可靠性。结果：聚类热图及矩阵图分析显示,EB病毒阳性胃癌细胞系与 阴性胃癌细胞系之间表达谱存在明显差异。差异表达基因涉及多种生物学过程。选取的6 条差异基因进行验证,其表达趋势与芯 片结果一致。结论：感染EB病毒可能会改变肿瘤相关基因的表达,进而在EB病毒相关胃癌的发生、发展及预后中发挥作用。筛 选出的肿瘤相关基因涉及多种生物学过程,提示多基因及相关基因的变异参与了EB病毒相关胃癌的形成。     

Dynamics of Pre-replicative Complex Assembly

The pre-replicative complex (pre-RC) is formed at all potential origins of replication through the action of the origin recognition complex (ORC), Cdc6, Cdt1, and the Mcm2-7 complex. The end result of pre-RC formation is the loading of the Mcm2-7 replicative helicase onto origin DNA. We examined pre-RC formation in vitro and found that it proceeds through separable binding events. Origin-bound ORC recruits Cdc6, and this ternary complex then promotes helicase loading in the presence of a pre-formed Mcm2-7-Cdt1 complex. Using a stepwise pre-RC assembly assay, we investigated the fate of pre-RC components during later stages of the reaction. We determined that helicase loading is accompanied by dissociation of ORC, Cdc6, and Cdt1 from origin DNA. This dissociation requires ATP hydrolysis at a late stage of pre-RC assembly. Our results indicate that pre-RC formation is a dynamic process.     

Entry and Exit Mechanisms at the cis-Face of the Golgi Complex

Vesicular transport of protein and lipid cargo from the endoplasmic reticulum (ER) to cis-Golgi compartments depends on coat protein complexes, Rab GTPases, tethering factors, and membrane fusion catalysts. ER-derived vesicles deliver cargo to an ER-Golgi intermediate compartment (ERGIC) that then fuses with and/or matures into cis-Golgi compartments. The forward transport pathway to cis-Golgi compartments is balanced by a retrograde directed pathway that recycles transport machinery back to the ER. How trafficking through the ERGIC and cis-Golgi is coordinated to maintain organelle structure and function is poorly understood and highlights central questions regarding trafficking routes and organization of the early secretory pathway.Newly synthesized secretory proteins and lipids are transported to early Golgi compartments in dissociative carrier vesicles that are formed from the ER (Palade 1975). Through the development of biochemical, genetic and morphological approaches, outlines for the molecular machinery that catalyze this transport step and the membrane structures that comprise the early secretory compartments have been developed (Rothman 1994; Schekman and Orci 1996). Initial images and studies suggested the early secretory pathway consisted of stable compartments with ER-derived carrier vesicles shuttling cargo to pre-Golgi and Golgi compartments. However, live cell and time-lapse imaging revealed highly dynamic structures with both secretory cargo and compartment residents detected in pleiomorphic intermediates (Presley et al. 1997; Scales et al. 1997; Shima et al. 1999; Ben-Tekaya et al. 2005). Several lines of evidence now indicate that active bidirectional transport cycles between the ER, ERGIC, and cis-Golgi compartments are balanced to maintain compartment structure and function (Lee et al. 2004). The coat protein complex II (COPII) produces vesicles for forward transport from the ER whereas the coat protein complex I (COPI) buds vesicles for retrograde transport from cis-Golgi compartments to the ER (Fig. 1). Indeed inhibition of either the forward or retrograde pathways results in a rapid loss of normal ER and Golgi organization (Lippincott-Schwartz et al. 1989; Rambourg et al. 1994; Morin-Ganet et al. 2000; Ward et al. 2001). Yet, under steady-state conditions, the cis-Golgi compartments retain a characteristic composition and structure as secretory cargo passes through. These observations indicate that the structure and function of early secretory compartments are maintained at dynamic equilibrium through coordination of multiple pathways.Open in a separate windowFigure 1.Trafficking in the early secretory pathway. A simplified model depicting bidirectional transport routes between the endoplasmic reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), and cis-Golgi cisternae. COPII vesicles bud from the ER and transport cargo in an anterograde direction for tethering and fusion with the ERGIC. The ERGIC then matures into the cis-Golgi compartment and/or fuses with the cis-Golgi. COPI vesicles bud from the ERGIC and cis-Golgi compartments in a retrograde transport pathway back to the ER to recycle transport machinery.Although much of the molecular machinery required for transport to and from cis-Golgi membranes has been identified, the current challenges are to understand the sequence of molecular events that underlie the observed structural organization. Moreover, the mechanisms that govern entry and exit rates to-from cis-Golgi membranes to maintain organization at dynamic equilibrium are poorly understood. In this perspective the known key machinery required for anterograde transport to, and retrograde exit from, cis-Golgi compartments will be described, and then current models for how compartmental structure is maintained while protein and lipid cargo fluxes through will be examined. This review will survey core machinery and principles from several experimental models although it is becoming clear that different species and different cell types within a species may employ variations on a basic theme depending on cellular function. For example, in many animal cells secretory cargo passes through a well-characterized ER-Golgi intermediate compartment (ERGIC) en route to cis-Golgi cisternae. The ERGIC may be necessary to span the distance between ER export sites and the Golgi stack; however, the relationship of this intermediate compartment to the cis-Golgi remains unclear (Appenzeller-Herzog and Hauri 2006). In other species including yeast, Golgi organization appears less coherent and may be considered more simply as a series of intermediate compartments. Here COPII vesicles are thought to fuse directly with the cis-Golgi or this first intermediate compartment (Fig. 2) (Mogelsvang et al. 2003). Despite these quite varied structural organizations, there is a remarkable level of conservation in molecular machinery. After consideration of this conserved molecular machinery, we will return to organizational issues in transport to and from the cis-Golgi compartment.Open in a separate windowFigure 2.ER/Golgi organization in the yeast P. pastoris. Three-dimensional models reconstructed from electron microscope tomography showing proximity of ER and cis-most cisterna of the Golgi complex. Putative COPII vesicles are detected in a narrow region between the ER and cis-Golgi. For further information, see Mogelsvang et al. (2003). Bar = 100 nm. (Reprinted, with permission, from Mogelsvang et al. 2003 [American Society for Cell Biology].)     

RNA诱导沉默复合体中的生物大分子及其装配

在RNA干扰机制中,双链RNA诱导同源RNA降解的过程依赖于RNA诱导沉默复合体（RISC）的活性。RISC由Dicer酶,Argonaute蛋白,siRNA等多种生物大分子装配而成,对这些大分子的结构和功能进行深入细致的研究,有助于进一步了解RISC的形成过程、作用方式,以及阐明整个RNAi过程的作用机制。研究表明,RISC中的Dicer具有RNaseIII结构域,在RNAi的起始阶段负责催化siRNA的产生,在RISC装配过程中起稳定RISC中间体结构和功能的作用;Argonaute蛋白是RISC中的核心蛋白,有PAZ和PIWI两个主要的结构域,前者为siRNA的传递提供结合位点,后者是RISC中的酶切割活性中心;siRNA是RISC完成特异性切割作用的向导,在成熟的RISC中虽然只包含siRNA的一条链,但siRNA在RISC形成过程中的双链结构是保证RNAi效应的决定因素。尽管RISC中还存在其他一些功能未知的蛋白质,但在RISC组分结构及功能研究方面取得的进展为建立一个可能的RISC装配模型提供了理论基础。     

Surface Architecture of Sperm Tail Entry into the Hamster Oocyte

At various times after artificial insemination in vivo , fertilized eggs were flushed from the ampulla of the oviduct of the hamster. The processes of sperm tail entry into the oocyte were studied with phase-contrast and electron microscopes. At 6–7 hr after insemination, the sperm head was incorporated completely into the ooplasm, but the entire length of the sperm tail still projected freely over the oocyte surface. The region on the oocyte surface where the second polar body was extruded was different from where the first polar body emerged. At 8–9 hr after insemination, the sperm tail was attached in a wave-like fashion to the oocyte surface. Where some portions of the tail were attached, they were trapped by the microvilli of the oocyte and had begun to sink into the ooplasm. Thus, the entire length of the sperm tail was incorporated into the ooplasm successively but almost synchronously. From the present observations, we have proposed a model for the mechanism of sperm tail entry into the vitellus in vivo .     

Structural Correlates of Rotavirus Cell Entry

Cell entry by non-enveloped viruses requires translocation into the cytosol of a macromolecular complex—for double-strand RNA viruses, a complete subviral particle. We have used live-cell fluorescence imaging to follow rotavirus entry and penetration into the cytosol of its ∼700 Å inner capsid particle (“double-layered particle”, DLP). We label with distinct fluorescent tags the DLP and each of the two outer-layer proteins and track the fates of each species as the particles bind and enter BSC-1 cells. Virions attach to their glycolipid receptors in the host cell membrane and rapidly become inaccessible to externally added agents; most particles that release their DLP into the cytosol have done so by ∼10 minutes, as detected by rapid diffusional motion of the DLP away from residual outer-layer proteins. Electron microscopy shows images of particles at various stages of engulfment into tightly fitting membrane invaginations, consistent with the interpretation that rotavirus particles drive their own uptake. Electron cryotomography of membrane-bound virions also shows closely wrapped membrane. Combined with high resolution structural information about the viral components, these observations suggest a molecular model for membrane disruption and DLP penetration.