Interaction between relaxase MbeA and accessory protein MbeC of the conjugally mobilizable plasmid ColE1

MbeA and MbeC are two key proteins in plasmid ColE1 conjugal mobilization. Isothermal titration calorimetry was used to detect and quantify an interaction between MbeA and MbeC. As a result of this interaction, the affinity of MbeA for single stranded DNA increased. The interaction was confirmed in vivo using a bacterial two-hybrid system, which revealed that MbeA-MbeC complexes are formed through the amino-terminal region of MbeA and the carboxy-terminal region of MbeC. To the best of our knowledge, this is the first report of direct interactions between conjugative proteins encoded by a mobilizable plasmid.     

An Extended Guinier Analysis for Intrinsically Disordered Proteins

Guinier analysis allows model-free determination of the radius of gyration (R_g) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred R_g within ～ 3% of the true R_g. The method is straightforward to implement and extends the range of validity to a maximum qR_g of ～ 2 versus ～ 1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to R_g, our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble.     

HIV-1附属蛋白特异性细胞毒性T细胞应答研究

人类免疫缺陷病毒(Human immunodeficiency virus, HIV)附属蛋白Nef、Vpu、Vpr和Vif 在病毒复制中起着关键作用,并能被细胞毒性T细胞(Cytotoxic T Lymphocyte, CTL)识别.然而,对我国HIV感染者体内附属蛋白特异性的CTL应答研究比较少.本研究应用覆盖HIV-1B、C亚型附属蛋白(Nef、Vpu、Vpr和Vif)的142个肽段作为抗原,通过酶联免疫斑点实验(Enzyme-Linked Immunospot,ELISPOT)检测61例中国HIV/AIDS患者和10例HIV-1血清阴性对照的HIV-1附属蛋白特异性CTL应答.无论对HIV-1B 亚型还是HIV-1C亚型附属蛋白都能产生特异性CTL 应答,特别是Nef区蛋白的反应频率和累积应答强度都较高(P＜0.001),B、C亚型间的应答频率和累积应答强度都无显著差别(P＞0.05),其免疫优势区也大致相同.附属蛋白特异性的累积CTL应答强度将近达到总应答的21%.这些结果表明尽管HIV-1附属蛋白的体积小,但它们在诱导特异性的CTL应答中发挥了重要作用,对评价HIV-1免疫应答的幅度和特异性以及研发针对中国人群的HIV疫苗有重要的意义.     

HIV-1附属蛋白特异性细胞毒性T细胞应答研究

人类免疫缺陷病毒(Humanimmunodeficiencyvirus,HIV)附属蛋白Nef、Vpu、Vpr和Vif在病毒复制中起着关键作用,并能被细胞毒性T细胞(CytotoxicTLymphocyte,CTL)识别。然而,对我国HIV感染者体内附属蛋白特异性的CTL应答研究比较少。本研究应用覆盖HIV-1B、C亚型附属蛋白(Nef、Vpu、Vpr和Vif)的142个肽段作为抗原,通过酶联免疫斑点实验(Enzyme-LinkedImmunospot,ELISPOT)检测61例中国HIV/AIDS患者和10例HIV-1血清阴性对照的HIV-1附属蛋白特异性CTL应答。无论对HIV-1B亚型还是HIV-1C亚型附属蛋白都能产生特异性CTL应答,特别是Nef区蛋白的反应频率和累积应答强度都较高(P<0.001),B、C亚型间的应答频率和累积应答强度都无显著差别(P>0.05),其免疫优势区也大致相同。附属蛋白特异性的累积CTL应答强度将近达到总应答的21%。这些结果表明尽管HIV-1附属蛋白的体积小,但它们在诱导特异性的CTL应答中发挥了重要作用,对评价HIV-1免疫应答的幅度和特异性以及研发针对中国人群的HIV疫苗有重要的意义。     

Analysis of the physiological control of replication of ColE1-type plasmids

The physiology of ColE1-type plasmid replication in a growing host has been examined both theoretically, using computer simulation, and experimentally, by observing replication of the plasmid pBR322 after a nutritional shift-up from glycerol minimal medium (doubling time 71 min) to LB medium (doubling time 24 min). The theory was based on a negative control model and uses three rate equations: for the accumulation of cell mass, for the accumulation of the replication inhibitor, and for the rate of plasmid synthesis. The implications of the theory were explored by simulating the effects of changes in the expression of replication control genes. The nutritional shift-up experiment showed that plasmid replication was blocked immediately after the shift for about half a mass doubling time; after that time, replication rapidly increased until plasmid numbers per unit volume of culture parallelled the increase in culture mass. After the establishment of steady-state growth in the post-shift medium, the plasmid concentration (plasmids per cell mass) was reduced in comparison to pre-shift growth in the same proportion as the culture doubling time. The results showed that plasmid replication factors are under metabolic control and that the changes in the control of these factors compensate one another during steady-state growth, but not immediately after the medium shift.     

Positive Selection on HIV Accessory Proteins and the Analysis of Molecular Adaptation After Interspecies Transmission

Studies examining positive selection on accessory proteins of HIV are rare, although these proteins play an important role in pathogenesis in vivo. Moreover, despite the biological relevance of analyses of molecular adaptation after viral transmission between species, the issue is still poorly studied. Here we present evidence that accessory proteins are subjected to positive selective forces exclusively in HIV. This scenario suggests that accessory protein genes are under adaptive evolution in HIV clades, while in SIVcpz such a phenomenon could not be detected. As a result, we show that comparative studies are critical to carry out functional investigation of positively selected protein sites, as they might help to achieve a better comprehension of the biology of HIV pathogenesis.     

Complementation of transfer deficient ColE1 mutants

Summary The transfer defect of some ColE1 mutants is complemented by ColE1 or ColK, but not by ColE2. This implies that at least one ColE1-specified protein or RNA is normally needed for ColE1 conjugal transfer. The gene(s) postulated for this function lies within a region whose length is at most 50% of the genome.     

A functional map of plasmid ColE1

Summary Examination of the properties of ColE1 derivatives containing either deletions or insertions of transposable genetic elements, has enabled a functional map of plasmid ColE1 to be constructed.     

Crystallization of the ColE1 Rop protein

Preliminary crystallographic data are given for Rop, a protein involved in the control of replication of plasmids of the ColE1 family.     

A Novel Family of Apicomplexan Glideosome-associated Proteins with an Inner Membrane-anchoring Role

The phylum Apicomplexa are a group of obligate intracellular parasites responsible for a wide range of important diseases. Central to the lifecycle of these unicellular parasites is their ability to migrate through animal tissue and invade target host cells. Apicomplexan movement is generated by a unique system of gliding motility in which substrate adhesins and invasion-related proteins are pulled across the plasma membrane by an underlying actin-myosin motor. The myosins of this motor are inserted into a dual membrane layer called the inner membrane complex (IMC) that is sandwiched between the plasma membrane and an underlying cytoskeletal basket. Central to our understanding of gliding motility is the characterization of proteins residing within the IMC, but to date only a few proteins are known. We report here a novel family of six-pass transmembrane proteins, termed the GAPM family, which are highly conserved and specific to Apicomplexa. In Plasmodium falciparum and Toxoplasma gondii the GAPMs localize to the IMC where they form highly SDS-resistant oligomeric complexes. The GAPMs co-purify with the cytoskeletal alveolin proteins and also to some degree with the actin-myosin motor itself. Hence, these proteins are strong candidates for an IMC-anchoring role, either directly or indirectly tethering the motor to the cytoskeleton.Apicomplexan parasites cause a multitude of illnesses through infection of both human and livestock hosts. Members of this phylum include the opportunistic human parasites Toxoplasma gondii and Cryptosporidium parvum, pathogens of livestock, including Theileria annulata and Eimeria tenalla, and most notably the Plasmodium species, the causative agents of malaria in humans. Infection with P. falciparum results in ∼1–3 million deaths and a further 500 million infections annually (1).During various stages of the Apicomplexan lifecycle the parasites require motility to migrate through their insect and vertebrate hosts and to invade and internalize themselves within targeted host cells (2–4). The parasite''s unique mechanism of gliding motility is powered by an Apicomplexan-specific motor complex termed the actin-myosin motor (5), which resides between the outer plasma membrane and inner membrane complex (IMC)⁴ (6). The IMC is a continuous patchwork of flattened vesicular cisternae located directly beneath the plasma membrane and overlying the cytoskeletal network (7, 8). The IMC appears to arise from Golgi-associated vesicles flattened during parasite maturation to form large membranous sheets, which envelope the parasite and leave only a small gap at the extreme parasite apex (9).The myosin component of the actin-myosin motor has previously been defined as a tetrameric complex consisting of a class XIV myosin termed Myo-A (10), a myosin tail interacting protein (also called myosin light chain) (7) and the two glideosome-associated proteins GAP45 and GAP50 (11). These motor components are linked to the outer IMC membrane via the membrane proteins GAP45/50 (11). Between the plasma membrane and the IMC are actin filaments held in place through aldolase-mediated contact with the C-terminal tails of plasma membrane-spanning adhesive proteins whose ectodomains bind substrate and host cells (2). To power the forward movement of apicomplexan zoite stages, myosin pulls the actin filaments and their attached adhesins rearward. For this to succeed the GAP-myosin complex must presumably be fixed to the IMC, possibly via interactions with unidentified proteins linking the motor to the underlying cytoskeleton. Studies of fluorescently tagged GAP50 confirm it is relatively immobile within the IMC, however attempts to identify potential anchoring proteins have not been successful and have instead indicated that GAP50 may be immobilized by the lipid-raft like properties of the IMC membranes (12).The actin-myosin complex is confined to the outer IMC membrane while the opposing innermost IMC membrane is studded with 9 nm intramembranous particles, revealed by electron microscopy of freeze fractured Toxoplasma tachyzoites and Plasmodium ookinetes (13, 14). The size of these particles suggests that the proteins involved are likely to form high molecular weight complexes that overlay the parasite''s cytoskeletal network and possibly anchor the IMC to the cytoskeleton (12–15). Due to the close apposition of the inner and outer IMC membranes (14, 16), it is possible that the intramembranous particles could bridge the IMC lumen and interact with the GAP-myosin complex contributing to its stabilization within the IMC.To identify putative proteins that might be components of the intramembranous particles, we examined data from the detergent-resistant membrane (DRM) proteome of schizont-stage P. falciparum parasites containing developing merozoites (17, 18). DRMs, or lipid-rafts, were of considerable interest, because they appeared to harbor proteins involved in host cell invasion such as glycosylphosphatidylinositol (GPI)-anchored merozoite surface proteins. Our data also indicated that P. falciparum schizont-stage DRMs contained the IMC proteins PfGAP45/50 (17), and recent studies in T. gondii have also suggested that the IMC is enriched in DRMs (12). Another study indicated that when P. falciparum DRM protein complexes were separated by blue native gel electrophoresis, a band was produced containing PfGAP45/50 and PfMyo-A as well as a novel six-pass transmembrane protein (PlasmoDB: PFD1110w, GenBank^TM: {"type":"entrez-protein","attrs":{"text":"CAD49269","term_id":"23498297","term_text":"CAD49269"}}CAD49269) (18). This protein was related to another six-pass transmembrane DRM protein (PlasmoDB: MAL13P1.130, GenBank^TM: {"type":"entrez-protein","attrs":{"text":"CAD52385","term_id":"23615394","term_text":"CAD52385"}}CAD52385) we had previously identified in P. falciparum schizont-stage DRMs (17).We show here that MAL13P1.130 and PFD1110w, termed PfGAPM1 and PfGAPM2 (glideosome-associated protein with multiple-membrane spans), respectively, belong to a family of proteins specific to the Apicomplexa and demonstrate that P. falciparum GAPM proteins, and their orthologues in T. gondii, localize to the parasite IMC. The GAPMs form high molecular weight complexes that are resistant to dissociation and solubilization by a variety of common detergents and could therefore be components of the intramembranous particles seen in electron microscopy. When isolated by immunoprecipitation, the GAPM complexes co-purify with components of the actin-myosin motor and particularly the parasite cytoskeletal network suggesting GAPMs could anchor the IMC to the cytoskeleton and perhaps even play a role in tethering the motor to cytoskeleton.     

Collapse Dynamics of Single Proteins Extended by Force

Single-molecule force spectroscopy has opened up new approaches to the study of protein dynamics. For example, an extended protein folding after an abrupt quench in the pulling force was shown to follow variable collapse trajectories marked by well-defined stages that departed from the expected two-state folding behavior that is commonly observed in bulk. Here, we explain these observations by developing a simple approach that models the free energy of a mechanically extended protein as a combination of an entropic elasticity term and a short-range potential representing enthalpic hydrophobic interactions. The resulting free energy of the molecule shows a force-dependent energy barrier of magnitude, ΔE = ɛ(F − F_c)^3/2, separating the enthalpic and entropic minima that vanishes at a critical force F_c. By solving the Langevin equation under conditions of a force quench, we generate folding trajectories corresponding to the diffusional collapse of an extended polypeptide. The predicted trajectories reproduce the different stages of collapse, as well as the magnitude and time course of the collapse trajectories observed experimentally in ubiquitin and I27 protein monomers. Our observations validate the force-clamp technique as a powerful approach to determining the free-energy landscape of proteins collapsing and folding from extended states.     

Dual-origin plasmids containing an amplifiable ColE1 ori; temperature-controlled expression of cloned genes

Dual-origin plasmids comprising an inducible ColE1-derived origin of replication controlled by the λ p_R promoter, the c1857 temperature-sensitive represser gene and the pSC101 origin of replication and its associated par sequence, were constructed. Such plasmids carrying cloned genes were stably maintained at four copies per chromosome, and were readily amplifiable by thermal induction. Cloned gene expression increased with copy number, and accumulation values of > 20% total cellular protein were detected. These vectors should prove useful for the production of foreign protein on a large scale, since they provide for stable plasmid maintenance during the growth phase, and high-level gene expression without plasmid loss during the production phase.     

Containment of Extended Length Polymorphisms in Silk Proteins

The spider silk gene family to the current date has been developed by gene duplication and homogenization events as well as conservation of crucial sequence parts. These evolutionary processes have created an amazing diversity of silk types each associated with specific properties and functions. In addition, they have led to allelic and gene variants within a species as exemplified by the major ampullate spidroin 1 gene of Nephila clavipes. Due to limited numbers of individuals screened to date little is known about the extent of these heterogeneities and how they are finally manifested in the proteins. Using expanded sample sizes, we show that sequence variations expressed as deletions or insertions of tri-nucleotides lead to different sized and structured repetitive units throughout a silk protein. Moreover, major ampullate spidroins 1 can quite dramatically differ in their overall lengths; however, extreme variants do not spread widely in a spider population. This suggests that a certain size range stabilized by purifying selection is important for spidroin 1 gene integrity and protein function. More than one locus for spidroin 1 genes possibly exist within one individual genome, which are homogenized in size, are differentially expressed and give a spider a certain degree of adaptation on silk’s composition and properties. Such mechanisms are shared to a lesser extent by the second major ampullate spidroin gene.