The Role of Solution Conditions in the Bacteriophage PP7 Capsid Charge Regulation

We investigate and quantify the effects of pH and salt concentration on the charge regulation of the bacteriophage PP7 capsid. These effects are found to be extremely important and substantial, introducing qualitative changes in the charge state of the capsid such as a transition from net-positive to net-negative charge depending on the solution pH. The overall charge of the virus capsid arises as a consequence of a complicated balance with the chemical dissociation equilibrium of the amino acids and the electrostatic interaction between them, and the translational entropy of the mobile solution ions, i.e., counterion release. We show that to properly describe and predict the charging equilibrium of viral capsids in general, one needs to include molecular details as exemplified by the acid-base equilibrium of the detailed distribution of amino acids in the proteinaceous capsid shell.     

Solution Structure of Bacteriophage T4D and Icosahedral Capsid Geometry Visualized in Freeze-Fractured,Deep-Etched Replicas

Abstract

The prolate icosahedral capsid geometry of wild type bacteriophage T4D has been determined by direct visualization of the triangular faces in stereoimages of transmission electron micrographs of phage particles. Bacteriophage T4 was prepared for transmission electron microscopy (TEM) following a protocol of freeze-fracturing, deep-etching (FDET) and replication by vertical deposition (80° angle) of a thin platinum-carbon (Pt-C) metal layer of 1.01 nm. From direct statistical measurements of the ratio of the head length to width and of stereometric angles on T4 heads, we have estimated a Q number of 21. This confirms previous indirect studies on T4 and agrees with determinations on bacteriophage T2. Many of the structural features of T4 observed in FDET preparations differ significantly from those observed by classical negative staining methods for TEM imaging. Most important among the differences are the conformation of the baseplate (a closed rosebud) and the positioning of the tail fibers (retracted). The retracted position of the tail fibers in the FDET preparations has been confirmed by negatively staining phage previously fixed suspended in solution with 2% glutaraldehyde. The FDET protocols appear to reveal important structural features not seen in negative stained preparations. These have implications for bacteriophage T4 conformation in solution, viral assembly and phage conformation states prior to tail contraction and DNA ejection.     

Involvement of a Bacterial Factor in Morphogenesis of Bacteriophage Capsid

A new bacterial factor has been found necessary for the activity of T4 gene 31, the only catalytic factor in the early stage of phage head formation, to process the assembly of head precursor proteins. In a mutant missing this factor, the precursors of phage head aggregate on the bacterial membrane.     

Morphological Study of the Role of Calcium in the Assembly of the Rotavirus Outer Capsid Protein VP7

Maturation of rotavirus occurs in the endoplasmic reticulum (ER), a site of intracellular calcium storage. It was demonstrated previously that calcium plays an important role in the maturation of bovine rotavirus. We used protein A colloidal gold conjugated to an antibody to localize VP7, the outer capsid protein of the simian rotavius SA11, in permeabilized infected cells in the presence and absence of calcium in the culture medium. In medium containing calcium, VP7 was associated with nonenveloped double-shelled particles and membranous structures of the ER. In calcium-free medium, gold particles were not associated with the ER or with virus particles. Gold particles were distributed through the cytoplasm and were mainly associated with granular structures, but did not assemble onto virus particles. Our data suggest that in calcium-free medium, VP7 is synthesized, but does not remain incorporated, in the ER.     

Production of Bacteriophage T7

Bacteriophage T7 was grown with Escherichia coli B as the host organism in 3- and 20-liter vessels. Under the best growth conditions devised, the yields of T7 in the culture lysates averaged 1.33 x 10(12) and 0.95 x 10(12) plaque-forming units per ml, respectively, compared with the best previously reported yields of 10(11) to 3 x 10(11) plaque-forming units per ml in 1-liter batches grown in the presence of air, or double this in similar batches grown in the presence of oxygen. The bacteriophage was purified by a simple method which gave average yields of 143 mg/liter and 131 mg/liter from the 3- and 20-liter batches, respectively. The efficiency of plating of the final material ranged from 18 to 42%. The purified bacteriophage is a convenient source of monodisperse deoxyribonucleic acid, the molecular weight of which is about 25 x 10(6).     

Capsid Size and Deoxyribonucleic Acid Length: the Petite Variant of Bacteriophage T4

A mutant which produces a small-headed ("petite") variant of bacteriophage T4 is described. The mutation (E920g) maps in a new gene (66) between genes 23 and 24. Petite phage particles composed up to 70% of the phage yield. The petite phage was nonviable upon single infection but produced progeny when two or more infected a cell. Its genome was shortened by a random deletion of about 30%, and deoxyribonucleic acid (DNA) extracted from the particles was 0.68 the length of normal T4 DNA. The reduction in DNA length was accompanied by a proportional reduction in head volume. Double mutants between E920g and head-defective mutants in gene 21 produced unusually high frequencies of spherical capsidlike structures (tau-particles).     

Rapid Detection of Escherichia coli O157:H7 by Using Green Fluorescent Protein-Labeled PP01 Bacteriophage

A previously isolated T-even-type PP01 bacteriophage was used to detect its host cell, Escherichia coli O157:H7. The phage small outer capsid (SOC) protein was used as a platform to present a marker protein, green fluorescent protein (GFP), on the phage capsid. The DNA fragment around soc was amplified by PCR and sequenced. The gene alignment of soc and its upstream region was g56-soc.2-soc.1-soc, which is the same as that for T2 phage. GFP was introduced into the C- and N-terminal regions of SOC to produce recombinant phages PP01-GFP/SOC and PP01-SOC/GFP, respectively. Fusion of GFP to SOC did not change the host range of PP01. On the contrary, the binding affinity of the recombinant phages to the host cell increased. However, the stability of the recombinant phages in alkaline solution decreased. Adsorption of the GFP-labeled PP01 phages to the E. coli cell surface enabled visualization of cells under a fluorescence microscope. GFP-labeled PP01 phage was not only adsorbed on culturable E. coli cells but also on viable but nonculturable or pasteurized cells. The coexistence of insensitive E. coli K-12 (W3110) cells did not influence the specificity and affinity of GFP-labeled PP01 adsorption on E. coli O157:H7. After a 10-min incubation with GFP-labeled PP01 phage at a multiplicity of infection of 1,000 at 4°C, E. coli O157:H7 cells could be visualized by fluorescence microscopy. The GFP-labeled PP01 phage could be a rapid and sensitive tool for E. coli O157:H7 detection.     

Translation of Pseudomonas aeruginosa Bacteriophage PP7 RNA by a Cell-Free Amino Acid Incorporating System from Escherichia coli

We have compared the activities of the RNA genomes of Pseudomonas aeruginosa phage PP7 and coliphages Qbeta and f2 in a cell-free amino acid incorporating system derived from Escherichia coli. The rate of incorporation of [(14)C]leucine in the PP7 RNA-directed system is greater than in the systems directed by either Qbeta or f2 RNA. The response to changes in phage RNA concentrations is similar in all the systems, reaching a saturation level at 0.75 to 1.0 mg of RNA per ml of reaction mixture. Analysis of complete reaction mixtures of the PP7 RNA and of the Qbeta RNA systems by sucrose gradient centrifugation shows generally similar patterns for both RNAs. The principal differences are that in the PP7 system a slightly higher percentage of RNA forms ribosome complexes and that the polysomes are somewhat smaller. PP7 RNA is also degraded more extensively during the reaction than is Qbeta RNA. Analysis of the products of the reactions by acrylamide gel electrophoresis shows that PP7 coat protein is the only identifiable product of the PP7 RNA-directed system, suggesting that only the coat protein cistron is translated by E. coli ribosomes.     

Role of the Air-Water-Solid Interface in Bacteriophage Sorption Experiments

Batch sorption experiments were carried out with the bacteriophages MS2 and X174. Two types of reactor vessels, polypropylene and glass, were used. Consistently lower concentrations of MS2 were found in the liquid phase in the absence of soil (control blanks) than in the presence of soil after mixing. High levels of MS2 inactivation (~99.9%) were observed in control tubes made of polypropylene (PP), with comparatively little loss of virus seen in PP tubes when soil was present. Minimal inactivation of MS2 was observed when the air-water interface was completely eliminated from PP control blanks during mixing. All batch experiments performed with reactor tubes made of glass demonstrated no substantial inactivation of MS2. In similar experiments, bacteriophage X174 did not undergo inactivation in either PP or glass control blanks, implying that this virus is not affected by the same factors which led to inactivation of MS2 in the PP control tubes. When possible, phage adsorption to soil was calculated by the Freundlich isotherm. Our data suggest that forces associated with the air-water-solid interface (where the solid is a hydrophobic surface) are responsible for inactivation of MS2 in the PP control tubes. The influence of air-water interfacial forces should be carefully considered when batch sorption experiments are conducted with certain viruses.     

MS2噬菌体衣壳蛋白与包装位点结合特异性及其生物学应用进展

MS2噬菌体为正义单链RNA噬菌体,基因组含有3569个核苷酸,编码成熟酶蛋白、衣壳蛋白、复制酶蛋白和裂解蛋白。MS2噬菌体复制酶编码基因5'端一个由19个碱基组成的茎环结构(又称包装位点)是衣壳蛋白二聚体与RNA相互作用的部位,二者相互作用形成的复合物是启动噬菌体自我包装的信号。MS2噬菌体衣壳蛋白与包装位点结合的特异性已被应用于RNA病毒核酸检测的标准物质、校准品和质控品的研究,实时动态监测活细胞内RNA的运动,以及RNA体内递送载体的研究等领域。     

Role of F Pili in the Penetration of Bacteriophage fl

Early stages of infection of Escherichia coli with the filamentous bacteriophage f1 were examined in the electron microscope. Purified phage-bacteria complexes were prepared at various time intervals after the initiation of synchronous infection. Cells were scored for the total number of F pili, the number of F pili with f1 attached, the number of intact phage particles which occurred at the surface of the cell, and F pilus length. Electron microscope autoradiographs were also prepared at each time interval. The results showed that the average number of F pili with f1 attached decreased with time as phage deoxyribonucleic acid (DNA) entered the cell. Concomitant with this loss, the remaining F pili became shorter. The rate of entry of phage DNA into the cell followed, with a short lag, the rate of loss of F pili with f1 attached. During the lag period, intact phage particles accumulated at the surface of the cell. The results from radioautographs showed that no phage DNA could be located within the F pilus. These results suggest that F pili are resorbed by the cell during infection with the bacteriophage f1. Parallel experiments with noninfected cultures further suggest that pilus resorption may be a normal cellular phenomenon.     

蛋白磷酸酶2A对微管的调控作用研究进展

微管是细胞骨架的主要成分之一,几乎存在于所有真核生物细胞之中,参与细胞众多生理功能。PP2A是真核生物体内存在最广泛的蛋白磷酸酶之一,可以调控大部分细胞生命活动,其中,包括微管所介导的许多生命活动。该文从以下方面介绍了PP2A在微管功能行使中的重要作用,包括PP2A参与微管蛋白翻译后修饰、调控分子马达和微管相关蛋白的活性、维持细胞周期中微管的动态平衡以及PP2A异常与微管类疾病的相关性。     

Adsorption of Bacteriophage eb7 on Streptococcus cremoris EB7

When M17 broth was used as growth medium before preparation of cell walls, adsorption of phage eb7 on Streptococcus cremoris EB7 at pH 4.0 was stimulated. When preparation included treatment with trypsin, absorption of phage was 65%. Without trypsin treatment, absorption was 81%. Only 10 to 20% of the adsorption was irreversible. Treatment with pepsin or commercial rennet but not pure chymosin prevented adsorption on non-trypsin-treated cell walls. d-Galactosamine treatment of phage eb7 had an inactivating effect which was enhanced by l-rhamnose.     

Structural Characterization of the Bacteriophage T7 Tail Machinery

Most bacterial viruses need a specialized machinery, called “tail,” to inject their genomes inside the bacterial cytoplasm without disrupting the cellular integrity. Bacteriophage T7 is a well characterized member of the Podoviridae family infecting Escherichia coli, and it has a short noncontractile tail that assembles sequentially on the viral head after DNA packaging. The T7 tail is a complex of around 2.7 MDa composed of at least four proteins as follows: the connector (gene product 8, gp8), the tail tubular proteins gp11 and gp12, and the fibers (gp17). Using cryo-electron microscopy and single particle image reconstruction techniques, we have determined the precise topology of the tail proteins by comparing the structure of the T7 tail extracted from viruses and a complex formed by recombinant gp8, gp11, and gp12 proteins. Furthermore, the order of assembly of the structural components within the complex was deduced from interaction assays with cloned and purified tail proteins. The existence of common folds among similar tail proteins allowed us to obtain pseudo-atomic threaded models of gp8 (connector) and gp11 (gatekeeper) proteins, which were docked into the corresponding cryo-EM volumes of the tail complex. This pseudo-atomic model of the connector-gatekeeper interaction revealed the existence of a common molecular architecture among viruses belonging to the three tailed bacteriophage families, strongly suggesting that a common molecular mechanism has been favored during evolution to coordinate the transition between DNA packaging and tail assembly.     

The Impact of Viral RNA on the Association Rates of Capsid Protein Assembly: Bacteriophage MS2 as a Case Study

A large number of single-stranded RNA viruses, which form a major class of all viruses, co-assemble their protein container and their genomic material. The multiple roles of the viral genome in this process are presently only partly understood. Recent experimental results indicate that RNA, in addition to its function as a repository for genetic information, could play important functional roles during the assembly of the viral protein containers. An investigation of the impact of genomic RNA on the association of the protein subunits may therefore provide further insights into the mechanism of virus assembly. We study here the impact of viral RNA on the association rates of the capsid proteins during virus assembly. As a case study, we consider the viral capsid of bacteriophage MS2, which is formed from 60 asymmetric (AB) and 30 symmetric (CC) protein dimers. Using Brownian dynamics simulations, we investigate the effect of the binding of an RNA stem-loop (the translational repressor) on the association rates of the capsid protein dimers. Our analysis shows that translational repressor binding results in self-association of AB dimers being inhibited, whilst association of AB with CC dimers is greatly enhanced. This provides an explanation for experimental results in which an alternating assembly pattern of AB and CC dimer addition to the growing assembly intermediate has been observed to be the dominant mode of assembly. The presence of the RNA hence dramatically decreases the number of dominant assembly pathways and thereby reduces the complexity of the self-assembly process of these viruses.     

The Role of PP2A A Subunits in Tumor Suppression

The protein phosphatase 2A (PP2A) family of heterotrimeric serine-threonine phosphatases participates in human cell transformation. Each functional PP2A complex contains one structural A subunit (Aα or Aβ), and mutations of both are found to occur at low frequency in human tumors. We have shown that Aα functions as haploinsufficient tumor suppressor gene by regulating in part phosphatidylinositol 3-kinase (PI3K) signaling. In contrast, loss of Aβ function due to biallelic alterations contributes to cancer progression through dysregulation of small GTPase RalA activity. These observations provide evidence that dysfunction of particular PP2A complexes regulate specific phosphorylation event necessary for cancer initiation.Key Words: protein phosphatase 2A, RalA, cancer, transformationReversible phosphorylation plays a key role in the regulation of signaling pathways relevant to cell transformation. Dysregulation of several kinase oncogenes have been shown to be required for cancer development, and several targeted therapies focused on inhibiting particular kinases have now been approved for clinical use. Although it is clear that phosphorylation is also regulated by phosphatases, initial biochemical studies suggested that unlike kinases, phosphatases act promiscuously and constitutively in vitro. However, recent work indicates that phosphatases play essential roles in malignant transformation by acting on specific substrates in vivo.Protein phosphatase 2A (PP2A) is a family of serine-threonine phosphatases implicated in the control of a diverse array of cellular processes. The PP2A core enzyme consists of a catalytic C subunit and a structural A subunit. In mammals, two distinct genes encode closely related versions of both the PP2A A and C subunits. The AC dimer recruits a third regulatory B subunit that has been predicted to dictate the substrate specificity and function of the PP2A heterotrimeric complex. Four unrelated families of B subunits have identified to date: B/B55/PR55/PPP2R2, B′/B56/PR61/PPP2R5, B″/PR72/PPP2R3 and Striatin¹ (Fig. 1). Recent genetic and proteomic studies implicate clear roles for PP2A subunits in regulating physiological functions and one emerging view is that specific PP2A complexes play critical roles in cell transformation by regulating particular substrates.Open in a separate windowFigure 1Disruption of PP2A complexes induces transformation. PP2A is a heterotrimeric protein complex, and several isoforms exist for each of the three subunits, creating a diverse family of related enzymes that regulate specific physiological functions. Alterations of PP2A structural subunits, Aα and Aβ, contribute to spontaneously arising human cancers by distinct mechanisms. Cancer-associated Aα haploinsufficiency may induce human cell transformation by activating PI3K/AKT pathway while PP2A Aβ loss-of-function permits the accumulation of activated RalA.Somatic alterations of the PP2A structural subunit Aβ (PPP2R1B) have been found to occur in colon, lung and breast cancers.^2–5 Notably, point mutations in one Aβ allele are commonly accompanied by loss of the second Aβ allele. We confirmed previous work⁶ that showed cancer-associated Aβ mutants form functionally null alleles.⁷ These studies indicate that Aβ is genetically inactivated in a subset of human cancers. In addition, we found that suppression of Aβ was found to cooperate with H-Ras, telomerase catalytic subunit hTERT and the SV40 Large T antigen to induce transformation of normal human cells while introduction of wild type Aβ into lung carcinoma cells lacking functional Aβ partially reverses this tumorigenic phenotype.⁷ Together, these data provide evidence that PP2A Aβ functions as a tumor suppressor gene.Previous work has shown cancer derived Aβ mutants exhibit markedly impaired ability to form complexes with the catalytic C subunit and the regulatory PR72 subunit.⁶ We have found that Aβ mutants also showed decreased ability to bind to regulatory Bα subunit and several members of B′ family. These data indicate that cancer-associated alterations of PP2A Aβ result in disruption of most if not all PP2A Aβ-containing complexes. Considering that distinct Aβ-B complexes are likely regulate the phosphorylation of particular substrates involved in transformation, further work is required to identify which B subunits participate in malignant transformation.Somatic mutations of the more abundant PP2A structural Aα subunit have also been reported in human cancers, although at low frequency.^2,8 We previously showed that cancer-associated PP2A Aα mutations contribute to cell transformation by creating a state of haploinsufficiency.⁹ Although these two distinct PP2A structural isoforms, Aα and Aβ, are 86% identical,¹⁰ it was unclear whether these two isoforms share overlapping functions.¹¹ We found that overexpression of Aα failed to revert the tumorigenic phenotype induced by Aβ suppression, suggesting that PP2A complexes containing Aα or Aβ are functionally distinct.To identify substrates specific for PP2A Aβ, we performed large scale immunopurification of PP2A Aα- and Aβ-containing complexes. We have found that PP2A Aβ complex, but not the PP2A Aα complex, binds to and inhibits activity of the small GTPase RalA through direct dephosphorylation at Ser183 and Ser 194. Cancer-associated Aβ mutants are unable to dephosphorylate RalA, suggesting that loss of Aβ function impairs the formation of complexes with RalA and deregulates its activity. Consistent with previous reports that implicated RalA in regulation of several signaling pathways relevant to cell transformation,^12–14 loss of function experiments revealed that RalA is crucial for transformation mediated by Aβ dysfunction. These findings strongly suggest that accumulation of phospho-RalA in PP2A Aβ deficient cells promotes tumorigenic phenotype (Fig. 1). However, we cannot exclude that other substrates of PP2A Aβ complexes also contribute to cell transformation.These observations also implicate phosphorylation of RalA as an alternative mechanism that may regulate RalA activity and cell transformation. Prior work has shown Aurora A kinase as one kinase that can induce RalA phosphorylation at Ser 194.¹⁵ However, further studies are required to identify the kinase(s) that are responsible for RalA phosphorylation at Ser 183 and Ser 194.While Aβ loss-of-function permits the accumulation of activated RalA, Aα haploinsufficiency seems to induce human cell transformation by activating AKT/PI3K signaling pathway⁹ (Fig. 1). However, it remains unclear whether PP2A A subunits determine the substrate specificity of heterotrimeric complexes by direct substrate binding, or by forming complex with particular set of B and C subunits. In consonance with the latter idea, Aα and Aβ have been reported to have different affinity to Cα, Bα, B''α1 and PR72 subunits.¹⁷ The systematic characterization of PP2A complex composition necessary for RalA dephosphorylation and Akt activation and further structural studies to resolve PP2A in complex with specific substrates will help elucidate the mechanistic details of how PP2A acts as a tumor suppressor.     

The Role of PP2A A Subunits in Tumor Suppression

The protein phosphatase 2A (PP2A) family of heterotrimeric serine-threonine phosphatases participates in human cell transformation. Each functional PP2A complex contains one structural A subunit (Aα or Aβ), and mutations of both are found to occur at low frequency in human tumors. We have shown that Aα functions as haploinsufficient tumor suppressor gene by regulating in part phosphatidylinositol 3-kinase (PI3K signaling). In contrast, loss of Aβ function due to biallelic alterations contributes to cancer progression through dysregulation of small GTPase RalA activity. These observations provide evidence that dysfunction of particular PP2A complexes regulate specific phosphorylation event necessary for cancer initiation.