"Phospholipids of virus-induced membranes in cytoplasm of Escherichia coli

Structure, Biology, and Applications of Filamentous Bacteriophages

The closely related Escherichia coli Ff filamentous phages (f1, fd, and M13) have taken a fantastic journey over the past 60 years, from the urban sewerage from which they were first isolated, to their use in high-end technologies in multiple fields. Their relatively small genome size, high titers, and the virions that tolerate fusion proteins make the Ffs an ideal system for phage display. Folding of the fusions in the oxidizing environment of the E. coli periplasm makes the Ff phages a platform that allows display of eukaryotic surface and secreted proteins, including antibodies. Resistance of the Ffs to a broad range of pH and detergents facilitates affinity screening in phage display, whereas the stability of the virions at ambient temperature makes them suitable for applications in material science and nanotechnology. Among filamentous phages, only the Ffs have been used in phage display technology, because of the most advanced state of knowledge about their biology and the various tools developed for E. coli as a cloning host for them. Filamentous phages have been thought to be a rather small group, infecting mostly Gram-negative bacteria. A recent discovery of more than 10 thousand diverse filamentous phages in bacteria and archaea, however, opens a fascinating prospect for novel applications. The main aim of this review is to give detailed biological and structural information to researchers embarking on phage display projects. The secondary aim is to discuss the yet-unresolved puzzles, as well as recent developments in filamentous phage biology, from a viewpoint of their impact on current and future applications.

Targeting a helix-in-groove interaction between E1 and E2 blocks ubiquitin transfer

The ubiquitin-proteasome system (UPS) is a highly regulated protein disposal process critical to cell survival. Inhibiting the pathway induces proteotoxic stress and can be an effective cancer treatment. The therapeutic window observed upon proteasomal blockade has motivated multiple UPS-targeting strategies, including preventing ubiquitination altogether. E1 initiates the cascade by transferring ubiquitin to E2 enzymes. A small molecule that engages the E1 ATP-binding site and derivatizes ubiquitin disrupts enzymatic activity and kills cancer cells. However, binding-site mutations cause resistance, motivating alternative approaches to block this promising target. We identified an interaction between the E2 N-terminal alpha-1 helix and a pocket within the E1 ubiquitin-fold domain as a potentially druggable site. Stapled peptides modeled after the E2 alpha-1 helix bound to the E1 groove, induced a consequential conformational change and inhibited E1 ubiquitin thiotransfer, disrupting E2 ubiquitin charging and ubiquitination of cellular proteins. Thus, we provide a blueprint for a distinct E1-targeting strategy to treat cancer.

Unifying principles of bifunctional, proximity-inducing small molecules

Nature uses a variety of tools to mediate the flow of information in cells, many of which control distances between key biomacromolecules. Researchers have thus generated compounds whose activities stem from interactions with two (or more) proteins simultaneously. In this Perspective, we describe how these 'bifunctional' small molecules facilitate the study of an increasingly wide range of complex biological phenomena and enable the drugging of otherwise challenging therapeutic targets and processes. Despite their structural and functional differences, all bifunctional molecules employ Nature's strategy of altering interactomes and inducing proximity to modulate biology. They therefore exhibit a shared set of chemical and biophysical principles that have not yet been appreciated fully. By highlighting these commonalities-and their wide-ranging consequences-we hope to chip away at the artificial barriers that threaten to constrain this interdisciplinary field. Doing so promises to yield remarkable benefits for biological research and therapeutics discovery.

Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small-molecule/protein interactions in human cells. Excavating clear structure-activity relationships from these 'ligandability' maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or 'enantioprobes', we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into fully functionalized fragment libraries provides a robust and streamlined method to discover ligandable proteins in cells.

Filamentous Phage: Structure and Biology

Ff filamentous phage (fd, M13 and f1) of Escherichia coli have been the workhorse of phage display technology for the past 30 years. Dominance of Ff over other bacteriophage in display technology stems from the titres that are about 100-fold higher than any other known phage, efficacious transformation ensuring large library size and superior stability of the virion at high temperatures, detergents and pH extremes, allowing broad range of biopanning conditions in screening phage display libraries. Due to the excellent understanding of infection and assembly requirements, Ff phage have also been at the core of phage-assisted continual protein evolution strategies (PACE). This chapter will give an overview of the Ff filamentous phage structure and biology, emphasizing those properties of the Ff phage life cycle and virion that are pertinent to phage display applications.

Localization and rearrangement modulation of the N-terminal arm of the membrane-bound major coat protein of bacteriophage M13

During infection the major coat protein of the filamentous bacteriophage M13 is in the cytoplasmic membrane of the host Escherichia coli. This study focuses on the configurational properties of the N-terminal part of the coat protein in the membrane-bound state. For this purpose X-Cys substitutions are generated at coat protein positions 3, 7, 9, 10, 11, 12, 13, 14, 15, 17, 19, 21, 22, 23 and 24, covering the N-terminal protein part. All coat protein mutants used are successfully produced in mg quantities by overexpression in E. coli. Mutant coat proteins are labeled and reconstituted into mixed bilayers of phospholipids. Information about the polarity of the local environment around the labeled sites is deduced from the wavelength of maximum emission using AEDANS attached to the SH groups of the cysteines as a fluorescent probe. Additional information is obtained by determining the accessibility of the fluorescence quenchers acrylamide and 5-doxyl stearic acid. By employing uniform coat protein surroundings provided by TFE and SDS, local effects of the backbone of the coat proteins or polarity of the residues could be excluded. Our data suggest that at a lipid to protein ratio around 100, the N-terminal arm of the protein gradually enters the membrane from residue 3 towards residue 19. The hinge region (residues 17-24), connecting the helical parts of the coat protein, is found to be more embedded in the membrane. Substitution of one or more of the membrane-anchoring amino acid residues lysine 8, phenylalanine 11 and leucine 14, results in a rearrangement of the N-terminal protein part into a more extended conformation. The N-terminal arm can also be forced in this conformation by allowing less space per coat protein at the membrane surface by decreasing the lipid to protein ratio. The influence of the phospholipid headgroup composition on the rearrangement of the N-terminal part of the protein is found to be negligible within the range thought to be relevant in vivo. From our experiments we conclude that membrane-anchoring and space-limiting effects are key factors for the structural rearrangement of the N-terminal protein part of the coat protein in the membrane.

The inhibitory effect of dithiothreitol on the assembly of the filamentous phage fd

Assembly of the filamentous phage fd is preceded by the formation of a complex between the viral single-stranded (ss) DNA and the virally coded gene 5 protein (gene 5 protein-ssDNA complex). The presence of 5 mM dithiothreitol in the growth medium prevents phage production; however, phage infection, phage DNA replication and phage genome expression are still observed. In contrast, the gene 5 protein-ssDNA complex is not formed in the presence of dithiothreitol in vivo, although the complex is not affected by the disulfide reducing agent in vitro. Furthermore, host lipid composition is altered by growth in the presence of dithiothreitol. The zwitterionic lipid, phosphatidylethanolamine, increases while the cationic phospholipid content, cardiolipin and phosphatidylglycerol, decreases. This suggests a role for lipids or membranous structures in the process of gene 5 protein-ssDNA complex formation.

Cloning and expression of the pnd gene of R16: determination of transcriptional direction and evolutionary analysis

The gene promoting nucleic-acid degradation (pnd) of IncB plasmid R16 was cloned into the vector plasmid pACYC177. The pnd gene was found to be located on a 0.55-kilobase (kb) AluI-PstI fragment by constructing subclones carrying various portions of the initially cloned fragment. The direction of transcription of the pnd gene was determined by inserting the gene in both orientations into the lacZ' gene of the plasmid pUR222. In the recombinant plasmid pCM2, transcription of the pnd gene was controlled by the lac promoter region. Addition of cAMP at 42 C resulted in rapid degradation of stable RNA in cells harboring pCM2. In contrast, no RNA degradation was observed in cells harboring pCM14, which has the same insert as pCM2 but in the opposite orientation. The equivalent gene, pnd of IncI alpha plasmid R483, has previously been cloned, and a detailed restriction map of the region has been constructed (Akimoto, S., and Ohnishi, Y. 1982. Microbiol. Immunol. 26: 779-793). We constructed a detailed restriction map of the pnd region of R16 and compared it with that of R483. Restriction analyses revealed a similar structure in these two pnd regions. The results suggest that the pnd genes of R16 and R483 have a common evolutional origin.

R483 and F plasmid genes promoting RNA degradation: comparative restriction mapping

The gene promoting nucleic-acid degradation (pnd) on IncIa plasmid R483 was cloned into pBR322. It is located on a 0.85 kilobase (kb) EcoRI-SalI fragment and is close to Tn7. The pnd gene has similar properties to the srnB gene on the F plasmid. A cleavage map of the 0.85 kb pnd fragment was constructed and compared with that of the 1.18 kb EcoRI-BamHI fragment containing the srnB gene. These two regions showed marked heterogeneity as evidenced by their distinctly different restriction maps. This result suggests separate paths of evolution of the two genes for stable RNA degradation.

Cloning of a 1.1-kb fragment including srnB+ gene in the F plasmid and isolation of an srnB mutant

The srnB+ gene, promoting stable RNA degradation at 42 C in the presence of rifampin, was cloned by using pBR322 as a vector; it was located on a 1.1-kilobase (kb) Eco RI/Bam HI fragment between 1.4 and 2.5 kb of the F plasmid. The region between 93.3 and 4.0 kb of the F plasmid was physically mapped by using restriction endonucleases EcoRI, HindIII, BamHI, PstI, and SmaI, with reference to a standard HindIII site in IS3. An srnB1 mutant was isolated from a chimeric plasmid, pOY54, after treatment of its DNA with hydroxylamine. The srnB1 allele on the F fragment of the mutant plasmid was recessive to the wildtype allele. Thermal elevation of cell cultures to 39 C was high enough to promote RNA degradation in strain YS12 carrying plasmid pOY54.

Membrane composition and virus susceptibility of Acholeplasma laidlawii

The membrane composition of 11 strains of Acholeplasma laidlawii, including three strains persistently infected with mycoplasmaviruses MVL51, MVL2, and MVL3, was studied and correlated with mycoplasmavirus sensitivity. Membranes of the strains had similiar sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns, and all strains were inhibited by an antiserum produced against membranes from one of the strains. The amounts of integral membrane proteins solubilized by the nonionic detergent Tween 20 differed considerably. Therefore, characteristic crossed immunoelectrophoresis patterns were obtained for each strain. Strains persistently infected with MVL2 and MVL3 were notably different from the noninfected host. The ability to propagate any of the viruses was not correlated with sodium dodecyl sulfate-polyacrylamide gel electrophoresis or crossed immunoelectrophoresis patterns. The persistently infected strains had a characteristic lipid composition. MVL51-resistant strains, including a resistant clone selected from a sensitive strain, were characterized by a large monoglucosyldiglyceride/diglucosyldiglyceride ratio and trace amounts of diphosphatidylglyceol (as opposed to the sensitive strains). Differences in lipid composition in A. laidlawii seem to affect the relationship between cells and viruses.

Effect of membrane-associated f1 bacteriophage coat protein upon the activity of Escherichia coli phosphatidylserine synthetase

The effects of insertion of the major coat protein of f1 bacteriophage into Escherichia coli membranes were investigated under conditions allowing in vivo analysis of phosphatidylserine synthesis. An E. coli strain possessing a temperature-sensitive phosphatidylserine decarboxylase was utilized under conditions in which the decarboxylase activity was reduced but nonlethal. The presence of the coat protein in the host membranes inhibits the activity of the phosphatidylserine synthetase and perhaps affects the activity of the phosphatidylserine decarboxylase.

Septation deficiency and phosphilipid perturbation in Escherichia coli genetically constitutive for the beta oxidation pathway

Mutants of Escherichia coli defective in the regulation of the fatty acids beta oxidation pathway show an ultrastructural deficiency in septum formation at high growth rate. Several independent pairs of parent and mutant strains have been analyzed biochemically. Each parent strain displays a well-defined pattern of cellular phospholipids, which varies with the growth conditions. High ratios of phosphatidylglycerol to cardiolipin characterize fast-growth conditions. None of the mutant strains, although they grow in mass nearly as rapidly as their respective parents, can reach these high ratios. The beta oxidation pathway regulatory mutation leads to an increased turnover of the glycerol moieties of these phospholipids in the inner as well as in the outer cell membrane.

Mesosomes: membranous bacterial organelles

Images

Altered phospholipid metabolism in Escherichia coli accompanying killing by disrupted granulocytes

The effect of bactericidal concentrations of disrupted rabbit granulocytes and of partially purified granulocyte fractions on phospholipid metabolism by Escherichia coli has been investigated. Previous studies in this laboratory have shown that, during and after killing of E. coli by granulocytes, bacterial macromolecular synthesis continues. Similarly, despite almost complete loss of viability within 15 min, incorporation of [1-(14)C]palmitate, [2-(14)C]glycerol, and [1-(14)C]acetate into E. coli phospholipids, in the presence of granulocyte preparations, remains the same as in control E. coli populations for at least 1 h. Incorporation of [1-(14)C]oleate into E. coli phospholipids is actually stimulated during the first 60 min of incubation in the presence of granulocyte preparations (more than twofold at 30 min and 40% at 60 min). With all labeled lipid precursors, bactericidal granulocyte preparations cause a relative increase in the labeling of E. coli cardiolipin, with a corresponding drop in labeled phosphatidyl-glycerol. Labeled lyso-compounds accumulate in the presence of granulocyte preparations when [1-(14)C]palmitate, but not when [1-(14)C]oleate is the labeled precursor. Since oleate occurs mainly in the 2-acyl position of E. coli phospholipids, whereas at least 50% of palmitate occurs in the 1 position, it appears that a phospholipase A(2) acts on the E. coli phospholipids. These various effects are also seen when E. coli are exposed to highly purified granulocyte preparations that possess potent bactericidal and phospholipase A(2) activities. We speculate that this phospholipase A(2) in the granulocyte preparations stimulates oleate but not palmitate incorporation by initiating increased turnover of the fatty acid in the 2-acyl position of E. coli phospholipids, causing formation of 1-acyl lyso-compounds likely to be preferentially reacylated with unsaturated fatty acids.

Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermophilus

The total phospholipid content of Bacillus stearothermophilus was constant during exponential growth, increased during the transition from the exponential to stationary phase of growth, and then slowly increased during the stationary phase. The first increase was a result of an increase in phosphatidylethanolamine; the second was a result of an increase in cardiolipin. Cessation of aeration of an exponentially growing culture or suspension in a nongrowth medium resulted in an immediate reduction in the rate of total phospholipid and phosphatidylethanolamine synthesis and a quantitative conversion of phosphatidylglycerol to cardiolipin. Cardiolipin appeared to be synthesized by the direct conversion of two molecules of phosphatidylglycerol to cardiolipin. After a 20-min pulse of (32)P, phosphatidylglycerol showed the most rapid loss of (32)P followed by cardiolipin, whereas phosphatidylethanolamine did not lose (32)P. The loss of (32)P from the total lipid pool, phosphatidylglycerol, and cardiolipin was biphasic, with rapid loss during the first two bacterial doublings followed by a greatly reduced rate of loss. The major loss of (32)P from the total phospholipid pool appeared to be by breakdown of cardiolipin. The loss of (32)P from the lipid pool was energy dependent (i.e., did not occur under anaerobic conditions or in the absence of an energy source) and was dependent on some factor other than the concentration of cardiolipin in the cells. The apparent conversion of phosphatidylglycerol to cardiolipin was independent of energy metabolism. Chloramphenicol reduced the rate of turnover of both phosphatidylglycerol and cardiolipin. The rate of lipid synthesis (all phospholipid components) was constant for about 10 min after the addition of chloramphenicol but diminished markedly after 20 min. Turnover of (32)P incorporated into phospholipid during a 30-min period prior to the addition of chloramphenicol was more rapid after the removal of chloramphenicol than that of (32)P incorporated during a 30-min period in the presence of chloramphenicol.

Ultrastructural properties of the extra membranes of Escherichia coli O111a as revealed by freeze-fracturing and negative-staining techniques

Escherichia coli O111a is a thermosensitive strain which, when grown at 40 C, accumulates large quantities of intracellular membranes. The ultrastructure of these membranes in cells which have been chemically fixed, embedded, and examined as thin sections has been compared with that of membranes in cells negatively stained or freeze-fractured. Results indicate that the extra membranes are present in the three types of preparations examined and, therefore, clearly are not artifacts of chemical fixation. Negative staining has proved also to be a valuable tool as a rapid means of monitoring cells for the accumulation of large amounts of extra membranes. Also, examination of thin sections has shown that distinct continuities between the plasma membrane and the extra membranes exist. In general, membrane surfaces in freeze-fractured cells containing extra membranes appear smooth and lack the particles associated with the plasma membranes of many cells.