Relative susceptibilities of caffeine-sensitive and caffeine-resistant strains of Candida albicans to inactivation and mutation by ultraviolet radiation

Summary Stable variants having increased resistance to growth inhibition by caffeine were obtained from four different absolute, amino acid auxotrophs of Candida albicans. Differences in growth rates and expression of auxotrophy between the resistant (Caf^R) variants and their sensitive (Caf^S) progenitors suggest that caffeine resistance arises through suppressor mutations which affect the fidelity of messenger RNA translation.Both Caf^S and Caf^R strains of C. albicans are more susceptible to inactivation by ultraviolet radiation (uv) when grown at 37°C rather than 25°C following exposure. Post irradiation growth on caffeine potentiates ultraviolet inactivation of all Caf^S strains at both temperatures. Depending on its origin, a Caf^R strain (i) may show greater, lesser or the same intrinsic susceptibility to uv inactivation as its Caf^S parent at 25°C or at 37°C and (ii) may or may not be refractory to post-irradiation contact with caffeine. Caf^R variants independently isolated from a given auxotroph are alike in inactivational responses whereas those obtained from different auxotrophs are dissimilar. This implies that different suppressor mutations are unique in the way they affect expression of potentially lethal uv damage and that only one kind of suppressor is obtained by selection for caffeine resistance in a particular auxotroph.The histidine requiring Caf^R strain WB-2CR is much more resistant to uv inactivation that its Caf^S parent WB-2. Moreover, post-irradiation survival of WB-2CR is unaffected by caffeine. However, WB-2CR and WB-2 are equally susceptible to uv-induced reversion to prototrophy. In both strains, caffeine does not enhance uv-induced reversion at 25°C or 37°C and exhibits an antimutagenic activity at high uv dosage at 37°C.The findings reinforce previously reported indications that, in C. albicans, (i) caffeine-sensitive excision-repair of uv damaged DNA does not occur and (ii) caffeine potentiates uv cellular inactivation by disturbing post-irradiation synthesis of protein essential for recovery from non-genetic damage.     

Effect of protein synthesis inhibition on recovery of UV- and γ-irradiated Schizosaccharomyces pombe from repair inhibition by caffeine

Summary The progress of repair in Schizosaccharomyces pombe may be followed during post-irradiation incubation by measuring, after various intervals, the ability of UV- or -irradiated cells to avoid enhanced lethality when exposed to the repair inhibitor caffeine (Gentner and Werner, 1975). This technique has now been used to investigate the effect of inhibition of protein synthesis on repair of UV- and -irradiation-induced damage in this organism.When protein synthesis was inhibited with cycloheximide in UV-irradiated wild-type cells, only a small amount of recovery from caffeine inhibition occurred; this indicated that post-irradiation protein synthesis was required for repair, and in particular for the recombinational repair pathway, which is a major mechanism for repair of UV damage in this organism.In -irradiated wild-type cells, inhibition of post-irradiation protein synthesis reduced the rate of recovery from repair inhibition by caffeine, but full recovery from caffeine-sensitive damage did occur at longer incubation times. We attribute the reduction in rate to the effect of protein synthesis inhibition on the recombinational repair pathway, because this pathway is known to be involved in the repair of both -ray and UV damage. The recovery that took place at the slower rate must reflect a caffeine-sensitive pathway which is involved only in repair of -ray damage and which does not require post-irradiation protein synthesis for activity.AECL Reference No. 5402     

The pigment system of the photoreceptor 7 yellow in the fly,a complex photoreceptor

Summary The 7y photoreceptor in the fly (Musca, Calliphora) retina harbours an unusually complex pigment system consisting of a bistable visual pigment (xanthopsin, X and metaxanthopsin, M), a blue-absorbing C₄₀-carotenoid (zeaxanthin and/or lutein) and a uv sensitizing pigment (3-OH retinol).The difference spectrum and photoequilibrium spectrum in single 7y rhabdomeres were determined microspectrophotometrically (Fig. 2).The extinction spectrum of the C₄₀-carotenoid has a pronounced vibrational structure, with peaks at 430, 450 and 480 nm (Fig. 3). The off-axis spectral sensitivity, determined electrophysiologically with 1 nm resolution shows no trace of this fine structure thus excluding the possibility that the C₄₀-carotenoid is a second sensitizing pigment (Fig. 4).The absorption spectra of X and M are derived by fitting nomogram spectra (based on fly R1–6 xanthopsin) to the difference spectrum. max for X is 425 nm, and for M 510 nm (Fig. 5). It is shown that the photoequilibrium spectrum and the difference spectrum can be used to derive the relative photosensitivity spectra of X and M using the analytical method developed by Stavenga (1975). The result (Fig. 6) shows a pronounced uv sensitivity for both, X and M, indicating that the uv sensitizing pigment transfers energy to both X and M. A value of 0.7 for, the relative efficiency of photoconversion for X and M, is obtained by fitting the analytically derived relative photosensitivity spectra to the absorption spectra at wavelengths beyond 420 nm.     

Differential effects of caffeine on DNA damage and replication cell cycle checkpoints in the fission yeast Schizosaccharomyces pombe

Caffeine potentiates the lethal effects of ultraviolet and ionising radiation on wild-type Schizosaccharomyces pombe cells. In previous studies this was attributed to the inhibition by caffeine of a novel DNA repair pathway in S. pombe that was absent in the budding yeast Saccharomyces cerevisiae. Studies with radiation-sensitive S. pombe mutants suggested that this caffeine-sensitive pathway could repair ultraviolet radiation damage in the absence of nucleotide excision repair. The alternative pathway was thought to be recombinational and to operate in the G₂ phase of the cell cycle. However, in this study we show that cells held in G₁ of the cell cycle can remove ultraviolet-induced lesions in the absence of nucleotide excision repair. We also show that recombination-defective mutants, and those now known to define the alternative repair pathway, still exhibit the caffeine effect. Our observations suggest that the basis of the caffeine effect is not due to direct inhibition of recombinational repair. The mutants originally thought to be involved in a caffeine-sensitive recombinational repair process are now known to be defective in arresting the cell cycle in S and/or G₂ following DNA damage or incomplete replication. The gene products may also have an additional role in a DNA repair or damage tolerance pathway. The effect of caffeine could, therefore, be due to interference with DNA damage checkpoints, or inhibition of the DNA damage repair/tolerance pathway. Using a combination of flow cytometric analysis, mitotic index analysis and fluorescence microscopy we show that caffeine interferes with intra-S phase and G₂ DNA damage checkpoints, overcoming cell cycle delays associated with damaged DNA. In contrast, caffeine has no effect on the DNA replication S phase checkpoint in reponse to inhibition of DNA synthesis by hydroxyurea. Received: 16 June 1998 / Accepted: 13 July 1998     

Differential effects of caffeine on DNA damage and replication cell cycle checkpoints in the fission yeast Schizosaccharomyces pombe

Caffeine potentiates the lethal effects of ultraviolet and ionising radiation on wild-type Schizosaccharomyces pombe cells. In previous studies this was attributed to the inhibition by caffeine of a novel DNA repair pathway in S. pombe that was absent in the budding yeast Saccharomyces cerevisiae. Studies with radiation-sensitive S. pombe mutants suggested that this caffeine-sensitive pathway could repair ultraviolet radiation damage in the absence of nucleotide excision repair. The alternative pathway was thought to be recombinational and to operate in the G₂ phase of the cell cycle. However, in this study we show that cells held in G₁ of the cell cycle can remove ultraviolet-induced lesions in the absence of nucleotide excision repair. We also show that recombination-defective mutants, and those now known to define the alternative repair pathway, still exhibit the caffeine effect. Our observations suggest that the basis of the caffeine effect is not due to direct inhibition of recombinational repair. The mutants originally thought to be involved in a caffeine-sensitive recombinational repair process are now known to be defective in arresting the cell cycle in S and/or G₂ following DNA damage or incomplete replication. The gene products may also have an additional role in a DNA repair or damage tolerance pathway. The effect of caffeine could, therefore, be due to interference with DNA damage checkpoints, or inhibition of the DNA damage repair/tolerance pathway. Using a combination of flow cytometric analysis, mitotic index analysis and fluorescence microscopy we show that caffeine interferes with intra-S phase and G₂ DNA damage checkpoints, overcoming cell cycle delays associated with damaged DNA. In contrast, caffeine has no effect on the DNA replication S phase checkpoint in reponse to inhibition of DNA synthesis by hydroxyurea.     

Contribution of a caffeine-sensitive recombinational repair pathway to survival and mutagenesis in UV-irradiated Schizosaccharomyces pombe

Summary Cells of wild-type Schizosacharomyces pombe exposed to UV radiation in either G1 or G2 phase show enhanced inactivation of colony-forming ability if plated in the presence of caffeine. This UV-sensitization by caffeine is abolished in both G1 and G2 phase cells by the rad1 mutation; since both caffeine and the rad1 mutation markedly reduce recombinational events, this suggests that a recombinational repair process is active in cells irradiated either in G1 or G2 phase. A prereplicative or sister chromatid exchange recombinational process appears to account for caffeine-sensitive repair of UV-damage in G2 cells (which possess at the time of radiation exposure the duplicated genome necessary for recombination), since caffeine-sensitive repair begins immediately and is completed before resumption of DNA synthesis. In contrast, since caffeine-sensitive repair of UV-damage in G1 cells displays a considerable lag and then occurs concomitantly with DNA synthesis, it appears that G1 cells must acquire a second genome in order to accomplish a caffeine-sensitive recovery process. Since a duplicated genome is required for caffeinesensitive repair, all such repair would seem to involve a recombinational mechanism. In G1 cells the process may be a post-replication recombinational mechanism. Since G2 phase cells are considerably more UV-resistant than G1 phase cells, the prereplicative recombinational process appears to be a much more efficient process for dealing with UV-induced damage than the post-replication mechanism.UV-induced mutagenesis was examined in wildtype and rad mutants using a forward mutation system. Rad mutants which show higher UV-induced mutation rates than wild-type retain UV-sensitization by caffeine (and thus presumably retain the recombinational mechanism). In contrast, rad strains which are relatively UV-immutable compared to wild-type do not possess the caffeine-sensitive UV-repair process. The recombinational process therefore may be the major pathway responsible for UV-induced mutation.AECL Reference No. 6251; NRC Publication No. 16999     

Genome-Wide Screen of Genes Required for Caffeine Tolerance in Fission Yeast

Background

An excess of caffeine is cytotoxic to all eukaryotic cell types. We aim to study how cells become tolerant to a toxic dose of this drug, and the relationship between caffeine and oxidative stress pathways.

Methodology/Principal Findings

We searched for Schizosaccharomyces pombe mutants with inhibited growth on caffeine-containing plates. We screened a collection of 2,700 haploid mutant cells, of which 98 were sensitive to caffeine. The genes mutated in these sensitive clones were involved in a number of cellular roles including the H₂O₂-induced Pap1 and Sty1 stress pathways, the integrity and calcineurin pathways, cell morphology and chromatin remodeling. We have investigated the role of the oxidative stress pathways in sensing and promoting survival to caffeine. The Pap1 and the Sty1 pathways are both required for normal tolerance to caffeine, but only the Sty1 pathway is activated by the drug. Cells lacking Pap1 are sensitive to caffeine due to the decreased expression of the efflux pump Hba2. Indeed, ?hba2 cells are sensitive to caffeine, and constitutive activation of the Pap1 pathway enhances resistance to caffeine in an Hba2-dependent manner.

Conclusions/Significance

With our caffeine-sensitive, genome-wide screen of an S. pombe deletion collection, we have demonstrated the importance of some oxidative stress pathway components on wild-type tolerance to the drug.     

Comparison of [35S]GTPγS binding to plasma membranes and endomembranes prepared from soybean and rat

Summary Plasma membranes were prepared from soybean hypocotyls and roots by aqueous two-phase partitioning and subsequent free-flow electrophoresis. The highly purified plasma membranes bound [³⁵S]GTPS with a relatively high affinity (K_d10nM). The binding was saturable and specific as it was indicated by the displacement of bound [³⁵S]GTPS by unlabeled GTPS and GTP, but not by ATPS, ATP, UTP or CTP. ITP was intermediate in its ability to displace [³⁵S]GTPS. When soybean plasma membrane proteins were separated by SDS-PAGE and displayed by autoradiography, two major [³⁵S]GTPS binding proteins were revealed with apparent molecular weights of 24 and 28 kDa. Results with plasma membranes from soybean hypocotyls and roots were similar but differed from those with plasma membranes prepared from rat liver and adipocytes where only a single major [³⁵S]GTPS binding activity with a molecular weight of 28 kDa was observed.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - G protein hetero-trimeric GTP binding protein with , , subunits - G_n protein GTP binding protein detected on nitrocellulose blots - GTPS guanosine 5-[-thio]triphosphate - IAA 3-indoleacetic acid - SDS-PAGE sodium dodecylsulfate-polyacrylamide gel electrophoresis     

Effect of caffeine in Fanconi anemia

Summary In Fanconi anemia (FA) cells the duration of the G₂ phase of the cell cycle prolonged. Such a slowing of the G₂ phase can be induced in normal cells by irradiation with rays during S phase, which also further increases the duration of G₂ in FA cells. The addition of caffeine during the last 7h of culture shortens the G₂ phase in both nonirradiated and irradiated FA cells. In nonirradiated normal cells it may have no effect or may increase G₂ phase duration, but in irradiated normal reduces the slowing of G₂ induced by the radiation. This suggests that FA cells recognize and repair preexisting DNA lesions during G₂ phase and that caffeine inhibits this process. The principal anomaly in FA may be a deficient repair during S phase, as manifest in the prolonged postreplication repair period during G₂ phase required to repair the larger number of lesions passing through S phase.     

Induction of respiration deficient mutants in Saccharomyces cerevisiae by Berenil

Summary Some characteristic details of mutagenesis by Berenil, a non-intercalating trypanocidal dye, that govern the change from wild type (⁺) to vegetative petite (^–) in Saccharomyces cerevisiae are presented and contrasted with the intercalating mutagens ethidium bromide and euflavine.The extent and rate of mutagenesis by Berenil is affected by a variety of parameters controlling the cellular and mitochondrial phenotype: among them are exposure to 45°; competition with EB but not euflavine; a requirement for an energy source during and subsequent to exposure to the mutagen; exposure to caffeine; and the presence of genetic blocks in various steps of the mitochondrial repair system for uv-induced lesions. It is, however, insensitive to exposure to Antimycin A. Except for the first of these observations, qualitative differences have emerged between the responses induced by Berenil and the other mutagens, especially ethidium bromide.Using these observations we have postulated a stepwise sequence of events that can account for the mutagenic action of Berenil.Publication No. 2122.     

Repair in Schizosaccharomyces pombe as measured by recovery from caffeine enhancement of radiation-induced lethality.

Inhibition of DNA repair by caffeine is manifested in Schizosaccharomyces pombe wild-type cells as an enhancement of UV- or gamma-irradiation-induced lethality. The progress of DNA repair processes involving one or more caffeine-sensitive steps may be conveniently followed by measuring the concomitant decrease of this lethal enhancement effect. By measuring, during post-irradiation incubation, the ability of cells to overcome susceptibility to repair inhibition by caffeine, we have determined the time course and requirements for repair in S. pombe. Recovery began immediately and took 150-200 min after gamma-irradiation and more than 500 min after UV-irradiation, for exposures which gave about 10% survival in the absence of caffeine. An incubation medium capable of supporting growth was required for caffeine-sensitive repair; no recovery occurred under liquid holding conditions. Survival curves after various recovery times indicated that a logarithmic phase cell population was homogeneous with respect to caffeine-sensitive repair of both UV- and gamma-ray-induced damage. Recovery from caffeine inhibition was compared for cells of different physiological states (logarithmic and stationary phase); although the importance of the physiological state was not the same for the two types of radiation, recovery was found to occur more rapidly in the more radiation-resistant state, in each case.     

Histamine in immunotherapy of advanced melanoma: a pilot study

Sixteen patients with advanced metastatic malignant melanoma were treated with a high-dose infusion of interleukin-2 (IL-2; 18×10⁶ IU/m^–2 day^–1) together with daily subcutaneous (s.c.) injections of interferon (IFN; 3×10⁶ U/m^–2 day^–1) in 5-day cycles. Nine of these patients were given histamine (1 mg s.c.) twice daily during treatment with IL-2 and IFN. In the seven patients who did not receive histamine, one partial response (that is a reduction of more than 50% in the total tumour burden) was observed in a patient with skin and lymph node melanoma. In the eight histamine-treated patients evaluable for response, four partial responses were observed. Two other patients showed regression at one site of metastasis but tumours remained unchanged at other sites. Two histamine-treated patients showed complete resolution of extensive liver metastasis. Sites of response in histamine-treated patients also included the subcutis, lymph nodes, skeleton, spleen and muscle. Lung melanoma did not respond to histamine/IL-2/IFN. Three patients with lung tumours responded with significant (more than 50%) reduction of the volume of soft-tissue tumours, suggesting that the response to histamine may be organotropic. Survival was significantly prolonged in patients receiving histamine. Our data suggest that treatment with histamine may improve the antitumour efficacy of immunotherapy in metastatic melanoma.     

Effects of ergosterol,palmitic acid and related simple lipids on the recovery of Candida albicans from ultraviolet irradiation

Summary Post-irradiation growth on sterols or long chain fatty acids promotes recovery of C. albicans from uv-induced lethal damage. The effect is observed only for cells which are not budding at the time of irradiation. Lipids have no effect on uv mutagenesis. A survey of a number of sporogenous and asporogenous yeasts indicates that the capacity for lipid-induced recovery from uv is a species specific characteristic of yeasts. The behaviors of cells damaged by uv and by amphotericin B, a membrane specific fungicidal antibiotic, suggest that lipids remediate an uv-induced derangement of the structure of the cell membrane critical for the initiation of cell division.     

Effects of immobilization on intrinsic kinetics and selectivity of trypsin

Summary There is few information available on effects of covalent coupling on the intrinsic kinetics of an enzyme excluding the interference of adsorption and transport phenomena. We present clear evidence for significant shifts in association constants for substrates and inhibitors due to covalent binding onto a rigid support. K_M and K_I values were changed by factors up to 6 and relative affinities were also different as compared to the native enzyme. Interference by other phenomena like adsorption or diffusion has been excluded. Protection of the enzyme by very strong inhibitors during binding can avoid such alterations.The effect of pH on K_I/K_M was not observed showing that there is no apparent effect of the solution pH on the relative affinities between pH-values 7 and 9. Similar findings were obtained for the maximal reaction rates.Symbols Ae Aerosil - Ae-NH₂ Aerosil with NH₂-groups - Am-BA p-Aminobenzamidinedihydrochloride - APTS Aminopropyltriethoxysilane - BA Benzamidinehydrochloride - BAEE N--Benzoyl-L-arginine-ethylesterhydrochloride - Bu-Am n-Butylamine - CDI 1-Cyclohexyl-3-(2-morpholinoethyl) carbodiimid metho-p-toluenesulfonate - D_e Effective diffusion coefficient - d_p Particle diameter - GA Glutardialdehyde - I Inhibitor concentration - K_I Inhibitor constant - K_M Michealis-Menten-constant - S Substrate concentration - Sh Sherwood number - STI Soybean trypsin inhibitor - Try Trypsin - Try-Ae Carrier bound trypsin - v Reaction rate - V_max Maximum reaction rate - Thiele modulus - Effectiveness     

Analysis of the excision repair of nondimer DNA damage induced by solar ultraviolet radiation in ICR 2A frog cells

The excision repair of solar uv-induced nondimer DNA damage was examined in ICR 2A frog cells through the use of the bromodeoxyuridine (BrdUrd) photolysis assay. A relatively pure population of nondimer DNA photoproducts was induced by irradiation of ICR 2A cells with the Mylar-filtered solar ultraviolet (uv) wavelengths produced by a fluorescent sunlamp followed by exposure to photoreactivating light (PRL) which removes most of the small yield of pyrimidine dimers induced by this treatment. Cultures of cells were also exposed to 254 nm uv, which induces primarily dimers, and 60Co gamma rays. Through use of a modification of the BrdUrd photolysis assay possessing enhanced sensitivity, it was found that the solar uv-induced nondimer DNA damage was repaired by a short patch repair mechanism in which less than approximately 20 nucleotides are inserted into a repaired region. Similar results were also obtained for gamma-irradiated cells. In contrast, excision repair of 254-nm-induced dimers was accomplished by a long-patch process in which an average of about 180 nucleotides are inserted into the repaired sites.     

Single-Particle Tracking Demonstrates that Actin Coordinates the Movement of the Ebola Virus Matrix Protein

The Ebola virus causes severe hemorrhagic fever and has a mortality rate that can be as high as 90%, yet no vaccines or approved therapeutics, to our knowledge, are available. To replicate and egress the infected host cell the Ebola virus uses VP40, its major matrix protein to assemble at the inner leaflet of the plasma membrane. The assembly and budding of VP40 from the plasma membrane of host cells seem still poorly understood. We investigated the assembly and egress of VP40 at the plasma membrane of human cells using single-particle tracking. Our results demonstrate that actin coordinates the movement and assembly of VP40, a critical step in viral egress. These findings underscore the ability of single-molecule techniques to investigate the interplay of VP40 and host proteins in viral replication.The actin cortex below the plasma membrane of mammalian cells is essential for maintenance of cell shape and for cell movement. This cortex has also been found to play an essential role in the replication process of a number of viruses including West Nile virus (1), respiratory syncytial virus (2), influenza (3), and vaccinia virus (4). Additionally, actin has been found to play a central role in the assembly and budding of HIV-1 (5) whereas Marburg virus has been shown to use actin-enriched filopodia to exit the host cell (6). Actin has also been found to be packaged into Ebola-virus-like particles (VLPs) (7). Ebola virus, which causes severe hemorrhagic fever, harbors a single-stranded negative-sense RNA genome encoding seven proteins. Of these seven proteins, VP40 is the most abundantly expressed and has been found to play a central role in the budding of the virus from the plasma membrane (8). Whereas actin has been found in Ebola VLPs (7), the role of actin in Ebola VP40 assembly is still seemingly unknown. Here, we have used Raster image correlation spectroscopy (RICS) (9) and three-dimensional single-particle tracking (see Fig. S1 in the Supporting Material) (10) to investigate the dynamics of Ebola VP40 and actin. We report that preassembled VLPs (pVLPs) of Ebola VP40 require actin for directed movement and assembly.Ebola VP40 has been demonstrated to colocalize with actin and actin is found in VP40 VLPs (7), suggesting an important role for actin in the replication cycle of the virus. To confirm the colocalization between VP40 and actin in HEK293 and CHO-K1 cells, we used confocal microscopy to examine the distribution of EGFP-VP40 and mCherry-actin. EGFP-VP40 and mCherry-actin displayed colocalization at the plasma membrane of HEK293 and CHO-K1 cells (see Fig. S2 A), which was markedly reduced in response to treatment with LAT-A (see Fig. S2 B and Fig. S3 A), an actin polymerization inhibitor. VP40 plasma membrane localization was not disrupted by LAT-A treatment (not unexpected, as VP40 is a lipid-binding protein (11) where high affinity for the PM drives its cellular localization (E. Adu-Gyamfi and R. V. Stahelin, unpublished)). To test whether this VP40-actin interaction is important to viral egress, we detected EGFP-VP40 with an anti-EGFP antibody used to measure VLPs formed from cells expressing EGFP-VP40. This was also performed to assess the effect of pharmacological treatment on EGFP-VP40-expressing cells with LAT-A or with the microtubule polymerization inhibitor nocodazole (see Fig. S3 B). LAT-A treatment led to a significant reduction in VLP formation whereas nocodazole did not display detectable effects.To test whether the VP40 and actin are engaged in synchronized movement, we performed time-lapse imaging in both the green and red channels. We observed that the pVLPs move with actin fibers extending from the plasma membrane (see Movie S1 in the Supporting Material). The movement was rapid, and caused smaller particles to merge into larger filamentous forms. To further demonstrate that the motion of actin and VP40 spatially overlapped, we used RICS to obtain correlation maps of EGFP-VP40 and mCherry-actin (Fig. 1). The spatial cross-correlation map indicated significant overlap of VP40 and actin movement (Fig. 2, A–C) at the plasma membrane (Fig. 1 and see Fig. S6), but not in the cytosol (see Fig. S5 and Fig. S7). In contrast, EGFP-VP40 and mCherry-α-tubulin (see Fig. S8, Fig. S9, and Fig. S10) displayed no significant spatial cross-correlation at the plasma membrane (Fig. S11) or other regions of the cell (see Fig. S12), supporting the VLP egress data where inhibition of microtubule polymerization did not influence viral egress.Open in a separate windowFigure 1EGFP-VP40 and mCherry-actin RICS analysis at the membrane. (A) HEK293 cells expressing EGFP-VP40 and mCherry-actin were imaged for 100 frames at 256 × 256 pixels. (White scale bar = 2 μm.) (B) Average intensity image of EGFP-VP40 across the 100 collected frames. (Pink box) Used to select a region of interest to yield the (C) average EGFP-VP40 intensity image. (D) Average intensity image of mCherry-actin taken for 100 frames at 256 × 256 pixels was used to select the same region of interest as in panel B (pink box) to yield the (E) average intensity image of the mCherry-actin signal in this region. (F) The two-dimensional spatial cross-correlation analysis of panels C and E demonstrates significant cross-correlation of VP40 and actin signals.Open in a separate windowFigure 2Three-dimensional RICS correlation maps of VP40 and actin cross-correlate at the plasma membrane. (A) EGFP-VP40 and (B) mCherry-actin (Fig. 1 and see Fig. S6 in the Supporting Material) RICS autocorrelation functions. (C) Appreciable cross-correlation is observed for EGFP-VP40 and mCherry-actin at the plasma membrane.To test whether the motion of the pVLPs is directed by actin, we applied the three-dimensional orbital tracking method first introduced by Levi et. al. (10). Tracking of isolated particles (Fig. 3 A) in five different cells allowed determination of the pVLPs trajectories (Fig. 3 D), which suggested that the VP40 particles undergo a directed motion. To verify this, we plotted the mean-square displacement (MSD) curves for the pVLPs (Fig. 3 C), which confirmed the trajectory was characteristic of directed motion. Analysis of the intensity profile of the dynamic VP40 particles suggested that the intensity of the particle changes with respect to time. Bleaching is expected if the molecule is exposed to the laser beam for an extended period of time; however, an increase in intensities was observed along the trajectory of the green channel due to addition of VP40 molecules. This suggests that the movement of the particles along actin fibers promote multimerization and maturation of the pVLPs. When actin polymerization was inhibited in four different cells with LAT-B, the rapid movement (see Fig. S13) and the directed trajectories of the pVLPs were lost (Fig. 3, E and F). This was reflected in a change from directed motion to movement indicative of random then constrained diffusion (Fig. 3, E and F).Open in a separate windowFigure 3Actin directs the movement of VP40 particles. HEK293 cells transfected with EGFP-VP40 were imaged with an electronic zoom of 2000 mV, corresponding to 72 nm/pixel in both X and Y. (A) An isolated and representative VP40 particle (highlighted by white box, inset) was tracked as described in the Supporting Material. (B) Intensity profile of the pVLP in A demonstrates increases in EGFP-VP40 intensity along the trajectory. (C) MSD of the pVLP, which follows a ballistic motion with a velocity of 0.067 ± 0.01 μm² s⁻¹. (D) The three-dimensional trajectory of the particle shown in panels A–C. (E) MSD curve of VP40 particles yields random then constrained diffusion after LAT-B treatment with a mean velocity of 0.017 ± 0.006 μm² s⁻¹ (p < 0.001). (F) Three-dimensional trajectory of the same particle shown in panel E displays a random then constrained diffusion.Taken together, our findings demonstrate that the movement of the pVLPs is driven by actin. Analysis of the pVLPs trajectories also suggests that the motion of pVLPs on actin enables further addition of VP40 molecules. These findings raise important questions regarding contemporary understanding of Ebola assembly and egress. VP40 lacks a consensus actin-binding motif, suggesting an adaptor protein such as an actin motor protein may function in this process. For instance, Myo10 has been found to be essential to Marburg virus release (6); however, Marburg VP40-Myo10 direct interactions were not observed, suggesting other cellular adaptor proteins may function in this process. Given the pathogenic nature of the Ebola virus and the necessity of VP40 to the assembly and egress of the virus (8), the VP40-actin coordination represents, to us, a novel target for therapeutic development.     

Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets

Octopus is an automated workflow management tool that is scalable for virtual high-throughput screening (vHTS). It integrates MOPAC2016, MGLTools, PyMOL, and AutoDock Vina. In contrast to other platforms, Octopus can perform docking simulations of an unlimited number of compounds into a set of molecular targets. After generating the ligands in a drawing package in the Protein Data Bank (PDB) format, Octopus can carry out geometry refinement using the semi-empirical method PM7 implemented in MOPAC2016. Docking simulations can be performed using AutoDock Vina and can utilize the Our Own Molecular Targets (OOMT) databank. Finally, the proposed software compiles the best binding energies into a standard table. Here, we describe two successful case studies that were verified by biological assay. In the first case study, the vHTS process was carried out for 22 (phenylamino)urea derivatives. The vHTS process identified a metalloprotease with the PDB code 1GKC as a molecular target for derivative LE&007. In a biological assay, compound LE&007 was found to inhibit 80% of the activity of this enzyme. In the second case study, compound Tx001 was submitted to the Octopus routine, and the results suggested that Plasmodium falciparum ATP6 (PfATP6) as a molecular target for this compound. Following an antimalarial assay, Tx001 was found to have an inhibitory concentration (IC₅₀) of 8.2 μM against PfATP6. These successful examples illustrate the utility of this software for finding appropriate molecular targets for compounds. Hits can then be identified and optimized as new antineoplastic and antimalarial drugs. Finally, Octopus has a friendly Linux-based user interface, and is available at www.drugdiscovery.com.br.

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Graphical Abstract Octopus: A platform for inverse virtual screening (IVS) to search new molecular targets for drugs.

     

An ultraviolet light induced bacteriophage inBeneckea gazogenes

An ultraviolet light induced prophage has been discovered in the red pigmented marine vibrioBeneckea gazogenes. Two spontaneously derived pigment mutants, one forming pink colonies and one lacking pigment and forming white colonies, were also irradiated. The presence of pigment was not related to phage induction; uv-induced cell lysis occurred in wildtype and mutant strains at the same dosages. Lysis was not prevented or retarded by exposure after irradiation to visible light indicating the phenomenon was not photoreactivable. Electron micrographs of the T-likeB. gazogenes phage are shown.A second beneckea was isolated from the anaerobic zone of cyanobacterial mats growing in the hypersaline environment of Laguna Mormona, Baja California. The Baja beneckea does not harbor a uv inducible prophage and is resistant to theB. gazogenes phage under all conditions tested.