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Development of an image-based screening system for inhibitors of the plastidial MEP pathway and of protein geranylgeranylation.

ABSTRACT: We have recently established an in vivo visualization system for the geranylgeranylation of proteins in a stably transformed tobacco BY-2 cell line, which involves expressing a dexamethasone-inducible GFP fused to the prenylable, carboxy-terminal basic domain of the rice calmodulin CaM61, which naturally bears a CaaL geranylgeranylation motif (GFP-BD-CVIL). By using pathway-specific inhibitors it was demonstrated that inhibition of the methylerythritol phosphate (MEP) pathway with oxoclomazone and fosmidomycin, as well as inhibition of protein geranylgeranyl transferase type 1 (PGGT-1), shifted the localization of the GFP-BD-CVIL protein from the membrane to the nucleus. In contrast, the inhibition of the mevalonate (MVA) pathway with mevinolin did not affect this localization. Furthermore, complementation assays with pathway-specific intermediates confirmed that the precursors for the cytosolic isoprenylation of this fusion protein are predominantly provided by the MEP pathway. In order to optimize this visualization system from a more qualitative assay to a statistically trustable medium or a high-throughput screening system, we established new conditions that permit culture and analysis in 96-well microtiter plates, followed by fluorescence microscopy. For further refinement, the existing GFP-BD-CVIL cell line was transformed with an estradiol-inducible vector driving the expression of a RFP protein, C-terminally fused to a nuclear localization signal (NLS-RFP). We are thus able to quantify the total number of viable cells versus the number of inhibited cells after various treatments. This approach also includes a semi-automatic counting system, based on the freely available image processing software. As a result, the time of image analysis as well as the risk of user-generated bias is reduced to a minimum. Moreover, there is no cross-induction of gene expression by dexamethasone and estradiol, which is an important prerequisite for this test system.

SUBMITTER: Hartmann M

PROVIDER: S-EPMC4536634 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Development of an image-based screening system for inhibitors of the plastidial MEP pathway and of protein geranylgeranylation.

Hartmann Michael M Gas-Pascual Elisabet E Hemmerlin Andrea A Rohmer Michel M Bach Thomas J TJ

F1000Research 20150116

We have recently established an <i>in vivo</i> visualization system for the geranylgeranylation of proteins in a stably transformed tobacco BY-2 cell line, which involves expressing a dexamethasone-inducible GFP fused to the prenylable, carboxy-terminal basic domain of the rice calmodulin CaM61, which naturally bears a CaaL geranylgeranylation motif (GFP-BD-CVIL). By using pathway-specific inhibitors it was demonstrated that inhibition of the methylerythritol phosphate (MEP) pathway with oxoclom ...[more]

PMID: 26309725

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Project description:The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.

Project description:BackgroundRecent research has led to the development of many information technology-supported systems for health care control, including systems estimating nutrition from images of meals. Systems that capture data about eating and exercise are useful for people with diabetes as well as for people who are simply on a diet. Continuous monitoring is key to effective dietary control, requiring systems that are simple to use and motivate users to pay attention to their meals. Unfortunately, most current systems are complex or fail to motivate. Such systems require some manual inputs such as selection of an icon or image, or by inputting the category of the user's food. The nutrition information fed back to users is not especially helpful, as only the estimated detailed nutritional values contained in the meal are typically provided.ObjectiveIn this paper, we introduce healthiness of meals as a more useful and meaningful general standard, and present a novel algorithm that can estimate healthiness from meal images without requiring manual inputs.MethodsWe propose a system that estimates meal healthiness using a deep neural network that extracts features and a ranking network that learns the relationship between the degrees of healthiness of a meal using a dataset prepared by a human dietary expert. First, we examined whether a registered dietitian can judge the healthiness of meals solely by viewing meal images using a small dataset (100 meals). We then generated ranking data based on comparisons of sets of meal images (850 meals) by a registered dietitian's viewing meal images and trained a ranking network. Finally, we estimated each meal's healthiness score to detect unhealthy meals.ResultsThe ranking estimated by the proposed network and the ranking of healthiness based on the dietitian's judgment were correlated (correlation coefficient 0.72). In addition, extracting network features through pretraining with a publicly available large meal dataset enabled overcoming the limited availability of specific healthiness data.ConclusionsWe have presented an image-based system that can rank meals in terms of the overall healthiness of the dishes constituting the meal. The ranking obtained by the proposed method showed a good correlation to nutritional value-based ranking by a dietitian. We then proposed a network that allows conditions that are important for judging the meal image, extracting features that eliminate background information and are independent of location. Under these conditions, the experimental results showed that our network achieves higher accuracy of healthiness ranking estimation than the conventional image ranking method. The results of this experiment in detecting unhealthy meals suggest that our system can be used to assist health care workers in establishing meal plans for patients with diabetes who need advice in choosing healthy meals.

Project description:BackgroundThe apicomplexan parasite Babesia orientalis, the causative agent of water buffalo babesiosis in China, is widespread in central and south China, resulting in a huge economic loss annually. Currently, there is no effective vaccine or drug against this disease. Babesia bovis and Plasmodium falciparum were reported to possess an apicoplast which contains the methylerythritol phosphate (MEP) pathway inhibitable by fosmidomycin, suggesting that the pathway could serve as a drug target for screening new drugs. However, it remains unknown in B. orientalis.MethodsPrimers were designed according to the seven MEP pathway genes of Babesia microti and Babesia bovis. The genes were cloned, sequenced and analyzed. The open reading frames (ORFs) of the first two enzyme genes, 1-deoxy-D-xylulose 5-phosphate synthase (BoDXS) and 1-Deoxy-D-xylulose 5-phosphate reductoisomerase (BoDXR), were cloned into the pET-32a expression vector and expressed as a Trx-tag fusion protein. Rabbit anti-rBoDXS and rabbit anti-rBoDXR antibodies were generated. Western blot was performed to identify the native proteins of BoDXS and BoDXR in B. orientalis. Fosmidomycin and geranylgeraniol were used for inhibition assay and rescue assay, respectively, in the in vitro cultivation of B. orientalis.ResultsThe seven enzyme genes of the B. orientalis MEP pathway (DXS, DXR, IspD, IspE, IspF, IspG and IspH) were cloned and sequenced, with a full length of 2094, 1554, 1344, 1521, 654, 1932 and 1056 bp, respectively. BoDXS and BoDXR were expressed as Trx-tag fusion proteins, with a size of 95 and 67 kDa, respectively. Western blot identified a 77 kDa band for the native BoDXS and a 49 kDa band for the native BoDXR. The drug assay results showed that fosmidomycin could inhibit the growth of B. orientalis, and geranylgeraniol could reverse the effect of fosmidomycin.ConclusionsBabesia orientalis has the isoprenoid biosynthesis pathway, which could be a potential drug target for controlling and curing babesiosis. Considering the high price and instability of fosmidomycin, further studies should focus on the screening of stable and cheap drugs.

Dataset Information

Development of an image-based screening system for inhibitors of the plastidial MEP pathway and of protein geranylgeranylation.

Publications

Development of an image-based screening system for inhibitors of the plastidial MEP pathway and of protein geranylgeranylation.

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