The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics

Drug resistance of bacterial pathogens is a growing problem that can be addressed through the discovery of compounds with novel mechanisms of antibacterial activity. Natural products, including plant phenolic compounds, are one source of diverse chemical structures that could inhibit bacteria through novel mechanisms. However, evaluating novel antibacterial mechanisms of action can be difficult and is uncommon in assessments of plant phenolic compounds. With systems biology approaches, though, antibacterial mechanisms can be assessed without the bias of target-directed bioassays to enable the discovery of novel mechanism(s) of action against drug resistant microorganisms. This review article summarizes the current knowledge of antibacterial mechanisms of action of plant phenolic compounds and discusses relevant methodology

Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus

The aqueous extract of yerba mate, a South American tea beverage made from Ilex paraguariensis leaves, has demonstrated bactericidal and inhibitory activity against bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). The gas chromatography-mass spectrometry (GC-MS) analysis of two unique fractions of yerba mate aqueous extract revealed 8 identifiable small molecules in those fractions with antimicrobial activity. For a more comprehensive analysis, a data analysis pipeline was assembled to prioritize compounds for antimicrobial testing against both MRSA and methicillin-sensitive S.aureus using forty-two unique fractions of the tea extract that were generated in duplicate, assayed for activity, and analyzed with GC-MS. As validation of our automated analysis, we checked our predicted active compounds for activity in literature references and used authentic standards to test for antimicrobial activity. 3,4-dihydroxybenzaldehyde showed the most antibacterial activity against MRSA at low concentrations in our bioassays. In addition, quinic acid and quercetin were identified using random forests analysis and 5-hydroxy pipecolic acid was identified using linear discriminant analysis. We also generated a ranked list of unidentified compounds that may contribute to the antimicrobial activity of yerba mate against MRSA. Here we utilized GC-MS data to implement an automated analysis that resulted in a ranked list of compounds that likely contribute to the antimicrobial activity of aqueous yerba mate extract against MRSA

The TcEG1 beetle (Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release

Background Genetically engineered biofuel crops, such as switchgrass (Panicum virgatum L.), that produce their own cell wall-digesting cellulase enzymes would reduce costs of cellulosic biofuel production. To date, non-bioenergy plant models have been used in nearly all studies assessing the synthesis and activity of plant-produced fungal and bacterial cellulases. One potential source for cellulolytic enzyme genes is herbivorous insects adapted to digest plant cell walls. Here we examine the potential of transgenic switchgrass-produced TcEG1 cellulase from Tribolium castaneum (red flour beetle). This enzyme, when overproduced in Escherichia coliand Saccharomyces cerevisiae, efficiently digests cellulose at optima of 50 °C and pH 12.0. Results TcEG1 that was produced in green transgenic switchgrass tissue had a range of endoglucanase activity of 0.16–0.05 units (µM glucose release/min/mg) at 50 °C and pH 12.0. TcEG1 activity from air-dried leaves was unchanged from that from green tissue, but when tissue was dried in a desiccant oven (46 °C), specific enzyme activity decreased by 60%. When transgenic biomass was “dropped-in” into an alkaline buffer (pH 12.0) and allowed to incubate at 50 °C, cellobiose release was increased up to 77% over non-transgenic biomass. Saccharification was increased in one transgenic event by 28%, which had a concurrent decrease in lignin content of 9%. Histological analysis revealed an increase in cell wall thickness with no change to cell area or perimeter. Transgenic plants produced more, albeit narrower, tillers with equivalent dry biomass as the control. Conclusions This work describes the first study in which an insect cellulase has been produced in transgenic plants; in this case, the dedicated bioenergy crop switchgrass. Switchgrass overexpressing the TcEG1 gene appeared to be morphologically similar to its non-transgenic control and produced equivalent dry biomass. Therefore, we propose TcEG1 transgenics could be bred with other transgenic germplasm (e.g., low-lignin lines) to yield new switchgrass with synergistically reduced recalcitrance to biofuel production. In addition, transgenes for other cell wall degrading enzymes may be stacked with TcEG1 in switchgrass to yield complementary cell wall digestion features and complete auto-hydrolysis

Overlay of initial yerba mate extract fraction chromatograms.

<p>A) The black chromatogram corresponds to a yerba mate extract fraction that demonstrated antibacterial activity against methicillin-resistant <i>Staphylococcus aureus</i> (MRSA); the red chromatogram corresponds to a yerba mate fraction that had no antibacterial activity against MRSA. B) Retention times of identified compounds and quantification in sorbitol equivalents were reported.</p

Growth of methicillin-sensitive (SA) and methicillin-resistant <i>Staphylococcus aureus</i> MRSA) in the presence of pure compounds.

<p>At concentrations of 10 μg/ml (chemical_1), 20 μg/ml (chemical_2) and 100 μg/ml (chemical_3), growth with compounds was compared to the positive growth control (no chemical added) to determine inhibitory activity. Statistically significant differences greater (*) or less (**) than control are marked by asterisks. Growth of A. SA 113, B. SA 27708, C. MRSA 35591, and D. MRSA 35593 are reported at 48 h. SA113 had a significant block by treatment interaction, so no conclusions can be drawn from it.</p

Predicted Functional Groups from Golm.

<p>Predicted Functional Groups from Golm.</p

Top ten results for each attribute ranking method.

<p>Top ten results for each attribute ranking method.</p

Top 20 unique retention times ranked by antimicrobial significance against MRSA using random forests.

<p>Top 20 unique retention times ranked by antimicrobial significance against MRSA using random forests.</p

Classification accuracy of a single major mz peak for each of the 3 identified compounds of interest.

<p>Classification accuracy of a single major mz peak for each of the 3 identified compounds of interest.</p

Rank biased overlap comparison of lists.

<p>Rank biased overlap comparison of lists.</p