Hierarchical metabolomics demonstrates substantial compositional similarity between genetically-modified and conventional potato crops

There is current debate whether genetically modified (GM) plants might contain unexpected, potentially undesirable changes in overall metabolite composition. However, appropriate analytical technology and acceptable metrics of compositional similarity require development. We describe a comprehensive comparison of total metabolites in field-grown GM and conventional potato tubers using a hierarchical approach initiating with rapid metabolome “fingerprinting” to guide more detailed profiling of metabolites where significant differences are suspected. Central to this strategy are data analysis procedures able to generate validated, reproducible metrics of comparison from complex metabolome data. We show that, apart from targeted changes, these GM potatoes in this study appear substantially equivalent to traditional cultivars

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.Peer reviewe

Species-selective killing of bacteria by antimicrobial peptide-PNAs

This is an open-access article distributed under the terms of the Creative Commons Attribution License, CC BY 4.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Broad-spectrum antimicrobials kill indiscriminately, a property that can lead to negative clinical consequences and an increase in the incidence of resistance. Species-specific antimicrobials that could selectively kill pathogenic bacteria without targeting other species in the microbiome could limit these problems. The pathogen genome presents an excellent target for the development of such antimicrobials. In this study we report the design and evaluation of species-selective peptide nucleic acid (PNA) antibacterials. Selective growth inhibition of B. subtilis, E. coli, K. pnuemoniae and S. enterica serovar Typhimurium in axenic or mixed culture could be achieved with PNAs that exploit species differences in the translation initiation region of essential genes. An S. Typhimurium-specific PNA targeting ftsZ resulted in elongated cells that were not observed in E. coli, providing phenotypic evidence of the selectivity of PNA-based antimicrobials. Analysis of the genomes of E. coli and S. Typhimurium gave a conservative estimate of >150 PNA targets that could potentially discriminate between these two closely related species. This work provides a basis for the development of a new class of antimicrobial with a tuneable spectrum of activity.Peer reviewedFinal Published versio

Use of peptide nucleic acids as species specific bactericides

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Bacterial strains used in this study.

a<p>American Type Culture Collection.</p>b<p><i>Salmonella</i> Genetic Stock Center.</p

Species-selective antibacterial peptide-PNAs in three-species mixed culture.

<p><i>B. subtilis</i> (dark grey), <i>K. pneumoniae</i> (white) and <i>S</i>. Typhimurium (light grey) in mixed culture were separately treated with Ec108 at 3.5 µM, Kp0001 or Se0001 at 4.5 µM or by combined treatment of Kp0001 and Se0001 both at 4.5 µM. All cultures were incubated for 16 hrs. Selective inhibition of either <i>K. pneumoniae</i> or <i>S</i>. Typhimurium individually or together, achieved with the peptide-PNAs, could not theoretically be achieved with any combination of the twenty known antimicrobial compounds tested in this study. Error bars as above.</p

Species-selective antibacterial peptide-PNAs in axenic and two-species mixed culture.

<p><i>E. coli</i> (dark grey), <i>K. pneumoniae</i> (white) and <i>S</i>. Typhimurium (light grey). All cultures were incubated for 16 hrs. A) axenic cultures of the species were treated with <i>E. coli</i>- specific Ec1000 at 3.2 µM, <i>K. pneumoniae</i>-specific Kp0001 at 3.2 µM and <i>S</i>. Typhimurium-specific Se0001 at 2.0 µM. Asterisks indicate species-selective growth inhibition of <i>E. coli</i>, <i>K. pneumoniae</i> and <i>S</i>. Typhimurium respectively. B) Two-species mixed cultures treated with peptide-PNAs as above. The control cultures show the relative proportion of the two species without treatment, the two treatments to the left of the control represent the same mixed culture treated with a peptide-PNA. Black arrows indicate non species-selective growth inhibition of <i>S</i>. Typhimurium by Ec1000. Error bars are standard error for biological replicates (<i>n</i> = 3).</p

<i>S</i>. Typhimurium-selective growth inhibition.

<p>Peptide-PNA Se0002 was designed to target the −5 to +5 region of the translational initiation region (TIR) of <i>ftsZ</i> in <i>S</i>. Typhimurium. Se0002 has 2 base pair mismatches in the TIR of <i>ftsZ</i> in <i>E. coli</i>. (A) Growth curve analysis of Se0002 in pure culture. <i>E. coli</i> growth in the presence of 1.25 µM Se0002 (solid line) was identical to that of untreated controls (not shown). <i>S</i>. Typhimurium growth was inhibited in the presence of 1.25 µM of Se0002 (dotted line) relative to the untreated control (dashed line). Growth in the treated samples after 10 hrs was not due to resistance (see text for details). (B) Mixed cultures of GFP-labeled <i>S</i>. Typhimurium AC02 and DsRed-labeled <i>E. coli</i> AC01 were treated with 1.25 µM Se0002; and imaged by fluorescence microscopy after 6 hrs of incubation. The filamentous growth phenotype was only observed in <i>S</i>. Typhimurium AC02 and is consistent with silencing of <i>ftsZ</i> expression.</p