For non-experts, we recommend to have a look at our article “Size matters – the importance of DNA packaging and the bacterial DNA Gyrase” first. The article introduces the importance and principles of DNA packaging by comparing the size of Escherichia coli DNA with its actual cell size. Additionally, we demonstrate a simple model of DNA packaging that you can try at home with strings and sticks. Lastly, we explain how the activity of enzymes involved in DNA packaging can be investigated by a technique called DNA gel electrophoresis, a technique used to obtain the results of the study discussed here in the following article.
The essential bacterial enzyme DNA gyrase is an important target for antibiotics. The enzyme helps to package DNA within the cell, an essential step in DNA- and cell replication. A recent study showed that the natural substance allicin from garlic is a potent DNA gyrase inhibitor, active at a concentration comparable to the antibiotic nalidixic acid. Allicin is a sulfur-containing defence substance synthesized by garlic upon cell damage, and it is responsible for the typical odour of freshly cut or crushed garlic.
Section 1 – Bacterial DNA gyrase is an antibiotic target
Antibiotics are substances that are used in medicine to kill microbes or inhibit their growth. Bacteria have a prokaryotic cell organisation and antibiotic targets can be for example bacterial protein- or DNA synthesis. The specificity of antibiotics is generally high enough so that eukaryotic host cells like human -or animal cells are not-, or only weakly, affected. A little side note here: It should always be kept in mind that the power-plants of our cells (mitochondria) are of bacterial origin and thus can also be sensitive to prokaryotic-targeting antibiotics as well 1,2.
A well-known bacteria-specific antibiotic is penicillin, synthesized by some fungi in the genus Penicillium, and which was described by Alexander Fleming in 1929 3. This antibiotic inhibits cell wall synthesis of many bacteria 4–6. Treatment with antibiotics and the emergence of antibiotic resistance often go hand in hand 7, so that an arsenal of antibiotics with different cellular targets becomes quite handy to combat this phenomenon.
One essential factor for DNA replication in bacteria that is exploited as a target for antibiotic treatment is the enzyme DNA gyrase 8, which belongs to the so-called topoisomerase protein family, that is important for DNA packaging 9.
Section 2 – Allicin from garlic inhibits DNA Gyrase Activity
Nalidixic acid (Figure 1), which is a purely chemically synthesized antibiotic, was the first antibiotic of the so-called quinolone class that turned out to be an effective inhibitor of DNA gyrase activity 10.
In 2020, a study by Jana Foerster (neé Reiter) and colleagues was published about the gyrase inhibitory mode of action of allicin 11, a natural sulfur compound from garlic (Figure 1). Allicin is a strong volatile antibiotic released from garlic cells after cellular damage and is the reason for the typical odour of freshly crushed garlic. Compared to other antibiotics with very specific targets, allicin attacks multiple targets in the cell at once because of its reactivity with available thiol groups in cysteines which are essential for the structure and activity of many enzymes 12,13.
When allicin reacts with a thiol group, this group becomes chemically oxidized and a so-called allyl group is added to it (Figure 2). This allyl-group addition also increases the mass of the proteins, and this mass difference was used by Foerster et al. to investigate which proteins became thioallylated after allicin treatment in Pseudomonas bacteria 11.
Foerster (neé Reiter) et al. were looking for potential resistance mechanisms against allicin by investigating the differences between thioallylated proteins in an allicin-resistant bacterium that was isolated from garlic, called Pseudomonas fluorescens Allicin Resistant-1 (PfAR-1), compared to its close, but allicin-sensitive, relative P. fluorescens Pf0-1 11. The working hypothesis was that proteins that were less thioallylated by allicin in PfAR-1 might be a resistance factor for bacterial survival during allicin stress.
By using a differential isotopic labelling method (OxICAT) pioneered by Professor Lars Leichert and colleagues 14, the thioallylated proteins, as well as the degree of allylation in the population of specific protein could be characterized in PfAR-1 and Pf0‑1 after allicin treatment. In this first part of Foerster (neé Reiter) et al.´s work, one candidate turned out to be the DNA gyrase protein subunit A (GyrA) because of a very significant difference observed between Pf0-1 and PfAR-1. In Pf0-1, the amount of oxidized GyrA proteins increased from 6.3 % to 56.1 %, while the amount of oxidized GyrA proteins in PfAR-1 only increased from 6.5 % to 10.8 %. The conclusion of these data was that up to 49.8 % of all GyrA protein molecules in Pf0‑1 became thioallylated, while only 4.3 % of all GyrA protein in PfAR‑1 became thioallylated 11.
Since the allylation of GyrA in Pf0-1 does not allow the conclusion that the DNA gyrase enzyme would also be inhibited by that modification, enzymatic assays were performed to address this question (Figure 3).
The assay was based on the different mobilities between relaxed and supercoiled DNA on electrophoresis in an agarose gel in a certain time. As the pUC19 plasmid DNA would be converted to supercoiled pUC19 by DNA gyrase, the more compact supercoiled DNA would move faster through an agarose gel compared to the relaxed pUC19 DNA. With boiled DNA gyrase compared to untreated DNA gyrase, the assay worked as expected, so that the effect of nalidixic acid and allicin pre-treatment of DNA gyrase could be investigated, showing that both substances are potent inhibitors of the enzyme in a concentration-dependent manner (Figure 3) 11.
Interestingly, both the DNA gyrase from Pf0-1 and PfAR-1 were inhibited by allicin in vitro to the same degree. The difference seen in thioallylation in vivo after allicin treatment reflected the ability of resistant PfAR-1 cells to protect their proteins against thioallylation compared to the sensitive Pf0-1 cells 15. The ability of allicin to inhibit DNA gyrase is an important observation and helps to explain allicin’s antibacterial activity 11.
However, at present, without more research and testing, allicin cannot be used as a substitute for other antibiotics and it should not be used for self-treatment, which can be very harmful.
Jan Borlinghaus, 13.10.2022
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