Bacterial Ribosome Gag

Russian scientists plugged the ribosome with a new antibiotic

Daria Spasskaya, N+1

A team of scientists from the institutes of Moscow and St. Petersburg in cooperation with the University of Illinois (USA) predicted the existence, isolated and characterized a new antimicrobial peptide – klebsazolicin. The substance belongs to the group of thiazole-oxazole-modified microcins and suppresses protein synthesis in bacteria. Structural analysis of the ribosome in combination with the peptide showed that the antibiotic blocks the release of the newly synthesized protein from the ribosome, acting as a plug. In the microcin group, this is the first characterized peptide with such a mechanism of action. The article was published in the journal Nature Chemical Biology.

Microcins ("little bacteriocins") are protein antibiotics that bacteria use to fight each other. A feature of microcins is the way they are synthesized. If more traditional antibiotics are synthesized by specialized enzymes from low-molecular-weight precursors, then microcins are encoded by ordinary genes and produced as ordinary proteins, on the ribosome. However, the initial short peptide always undergoes a strong modification, and only after that it turns into an active substance. There are, for example, microcines in which the residues of cysteine, serine and threonine form heterocycles, they are called thiazole-oxazole-modified microcines. Other microcins form loops from the peptide chain. Different microcins act on different targets, among them there is bacterial gyrase (an enzyme necessary to maintain the structure of DNA) and RNA polymerase.

Since microcins are of a protein nature, their sequence is encoded in the genome. Usually, the microcin gene is located in the same cluster with genes encoding enzymes for its modification. Based on the sequences of these enzymes, it is possible to search in bacterial genomes for cassettes of genes responsible for the synthesis of previously unknown antimicrobial peptides. This is the approach used by the researchers who discovered klebsazolicin.

The gene encoding the putative precursor of microcin was found as part of a cluster found in the genome of the bacterium Klebsiella pneumoniae by homology with the gene cluster of synthesis of the well-studied microcin B17 of E.coli coli. The scientists introduced this gene and the putative genes of microcin-modifying enzymes into a laboratory strain of E.coli and isolated a biologically active substance from the growth medium. Physico-chemical analysis showed that it is a peptide of 23 amino acids, of which the first two are closed in a cycle. Since the natural producer of the peptide is Klebsiella, it was named klebsazolicin.

The antimicrobial activity test showed that klebsazolicin inhibits the growth of several strains of E. coli, pathogenic bacteria Yersinia pseudotuberculosis and the Klebsiella pneumoniae. Thus, the peptide has a rather narrow spectrum of antibacterial activity. However, as the authors of the work have shown, this is not due to the mechanism of action of the antibiotic, but most likely due to insufficiently efficient transport into the cell.

The researchers determined that the target of klebsazolicin is a protein synthesis apparatus, namely the ribosome. To clarify the mechanism of its action, the authors, in collaboration with American colleagues, obtained the structure of a working ribosome using X-ray diffraction analysis (that is, in the presence of matrix and transport RNA) in combination with an antibiotic.

Ribosome exit channel without antibiotic (left) and in the presence of klebsazolicin (right). Mikhail Metelev et al / Nature Chemical Biology 2017

It turned out that klebsazolicin interacts with the ribosome channel in the place where the newly synthesized protein comes out and literally plugs it. Some macrolide antibiotics, for example, erythromycin and streptogramin B, work in a similar way. Nevertheless, klebsazolicin is the first representative in its group that acts by such a mechanism, so it was isolated into a separate new class of protein synthesis inhibitors.

Functional analysis of individual fragments of the peptide showed that only the first 14 amino acid residues interact with the ribosome, and the remaining 9, apparently, are needed for the penetration of the substance molecule into the cell. This means that the functional part of klebsazolicin can be used separately, including as part of hybrid molecules that penetrate cells more effectively. By itself, the new antibiotic most likely will not have clinical use due to difficulties with penetration into cells. According to one of the authors of the article, Dmitry Gilyarov, it is much more interesting to discover the mechanism of action itself: "the most important thing is that we are talking about the discovery of a new "scaffold", i.e. the basis for the rational design of modified analogues of klebsazolicin, which can potentially be more active and better than itself."

The new work of Russian scientists is the result of a targeted search for genes related to the metabolism of antimicrobial compounds using computer analysis. Recently we wrote about a new antibiotic isolated from natural sources by testing a large number of different substances for antimicrobial activity. And here you can read a lot of material about antibiotics and resistance to them.

Portal "Eternal youth" http://vechnayamolodost.ru  31.08.2017