Flow-Seq Method: Features and Application in Bacterial Translation Studies

The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.

Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome

Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.