Anastasia Metlitskaya

Aspartyl-tRNA Synthetase Is the Target of Peptide Nucleotide Antibiotic Microcin C

Microcin C is a ribosome-synthesized heptapeptide that contains a modified adenosine monophosphate covalently attached to the C-terminal aspartate. Microcin C is a potent inhibitor of bacterial cell growth. Based on the in vivo kinetics of inhibition of macromolecular synthesis, Microcin C targets translation, through a mechanism that remained undefined. Here, we show that Microcin C is a subject of specific degradation inside the sensitive cell. The product of degradation, a modified aspartyl-adenylate containing an N-acylphosphoramidate linkage, strongly inhibits translation by blocking the function of aspartyl-tRNA synthetase.

High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli.

In Escherichia coli, the acquisition of new CRISPR spacers is strongly stimulated by a priming interaction between a spacer in CRISPR RNA and a protospacer in foreign DNA. Priming also leads to a pronounced bias in DNA strand from which new spacers are selected. Here, ca. 200,000 spacers acquired during E. coli type I-E CRISPR/Cas-driven plasmid elimination were analyzed. Analysis of positions of plasmid protospacers from which newly acquired spacers have been derived is inconsistent with spacer acquisition machinery sliding along the target DNA as the primary mechanism responsible for strand bias during primed spacer acquisition. Most protospacers that served as donors of newly acquired spacers during primed spacer acquisition had an AAG protospacer adjacent motif, PAM. Yet, the introduction of multiple AAG sequences in the target DNA had no effect on the choice of protospacers used for adaptation, which again is inconsistent with the sliding mechanism. Despite a strong preference for an AAG PAM during CRISPR adaptation, the AAG (and CTT) triplets do not appear to be avoided in known E. coli phages. Likewise, PAM sequences are not avoided in Streptococcus thermophilus phages, indicating that CRISPR/Cas systems may not have been a strong factor in shaping host-virus interactions.

The Escherichia coli Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C

Microcin C (McC), a peptide-nucleotide antibiotic, targets aspartyl-tRNA synthetase. By analyzing a random transposon library, we identified Escherichia coli mutants resistant to McC. Transposon insertions were localized to a single locus, yejABEF, which encodes components of a putative inner membrane ABC transporter. Analysis of site-specific mutants established that all four components of the transporter are required for McC sensitivity. Since aspartyl-tRNA synthetase in yej mutant extracts was fully sensitive to McC, we conclude that yej mutations interfere with McC uptake and that YejABEF is the only inner membrane transporter responsible for McC uptake in E. coli. Other substrates of YejABEF remain to be identified.

Escherichia coli Peptidase A, B, or N Can Process Translation Inhibitor Microcin C

The heptapeptide-nucleotide microcin C (McC) targets aspartyl-tRNA synthetase. Upon its entry into a susceptible cell, McC is processed to release a nonhydrolyzable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase, leading to the cessation of translation and cell growth. Here, we surveyed Escherichia coli cells with singly, doubly, and triply disrupted broad-specificity peptidase genes to show that any of three nonspecific oligopeptidases (PepA, PepB, or PepN) can effectively process McC. We also show that the rate-limiting step of McC processing in vitro is deformylation of the first methionine residue of McC.

Quorum sensing regulation of gene expression: A promising target for drugs against bacterial pathogenicity

Bacteria are sensitive to an increase in population density and respond quickly and coordinately by induction of certain sets of genes. This mode of regulation, known as quorum sensing (QS), is based on the effect of low-molecular-weight signal molecules, autoinducers (AIs). When the population density is high, AIs accumulate in the medium and interact with regulatory receptor proteins. QS systems are global regulators of bacterial gene expression and play a key role in controlling many metabolic processes in the cell, including bacterial virulence. The review considers the molecular mechanisms of QS in different taxonomic groups of bacteria and discusses QS regulation as a possible target in treating bacterial infections. This is a new, alternative strategy of antibacterial therapy, which includes the construction of drugs acting directly against bacterial pathogenicity by suppressing QS (antipathogenicity drugs). This strategy makes it possible to avoid a wide distribution of antibiotic-resistant pathogenic bacteria and the formation of biofilms, which dramatically increase drug resistance.

Synthetic Microcin C Analogs Targeting Different Aminoacyl-tRNA Synthetases

Microcin C (McC) is a potent antibacterial agent produced by some strains of Escherichia coli. McC consists of a ribosomally synthesized heptapeptide with a modified AMP attached through a phosphoramidate linkage to the alpha-carboxyl group of the terminal aspartate. McC is a Trojan horse inhibitor: it is actively taken inside sensitive cells and processed there, and the product of processing, a nonhydrolyzable aspartyl-adenylate, inhibits translation by preventing aminoacylation of tRNA(Asp) by aspartyl-tRNA synthetase (AspRS). Changing the last residue of the McC peptide should result in antibacterial compounds with targets other than AspRS. However, mutations that introduce amino acid substitutions in the last position of the McC peptide abolish McC production. Here, we report total chemical synthesis of three McC-like compounds containing a terminal aspartate, glutamate, or leucine attached to adenosine through a nonhydrolyzable sulfamoyl bond. We show that all three compounds function in a manner similar to that of McC, but the first compound inhibits bacterial growth by targeting AspRS while the latter two inhibit, respectively, GluRS and LeuRS. Our approach opens a way for creation of new antibacterial Trojan horse agents that target any 1 of the 20 tRNA synthetases in the cell.

Maturation of the Translation Inhibitor Microcin C

Microcin C (McC), an inhibitor of the growth of enteric bacteria, consists of a heptapeptide with a modified AMP residue attached to the backbone of the C-terminal aspartate through an N-acyl phosphamidate bond. Here we identify maturation intermediates produced by cells lacking individual mcc McC biosynthesis genes. We show that the products of the mccD and mccE genes are required for attachment of a 3-aminopropyl group to the phosphate of McC and that this group increases the potency of inhibition of the McC target, aspartyl-tRNA synthetase.

Structure of microcin C51, a new antibiotic with a broad spectrum of activity

The structure of microcin C51, a new antibiotic produced by E. coli, has been determined. This antibiotic was shown to be a 1.18 kDa nucleotide peptide. It consists of a heptapeptide with formylmethionine as the N‐terminus and a C‐terminal asparagine linked with nebularin‐5′‐monophosphate through the three‐methylene bridge. The OH‐group of threonine is substituted. The peptide chain of microcin C51 synthesized on ribosomes is the longest among the known biologically active nucleotide peptides.

Production of N-acylhomoserine lactone signal molecules by gram-negative soil-borne and plant-associated bacteria.

Quorum-sensing control mediated byN-acylhomoserine lactone (AHL) signal molecules has been established as a key feature in the regulation of various metabolic traits in many bacteria. Approximately 300 strains representing 6 genera and 18 species of soil-borne and plant-associated Gram-negative bacteria isolated in various regions of the former USSR using two reporter systems were screened for AHL production. The production was observed in 17.5 % of the screened bacterial strains. Positive response was detected in all of the 14 tested strains ofErwinia herbicola, in 41 of the 239 strains ofPseudomonas species; in all 5 strains ofXanthomonas ampelina, X. campestris pv.malvacearum, pv.translucens, pv.vesicatoria and in one strain ofPantoea stewartii. AHL assay of 41 strains ofX. maltophilia (syn.Stenotrophomonas maltophilia) isolated from soils withChromobacterium violaceum reporter has revealed no strains synthesizing these signal molecules; 26 strains analyzed withAgrobacterium tumefaciens reporter showed the same result.

Cloning and mapping of the genetic determinants for microcin C51 production and immunity

Microcin C51 is a small peptide antibiotic produced by Escherichia coli cells harbouring the 38 kb low copy number plasmid pC51, which codes for microcin production and immunity. The genetic determinants for microcin synthesis and immunity were cloned into the vectors pBR325, pUC19 and pACYC184. Physical and phenotypic analysis of deletion derivatives and mutant plasmids bearing insertions of transposon Tn5 showed that a DNA fragment of about 5 kb is required for microcin C51 synthesis and expression of complete immunity to microcin. Partial immunity can be provided by a 2 kb DNA fragment. Mutant plasmids were tested for their ability to complement Mic− mutations. Results of these experiments indicate that at least three plasmid genes are required for microcin production. The host OmpR function is also necessary for microcin C51 synthesis.