Complementation of an Escherichia coli polypeptide deformylase mutant with a gene from Clostridium acetobutylicum ATCC 824

Cotranslational processing mechanisms: towards a dynamic 3D model

Recent major advances have been made in understanding how cotranslational events are achieved in the course of protein biosynthesis. Specifically, several studies have shed light into the dynamic process of how nascent chains emerging from the ribosome are supported by protein biogenesis factors to ensure both processing and folding mechanisms. To take into account the awareness that coordination is needed, a new 'concerted model' recently proposed simultaneous action of both processes on the ribosome. In the model, any emerging nascent chain is first encountered by the chaperone trigger factor (TF), which forms an open cradle underneath the ribosomal exit tunnel. This cradle serves as a passive router that channels the nascent chains to the first cotranslational event, the proteolysis event performed by the N-terminal methionine excision machinery. Although fascinating, this model clearly raises more questions than it answers. Does the data used to develop this model stand up to scrutiny and, if not, what are the alternative mechanisms that the data suggest?

Peptide deformylase: a target for novel antibiotics?

Peptide deformylase (PDF) catalyses the hydrolytic removal of the N-terminal formyl group from nascent ribosome-synthesised polypeptides. Its activity is essential and it is present in all eubacteria. It is also present in the organelles of some eukaryotes. PDF represents a novel class of mononuclear iron protein, utilising an Fe(2+) ion to catalyse the hydrolysis of an amide bond. Due to its extreme lability, isolation and characterisation of PDF was not possible until very recently. This review will discuss the recent progress in the elucidation of the the structure and function of PDF, evaluating its suitability as a target for antibiotic design and summarising the current approaches to designing drugs that target PDF.

YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases

Peptide deformylation is an essential process in eubacteria. The peptide deformylase Def has been suggested to be an attractive target for antibacterial drug discovery. Some eubacteria including medically important pathogens possess two def-like genes. Until now, the functionality of both genes has been tested only in Staphylococcus aureus with the result that one gene copy was functional. Here, expression of two functional def-like gene products in Bacillus subtilis is demonstrated. Besides the def gene, which is chromosomally located close to the formyltransferase gene fmt and which was overexpressed and biochemically tested previously, B. subtilis possesses a second def-like gene, called ykrB. The encoded protein is 32% identical to the def gene product. It was shown that either def or ykrB had to be present for growth of B. subtilis in rich medium (each was individually dispensable). Studies with a def/ykrB double deletion strain with xylose-inducible ykrB copy demonstrated that, besides def, the gene ykrB is a second cellular target of deformylase inhibitors such as the antibiotic actinonin. The gene products exhibited similar enzymic properties, exemplified by similar inhibition efficacy of actinonin in biochemical assays. Antibiotic susceptibility tests with different deletion strains and Northern analyses indicated that YkrB is probably the predominant deformylase in B. subtilis. It was shown that duplication of the deformylase function does not lead to an increased actinonin-resistance frequency in comparison to B. subtilis mutants carrying only one deformylase gene.

Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents

Peptide deformylase was discovered 30 years ago, but as a result of its unusually unstable activity it was not fully characterized until very recently. The aim of this paper is to review the many recent data concerning this enzyme and to try to assess its potential as a target for future antimicrobial drugs.