PhD topic / position – the role of ABCF proteins in the regulation of translation and antibiotic resistence

Institute of Microbiology of the CAS, v. v. i.

Laboratory for Biology of Secondary Metabolism (Lab 111) in research center BIOCEV (Vestec) is seeking motivated students to study the role of ABCF proteins in the regulation of translation and antibiotic resistence

ABCF proteins are cytosolic ATPases of the ABC superfamily, which includes proteins involved in regulation of translation or in ribosome protection from antibiotics targeting the 50S ribosomal subunit. Despite their different biological functions, all characterized ABCFs bind to the same site on the ribosome, and their common feature is ATP-dependent modulation of the peptidyl-transferase site. However, the vast majority of the 30 bacterial ABCF subfamilies have not yet been characterized. The number of ABCFs in the genome correlates with the complexity of the bacterial life cycle (sporulation, production of specialized metabolites, occurrence in the environment). This suggests that these proteins are an important tool for bacterial adaptation to the external environment.

We study the biological function of ABCF proteins and their molecular mechanism of action in two bacterial models: environmentally occurring antibiotic-producing filamentous bacteria of the genus Streptomyces (8-11 ABCFs per genome) and an important human pathogen, Staphylococcus aureus (usually 3 chromosomal ABCFs per chromosome and several resistance ).

We will work with the prospective candidates to „tailor“ the PhD, Master's or Bachelor's project according to their previous experience and current interests. For PhD. students we offer part-time employment. Methodological approaches that can be learned in our lab include genetic manipulations (DNA cloning, site-directed mutagenesis, CRISPR genome editing), working with ribosomes (cell-free transcription-translation assay, polysome profiling), Work with proteins (heterologous expression and purification, Western bloting), omics approaches ( genomic sequencing, proteomics, potentially RNAseq and ribosomal footprint profiling) and in collaboration structural analysis of ribosomal complexes using CryoEM.

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