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Comparative Analyses of Extrachromosomal Bacterial Replicons, Identification of Chromids, and Experimental Evaluation of Their Indispensability

  • Lukasz DziewitEmail author
  • Dariusz Bartosik
Part of the Methods in Molecular Biology book series (MIMB, volume 1231)

Abstract

Bacterial genomic information can be divided between various replicons, including chromosomes, plasmids, and chromids (essential plasmid-like replicons with properties of both chromosomes and plasmids). Comparative analyses of bacterial plasmids, including homology searches, phylogenetic and phylogenomic analyses, as well as network construction for the characterization of their relationships, are good starting points for the identification of chromids. Chromids possess several chromosome-like genetic features (e.g., codon usage, GC content), but most significantly, they carry housekeeping genes, which make them indispensable for cell viability. However, it is important to confirm in silico predictions experimentally. The essential nature of a predicted chromid is usually verified by the application of a target-oriented replicon curing technique, based on the incompatibility phenomenon. Further tests examining growth in various media are used to distinguish secondary chromids from plasmids, and mutational analysis (e.g., using the yeast FLP/FRT recombination system) is employed to identify essential genes carried by particular chromids.

Key words

Extrachromosomal bacterial replicon Plasmid Chromid Comparative genomics Target-oriented replicon curing technique Growth assay Mutational analysis 

Notes

Acknowledgement

This work was supported by the National Science Centre, Poland (grant 2013/09/B/NZ1/00133).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Bacterial Genetics, Institute of MicrobiologyUniversity of WarsawWarsawPoland

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