Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of ?-Lactam and Vancomycin Resistance in Enterococcus faecium

The transfer of DNA between Enterococcus faecium strains has been characterized by both the movement of well-defined genetic elements and by the large-scale transfer of genomic DNA fragments. In this work we report on the whole genome analysis of transconjugants resulting from mating events between the vancomycin-resistant E. faecium C68 strain and vancomycin susceptible D344RRF to discern the mechanism by which the transferred regions enter the recipient chromosome. Vancomycin-resistant transconjugants from five independent matings were analysed by whole genome sequencing. In all cases but one, the penicillin binding protein 5 gene (pbp5) and the Tn5382-vancomycin resistance transposon were transferred together and replaced the corresponding pbp5 region of D344RRF. In one instance, Tn5382 inserted independently downstream of the D344RRF pbp5. Single nucleotide variants (SNV) analysis suggests that entry of donor DNA into the recipient chromosome occurred by recombination across regions of homology between donor and recipient chromosomes, rather than through insertion sequence-mediated transposition. Transfer of genomic DNA was also associated with transfer of C68 plasmid pLRM23 and another putative plasmid. Our data are consistent with transfer initiated by a cointegration of a transferable plasmid with the donor chromosome, with subsequent circularization of the plasmid/chromosome cointegrate in the donor prior to transfer. Entry into the recipient chromosome occurs most commonly across regions of homology between donor and recipient chromosomes

Evolution of early development in dipterans: reverse-engineering the gap gene network in the moth midge Clogmia albipunctata (Psychodidae)

Includes supplemental materials for the online appendix.Understanding the developmental and evolutionary dynamics of regulatory networks is essential if we are to explain the non-random distribution of phenotypes among the diversity of organismic forms. Here, we present a comparative analysis of one of the best understood developmental gene regulatory networks today: the gap gene network involved in early patterning of insect embryos. We use gene circuit models, which are fitted to quantitative spatio-temporal gene expression data for the four trunk gap genes hunchback (hb), Krüppel (Kr), giant (gt), and knirps (kni)/knirps-like (knl) in the moth midge Clogmia albipunctata, and compare them to equivalent reverse-engineered circuits from our reference species, the vinegar fly Drosophila melanogaster. In contrast to the single network structure we find for D. melanogaster, our models predict four alternative networks for C. albipunctata. These networks share a core structure, which includes the central regulatory feedback between hb and knl. Other interactions are only partially determined, as they differ between our four network structures. Nevertheless, our models make testable predictions and enable us to gain specific insights into gap gene regulation in C. albipunctata. They suggest a less central role for Kr in C. albipunctata than in D. melanogaster, and show that the mechanisms causing an anterior shift of gap domains over time are largely conserved between the two species, although shift dynamics differ. The set of C. albipunctata gene circuit models presented here will be used as the starting point for data-constrained in silico evolutionary simulations to study patterning transitions in the early development of dipteran species.The laboratory of Johannes Jaeger and this study in particular was funded by the MEC-EMBL agreement for the EMBL/CRG Research Unit in Systems Biology, by SGR Grant 406 from the Catalan funding agency AGAUR, by grants BFU2009-10184 and BFU2012-33775 from the Spanish Ministry of Science (MICINN, now called MINECO), and by European Commission grant FP7-KBBE-2011-5/289434 (BioPreDyn). Early stages of this work were funded by a Conacyt scholarship to MG-S, and by BBSRC grant no. BB/D000513/1 supporting JJ. The Centre for Genomic Regulation (CRG) acknowledges support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208