R. Kogay

Defense systems and horizontal gene transfer in bacteria

The paper examines whether bacterial defense systems reduce horizontal gene transfer by analyzing HGT rates and the presence of 73 defense systems in 12 bacterial species.

Co-evolution of gene transfer agents and their alphaproteobacterial hosts

The paper identifies 59 gene families co-evolving with GTA genes in alphaproteobacteria, suggesting they are involved in stress response, DNA repair, and biofilm formation, supporting a model for GTA persistence in microbial populations.

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes

The paper characterizes the Kiwa defence system as a bacterial membrane supercomplex that detects phage-induced membrane changes and inhibits phage replication.

Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents

The paper identifies codon usage bias in GTA genes of alphaproteobacteria, suggesting selection for translational efficiency during GTA production, and finds genes potentially involved in DNA integration.

Formal Recognition and Classification of Gene Transfer Agents as Viriforms

The paper argues that gene transfer agents (GTAs) should be classified as viriforms rather than viruses due to their unique lifecycle and genetic characteristics.

Phylogenetic evidence of headful packaging strategy in gene transfer agents

The paper reconstructs the evolutionary history of GTA terminase to show RcGTA evolved from a headful packaging virus.

Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents

This paper shows that GTA genes evolve under positive selection for reduced energy cost of protein production, suggesting GTAs are bacterial adaptations for horizontal gene transfer under nutrient stress.