Chromosome architecture constrains horizontal gene transfer in bacteria

Area of Science:

• Genomics
• Microbial Ecology
• Molecular Biology

Background:

• Bacteria exhibit ecological and phenotypic cohesion despite frequent lateral gene transfer.
• Barriers to panmictic gene dissemination suggest mechanisms limiting horizontal gene transfer (HGT).
• Architecture IMparting Sequences (AIMS) are hypothesized to impose functional genome architecture.

Purpose of the Study:

• To investigate the role of AIMS in constraining DNA rearrangement within bacterial genomes.
• To determine if AIMS influence the acceptance and retention of horizontally transferred genes.
• To predict pathways of HGT based on AIMS compatibility between bacterial species.

Main Methods:

• Identification and analysis of AIMS (8 bp sequences) in bacterial genomes.
• Correlation of AIMS abundance and strand-bias with proximity to the replication terminus.
• Analysis of inversions and laterally acquired genes in relation to AIMS distribution.
• Development of a predictive model for HGT pathways based on AIMS compatibility.

Main Results:

• AIMS abundance and strand-bias correlate positively with proximity to the replication terminus.
• Inversions are less frequent near the replication terminus, consistent with selection on AIMS function.
• Strand-bias of AIMS in acquired genes is negatively correlated with distance from the replication terminus.
• Selection for AIMS function leads to the loss of at least 18% of transferred genes in terminus-proximal regions.

Conclusions:

• AIMS impose functional architecture on bacterial genomes, constraining DNA rearrangement and HGT.
• Selection for AIMS compatibility acts as a barrier to gene acquisition, preserving species integrity.
• Genome architecture, dictated by AIMS, plays a crucial role in bacterial evolution and speciation.