Chromosome organization affects genome evolution in Sulfolobus archaea.

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Organismal DNA sequence and chromosome structure influence gene expression.
• The extremophilic crenarchaeon Sulfolobus possesses a single circular chromosome with three replication origins.
• Previous studies identified distinct A (high gene expression, replication origins) and B (low gene expression) chromosomal compartments in Sulfolobus.

Purpose of the Study:

• To investigate the impact of three-dimensional chromosomal organization on primary sequence evolution in eleven Sulfolobus species.
• To determine the effects of replication origins and compartmentalization on genome evolution.
• To understand how chromosomal architecture influences mutation rates and selection pressures.

Main Methods:

• Single-nucleotide polymorphism (SNP) analysis across eleven Sulfolobus species.
• Mutational analyses to assess sequence variation.
• Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to evaluate chromatin accessibility.

Main Results:

• Mutation rates increased with distance from replication origins in the B compartment, but not in the A compartment.
• Sequences within the A compartment exhibited lower mutation rates and stronger purifying selection compared to the B compartment.
• The B compartment demonstrated reduced chromatin accessibility compared to the A compartment.

Conclusions:

• Chromosomal compartmentalization significantly influences genome evolution in Sulfolobus.
• The A compartment acts as a stable reservoir for gene sequences.
• The B compartment facilitates sequence diversification, potentially driven by replication termination events.