Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the...

Area of Science:

• Genomics
• Molecular Biology
• Microbial Genetics

Background:

• The Escherichia coli chromosome harbors unique GC-rich genomic structures.
• Replication fork progression can be impeded by specific DNA sequences.
• Understanding DNA replication challenges is crucial for genome stability.

Purpose of the Study:

• To identify and characterize novel genomic structural elements in E. coli.
• To investigate the role of these elements in DNA replication and genome topology.
• To explore the potential conserved function of these elements in other organisms.

Main Methods:

• Bioinformatic analysis to identify conserved DNA sequences.
• Genetic manipulation (deletion studies) to assess functional impact.
• DNA replication assays to detect post-replication gaps and DNA polymerase extension impediments.

Main Results:

• Discovery of two novel, conserved 222 bp repeats named Replication Risk Sequences (RRS).
• RRS are located near the dif and Ter macrodomain, flanking the terminus.
• RRS impede DNA polymerase extension on the lagging strand, forming single-stranded DNA gaps up to 2000 bp.
• Deletion of RRS significantly alters global genome structure and topology.
• At least one RRS is essential for viability unless a specific genomic region is amplified.

Conclusions:

• RRS are essential genomic elements that induce transient post-replication gaps in E. coli.
• These sequences contain G-quadruplexes that likely cause replication stress.
• RRS may function as topological relief valves during chromosome replication and segregation.
• Functional analogs of RRS might be widespread, potentially including eukaryotic G-quadruplexes.