Spaghettification: How extreme replichore imbalance impacts bacterial replication and morphology

Abstract

Bacterial chromosomes are typically organized into two similarly sized replichores to synchronize bidirectional replication and fusion within a Tus/ter-defined termination zone. Previous studies have suggested that replichore balance in both Salmonella and E. coli is maintained by selection for efficient and properly coordinated replication termination and chromosome segregation. However, there is a lack of understanding of the causal relationship between replichore asymmetry, cellular fitness, and replication-fork convergence, as well as how the termination machinery behaves when the two replichores differ substantially in length. Here we dissect the impact of replichore asymmetry by engineering 41 isogenic Salmonella inversion mutants spanning progressive imbalances, complemented by duplication-based asymmetries. Our constructed strains show that even cells with severely imbalanced chromosomes, where one replichore is 11-fold longer in size than the other (0.38 Mb vs. 4.48 Mb) are viable. However, relative fitness declined linearly with replichore size difference at approximately -0.17 per Mb. Additionally, highly imbalanced strains exhibited substantial division defects with severe cell elongation and lysis. Replication profiling showed that, even under extreme replichore asymmetry, forks consistently converge at the innermost ter sites of the shorter replichore and that two sequential Tus/ter barriers were sufficient for complete replication fork arrest. Together, these results establish a quantitative rule linking replichore asymmetry to fitness, define the termination position under imbalance, and reveal a dual Tus/ter barrier that safeguards termination when one replichore reaches the terminus region ahead of the other. Collectively these results connect chromosome architecture to replication mechanics and cell-division outcomes.