Abstract
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
Highlights
Replication is assumed to be a key factor in the evolution of genome structure and organization (Rocha 2004; Rocha 2008; Cagliero et al 2013; Jun et al 2018)
In contrast to eukaryotes and archaea, where the chromosome replication proceeds simultaneously from multiple sites, replication of bacterial chromosomes starts from a single origin of replication and continues along both replichores up to the terminus of replication
We focused on Rhodobaca (R.) barguzinensis and Loktanella (L.) vestfoldensis, the species with the highest slopes and the conserved genes mostly clustered around terminus of replication (terC)
Summary
Replication is assumed to be a key factor in the evolution of genome structure and organization (Rocha 2004; Rocha 2008; Cagliero et al 2013; Jun et al 2018). Since cell division is often shorter than the time required for the replication of the chromosome itself, it leads to the occurrence of multiple replication complexes in the cell. The genes located in the early replicating regions near the oriC can be present in multiple copies and have a higher expression level compared with genes in the late replicating regions. This so-called gene-dosage effect is especially pronounced in fast-growing bacteria, where strongly expressed genes are preferentially concentrated near the oriC (Rocha 2004; Couturier and Rocha 2006). Bacterial chromosome architecture can be shaped by large-scale interreplichore translocations, as was recently shown using genome sequence comparisons between 262 closely related pairs of bacterial species (Khedkar and Seshasayee 2016)
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