Bipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes

Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this study extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.

Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

Background

The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.

Results

We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.

Conclusion

The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.