The Proximity of Ribosomal Protein Genes to oriC Enhances Vibrio cholerae Fitness in the Absence of Multifork Replication

Abstract

Recent works suggest that bacterial gene order links chromosome structure to cell homeostasis. Comparative genomics showed that, in fast-growing bacteria, ribosomal protein genes (RP) locate near the replication origin (oriC). We recently showed that Vibrio cholerae employs this positional bias as a growth optimization strategy: under fast-growth conditions, multifork replication increases RP dosage and expression. However, RP location may provide advantages in a dosage-independent manner: for example, the physical proximity of the many ribosomal components, in the context of a crowded cytoplasm, may favor ribosome biogenesis. To uncover putative dosage-independent effects, we studied isogenic V. cholerae derivatives in which the major RP locus, S10-spc-α (S10), was relocated to alternative genomic positions. When bacteria grew fast, bacterial fitness was reduced according to the S10 relative distance to oriC. The growth of wild-type V. cholerae could not be improved by additional copies of the locus, suggesting a physiologically optimized genomic location. Slow growth is expected to uncouple RP position from dosage, since multifork replication does not occur. Under these conditions, we detected a fitness impairment when S10 was far from oriC. Deep sequencing followed by marker frequency analysis in the absence of multifork replication revealed an up to 30% S10 dosage reduction associated with its relocation that closely correlated with fitness alterations. Hence, the impact of S10 location goes beyond a growth optimization strategy during feast periods. RP location may be important during the whole life cycle of this pathogen.

High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

“…Even though rRNA operons in S. pneumoniae are also initiated with GTP (BioRxiv: https://doi.org/10.1101/283663), we did not observe a correlation between initiating nucleotide and gene expression levels in cells growing in different media (Supplementary Figure S2C). Nevertheless, in prokaryotes including S. pneumoniae, genes encoding ribosomal RNAs and proteins are conserved in a location close to the origin of replication (50)(51)(52). The ori-proximal location of the four pneumococcal rRNA loci results in a higher gene copy number of rRNAs in fast-growing cells, such as in C+Y, as a direct consequence of the increase in replication initiation frequency.…”

Macromolecular crowding links ribosomal protein gene dosage to growth rate inVibrio cholerae

“…In line with prior bioinformatics studies (16, 17), we showed that oriC -proximity of S10 provides optimal dosage and expression to attain the maximal growth capacity (19). We also found that S10 position impacts bacterial fitness in absence of multi-fork replication (20). This suggests that the RP gene location affects cell physiology even in slow-growing bacteria (20).…”

“…In previous works (19, 20), we tackled this issue in Vibrio cholerae , the causative agent of cholera disease. This microorganism is also a model for multi-chromosomal bacteria, a trait found in ~10% of these microorganisms (21).…”

“…1b and 1c). Also, S10 genomic location impacted on V. cholerae fitness and infectivity (19, 20). In line with prior bioinformatics studies (16, 17), we showed that oriC -proximity of S10 provides optimal dosage and expression to attain the maximal growth capacity (19).…”

The impact of global transcriptional regulation on bacterial gene order

“…Indeed, the increase in gene dosage due to bacterial multifork replication appears as an added control mechanism of natural genetic circuits (37,38). However, the relevance of genome organization goes beyond gene dosage fluctuations in fast growth (39,40), and it may be influenced by chromosomal structure (39) and gene essentiality (41).…”