Evolutionary Constraints on RNA Polymerase Gene Positioning in the Genome of Fast-Growing Bacteria..

Larotonda, L. I.; Ojeda, E.; Bordignon, M. B.; Fulgenzi, F. R.; Comerci, D. J.; Val, M.-E.; Llorente, B. E.; Mazel, D.; Soler-Bistue, A.

doi:10.1101/2025.04.14.645983

bioRxiv · 10.1101/2025.04.14.645983

Evolutionary Constraints on RNA Polymerase Gene Positioning in the Genome of Fast-Growing Bacteria..

Larotonda, L. I.·Ojeda, E.·Bordignon, M. B.·Fulgenzi, F. R.·Comerci, D. J.·Val, M.-E.·Llorente, B. E.·Mazel, D.·Soler-Bistue, A.

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Abstract

How gene order along chromosomes affects cellular homeostasis and genome evolution remains poorly understood. Bacterial chromosomes are organized along the replication origin (oriC)-terminus (ter) axis. The spatial arrengement of genes within this axis may influence cellular physiology, genome evolution, and transcriptional regulation. The catalytic core of the sole bacterial RNA polymerase (RNAP) is encoded by rpoB and rpoC within the universally conserved rplKAJL-rpoBC locus. In fast growing bacteria this locus is located near oriC potentially linking genome organization to cellular physiology. Here, we investigated the functional relevance of rplKAJL-rpoBC chromosomal positioning by relocating it within Vibrio cholerae genome. While viable, strains harboring rplKAJL-rpoBC far from oriC exhibited nutrient-dependent fitness defects. These phenotypes correlated with reduced locus copy number and RNAP abundance, without changes in its subcellular distribution. Introducing a second copy of rpIKAJL-rpoBC at a distal genomic location from oriC abolished the phenotypes, demonstrating that replication-associated gene dosage effects were the main mechanism behind the observed physiological changes. Further uncoupling rpoB and rpoC from the rplKAJL-rpoBC locus revealed that fitness costs were specifically linked to RNAP gene relocation. Our results reveal that selective pressures act to maintain RNAP-encoding genes near oriC to optimize replication-associated dosage effects, ensuring efficient RNAP production during exponential growth. We discuss the relationship between gene order and ecological strategies linked to bacterial growth. Our work underscores gene order as an underestimated but critical factor shaping cellular physiology and genome evolution. SignificanceBacterial chromosomes have a highly plastic gene content but the importance of their spatial organization and gene order is started to be appreciated as a driver of cellular physiology. Growing evidence suggests that the spatial organization of bacterial genomes plays a critical role in gene expression, replication dynamics, and fitness. In this study, we demonstrate that the conserved positioning of rpoB and rpoC, encoding the catalytic core of RNA polymerase (RNAP), near the replication origin (oriC) is essential for optimal bacterial growth. By relocating the rplKAJL-rpoBC locus in Vibrio cholerae, we show that its chromosomal position directly impacts nutrient-dependent fitness, RNAP abundance, and replication-associated gene dosage effects. These findings suggest that selective pressures maintain genes encoding RNAP near oriC to ensure efficient transcriptional output during exponential growth. More broadly, our study highlights gene order as an underappreciated factor in bacterial genome evolution, beyond its known roles in operon structure and transcriptional regulation. Given the fundamental role of RNAP, our results have implications for understanding bacterial ecological strategies, adaptation, and synthetic genome design. By integrating positional genomics with physiological studies, we provide a theoretical and experimental framework for investigating how genome architecture shapes cellular function.

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Larotonda, L. I., Ojeda, E., Bordignon, M. B., Fulgenzi, F. R., Comerci, D. J., Val, M.-E., Llorente, B. E., Mazel, D., Soler-Bistue, A.. 2025-04-14. Evolutionary Constraints on RNA Polymerase Gene Positioning in the Genome of Fast-Growing Bacteria... https://doi.org/10.1101/2025.04.14.645983

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