Biology subjects

Soler-Bistue, A.

Publications and source records attributed to Soler-Bistue, A..

6 recordsLinked to original sources

bioRxiv2026

Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change

The ability to generate genomic diversity expands opportunities for understanding and engineering biology. Here, we demonstrate on-demand generation of diversity in bacterial genome configurations and its application to probing physiology under altered genome organization. We engineered the fast-growing bacterium Vibrio natriegens to enable large-scale stochastic duplications, translocations, inversions, and deletions, producing populations with a wide range of genome arrangements. We investigated phenotypic robustness to genome reconfigurations and found that distinct genome organizations can support stable physiology, indicating that bacteria may tolerate chromosomal alterations more readily than previously appreciated. Our work provides a framework for advancing the understanding and engineering of bacterial genomes and suggests that genome reconfigurations may contribute to phenogenetic drift, allowing for evolutionary exploration while preserving phenotype.

synthetic biology↗

bioRxiv2025

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

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.

microbiology↗

bioRxiv2025

Role of Tad Pili during the transition from Planktonic to Biofilm State in Bradyrhizobium diazoefficiens USDA 110

Free-living soil bacteria may exist in two states: planktonic as swimmer cells, and sessile within biofilms. In biofilms, bacterial cells are embedded into an extracellular matrix, which confers protection against environmental stresses and extends bacterial survival. The transition from planktonic to biofilm state involves surface sensing and attachment mediated by flagella and pili. Here, we explored the role of Tad pili (Type IVc) in surface sensing, adhesion, and biofilm formation in Bradyrhizobium diazoefficiens, a nitrogen-fixing symbiont of soybean. Bioinfor-matic analyses revealed that Tad pili are widely distributed and highly conserved in Bradyrhi-zobium. In other model bacteria, pili deletion leads to decrease in biofilm-forming capacity, but other functions are also affected depending on the microorganism. Surprisingly, deletion of the most conserved genomic cluster encoding Tad pili in B. diazoefficiens caused an increased ad-hesion to abiotic surfaces and loss of movement, indicating a physiological shift towards a bio-film state. These observations suggest a sensor or regulatory role for this apparatus that could affect cell-cell interactions or interactions with the extracellular matrix. Additionally, a connec-tion between pili and c-di-GMP levels in the cell was established. These findings highlight the critical role of Tad pili in B. diazoefficiens physiology, providing insights into bacterial adaptabil-ity and potential applications in agriculture and biotechnology. Understanding these mecha-nisms is key to improving biofilm management strategies and generating novel approaches to enhance bacterial viability in soil and inoculants as well as to optimize the symbiosis. ImportanceBiofilm formation is critical for bacterial survival in the soil. In this study we analyzed the role of Tad pili in Bradyrhizobium diazoefficiens biofilm forming capacity and its connection with the second messenger c-di-GMP, which is involved in regulating the transition between plank-tonic and sessile states. Since bacteria applied in inoculants are in the planktonic state, where-as bacterial survival is optimal in the sessile (biofilm) state, our findings may contribute to im-prove the switch towards the sessile state in novel inoculant formulations, enhancing bacterial persistence in formulations and soil.

microbiology↗

bioRxiv2024

Inside Out: the physiology of Brucella Vegetative and Intracellular Growth.

Growth rate is a key prokaryotic trait that allows estimating fitness and understanding cell metabolism. While in some clades it has been well studied in model organisms, there is little data on slow-growing bacteria. In particular, there is a lack of quantitative studies on the species of the Brucella genus. This is an important microorganism since it is the causative agent of brucellosis, one of the most widespread bacterial zoonoses affecting several species of animals, including humans. Brucella species exhibit approximately 97% genomic similarity. Despite this, Brucella species show different host preferences, zoonotic risks, and pathogenicity. After more than one hundred years of research, numerous aspects of Brucella biology, such as in vivo and in vitro growth remain poorly characterized. In this work, we analyzed vegetative and intracellular growth of the classical Brucella species (B. abortus 2308, B. melitensis 16M. B. suis 1330, B. ovis, and B. canis). Strikingly, each species displayed particular growth parameters in culture. Doubling time (DT) spanned from 2.7 hs-1 in B. suis to 18h-1 for B. ovis. In the context of intracellular infection of J774A.1 phagocytic cells, DT was higher, but it widely varied across species, closely correlating to the growth observed in vitro. Overall, despite high similarity of the genomes, we found species-specific growth parameters in the intracellular cell cycle.

microbiology↗

bioRxiv2019

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae.

Ribosomal protein (RP) genes locate near the replication origin (oriC) in fast-growing bacteria, which is thought to have been selected as a translation optimization strategy. Relocation of S10-spc- locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. Deep-sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Strikingly, in this work we observed that protein production capacity was independent of S10 position. Since RP constitute a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains. Therefore, on top of its essential function in translation, RP genomic location contributes to sustain optimal macromolecular crowding. This is a novel mechanism coordinating DNA replication with bacterial growth.

microbiology↗

bioRxiv2018

Interspecies DNA acquisition by a naturally competent Acinetobacter baumannii strain

Acinetobacter baumannii is a human pathogen that frequently acquires antibiotic resistance genes leading to the emergence of multi-drug-resistant (MDR) strains. To investigate the role of transformation in the acquisition of resistance determinants by this species, the susceptible strain A118 was exposed to genomic DNA of carbapenem-resistant Klebsiella pneumoniae (CRKp). Resistant transformants were obtained and an increase in the resistance level to all {beta}-lactam antibiotics was observed. Whole genome analysis of transformant clones demonstrated the acquisition of CRKp DNA. The most frequently acquired genes correspond to mobile elements, antibiotic resistance genes, and operons involved in metabolism. Bioinformatic analyses and in silico gene flow prediction strengthen our findings, showing that a continuing exchange of genetic material between A. baumannii and K. pneumoniae occurs when they share the same niche. Our results reinforce the idea that natural transformation may play a key role in the increasing emergence of A. baumannii MDR.\n\nIMPORTANCESince the characterization of antibiotic resistance in the late 50s, antibiotic resistance propagation was classically associated with horizontal gene transfer (HGT) mediated by plasmids bearing multiple resistance genes. Here we show that, at least in the human pathogen A. baumannii, transformation also plays a major role in the acquisition of antibiotic resistance determinants. This study unravels that at least for certain pathogens the propagation of resistance genes occurs by alternative HGT mechanisms which in the past have been unappreciated.

microbiology↗