Biology subjects

Skovgaard, O.

Publications and source records attributed to Skovgaard, O..

5 recordsLinked to original sources

bioRxiv2025

Replication coordination marks the domestication of large extrachromosomal replicons in bacteria

Bacterial genomes often include extrachromosomal replicons (ERs), ranging from small plasmids to nearly chromosome-sized elements, that foster genome plasticity and adaptation. Despite their prevalence, the mechanisms underlying ER domestication and their long-term adaptation within bacterial hosts remain largely unexplored. By analyzing over 40,000 complete bacterial genomes, we identified two main ER categories: small ERs with diverse GC content and large ERs ([≥]10% the size of the main chromosome) that closely match the GC content of the chromosome. Across multiple phyla, marker frequency analyses showed that large ERs maintain a 1:1 copy number with the chromosome. Another key finding of this study is that large ERs terminate replication in synchrony with the chromosome. Hi-C contact maps revealed consistent ori-ori interactions between chromosomes and ERs. In large ERs, inter-replichore and ter-ter interactions, along with the recruitment of key chromosomal segregation motifs, suggest the co-option of chromosome-associated replication and segregation machineries. Together, our findings indicate that as ERs become larger, they become increasingly reliant on chromosome-driven processes for stable inheritance, potentially explaining why they do not exceed the size of the chromosome.

microbiology↗

bioRxiv2024

Chromosomal plasticity can drive rapid adaptation in bacteria

Understanding the molecular mechanisms underlying rapid adaptation to stress is a fundamental question in evolutionary biology. A common mechanism is copy number changes, which can affect single genes, larger genomic regions, or even entire chromosomes in the case of eukaryotes (aneuploidy). Bacterial species with genomes comprising more than one chromosome are common, yet the role of adaptive copy number changes affecting entire chromosomes is unknown. Here, by using a bacterium with two chromosomes (chrI and chrII) as model system and combining evolution experiments in the presence of severe nutrient stress with whole-genome sequencing, we show that chromosomal copy number changes can drive rapid adaptation. We detected increased copy number of the entire chrII in almost half of the sequenced clones, isolated from twelve independent populations. In most cases, copy number increases were driven by mutations in the replication protein of chrII. A higher chrII copy number is likely to be beneficial because chrII codes for the operon responsible for metabolizing D-gluconic acid, the only carbon source present in the medium. Our results revealed a novel mechanism for rapid adaptation in bacteria. Given the prevalence of bacteria with secondary chromosomes, and the enrichment of secondary chromosomes in genes associated with interaction with the environment, this may be an important mechanism for adapting to novel environments that has been overlooked.

evolutionary biology↗

bioRxiv2023

Chromosomal Integrons are Genetically and Functionally Isolated Units of Genomes

Integrons are genetic elements that increase the evolvability of bacteria by capturing new genes and stockpiling them in arrays. Sedentary chromosomal integrons (SCIs), can be massive and highly stabilized structures encoding hundreds of genes, whose function remains generally unknown. SCIs have co-evolved with the host for aeons and are highly intertwined with their physiology from a mechanistic point of view. But, paradoxically, other aspects, like their variable content and location within the genome, suggest a high genetic and functional independence. In this work, we have explored the connection of SCIs to their host genome using as a model the Superintegron (SI), a 179-cassette long SCI in the genome of Vibrio cholerae N16961. We have relocated and deleted the SI using SeqDelTA, a novel method that allows to counteract the strong stabilization conferred by toxin-antitoxin systems within the array. We have characterized in depth the impact in V. choleraes physiology, measuring fitness, chromosome replication dynamics, persistence, transcriptomics, phenomics and virulence. The deletion of the SI did not produce detectable effects in any condition, proving that -despite millions of years of co-evolution-, SCIs are genetically and functionally isolated units of genomes.

microbiology↗

bioRxiv2022

Genetic drivers of chromosomal integron stability

Integrons are adaptive bacterial devices that rearrange promoter less gene cassettes into variable ordered arrays under stress conditions, to sample combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as abortive systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes. TeaserThe accumulation of cassette functions in integrons is ensured by toxin-antitoxin systems which kill the cell when the cassette excision rate is too high.

genetics↗

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↗