Biology subjects

Huelter, N. F.

Publications and source records attributed to Huelter, N. F..

7 recordsLinked to original sources

bioRxiv2026

Regulatory and metabolic integration accompany plasmid domestication during adaptation to a plant-associated lifestyle

Plasmids are major drivers of evolutionary innovation and ecological adaptation in prokaryotes. Plasmids that confer beneficial functions on their host may become domesticated through long-term coevolution, resulting in stable vertical inheritance within a bacterial lineage. How this process contributes to the evolution of bacteria associated with eukaryotic hosts remains poorly understood. Here, we investigate the function of the two large domesticated plasmids, LPP1 and LPP2, in Pantoea agglomerans associated with wheat. We show that loss of LPP1 reduces bacterial fitness during wheat colonization and impairs the utilization of diverse carbon sources. Comparative transcriptomics further reveal that curing of either plasmid extensively remodels chromosomal gene expression under both laboratory and wheat-associated conditions, whereas genome-scale metabolic reconstruction predicts that many metabolic pathways are jointly encoded by plasmid and chromosome. This functional integration extends beyond plasmid-specific pathways, as plasmid curing disrupts the utilization of substrates metabolized exclusively by chromosomally-encoded enzymes. Our results indicate that LPP1 promotes P. agglomerans association with wheat primarily through its regulatory and metabolic integration with the chromosome rather than through the simple addition of accessory genes. We propose that LPP1, and likely LPP2, represent chromosome-like symbiosis plasmids whose domestication reflects long-term selection for plant-associated lifestyle in Pantoea. Our findings suggest that persistent selection imposed by symbiotic lifestyles drives plasmid domestication, progressively transforming mobile plasmids into chromosome-like replicons that are integral components of bacterial genomes.

microbiology↗

bioRxiv2026

Horizontal transfer promotes allele segregation in multicopy plasmids

Plasmids reside within prokaryotic cells in multiple copies and can spread horizontally between hosts. Their multicopy nature enables intracellular allele diversity (heteroplasmy), and their segregation depends on the modes of plasmid replication and partition. Horizontal plasmid transfer has the potential to alter plasmid allele composition, however its impact on plasmid allele dynamics remains poorly understood. Here, we show that conjugative plasmid transfer accelerates the segregation of plasmid heteroplasmy by promoting the emergence of homoplasmic hosts. Using a quantitative experimental system to track plasmid allele dynamics in Acinetobacter baylyi under non-selective conditions, we followed the fate of a novel antibiotic resistance allele introduced into an ancestral donor population. While alleles in heteroplasmic donors segregated over time, conjugation produced almost only homoplasmic recipients whose allele composition closely mirrored that of the donor pool. Heteroplasmic recipients were rare and arose primarily from multiple plasmid transfer events prior to plasmid establishment. A mathematical model calibrated to the experimental setup predicts that conjugation accelerates plasmid allele segregation, with effects scaling with plasmid copy number and conjugation frequency. Our findings identify horizontal transfer as a previously unrecognized segregation pathway shaping the evolution of mobile genetic elements.

evolutionary biology↗

bioRxiv2025

Persistence of large conjugative plasmids relies on the combination of active partitioning and addiction mechanisms

Extrachromosomal and mobile genetic elements, including transposable elements, plasmids, and accessory chromosomes, are found across all domains of life. The replication and segregation of elements integrated into the host chromosome are ensured by the host life cycle. In contrast, the persistence of autonomously replicating elements relies on their ability to remain within the host population. Here, we compare the evolutionary advantage of different persistence strategies found in prokaryotic plasmids. Through intracellular competitions between plasmid genotypes, we find that the combination of active partitioning during cell division with a toxin-antitoxin (TA) system for post-segregational killing increases plasmid fitness more than either strategy alone. Mathematical modeling of long-term plasmid evolution, calibrated with empirical plasmid loss dynamics, further supports these findings. A survey of enterobacterial genomes indicates that partitioning and TA systems are core features of large conjugative plasmids. Indeed, we confirm the presence of a previously unrecognized type I TA system in IncX3 plasmids, which serve as important vectors of antibiotic resistance in human pathogens. These findings suggest that large conjugative plasmids encode TA systems, including those yet to be identified. The combination of TA and partitioning systems emerges as the most effective strategy for the evolutionary success of low-copy extrachromosomal elements.

microbiology↗

bioRxiv2024

Evolution of plasmid domestication in plant-associated Pantoea: massive gain of genetic redundancy followed by differential gene loss

Plasmids are important drivers of evolutionary transformations and ecological adaptation in prokaryotes. Plasmids supplying the host with beneficial functions may become domesticated and gain a stable inheritance within the host lineage in the form of secondary chromosomes. Chromosomes descendent from plasmids (termed chromids) comprise core genes that are universally present in all taxon members. The origin of plasmid core genes remains poorly understood and alternative hypotheses entailing gene translocation or genetic redundancy are debated. Studying plasmid evolution in plant-associated Pantoea, we show that the large Pantoea plasmid (LPP) and plasmid pPag1 comprise core genes in the host taxa. We infer the LPP acquisition in plant-associated ancestors, while the pPag1 acquisition is traced to the ancestor of plant growth-promoting species. We show that both plasmids are vertically inherited and the LPP replication is furthermore coordinated with cell division, hence they are better described as chromids. Using phylogenomics we infer that the plasmid acquisition manifested in massive gene gain, some redundant with the chromosome, followed by differential gene loss. Our results provide an explanation for the evolution of core plasmid genes that entails plasmid-driven species divergence, which preliminarily manifests in genetic redundancy, and is followed by gradual loss of redundant genes. Significance statementAdaptation to host-associated lifestyle in bacteria can be promoted by the acquisition of plasmids, which are mobile extra-chromosomal genetic elements. A canonic example is the symbiosis Rhizobia plasmids, where essential traits to interact with Legumes are plasmid-encoded. Symbiosis plasmids are likely to evolve into stably inherited domesticated plasmids (termed chromids). Recent research reveals that potential chromids are widely distributed among plant-associated bacteria. Studying the origin of plasmids in the plant-associated genus Pantoea, we show that the large Pantoea plasmid (LPP) and plasmid pPag1 are domesticated. Phylogenomic analyses trace back the plasmid origin to ancestral nodes in the Pantoea species tree. We reconstruct main events in chromid evolution, including massive gene gain, some redundant with the chromosome, and differential gene loss.

evolutionary biology↗

bioRxiv2023

T6SS-mediated competitive exclusion among Pantoea agglomerans associated with plants

Establishment of symbiotic interactions with a host habitat depends on colonization success of the microbiome members. One route to success is increasing competitiveness against genotypes having similar adaptations. Many bacteria deploy the type VI secretion system (T6SS) to deliver toxic effector proteins into the cytoplasm of competing cells, whereas the attacking cells are protected from self-intoxication by immunity proteins. While the evolution of antagonistic interactions between species competing for similar niches is expected, the interactions between closely related strains having a similar core genetic makeup, remains understudied. Here we show that the strength of T6SS-mediated competition between closely related P. agglomerans strains is not associated with phylogenetic relatedness and rather depends on their effector and immunity genes repertoire. Annotating the T6SS components in eleven P. agglomerans isolates from wheat seeds, we observed a heterogeneous composition of effector and immunity determinants. Competition experiments further showed profound differences in the strain survival following reciprocal T6SS-mediated interactions. Reconstructing the evolution of T6SS loci across plant-associated P. agglomerans isolates indicates intra-chromosomal recombination as the main driver of effector and immunity gene diversification. Our results provide empirical data on intraspecific interactions during microbiota assembly likely to be at play during colonization of germinating plant seeds.

microbiology↗

bioRxiv2023

Segregational drift hinders the evolution of antibiotic resistance on polyploid replicons

The emergence of antibiotic resistance under treatment depends on the availability of resistance alleles and their establishment in the population. Novel resistance alleles are encoded either in chromosomal or extrachromosomal genetic elements; both types may be present in multiple copies within the cell. However, the effect of polyploidy on the emergence of antibiotic resistance remains understudied. Here we show that the establishment of resistance alleles in microbial populations depends on the ploidy level. Evolving bacterial populations under selection for antibiotic resistance, we demonstrate that resistance alleles in polyploid elements are lost frequently in comparison to alleles in monoploid elements due to segregational drift. Integrating the experiments with a mathematical model, we find an agreement between the theoretical and empirical allele dynamics, confirming our understanding of the allele segregation process. Using the mathematical model, we further show that the effect of polyploidy on the establishment probability of beneficial alleles is strongest for low replicon copy numbers and plateaus for high replicon copy numbers. Our results suggest that the distribution of fitness effects for mutations that get fixed in a population depends on the replicon ploidy level. Our study indicates that strategies for drug treatment of bacterial infections should take into consideration the pathogen ploidy level.

microbiology↗

bioRxiv2018

Segregational drift and the interplay between plasmid copy number and evolvability

The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. We investigate the implications of random genetic drift of multicopy plasmids during cell division - termed here segregational drift - to plasmid evolution. Performing experimental evolution of low- and high-copy non-mobile plasmids in Escherichia coli, we find that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. In addition, simulated evolution of multicopy plasmid alleles demonstrates that segregational drift leads to increased loss frequency and extended fixation time of plasmid mutations in comparison to haploid chromosomes. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. Our study demonstrates that segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. We suggest that plasmid copy number is an important determinant of plasmid evolvability due to the manifestation of segregational drift.

microbiology↗