Biology subjects

Colp, M. J.

Publications and source records attributed to Colp, M. J..

4 recordsLinked to original sources

bioRxiv2025

Single nucleotide polymorphisms and structural variants reveal complex and variable ploidy in the amoebozoan Acanthamoeba castellanii

Acanthamoeba castellanii is a free-living amoeba that is emerging as a model organism for the study of eukaryotic microbiology. It is one of the most widely studied members of the Amoebozoa, and is both an important grazer in soil communities and an opportunistic human pathogen; A. castellanii is thus of evolutionary, ecological, and biomedical significance. Despite its potential as a lab workhorse, the genome biology of A. castellanii is complex and poorly understood. Polyploidy is a common feature of many amoebozoan genomes, and members of the genus Acanthamoeba are no exception; they appear to be not only polyploid, where genome copy number is inflated beyond the conventional haploid and diploid states, but also aneuploid, i.e., with inter-chromosomal copy number variation. To better understand aneuploidy in A. castellanii and how it may vary over time and between closely related strains, we analyzed nanopore and Illumina sequence datasets from several wild-type and mutant A. castellanii lines, with a focus on quantifying single nucleotide polymorphism (SNP) and structural variant allele frequencies across chromosome-scale scaffolds. Our findings suggest that intragenomic chromosome copy number is highly variable in Acanthamoeba and can change dynamically even over laboratory time scales. Significance StatementAcanthamoeba castellanii is becoming an important model organism for basic and applied research. However, its apparent polyploidy and aneuploidy has the potential to complicate the interpretation of results that depend on knowledge of gene copy number. In this study, we reveal the complex nature of ploidy in this organism by analyzing long- and short-read sequence data. Our results provide a reference point against which genomic and experimental data from A. castellanii can be interpreted, and guide future efforts aimed at more precisely characterizing how the organism regulates its genome and chromosome copy number.

genomics↗

bioRxiv2024

Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba

Acanthamoeba is a cosmopolitan freshwater amoebae known for its association with Nucleocytoplasmic Large DNA Viruses (NCLDVs). Previous studies have shown that Acanthamoeba spp. undergo lateral gene transfer (LGT) with NCLDVs. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba castellanii, Neff and C3, to investigate the occurrence and genomic context of viral LGT in Acanthamoeba. We show that the viral footprints in the C3 and Neff genomes are largely non-overlapping and that viral genes in Neff are found disproportionately in large sub-telomeric insertions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed and do not encode functions for their own mobility. Viral regions are hyper-methylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions. We propose a three-step model for the origin and fate of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, which allows them to persist in the genome, and (iii) deterioration of viral genomes by point mutation and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the host amoeba. Our work strengthens a growing body of work showing widespread but transient integration of viral DNA in protists and extends the relevance of epigenetic silencing mechanisms to the evolution of Amoebozoa. We highlight the importance of host genome dynamics for understanding the evolution of endogenized viral elements.

genomics↗

bioRxiv2024

The fate of artificial transgenes in Acanthamoeba castellanii

In this study, artificial transformation experiments were performed to investigate how the A. castellanii genome responds to foreign DNA presented in both circular and linear plasmid form. Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance in A. castellanii is proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends. This nascent linear molecule is maintained as a transgene-bearing minichromosome, while also allowing for chromosomal integration.

molecular biology↗

bioRxiv2021

Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin re-organization

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain, and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila. Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization, suggesting that changes in chromosomal folding are associated with host cell biology during infection.

genomics↗