Biology subjects

Hanke, D. M.

Publications and source records attributed to Hanke, D. M..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape

Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low-copy plasmids. In multicellular cyanobacteria like Anabaena sp., we found that a chromosomally-encoded ParMR has evolved into a novel cytoskeleton-termed CorMR-with a function in cell shape control rather than DNA segregation. Using live-cell imaging, in vitro reconstitution and Cryo-EM, we demonstrate that CorM forms dynamically unstable, antiparallel double-stranded filaments, which are recruited to the membrane by CorR via an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments are regulated by MinC, which excludes them from the poles and division plane. Comparative genomics reveal that the repurposing of ParMR and Min systems co-evolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.

microbiology↗

bioRxiv2025

SegMantX: a novel tool for detecting DNA duplications uncovers prevalent duplications in plasmids

Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification and the emergence of novel functions. The detection of segmental duplications is challenging due to heterogeneous amelioration of sequence similarity among duplicates, which hinders the reconstruction of continuous sequence alignment. Here we introduce SegMantX, a novel approach for the identifcation of diverged segmental duplications using local alignment chaining. In this approach, local alignments resulting from a preliminary sequence similarity search (e.g., BLASTn) are chained into continuous segments. Evaluating the performance of SegMantX simulated sequences shows that the tool can detect diverged duplications beyond the sensitivity limits of standard alignment-based methods. Applying SegMantX to 6,784 enterobacterial plasmids, we find that 74% plasmids contain duplicated regions, most of which correspond to duplicated mobile genetic elements (MGEs; e.g., transposons and insertion sequences). Furthermore, we demonstrate the applicability of SegMantX for the identification of diverged gene transfers between replicons, and plasmid hybridization events. Our findings highlight MGEs as drivers of segmental duplications in plasmid evolution, leading to the amplification of their cargo genes, including antibiotic resistance genes. SegMantX provides a powerful framework for reconstructing diverged segmental duplications and other alignment problems.

bioinformatics↗

bioRxiv2023

Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility

Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g., obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g., mobility, or their effect on the host. Analyzing 10, 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.

evolutionary biology↗