Biology subjects

Thormann, K.

Publications and source records attributed to Thormann, K..

4 recordsLinked to original sources

bioRxiv2025

Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms

Extracellular DNA (eDNA) plays crucial roles in biofilm formation and function, yet the role of bacteriophages (phages) in controlling eDNA synthesis, structure and activity remains obscure. Here, we demonstrate that phages harbored by environmental bacteria can be exploited for programmable synthesis of functional eDNA superstructures. We designed a 112-nucleotide circular template (T1) and used it to direct rolling circle replication (RCR) of G-quadruplex (GQ) motifs in Shewanella oneidensis and Bacillus subtilis. Under nutrient-limiting conditions, prophage activation triggered cell lysis and subsequent extracellular DNA synthesis, producing multimeric GQ concatemers that self-assembled into distinct morphologies: spherical structures ([≤]10 m) in S. oneidensis and wire-like structures (>50 m) in B. subtilis. Real-time monitoring using fluorescent reporter strains revealed that DNA synthesis occurred predominantly after bacterial lysis, coinciding with prophage replication. The resulting DNA superstructures exhibited peroxidase activity through GQ-hemin DNAzyme formation and enhanced the electrochemical properties of S. oneidensis biofilms, showing a 3-fold increase in current density. This work unveils a previously unknown mechanism by which prophages contribute to biofilm architecture and establishes a biotechnological platform for engineering functional DNA materials in living bacterial communities, with potential applications in biotechnology and synthetic biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/691978v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@aec065org.highwire.dtl.DTLVardef@d94709org.highwire.dtl.DTLVardef@c6c228org.highwire.dtl.DTLVardef@f4f465_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Polar confinement of a macromolecular machine by an SRP-type GTPase

The SRP-type GTPase FlhF, along with its regulator FlhG, orchestrates the localization and quantity of flagella in bacteria. Our study reveals that FlhF anchors developing flagellar structures to the polar landmark protein HubP/FimV, thereby restricting their formation to the cell pole. Specifically, the GTPase domain of FlhF interacts with HubP, while an as-yet-uncharacterized structured domain at the N-terminus of FlhF binds to FliG. This FlhF-bound FliG subsequently engages with the MS-ring protein FliF, but not with the C-ring proteins FliM/FliN. Consequently, FlhFs interaction with HubP/FliG recruits a functional FliF/FliG complex to the pole, while FlhGs modulation of FlhF controls FliGs interaction with FliM/FliN, thereby regulating the progression of flagellar assembly at the pole. Significance statementFlagella serve as bacterial locomotion organelles, with their number and location, known as the flagellation pattern, being species-specific and among the earliest taxonomic criteria in microbiology. Bacteria replicate their flagellation pattern with each cell division. Flagella localization and abundance depends on the SRP-type GTPase FlhF, together with its regulator FlhG. Our study clarifies the mechanism through which FlhF coordinates the polar positioning of the flagellum, working in tandem with the polar landmark protein HubP and aiding in the assembly of flagellar MS-ring/C-ring components at the cellular pole.

microbiology↗

bioRxiv2024

Discovery of a pentose as a cytosine nucleobase modification in Shewanella phage Thanatos-1 genomic DNA mediating enhanced resistance towards host restriction systems

Co-evolution of bacterial defense systems and phage counter defense mechanisms has resulted in an intricate biological interplay between bacteriophages and their prey. To evade nuclease-based mechanisms targeting the DNA, various bacteriophages modify their nucleobases, which impedes or even inhibits recognition by endonucleases. We found that Shewanella phage Thanatos-1 DNA is insensitive to multiple restriction enzymes and, partially, also to Cas I-Fv and Cas9 cleavage. Furthermore, the phage genome shows strongly impaired basecalling with nanopore sequencing. We characterised the phage adenine methyltransferase TH1_126 in methylase-free E. coli ER3413 and derived and confirmed its recognition motif 5-ATC-3. Moreover, the data pointed to an additional, much more substantial nucleobase modification. Using LC-MS, we identified a deoxypentose of unknown configuration attached to cytosine as a yet undiscovered phage DNA modification, which is present in Thanatos-1 genomic DNA, likely mediates the observed resistance to restriction endonucleases, as well as a strong reduction in Cas nuclease activity. To elucidate the underlying enzyme functions, we determined structural homologs of Thanatos-1 proteins among known glycosyltransferase folds and experimentally proved a UDP-xylose pyrophosphorylase function of phage protein TH1_063 by in vitro enzyme assays.

molecular biology↗

bioRxiv2020

Obligate cross-feeding expands the metabolic niche of bacteria

Bacteria frequently engage in obligate metabolic mutualisms with other microorganisms. However, it remains generally unclear how the resulting metabolic dependencies affect the ecological niche space accessible to the whole consortium relative to the niche space available to its constituent individuals. Here we address this issue by systematically cultivating metabolically dependent strains of different bacterial species either individually or as pairwise coculture in a wide range of carbon sources. Our results show that obligate cross-feeding is significantly more likely to expand the metabolic niche space of interacting bacterial populations than to contract it. Moreover, niche expansion occurred predominantly between two specialist taxa and correlated positively with the phylogenetic distance between interaction partners. Together, our results demonstrate that obligate cross-feeding can significantly expand the ecological niche space of interacting bacterial genotypes, thus explaining the widespread occurrence of this type of ecological interaction in natural microbiomes.

evolutionary biology↗