Search bioRxiv⌕ Search

Biology subjects

Ajunwa, O. M.

Publications and source records attributed to Ajunwa, O. M..

4 recordsLinked to original sources

Spatial organization of self-assembled G-quadruplex nucleic acids tunes extracellular electron transfer in pathogenic biofilms

Extracellular electron transfer (EET) allows bacteria to sustain metabolism when soluble electron acceptors such as oxygen are scarce, a situation typical of the biofilm interior. These mechanisms are well characterised in environmental metal-reducing bacteria but poorly defined in the biofilms of pathogens, where they may contribute to persistence at infection sites. We previously found that synthetic guanine-quadruplex (G4) nucleic acids bound to hemin can conduct electrons1, yet whether bacteria self-assemble such structures in electroactive form was unknown. Here we show that Staphylococcus aureus biofilms naturally assemble G4-rich extracellular nucleic acids that bind hemin to form a catalytically active, electron-conducting complex, without exogenous G4 addition. Nutrient starvation, rather than biofilm age or cell density, triggers extracellular G4 accumulation, and as biofilms develop, the G4 reorganise from intercellular networks to being primarily located at the cell-envelope. Using electrochemistry, peroxidase imaging and different types of nucleases, we show that these architectures impose distinct modes of electron transfer through the matrix or at the cell surface. Degradation of G4 abolishes electroactivity whereas removing canonical B-DNA does not. S. aureus thus builds and organises its own electroactive nucleic-acid network, identifying biofilm architecture as a tunable determinant of extracellular electron flow.

microbiology↗

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↗

Extracellular RNA drives Electromethanogenesis in a Methanogenic Archaeon

Methanogenic archaea account for two-thirds of global methane emissions. Some species, including Methanosarcina barkeri, reduce CO2 by directly acquiring electrons from solid substrates. However, the mechanism of electron acquisition in M. barkeri has remained unclear because this archaeon lacks the multiheme c-type cytochromes that drive extracellular electron transfer in many other microbes. Here we show that M. barkeri releases abundant extracellular nucleic acids during early growth, primarily short RNAs (78%). These extracellular nucleic acids assemble into G-quadruplexes (G4s) and B-DNA architectures that decorate cell surfaces and link aggregates. Surface-associated G4s are folded in vivo in a conformation compatible with cofactor binding and redox chemistry. Enzymatic degradation of extracellular nucleic acids abolished electron uptake and electromethanogenesis, whereas addition of synthetic G4-RNAs doubled methane yields and lowered cell-electrode interfacial resistance. These effects were not observed when cells were grown on soluble substrates. Together, these findings identify eRNA as a previously unrecognized electron conduit in methanogens, raising the possibility that RNA-based electron transfer may predate more elaborate protein-based electron conduits, with implications for models of early earth metabolism and for the design of next-generation bioenergy systems.

microbiology↗

Hemin-binding DNA structures on the surface of bacteria promote extracellular electron transfer

Recent research has shown that bacteria in anoxic layers of Pseudomonas aeruginosa biofilms can respire by transferring electrons to oxygen via extracellular DNA (eDNA) and DNA-binding redox mediators that are unique to this species1. In this study, we propose a similar but generic mechanism by which bacteria can transfer electrons via DNA in biofilms, using hemin as a redox-mediator and hemin-binding G-quadruplex (G4) DNA structures in the extracellular matrix. Using Staphylococcus epidermidis as a model organism, voltammetry showed that eDNA and hemin were needed for extracellular electron transfer (EET). Surface-associated G4-DNA formed a complex with hemin, which transferred electrons from the bacteria to an electrode under anoxic conditions. Addition of G4-DNA and hemin to growing biofilms promoted EET which was stable for days. G4-DNA/hemin is also a peroxidase-like DNAzyme, capable of transferring electrons from bacteria to H2O2. G4-DNA were only recently discovered to be abundant in the extracellular matrix of biofilms2,3. We now show that hemin turns these structures into conduits for EET. The study opens the door to new and generic mechanisms for bacterial energy conservation under oxygen-limiting conditions, and for tackling H2O2, a common host defense mechanism against bacterial infections.

microbiology↗