Biology subjects

Dzurik, K. G.

Publications and source records attributed to Dzurik, K. G..

4 recordsLinked to original sources

bioRxiv2026

The E. coli DEAD box ATPase CsdA, is a NAD+ capped RNA binding protein

5' nicotinamide adenine dinucleotide (NAD+) caps are one of the most common metabolites derived non-canonical caps reported on bacterial RNAs. Multiple decapping proteins are known to regulate the stability of NAD+ capped transcripts. However, no other proteins have been identified that preferentially interact with these NAD+ caps, and mechanistic details of the cap-dependent recognition remain poorly understood. Using an affinity capture approach, we identified multiple E. coli proteins that selectively recognize NAD+ caps, including the ATP-dependent RNA helicase, CsdA. CsdA preferentially interacts directly with NAD+ capped RNAs and can discriminate between 5' NAD+ capped and 5' triphosphate end transcripts. Binding to NAD+ capped RNA versus 5' triphosphate RNA more greatly enhances the ATPase activity of CsdA and the presence of NAD+ caps on transcripts modulates the ability of CsdA to form RNA condensates. Furthermore, we find that CsdA enhances the decapping activity of the NADH hydrolase NudC, suggesting CsdA plays a role in regulating the degradation of NAD+ capped transcripts. CsdA is the first identified NAD+ cap reader protein and its preference for binding NAD+ capped RNA provides a mechanism by which E. coli cells link RNA stability to the identity of the 5' cap. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/730015v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@115a057org.highwire.dtl.DTLVardef@d1c2c6org.highwire.dtl.DTLVardef@14a6d2dorg.highwire.dtl.DTLVardef@145ccff_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Bacterial Ribonucleoprotein bodies maintain an acidic pH environment as a mechanism of enzyme regulation

Phase separated biomolecular condensates create subcellular niches, yet their role in client regulation remains unclear. Here, we demonstrate that Bacterial Ribonucleoprotein bodies (BR-bodies) are acidic. Using ratiometric fluorescent probes in vivo, we find BR-bodies exhibit a dense-phase pH of [~]5.1, significantly lower than the near-neutral cytoplasm. Single-molecule localization microscopy and fluorescence lifetime imaging reveals that Caulobacter crescentus BR-bodies have spatially variable and acidic nanoscale RNase E clusters. These results question the notion of homogeneous condensates, suggesting that BR-bodies exhibit structural and biochemical diversity, which may facilitate RNA processing under stress. In vitro, pH gradients observed with C-SNARF-4F and RNase E CTD-pHluorin2 deteriorate with increasing buffer concentrations. Notably, the acidic microenvironment within BR-bodies enhances PNPase activity, highlighting the significance of condensate pH regulation. These findings suggest that pH modulation is intrinsic to condensates, directly influencing biochemical reactions and offering a new strategy for designing pH-sensitive drugs to target enzymes within condensates.

microbiology↗

bioRxiv2025

BR-Bodies Facilitate Adaptive Responses and Survival During Copper Stress in Caulobacter crescentus

Microbes must rapidly adapt to environmental stresses, including toxic heavy metals like copper, by sensing and mitigating their harmful effects. Here, we demonstrate that the phase separation properties of bacterial ribonucleoprotein bodies (BR-bodies) enhance Caulobacter crescentus fitness under copper stress. To uncover the underlying mechanism, we identified two key interactions between copper and the central scaffold of BR-bodies, RNase E. First, biochemical assays and fluorescence microscopy experiments show that reductive chelation of Cu{superscript 2} leads to cysteine oxidation, driving the transition of BR-bodies into more solid-like condensates. Second, tryptophan fluorescence and EPR assays reveal that RNase E binds Cu{superscript 2} at histidine sites, creating a protective microenvironment that prevents mismetallation and preserves PNPase activity. More broadly, this example highlights how metal-condensate interactions can regulate condensate material properties and establish specialized chemical environments that safeguard enzyme function.

microbiology↗

bioRxiv2025

Bacterial IF2's N-terminal IDR drives cold-induced phase separation and promotes fitness during cold stress

Translation initiation factor 2 (IF2) plays an essential role in bacterial cells by delivering the fMet-tRNAfMet to the ribosome pre-initiation complex. IF2 is known to have an N-terminal disordered region which is present across bacterial species, yet its function is not fully understood. Deletion of the IDR in E. coli showed no phenotypes at normal growth temperature (37{degrees}C); however, this IDR was found to be required for growth at cold temperatures (15{degrees}C). Since large IDRs can drive phase separation of various RNA binding proteins into biomolecular condensates, we investigated whether E. coli IF2 could phase separate. We discovered that IF2s N-terminal IDR drives phase separation in E. coli and C. crescentus, suggesting that IF2 condensation is a conserved property. Finally, using E. coli, we found that the IDR strongly drives phase separation in the cold, suggesting IF2 condensates promote fitness during cold stress. HighlightsO_LIIF2s IDR promotes phase separation with RNA. C_LIO_LICold temperature promotes IF2 condensation with RNA. C_LIO_LIIF2s IDR promotes fitness during cold shock. C_LI

microbiology↗