Biology subjects

Prakapaite, R.

Publications and source records attributed to Prakapaite, R..

3 recordsLinked to original sources

bioRxiv2026

A bacterial nucleolus for cold adaptation

Compartmentalisation enables cells to spatially organise essential biochemical processes. This is exemplified by the eukaryotic nucleolus, which concentrates the machinery for ribosome biogenesis. Bacteria are generally thought to lack an equivalent compartment. Here we discover a nucleolus-like condensate in Escherichia coli that emerges at rDNA loci during cold adaptation to spatially organise and promote ribosome biogenesis. Low temperatures, which stabilise RNA secondary structures, induce accumulation of the RNA-remodelling enzyme CsdA. This raises the cellular CsdA concentration above its condensation threshold, driving condensate formation at rDNA loci when rRNA transcription is active. CsdA compartments enrich the rRNA transcription machinery and ribosome-biogenesis factors, spatially linking rRNA synthesis to downstream processing and assembly. Disrupting CsdA condensation impairs ribosome maturation and reduces bacterial adaptation to cold temperature, demonstrating functional importance of condensate formation. Comparative genomics suggests that analogous condensate-forming RNA remodelling enzymes have evolved repeatedly across diverse bacterial lineages. Our findings establish biomolecular condensates as a unifying organisational principle of ribosome biogenesis across the tree of life and suggest that adaptive compartmentalisation can emerge when environmental conditions challenge the efficiency of essential biochemical processes.

cell biology↗

bioRxiv2025

Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine

Urinary tract infections (UTIs) are among the most common infectious diseases, causing over 400 million cases and 260,000 deaths annually. Women are disproportionately affected, with [~]50% experiencing at least one UTI during their lifetime and 20-30% suffering from recurrent infections. Uropathogenic Escherichia coli (UPEC), which accounts for [~]75% of cases, employs diverse virulence factors to persist and evade host immunity. Rising antibiotic resistance, driven by widespread antimicrobial misuse, is eroding treatment efficacy and highlights the urgent need for alternative therapeutic strategies. To uncover novel vulnerabilities under physiologically relevant conditions, we constructed a genome-wide CRISPR interference (CRISPRi) library in the UPEC reference strain E. coli CFT073 and systematically profiled gene fitness in rich media versus human urine. The screen revealed multiple pathways that are conditionally essential for UPEC growth in urine, including iron uptake, envelope maintenance, and the biosynthesis of arginine, methionine, and branched-chain amino acids. Notably, we identified acetolactate synthase (ALS) II as the sole active isoform supporting branched-chain amino acid synthesis in urine. Functional validation further demonstrated its druggability: introducing a re-sensitizing mutation overcame the proteins intrinsic resistance to the ALS-targeting herbicide sulfometuron methyl, restoring sensitivity. These findings establish ALS II as a promising therapeutic target against UPEC.

microbiology↗

bioRxiv2021

A new sugar for an old phage: A c-di-GMP dependent polysaccharide pathway sensitizes E. coli for bacteriophage infection

Bacteriophages are ubiquitous parasites of bacteria and major drivers of bacterial ecology and evolution. Despite an ever-growing interest in their biotechnological and therapeutic applications, detailed knowledge of the molecular mechanisms underlying phage-host interactions remains scarce. Here, we show that bacteriophage N4 exploits a novel surface glycan, NGR, as a receptor to infect its host Escherichia coli. We demonstrate that this process is regulated by the second messenger c-di-GMP and that N4 infection is specifically stimulated by the diguanylate cyclase DgcJ while the phosphodiesterase PdeL effectively protects E. coli from N4-mediated killing. PdeL-mediated protection requires its catalytic activity to reduce c-di-GMP and includes a secondary role as a transcriptional repressor. We demonstrate that PdeL binds to and represses the promoter of the wec operon, which encodes components of the ECA exopolysaccharide pathway. However, only the acetylglucosamine epimerase WecB but none of the other ECA components is required for N4 infection. Based on this, we postulate that NGR is an N-acetylmannosamine-based carbohydrate polymer that is produced and exported to the cell surface of E. coli in a c-di-GMP dependent manner where it serves as a receptor for N4. This novel carbohydrate pathway is conserved in E. coli and other bacterial pathogens, serves as the primary receptor for a range of N4-like bacteriophages, and is induced at elevated temperature and by specific amino acid-based nutrients. These studies provide an entry point into understanding how bacteria use specific regulatory mechanisms to balance costs and benefits of highly conserved surface structures. ImportanceBecause bacterial surface glycans are in direct contact with the environment they can provide essential protective functions during infections or against competing bacteria. But such structures are also Achilles heels as they can serve as primary receptors for bacteriophages. Bacteria thus need to carefully control the exposure of conserved surface glycans to balance costs and benefits. Here, we identify a novel exopolysaccharide that is widely conserved in E. coli and is used by N4 and related bacteriophages as primary receptor. We demonstrate that the synthesis of NGR (N4 glycan receptor) is tightly controlled by the second messenger c-di-GMP in a highly specific manner and by a single diguanylate cyclase. These studies provide an example of how bacteria can alleviate the strong selective pressure imposed on them by bacteriophages entering through conserved surface structures by carefully regulating their synthesis and secretion.

microbiology↗