Biology subjects

Ilioaia, O.

Publications and source records attributed to Ilioaia, O..

5 recordsLinked to original sources

bioRxiv2026

F1F0-ATP-synthase subunit b head-to-head interactions shape intracellular membranes in Escherichia coli

1Intracellular membrane (ICM) compartments in bacteria remain poorly understood. In Escherichia coli, ICMs form upon the overproduction of certain membrane proteins. Here, we investigate at the molecular level how overproduction of subunit b of the F1Fo-ATP synthase complex shapes ICMs. Through a combination of subunit b deletions, electron microscopy, and biochemical analyses, we demonstrate that ICMs network structuration is mediated by the C-terminal domain of subunit b. High-resolution cryo-electron tomography and molecular dynamics simulations reveal that this domain forms tetrameric assemblies, bridging membranes and maintaining a regular 26 nm spacing. Transcriptomic and proteomic analyses further show that the cell responds to ICMs formation by upregulating energy metabolism genes and the ESCRT-III homolog PspA, while downregulating ribosomal and translational machinery. These results uncover a novel mechanism by which the C-terminal domain of subunit b drives the structuring of intracellular membranes. Additionally, they highlight how E. coli adapts to membrane stress by overexpressing membrane-remodeling proteins, a response that shares similarities with intracellular membrane homeostasis mechanisms in photosynthetic bacteria and unicellular algae.

microbiology↗

bioRxiv2025

Transient telomere uncapping triggers telomeric and subtelomeric rearrangements

Telomeres are nucleoprotein structures that cap the extremities of eukaryotic linear chromosomes, thus preventing them from being detected as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, the Cdc13-Stn1-Ten1 complex caps telomeres and limits resection, which would otherwise lead to DNA damage checkpoint activation. Here, using the temperature-sensitive cdc13-1 allele, we demonstrate that even transient telomere uncapping induces extensive genomic rearrangements within a few cell cycles, despite a functional DNA damage checkpoint. Two distinct rearrangement signatures were observed in cells surviving transient uncapping: one characterized by the reorganization and recombination of the subtelomeric region, mostly involving the Y elements, and the other exhibiting massively elongated telomeres up to 10 kb, corresponding to a [~]30-fold increase. Long-read sequencing revealed that the genomic instability was confined to the subtelomere and telomere regions, and evidenced Y' element loss/amplification, terminal duplication of chromosome ends, and telomeric-circle-driven amplification of telomere repeats. Rearrangements unfold over multiple generations and require the homologous recombination factor Rad52 and the Pol{delta} subunit Pol32, which is essential for break-induced replication. The recombination proteins Rad51 and Rad59 also contribute to the rearrangements in partially independent pathways. Remarkably, survivors with elongated telomeres demonstrate robust resistance to subsequent telomere uncapping, in a Rad52-dependent manner. Our findings provide novel insights into the consequences of transient telomere uncapping for genome stability, a process that might contribute to subtelomere and telomere dynamics and evolution.

molecular biology↗

bioRxiv2025

Natural diversity of telomere length distributions across 100 yeast strains

Telomeres gradually shorten at each cell division and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. We developed a method for detecting telomeric sequences in Saccharomyces cerevisiae genomes from raw Oxford Nanopore Technologies (ONT) sequencing reads, providing a comprehensive view of TL distributions both genome-wide and at individual chromosome extremities. We analyzed the TL distribution in 100 S. cerevisiae strains, representing the genetic and ecological diversity of the species. Our analysis revealed a large diversity in TL distributions within the species, largely driven by inter-extremity differences, ploidy level, and subtelomere structure. Polyploid strains displayed significantly longer telomeres than diploid and haploid strains, and experiments with artificially generated polyploids in two independent genetic backgrounds confirmed that higher ploidy levels lead to telomere elongation. Furthermore, we found that the subtelomeric Y element exerts two distinct and opposing effects: (i) the presence of Y elements at a chromosome extremity is associated with shorter telomeres in cis, but (ii) the overall Y element content in a strain correlates with longer telomeres. Interestingly, the length of the shortest telomeres remained relatively constant across strains, suggesting a selective constraint at the species level. This study reveals the diversity of TL in S. cerevisiae and highlights key factors shaping TL distributions both genome-wide and at individual chromosome extremities.

genomics↗

bioRxiv2025

The CST complex mediates a post-resection non-homologous end-joining repair pathway and promotes local deletions

Repair of a DNA double-strand break (DSB) by non-homologous end-joining (NHEJ) generally leaves an intact or minimally modified DNA sequence. Resection initiation exposes single-stranded DNA and directs repair towards homology-dependent pathways and away from NHEJ. Therefore, NHEJ is not thought to be an available repair pathway once the DSB is resected. Here, we report that the Cdc13/Stn1/Ten1 (CST) complex, well characterized for its telomere-associated functions, acts after resection initiation to mediate a backup NHEJ repair. We found a CST-specific mutation signature after DSB repair, characterized by deletions of 5-85 bp, mostly dependent on NHEJ. In contrast, NHEJ-mediated small deletions of 1-4 bp and insertions are not affected in CST mutants. The interaction between CST and Pol-primase is critical for these intermediate size deletions, suggesting a role for fill-in synthesis. Consistently, in stn1{Delta} and Pol-primase mutant deficient for interaction with CST, resection is increased, leading to larger deletions of several kilobases mediated by microhomologies. Collectively, these results depict a more complex picture of repair pathway choice where CST allows a post-resection NHEJ repair, promoting local deletions but guarding against much larger and potentially more deleterious deletions and rearrangements.

molecular biology↗

bioRxiv2021

The Polo kinase Cdc5 is regulated at multiple levels in the adaptation response to telomere dysfunction

Telomere dysfunction activates the DNA damage checkpoint to induce a cell cycle arrest. After an extended period of time, however, cells can bypass the arrest and undergo cell division despite the persistence of the initial damage, a process called adaptation to DNA damage. The Polo kinase Cdc5 in Saccharomyces cerevisiae is essential for adaptation and for many other cell-cycle processes. How the regulation of Cdc5 in response to telomere dysfunction relates to adaptation is not clear. Here, we report that Cdc5 protein level decreases after telomere dysfunction in a Mec1-, Rad53- and Ndd1-dependent manner. This regulation of Cdc5 is important to maintain long-term cell cycle arrest but not for the initial checkpoint arrest. We find that both Cdc5 and the adaptation-deficient mutant protein Cdc5-ad are heavily phosphorylated and several phosphorylation sites modulate adaptation efficiency. The PP2A phosphatases are involved in Cdc5-ad phosphorylation status and contribute to adaptation mechanisms. We finally propose that Cdc5 orchestrates multiple cell cycle pathways to promote adaptation.

genetics↗