Biology subjects

Ershova, A. S.

Publications and source records attributed to Ershova, A. S..

6 recordsLinked to original sources

bioRxiv2026

Contributions of plasmid p1AB5075-encoded antibiotic resistance genes to multidrug resistance of Acinetobacter baumannii AB5075

Infections with multidrug resistant Acinetobacter baumannii are considered a threat to human and animal health. The widely studied A. baumannii strain AB5075 displays a high degree of antibiotic resistance. In this study, we experimentally validated that antibiotic resistance is largely mediated by resistance genes located on plasmid p1AB5075. We used a p1AB5075-deficient AB5075 strain to assess individual contributions of p1AB5075-encoded antibiotic resistance genes by ectopically (over-)expressing each gene in the {Delta}p1AB5075 background. By determining individual contributions of seven p1AB5075-encoded antibiotic resistance genes, we show individual and overlapping roles of genes for aminoglycoside resistance and uncover the importance of extended-spectrum {beta}-lactamase blaGES-11 for cephalosporin resistance in A. baumannii AB5075. We discovered that aminoglycoside N-acetyltransferase aaC(6)-Ib3 (aacA4), which was considered a potential pseudogene in A. baumannii AB5075, to be functional providing broad resistance to gentamicin, kanamycin, amikacin, streptomycin and tobramycin when overexpressed in A. baumannii AB5075. Because p1AB5075 is transferrable to a wide range of environmental and clinical A. baumannii strains and non-baumannii Acinetobacter species, the relevance of our findings extends beyond A. baumannii AB5075.

microbiology↗

bioRxiv2026

Methylome and transcriptome mapping reveal miniscule DNA methyltransferase regulons in Salmonella enterica serovar Typhimurium

DNA methylation is a regulator of bacterial gene expression and adaptation, influencing traits such as virulence and antimicrobial resistance. The dynamic nature of DNA methylation enables rapid responses to changing environments and is a source of heterogeneity in bacterial populations. However, condition-dependent DNA methylation and consequences for transcriptional output remain poorly understood. We applied Oxford Nanopore sequencing to profile DNA methylation during exponential growth and late stationary phase of Salmonella enterica serovar Typhimurium and integrated these data with transcriptomic analyses. We found that each DNA methyltransferase (MTases) exhibits a distinct activity pattern across growth stages, which could not be explained by transcriptional levels of the corresponding enzymes. As predicted, DNA methylation patterns determined by regulatory MTases were dynamic across growth conditions whereas methylation patterns of MTases belonging to R-M systems were comparatively stable. We identified growth stage-specific methylation patterns for all studied MTases and correlations between methylation states and gene expression patterns. Together, these findings chart DNA methylation networks in the epigenetic regulation of bacterial physiology. Author summaryDNA methylation in bacteria is best known for its role protecting DNA from endonucleases, such as restriction-modification, and coordinating chromosome replication and mutation repair, yet DNA methylation also regulates gene expression and cell physiology. Previous studies primarily examined bacterial DNA methylation at single time points or in limited genomic regions, providing only a partial view of its biological significance. In this study, we used Oxford Nanopore sequencing to compare DNA methylation patterns in Salmonella enterica during exponential growth and late stationary phase then integrated these data with corresponding gene expression profiles. We identified numerous methylation target motifs, all of which demonstrated constitutively methylated or unmethylated regions. This systems-level analysis clarifies the role of DNA methylation in bacterial adaptation across growth stages and demonstrates the utility of Oxford Nanopore sequencing for genome-wide methylation profiling.

microbiology↗

bioRxiv2025

DNA uptake and twitching motility are controlled by the small RNA Arp through repression of pilin translation in Acinetobacter baumannii

Acinetobacter baumannii is a major opportunistic pathogen capable of natural transformation, a process driven by type IV pili (T4P) that facilitates horizontal gene transfer and accelerates the spread of antimicrobial resistance. While the transcriptional regulation of T4P is increasingly understood, post-transcriptional mechanisms controlling pilus assembly remain unexplored. Here, we identify and characterise a small RNA, Arp (Acinetobacter repressor of pilin), as a post-transcriptional repressor of T4P-mediated functions in A. baumannii. In a previous Hi-GRIL-seq experiment, we detected specific ligation events between Arp and the ribosome binding site of the pilA mRNA, encoding the major pilin subunit PilA. In-line probing and translational reporter assays revealed that Arp represses pilA translation by sequestering the Shine-Dalgarno sequence and the first 17 codons of the mRNA. Overexpression of Arp significantly impairs DNA uptake and twitching motility, two hallmark T4P-dependent phenotypes. Together, our findings identify a native A. baumannii sRNA that modulates natural competence by targeting pilin synthesis, revealing a new regulatory layer that could be exploited to disrupt horizontal gene transfer in multidrug-resistant strains. Significance StatementAcinetobacter baumannii is a multidrug-resistant WHO #1 priority pathogen that acquires antibiotic resistance genes through natural transformation, a process dependent on type IV pili (T4P). This work reveals Arp, the first native post-transcriptional repressor of natural competence in A. baumannii, uncovering a novel regulatory layer that modulates horizontal gene transfer. The widespread presence of arp in pathogenic Acinetobacter strains suggests that sRNA is an important regulator in those organisms. Furthermore, these findings broaden our understanding of RNA-based regulation in this priority pathogen and open potential avenues for interfering with antibiotic resistance dissemination.

microbiology↗

bioRxiv2025

Differential roles of the type I and II secretion systems for the intracellular ABC141 Acinetobacter baumannii infection, which elicits an atypical hypoxia response in endothelial cells

Acinetobacter baumannii poses a substantial global health threat, causing severe multi-drug-resistant infections in hospitalized patients. Circulating clinical isolates present remarkable diversity, with a proportion capable of establishing a transient intracellular niche suitable for persistence, multiplication, and spread. Yet, it remains unknown which bacterial factors mediate the formation and maintenance of this niche, especially within non-phagocytic cells, nor what host responses are elicited. This work demonstrates that the invasive A. baumannii ABC141 strain does not secrete ammonia in endothelial cells as previously shown for other A. baumannii strains multiplying within macrophages but resides in an acidic vacuole devoid of active lysosomal degradative enzymes. This compartment mediates bacterial egress and infection of neighboring cells, promoting dissemination. Using a Dual-RNAseq approach, we mapped the host and bacterial gene expression during the replicative stage of the infection. An atypical hypoxia cell response was observed without significant induction of the HIF1 pathway, with no metabolic shift or disturbance of mitochondria. Surprisingly, ABC141 efficiently grew in hypoxic conditions in culture and within host cells. In addition, we found a bacterial signature reflective of an adaptation to a nutrient-deprived environment. Our work also highlights a differential role for ABC141 secretion systems, with the T1SS assisting intracellular multiplication and the T2SS required for host cell invasion, implicating for the first time the T2SS in the intracellular lifecycle of invasive ABC141 in endothelial cells. Author summaryAcinetobacter baumannii is a major burden for healthcare facilities worldwide, causing severe infections in hospitalized and intensive care patients that are challenging to treat because of extremely high levels of resistance to most antimicrobials. Traditionally seen as extracellular, recent studies have highlighted that a proportion of clinical isolates currently circulating in clinics can invade and multiply inside epithelial and endothelial cells. Yet, how these strains establish an intracellular protected niche remains unknown. Here, we undertook a detailed characterization of the intracellular compartment enclosing multiplying bacteria, the induced host response, and the bacterial genes that contribute to the adaptation to this intracellular environment. We found that the A. baumannii ABC141 clinical strain is well equipped to resist acidic, low oxygen, and low nutrient environments. Furthermore, we discovered it uses its type II secretion system to invade human endothelial cells, the first step of this intracellular lifecycle. This study opens new avenues of research to help develop new antimicrobial strategies to combat this bacteria when shielded within intracellular compartments in the host.

microbiology↗

bioRxiv2023

Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to functionally characterise environmental adaptation, antibiotic resistance and pathogenicity of this organism and their genetic regulators to inform intervention strategies. Critical to rapid adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners in A. baumannii, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. We found that 40 sRNA candidates were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii and that sRNAs act as direct regulators of mRNA molecules through antisense base-pairing. In-depth characterisation uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including that of the outer membrane protein CarO and the siderophore receptor BfnH. We show that Aar initiates base-pairing with these mRNA molecules using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in response to multiple stress stimuli suggesting a role in fine-tuning translation of the Aar-target molecules in A. baumannii under hostile conditions. Together, our study provides mechanistic insights into sRNA-mediated gene expression control in A. baumannii and represents a valuable resource for future RNA-centric research endeavours in this ESKAPE pathogen.

microbiology↗

bioRxiv2020

Enhanced C/EBPs binding to C>T mismatches facilitates fixation of CpG mutations

Knowledge of mechanisms responsible for mutagenesis of adult stem cells is crucial to track genomic alterations that may affect cell renovation and provoke malignant cell transformation. Mutations in regulatory regions are widely studied nowadays, though mostly in cancer. In this study, we decomposed the mutation signature of adult stem cells, mapped the corresponding mutations into transcription factor binding regions, and assessed mutation frequency in sequence motif occurrences. We found binding sites of C/EBP transcription factors strongly enriched with [C>T]G mutations within the core CG dinucleotide related to deamination of the methylated cytosine. This effect was also exhibited in related cancer samples. Structural modeling predicted enhanced CEBPB binding to the consensus sequence with the [C>T]G mismatch, which was then confirmed in the direct experiment. We propose that it is the enhanced binding of C/EBPs that shields C>T transitions from DNA repair and leads to selective accumulation of the [C>T]G mutations within binding sites.

genomics↗