Biology subjects

Arai, N.

Publications and source records attributed to Arai, N..

5 recordsLinked to original sources

bioRxiv2025

Genetic basis of R-phase H:z27 antigen expression and phylogenetic relationships of Salmonella enterica serovar Senftenberg

Salmonella enterica serovar Senftenberg (S. Senftenberg) is one of the most prevalent Salmonella serovars and can be isolated from various animals and humans. According to the White-Kauffmann-Le Minor (WKL) scheme, the antigenic formula of S. Senftenberg is defined as 1,3,19:g,[s],t:-. Although the antigenic formula 1,3,19:z27:- was formerly designated as serovar Simsbury, this name was later removed from the WKL scheme due to reports of interconvertibility between serovars Senftenberg and Simsbury. The H:z27 antigen is currently recognized as one of the R-phase H antigens of S. Senftenberg. To elucidate the genetic basis of H:z27 antigen expression in S. Senftenberg, we determined the whole-genome sequences of isolates expressing the H:z27 antigen. These isolates belonged to sequence type (ST) 185 and harbored a horizontally acquired chromosomal region containing the fljA, fljB, and pinR genes, which are predicted to encode a translational repressor of fliC mRNA, a phase 2 flagellin, and an invertase, respectively. A deletion mutant lacking this region expressed the H:g,s,t antigen instead of H:z27, as confirmed by serotyping and Western blot analysis. Phylogenetic analysis based on S. Senftenberg genome archives, together with the sequences obtained in this study, suggested that the S. Senftenberg ST185 lineage acquired the fljAB-pinR locus around 1867. In contrast, our broader phylogenetic analysis of Salmonella serovars indicated that S. Senftenberg ST14 is genetically closer to certain other serovars than to ST185, while ST185 shows a closer relationship to a different serovar than to ST14. These findings suggest that S. Senftenberg comprises at least two distinct genomic lineages. IMPORTANCELimited information is available on the genetic basis of R-phase H antigen expression in S. enterica. In this study, we first demonstrated that the R-phase H:z27 antigen of S. Senftenberg is determined by a horizontally acquired chromosomal region. The ST 185 lineage of S. Senftenberg appears to have acquired this chromosomal region around 1867 and subsequently disseminated worldwide. We also demonstrated that S. Senftenberg comprises at least two distinct genomic lineages. The combined use of serotyping and multilocus sequence typing may provide a typing framework that better reflects the disease potential of Salmonella.

microbiology↗

bioRxiv2021

Pilot study: Trehalose-induced remodelling of the human microbiota affects Clostridioides difficile infection outcome in an in vitro colonic model

Within the human intestinal tract, dietary, microbial- and host-derived compounds are used as signals by many pathogenic organisms, including Clostridioides difficile. Trehalose has been reported to enhance virulence of certain C. difficile ribotypes; however, such variants are widespread and not correlated with clinical outcomes for patients suffering from C. difficile infection (CDI). Here, we make preliminary observations to how to trehalose supplementation affects the microbiota in an in vitro model and show that trehalose can reduce the outgrowth of C. difficile, preventing simulated CDI. Three clinically reflective human gut models simulated the effects of sugar (trehalose or glucose) or saline ingestion on the microbiota. Models were instilled with sugar or saline and further exposed to C. difficile spores. The recovery of the microbiota following antibiotic treatment and CDI induction was monitored in each model. The human microbiota remodeled to utilise the bioavailable trehalose. Clindamycin induction caused simulated CDI in models supplemented with either glucose or saline; however, trehalose supplementation did not result in CDI, although limited spore germination did occur. The absence of CDI in trehalose model was associated with enhanced abundances of Finegoldia, Faecalibacterium and Oscillospira, and reduced abundances of Klebsiella and Clostridium spp., compared with the other models. Functional analysis of the microbiota in the trehalose model revealed differences in the metabolic pathways, such as amino acid metabolism, which could be attributed to prevention of CDI. Our data show that trehalose supplementation remodelled the microbiota, which prevented simulated CDI, potentially due to enhanced recovery of nutritionally competitive microbiota against C. difficile.

microbiology↗

bioRxiv2020

Identification of a recently dominate sublineage in Salmonella 4,,12:i:- sequence type 34 isolated from food animals in Japan

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are classified into nine clades. Clade 9 is composed of ST34 strains, including the Salmonella 4,[5],12:i:-European clone, which has rapidly disseminated in humans and animals worldwide since the 2000s. To reveal the microevolution of ST34/clade 9, we analyzed the whole-genome-based phylogenetic relationships of 230 Salmonella Typhimurium and Salmonella 4,[5],12:i:-strains isolated between 1998 and 2017 in Japan and other countries. We identified clade 9-2, a novel sublineage derived from the conventional Salmonella 4,[5],12:i:-clade 9 that exclusively consists of Japanese isolates. Clade 9-2 was generated by mobile genetic element-mediated stepwise genome reductions caused by IS26 and prophages. Furthermore, the recently identified strains developed further resistance to antimicrobials via the acquisition of resistance genes. During this microevolution, Salmonella 4,[5],12:i:-clade 9-2 has dominated among recent isolates from food animals in Japan via the emergence of clonally expanding and/or multiple host-adapted subclades.

microbiology↗

bioRxiv2019

Salmonella genomic island 3 is an integrative and conjugative element and contributes to copper and arsenic resistance of Salmonella enterica

Salmonella genomic island 3 (SGI3) was first described as a chromosomal island in Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella enterica subsp. enterica serovar Typhimurium. The SGI3 DNA sequence detected from Salmonella 4,[5],12:i:-isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic resistance operon in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter mating experiments using the S. enterica serovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3' end of the tRNA genes pheV or pheR. The length of the target site was 52 or 55 bp, and a 55-bp attI sequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4 compared with the recipient strains under anaerobic conditions. Resistance was defined by the cus gene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4 compared with recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic resistance of S. enterica.

microbiology↗

bioRxiv2018

HERC2 promotes BLM and WRN to suppress G-quadruplex DNA

BLM and WRN are RecQ DNA helicases essential for genomic stability. Here we demonstrate that HERC2, a HECT E3 ligase, is critical for their functions to suppress G-quadruplex (G4) DNA. HERC2 interacts with BLM, WRN, and replication protein A (RPA) complexes during S-phase of the cell cycle. Depletion of HERC2 dissociates RPA from BLM and WRN complexes and significantly increases G4 formation. Triple depletion revealed that HERC2 has an epistatic relationship with BLM and WRN in their G4- suppressing function. In vitro, HERC2 releases RPA onto single-stranded DNA (ssDNA), rather than anchoring onto RPA-coated ssDNA. CRISPR/Cas9-mediated deletion of the catalytic ubiquitin-binding site of HERC2 causes RPA accumulation in the helicase complexes and increases G4, indicating an essential role for E3 activity in G4 suppression. Both HERC2 depletion and E3 inactivation sensitize cells to the G4-interacting compounds, telomestatin and pyridostatin. Overall, HERC2 is a master regulator of G4 suppression and affects the sensitivity of cells to G4 stabilizers.

molecular biology↗