Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome, with implications for microbial pathogenesis and host defense. Among these, transfer RNA-derived small RNAs (tsRNAs) have garnered attention for their roles in modulating microbial behavior. However, the bacterial factors mediating tsRNA interaction and functionality remain poorly understood. In this study, using RNA affinity pull-down assay in combination with mass spectrometry, we identified a putative membrane-bound protein, annotated as P-type ATPase transporter (PtaT) in Fusobacterium nucleatum (Fn), which binds Fn-targeting tsRNAs in a sequence-specific manner. Through targeted mutagenesis and phenotypic characterization, we showed that in both the Fn type strain and a clinical tumor isolate, deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition. Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant, highlighting the functional significance of PtaT in purine and pyrimidine metabolism. Furthermore, AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA. By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs (sRNAs), our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.
Fusobacterium nucleatum/growth & development* ; RNA-Binding Proteins/genetics* ; Bacterial Proteins/genetics* ; RNA, Bacterial/metabolism* ; Humans ; RNA, Transfer/metabolism*

For the purpose of seeking new antibiotics, researchers usually modify the already-existing ones. However, this strategy has been extensively used and is close to its limits, especially in the case of aminoglycosides, and it is difficult to find a proper aminoglycoside antibiotic for novel modification. In this paper, we reported the design, synthesis, and evaluation of a series of 5-epi-neamine derivatives based on the structural information of bacterial 16S RNA A-site binding with aminoglycosides. Bioassay results showed that our design strategy was feasible. Our study offers a new way to search for structurally novel aminoglycosides. Meanwhile, our study provides valuable structure-activity relationship information, which will lead to better understanding and exploitation of the drug target, and improved development of new aminoglycoside antibiotics.
Aminoglycosides/chemistry* ; Anti-Bacterial Agents/chemistry* ; RNA, Ribosomal, 16S/metabolism* ; Structure-Activity Relationship ; Biological Assay

Rifamycins, a group of bacterial RNA polymerase inhibitors, are the firstline antimicrobial drugs to treat tuberculosis. In light of the emergence of rifamycinresistant bacteria, development of new RNA polymerase inhibitors that kill rifamycinresistant bacteria with high bioavailability is urgent. Structural analysis of bacterial RNA polymerase in complex with inhibitors by crystallography and cryo-EM indicates that RNA polymerase inhibitors function through five distinct molecular mechanisms:inhibition of the extension of short RNA; competition with substrates; inhibition of the conformational change of the'bridge helix'; inhibition of clamp opening;inhibition of clamp closure. This article reviews the research progress of these five groups of RNA polymerase inhibitors to provide references for the modification of existing RNA polymerase inhibitors and the discovery of new RNA polymerase inhibitors.
Antitubercular Agents ; therapeutic use ; Bacteria ; drug effects ; enzymology ; DNA-Directed RNA Polymerases ; metabolism ; Drug Discovery ; trends ; Drug Resistance, Bacterial ; Enzyme Activation ; drug effects ; Enzyme Inhibitors ; pharmacology ; Humans ; RNA, Bacterial ; Tuberculosis ; drug therapy ; enzymology

In order to clarify dynamic change of microbial community composition and to identify key functional bacteria in the cellulose degradation consortium, we studied several aspects of the biodegradation of filter papers and rice straws by the microbial consortium, the change of substrate degradation, microbial biomass and pH of fermentation broth. We extracted total DNA of the microbial consortium in different degradation stages for high-throughput sequencing of amplicons of bacterial 16 S rRNA genes. Based on the decomposition characteristics test, we defined the 12th, 72nd and 168th hours after inoculation as the initial stage, peak stage and end stage of degradation, respectively. The microbial consortium was mainly composed of 1 phylum, 2 classes, 2 orders, 7 families and 11 genera. With cellulose degradation, bacteria in the consortium showed different growth trends. The relative abundance of Brevibacillus and Caloramator decreased gradually. The relative abundance of Clostridium, Bacillus, Geobacillus and Cohnella increased gradually. The relative abundance of Ureibacillus, Tissierella, Epulopiscium was the highest in peak stage. The relative abundance of Paenibacillus and Ruminococcus did not change obviously in each stage. Above-mentioned 11 main genera all belonged to Firmicutes, which are thermophilic, broad pH adaptable and cellulose or hemicellulose degradable. During cellulose degradation by the microbial consortium, aerobic bacteria were dominant functional bacteria in the initial stage. However, the relative abundance of anaerobic bacteria increased gradually in middle and end stage, and replaced aerobic bacteria to become main bacteria to degrade cellulose.
Bacteria ; classification ; metabolism ; Biodegradation, Environmental ; Cellulose ; metabolism ; DNA, Bacterial ; genetics ; Microbial Consortia ; RNA, Ribosomal, 16S ; genetics

No abstract available.
Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Cefotaxime/analogs & derivatives/therapeutic use ; Cholangiopancreatography, Endoscopic Retrograde ; Gallstones/surgery ; Gram-Negative Anaerobic Bacteria/drug effects/genetics/*isolation & purification ; Gram-Negative Bacterial Infections/*diagnosis/drug therapy/microbiology ; Humans ; Male ; Metronidazole/therapeutic use ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Tomography, X-Ray Computed

Objective: To explore the effects of Zhibai Dihuang Decoction (ZDD) on mitochondrial cytochrome oxidase (COX) in the spermatogenic cells of rats with ureaplasma urealyticum (UU) infection. METHODS: From forty 4－5 months old SD rats, 30 were randomly selected for the establishment of the model of testicular UU infection by inoculating the bladder with UU suspension and the other 10 injected with normal saline as controls (group A). At 7 days after inoculation, the rat models of testicular UU infection were treated orally with normal saline (group B), ZDD at 1 g per kg of the body weight per day (group C), and azithromycin at 0.105 g per kg of the body weight per day (group D), respectively, once daily for 21 days. Then all the animals were sacrificed and the epididymal and testicular tissues collected for examination of sperm motility with the color sperm dynamic detection system, measurement of the COX activity with the immunohistochemical DAB method, and determination of the mRNA expressions of COXⅠ and COXⅡ by RT-PCR. RESULTS: Compared with group A, group B showed significant decreases in such sperm parameters as grade a sperm (［1.03 ± 0.09］ vs ［0.07 ± 0.03］ %, P<0.01), grade b sperm (［2.07 ± 0.52］ vs ［0.35 ± 0.13］ %, P<0.01), straight line velocity (VSL) (［10.95 ± 0.98］ vs ［6.78 ± 1.05］ μm/s, P<0.01), curvilinear velocity (VCL) (［42.03 ± 1.35］ vs ［38.10 ± 7.65］ μm/s, P>0.05), average path velocity (VAP) (［16.22 ± 1.52］ vs ［10.05 ± 1.80］ μm/s, P<0.01), and the mRNA expressions of COX Ⅰ (［2.25 ± 0.24］ vs ［0.93 ± 0.10］ %, P<0.01) and Ⅱ (［6.72 ± 0.37］ vs ［2.95 ± 0.78］ %, P<0.01). After treatment, all the parameters were remarkably increased in groups C and D (grade a sperm: ［1.11 ± 0.30］ and ［0.60 ± 0.19］%; grade b sperm: ［2.40 ± 0.59］ and ［1.32 ± 0.27］ %; VSL: ［12.11 ± 1.62］ and ［11.47 ± 1.21］ μm/s; VCL: ［54.30 ± 2.35］ and ［45.75 ± 1.64］ μm/s; VAP ［18.40 ± 1.27］ and ［16.69 ± 1.02］ μm/s; expression of COXⅠ mRNA: ［1.86 ± 0.30］ and ［1.74 ± 0.17］ %) as compared with those in group B (P<0.05or P<0.01) except the COX activity and the expression of COX Ⅱ mRNA (P>0.05), and all the parameters were significantly higher in group C than in D (P<0.05or P<0.01). CONCLUSIONS UU infection can reduce grades a and b sperm, linear, curvilinear and mean sperm velocities, and the mRNA expressions of COX Ⅰ and Ⅱ while ZDD can improve these parameters. The improvement of sperm motility may not be associated with the activity of COX, and the COX activity may be related to the mRNA expression of COX II but not that of COXⅠ.
Animals ; Anti-Bacterial Agents ; therapeutic use ; Azithromycin ; therapeutic use ; Drugs, Chinese Herbal ; pharmacology ; Electron Transport Complex IV ; metabolism ; Epididymis ; drug effects ; enzymology ; Humans ; Male ; Mitochondria ; drug effects ; enzymology ; RNA, Messenger ; metabolism ; Rats ; Rats, Sprague-Dawley ; Sperm Motility ; Spermatozoa ; drug effects ; enzymology ; physiology ; Ureaplasma Infections ; drug therapy ; enzymology ; Ureaplasma urealyticum

Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease-causing mutations in patients. However, problems such as mosaicism and low mutagenesis efficiency continue to pose challenges to clinical application of such approaches. Recently, a base editor (BE) system built on cytidine (C) deaminase and CRISPR/Cas9 technology was developed as an alternative method for targeted point mutagenesis in plant, yeast, and human cells. Base editors convert C in the deamination window to thymidine (T) efficiently, however, it remains unclear whether targeted base editing in mouse embryos is feasible. In this report, we generated a modified high-fidelity version of base editor 2 (HF2-BE2), and investigated its base editing efficacy in mouse embryos. We found that HF2-BE2 could convert C to T efficiently, with up to 100% biallelic mutation efficiency in mouse embryos. Unlike BE3, HF2-BE2 could convert C to T on both the target and non-target strand, expanding the editing scope of base editors. Surprisingly, we found HF2-BE2 could also deaminate C that was proximal to the gRNA-binding region. Taken together, our work demonstrates the feasibility of generating point mutations in mouse by base editing, and underscores the need to carefully optimize base editing systems in order to eliminate proximal-site deamination.
APOBEC-1 Deaminase ; genetics ; metabolism ; Animals ; Bacterial Proteins ; genetics ; metabolism ; Base Sequence ; CRISPR-Associated Protein 9 ; CRISPR-Cas Systems ; Cytidine ; genetics ; metabolism ; Embryo Transfer ; Embryo, Mammalian ; Endonucleases ; genetics ; metabolism ; Gene Editing ; methods ; HEK293 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Mice ; Mice, Inbred C57BL ; Microinjections ; Plasmids ; chemistry ; metabolism ; Point Mutation ; RNA, Guide ; genetics ; metabolism ; Thymidine ; genetics ; metabolism ; Zygote ; growth & development ; metabolism ; transplantation

BACKGROUND: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. METHODS: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. RESULTS: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). CONCLUSIONS: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
Area Under Curve ; Bacteria/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Candida/*genetics/isolation & purification ; Female ; Fungal Proteins/genetics ; Gardnerella vaginalis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; ROC Curve ; Sequence Analysis, DNA ; Trichomonas vaginalis/genetics/isolation & purification ; Vagina/*microbiology ; Vaginitis/*diagnosis/microbiology

BACKGROUND: Acinetobacter baumannii has a greater clinical impact and exhibits higher antimicrobial resistance rates than the non-baumannii Acinetobacter species. Therefore, the correct identification of Acinetobacter species is clinically important. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has recently become the method of choice for identifying bacterial species. The purpose of this study was to evaluate the ability of MALDI-TOF MS (Bruker Daltonics GmbH, Germany) in combination with an improved database to identify various Acinetobacter species. METHODS: A total of 729 Acinetobacter clinical isolates were investigated, including 447 A. baumannii, 146 A. nosocomialis, 78 A. pittii, 18 A. ursingii, 9 A. bereziniae, 9 A. soli, 4 A. johnsonii, 4 A. radioresistens, 3 A. gyllenbergii, 3 A. haemolyticus, 2 A. lwoffii, 2 A. junii, 2 A. venetianus, and 2 A. genomospecies 14TU. After 212 isolates were tested with the default Bruker database, the profiles of 63 additional Acinetobacter strains were added to the default database, and 517 isolates from 32 hospitals were assayed for validation. All strains in this study were confirmed by rpoB sequencing. RESULTS: The addition of the 63 Acinetobacter strains' profiles to the default Bruker database increased the overall concordance rate between MALDI-TOF MS and rpoB sequencing from 69.8% (148/212) to 100.0% (517/517). Moreover, after library modification, all previously mismatched 64 Acinetobacter strains were correctly identified. CONCLUSIONS: MALDI-TOF MS enables the prompt and accurate identification of clinically significant Acinetobacter species when used with the improved database.
Acinetobacter Infections/*microbiology/pathology ; Acinetobacter baumannii/*chemistry/classification/isolation & purification ; Bacterial Proteins/chemistry/genetics/metabolism ; Databases, Factual ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

The epithelial cytokine response, associated with reactive oxygen species (ROS), is important in Helicobacter pylori (H. pylori)-induced inflammation. H. pylori induces the production of ROS, which may be involved in the activation of mitogen-activated protein kinases (MAPK), janus kinase/signal transducers and activators of transcription (Jak/Stat), and oxidant-sensitive transcription factor, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappaB), and thus, expression of interleukin-8 (IL-8) in gastric epithelial cells. alpha-lipoic acid, a naturally occurring thiol compound, is a potential antioxidant. It shows beneficial effects in treatment of oxidant-associated diseases including diabetes. The present study is purposed to investigate whether alpha-lipoic acid inhibits expression of inflammatory cytokine IL-8 by suppressing activation of MAPK, Jak/Stat, and NF-kappaB in H. pylori-infected gastric epithelial cells. Gastric epithelial AGS cells were pretreated with or without alpha-lipoic acid for 2 h and infected with H. pylori in a Korean isolate (HP99) at a ratio of 300:1. IL-8 mRNA expression was analyzed by RT-PCR analysis. IL-8 levels in the medium were determined by enzyme-linked immunosorbent assay. NF-kappaB-DNA binding activity was determined by electrophoretic mobility shift assay. Phospho-specific and total forms of MAPK and Jak/Stat were assessed by Western blot analysis. ROS levels were determined using dichlorofluorescein fluorescence. As a result, H. pylori induced increases in ROS levels, mRNA, and protein levels of IL-8, as well as the activation of MAPK [extracellular signal-regulated kinase 1/2 (ERK1/2), c-Jun NH2-terminal kinase 1/2 (JNK1/2), p38], Jak/Stat (Jak1/2, Stat3), and NF-kappaB in AGS cells, which was inhibited by alpha-lipoic acid. In conclusion, alpha-lipoic acid may be beneficial for prevention and/or treatment of H. pylori infection-associated gastric inflammation.
Enzyme-Linked Immunosorbent Assay ; Epithelial Cells/metabolism ; Gastric Mucosa/*drug effects/metabolism/microbiology ; Gene Expression Regulation, Bacterial ; Helicobacter Infections/immunology/*metabolism ; Helicobacter pylori/drug effects/*pathogenicity ; Humans ; Interleukin-8/genetics/*metabolism ; JNK Mitogen-Activated Protein Kinases ; Janus Kinase 1 ; Mitogen-Activated Protein Kinases/*biosynthesis ; NF-kappa B/*metabolism ; RNA, Messenger/isolation & purification/metabolism ; Reactive Oxygen Species/metabolism ; STAT3 Transcription Factor ; Stomach/metabolism/*microbiology ; Thioctic Acid/*pharmacology