Mobile Elements Research Articles

Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems.

The DndABCDE systems catalysing the unusual phosphorothioate (PT) DNA backbone modification, and the DndFGH systems, which restrict invasive DNA, have enigmatic and paradoxical features. Using comparative genomics and sequence-structure analyses, we show that the DndABCDE module is commonly functionally decoupled from the DndFGH module. However, the modification gene-neighborhoods encode other nucleases, potentially acting as the actual restriction components or suicide effectors limiting propagation of the selfish elements. The modification module's core consists of a coevolving gene-pair encoding the DNA-scanning apparatus - a DndD/CxC-clade ABC ATPase and DndE with two ribbon-helix-helix (MetJ/Arc) DNA-binding domains. Diversification of DndE's DNA-binding interface suggests a multiplicity of target specificities. Additionally, many systems feature DNA cytosine methylase genes instead of PT modification, indicating the DndDE core can recruit other nucleobase modifications. We show that DndFGH is a distinct counter-invader system with several previously uncharacterized domains, including a nucleotide kinase. These likely trigger its restriction endonuclease domain in response to multiple stimuli, like nucleotides, while blocking protective modifications by invader methylases. Remarkably, different DndH variants contain a HerA/FtsK ATPase domain acquired from multiple sources, including cellular genome-segregation systems and mobile elements. Thus, we uncovered novel HerA/FtsK-dependent defense systems that might intercept invasive DNA during replication, conjugation, or packaging.

Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.

Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.

The Relevance of Prismatic Sala Model to Village Administration in Otuke District: A Critical Look at Kamdini as a Presidential “Neighbourhood” Village

The paper aims at analyzing the relevance of Prismatic Sala Model to village administration. Village administration in Uganda was formalized by Article 181 of the Constitution of the Republic of Uganda (1995), and CAP 243 of the Local Government Act (1997). Conceptually, in Kamdini village, traditional elements of village administration covered the field of agriculture, health and environment. Heterogeneity was categorized under constructs such as political diversity, religious affiliations, literacy levels, and employment status while village administration was looked at the elements of mobilization and conflict resolution. The Prismatic Sala Model was highly considered to guide the development of this paper. Despite having over 70,626 villages in Uganda, there are currently limited empirical researches that provide comprehensive analyses of in-house challenges of village administration, thus this paper was premised with a view of analyzing the relevance of Prismatic Sala Model to village administration with two specific objectives set: to identify the traditional elements posing threats to Kamdini village administration, and to analyze the effects of heterogeneity on the administration of Kamdini village. The paper adopted a mixed research approach and descriptive design. It targeted the entire population of Kamdini village but purposively sampled the 20 elders, 09 Local Council One executive members and 01 Parish Chief to provide interview and avail the necessary secondary data. Data was analyzed using computer generated software, notably SPSS and STATA to generate both descriptive and inferential statistics. In the first study objective, the finding reveals that Kamdini village is still majorly a traditional community, and that tradition negatively affects the village administration in the study area. In the second study objective, the finding from correlation analysis reveals that heterogeneity positively affects village administration where political diversity (r=.811; p-value = 0.05) was found to be positive, very strong and statistically significant at the 0.05 alpha level; that religious affiliation (r=.449; p-value = 0.05) was positive, moderate and statistically significant at the 0.05 alpha level; that literacy level (r=.614; p-value = 0.05) was positive, strong and statistically significant at the 0.05 alpha level; and that employment status (r=.179; p-value = 0.05) was positive, very weak and statistically significant at the 0.05 alpha level. The paper concludes that traditional practices negatively affect the administration of a village; and that having heterogenic village is more conducive in enhancing better village administration. The study recommends that a spirited campaign be made to transform villages from the elements of prismatic societies to a modernized society.

Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.

Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.

Whole genome sequencing of Lacticaseibacillus casei KACC92338 strain with strong antioxidant activity, reveals genes and gene clusters of probiotic and antimicrobial potential.

Lacticaseibacillus casei KACC92338 was originally isolated from Korean raw milk. The antioxidant activities and protective effect in vitro of this strain were evaluated extensively. The results showed that KACC92338 can tolerate hydrogen peroxide up to 2 mM and cell-free supernatant (CFS) had higher scavenging rates for DPPH, hydroxyl radical, reducing power, and iron chelating activities with 95.61 ± 1.59%, 34.10 ± 1.93%, 2.220 ± 0.82 and 81.06 ± 1.06%, respectively. Meanwhile, the CFS showed a protective effect on yeast cells against 10 mM hydrogen peroxide with a survival rate of 76.05 ± 5.65%. To explore the probiotic potential of KACC92338, whole genome assembly and gene clusters with probiotic properties were further analyzed. The genome size was 3,050,901 bp with a 47.96% GC ratio, and 63 contigs. The genome contains 3,048 genes composed of 2,981 coding sequences and 67 RNAs (including 57 tRNAs +9 rRNAs +1 tmRNA). Average Nucleotide Identity and genome-based taxonomy showed that the KACC92338 genome had close similarity with L. casei strains with 96% ANI. Functional annotation by EggNOG and KEGG revealed the presence of numerous genes putatively involved in carbohydrate- and amino acid-transport and metabolism, genetic information processing, and signaling and cellular processes. Additionally, several genes conferring probiotic characteristics such as tolerance to stress, heat, cold, acid, bile salts, oxidative stress, immunomodulation, and adhesion to intestinal epithelium were identified. Notably absent were acquired antibiotic resistance genes, virulence, and pathogenic factors, that prove KACC92338 is a safe strain. Besides, the defense mechanisms of KACC92338 include six prophage regions and three clustered regularly interspaced short palindromic repeat (CRISPR) arrays as acquired immune systems against mobile elements. Further, the BAGEL4 database determined antimicrobial bacteriocin clusters of class IIb: sakacin-P, Enterolysin_A, sactipeptides, and Enterocin X, which suggests the strain could exhibit a wide range of antimicrobial functions. Together, these findings show that the L. casei KACC92338 strain can be a potential probiotic candidate in producing functional fermented foods-, health care- and skin care products- with antioxidant properties. However, a few more mechanistic studies are necessary on the safety assurance and potential application of the strain as a probiotic agent.

First comparative genomics analysis of Corynebacterium auriscanis.

Corynebacterium auriscanis is a bacterial species frequently isolated from dogs with external otitis or dermatitis and a zoonotic pathogen transmitted by dog bite. It is considered an opportunistic pathogen, but its pathogenicity mechanisms are poorly studied. Comparative genomics can identify virulence and niche factors that could contribute to understanding its lifestyle. The objectives of this project was to compare genomes of C. auriscanis to identify genes related to its virulence and lifestyle. The genome of strain 32 was sequenced using Illumina HiSeq 2500 (Illumina, CA, USA) and assembled using Unicycler. The two other non-redundant genomes from the same species available in GenBank were included in the analysis. All genomes were annotated and checked for taxonomy, assembly quality, mobile elements, CRISPR-Cas systems, and virulence and antimicrobial resistance genes. The virulence genes in the three genomes were compared to the ones from other pathogens commonly isolated with C. auriscanis. The species has 42 virulence factors that can be classified as niche factors, due to the absence of true virulence factors found in primary pathogens. The gene rbpA could confer basal levels of resistance to rifampin. The absence of true virulence factors in the three genomes suggests C. auriscanis has an opportunistic pathogen lifestyle.

Nursing care for hospitalized older adults - fall accidents versus safe mobility: a scoping review.

to map the constituent elements of the safe mobility concept present in hospital care for older adults. a scoping review of 35 articles searched in databases and gray literature - BDENF/VHL, Scopus, CINAHL/EBSCO, Embase, Web of Science, PEDro, MEDLINE/PubMed and CAPES Theses and Dissertations Catalog. No time or language cut-off was established. none of the studies presented a clear safe mobility concept, however its constituent elements involve factors related to patient (behavioral factors, conditions, diseases, signs and symptoms, nutritional status, age, balance, strength, gait quality, sleep), the institution (environment, treatment devices, guidelines, medications and polypharmacy, material and human resources and clothing/shoes) and the nature of the interventions (related to the patient, institution and family). the constituent elements of safe mobility express hospital units' capacity to guarantee care and protection from fall accidents for hospitalized older adults.

REE and trace element mobility during the transformation of basalt to laterite and bauxite, Payas Province, Türkiye

The bauxites of the Payas area in the eastern Mediterranean region of Turkey occur as a stratigraphically continuous layer between Early and Late Cretaceous shallow marine carbonates. The laterites represent an in situ formation and mark a key stratigraphic layer in the region. Bauxite pockets are also present in the laterites, formed from the reworking of the laterites and accumulated in depressions in the karst terrain. Therefore, bauxite occurrences are found locally in this stratigraphic layer. The parental rock was a Ti-rich basalt that is compositionally similar to Hawaiian basalts, as indicated by petrographic features and distinctive trace element composition (Zr/TiO2 and Nb/Y). The behavior of elements during the lateritization and bauxitization processes was interpreted using the composition of the Hawaiian basalts with the iron laterite and Ti-rich bauxites of the Payas Region. During lateritization, Fe, Al, Ti, Cr, Nb, and Ta, were largely immobilie while REE and other trace elements, except for Rb, Ni, Co, and Pb were significantly removed. Approximately 75 % of the REE were removed at the end of the bauxitization and/or transportation of the lateritic soil into the karstic depressions. REE were not equally mobile with La to Ce and Lu to Yb having a relatively lower mobility than highly mobile middle REE. During the transformation of laterite to bauxite, low mobility elements such as Ti, Nb, Th, Cr, Hf, and Sn were enriched in the bauxite phase. In comparison to other elements, Rb, As, Pb, Mo, and Ni were strongly removed from the lateritic material during the bauxitization processes. The transfer of MREE during lateritization and bauxitization would have resulted in the enrichment of both light and heavy REE (concave pattern) in contemporaneous seawater. In other words, silicate weathering periods on land should be marked by a concave REE pattern with positive Eu anomaly in marine sediments throughout the geological period.

Antibiotic Resistances of Clostridioides difficile.

The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.

Distribution and spread of tigecycline resistance gene tet(X4) in Escherichia coli from different sources.

Tigecycline serves as a last-resort antimicrobial agent against severe infections caused by multidrug-resistant bacteria. Tet(X) and its numerous variants encoding flavin-dependent monooxygenase can confer resistance to tigecycline, with tet(X4) being the most prevalent variant. This study aims to investigate the prevalence and characterize tigecycline resistance gene tet(X) in E. coli isolates from various origins in Yangzhou, China, to provide insights into tet(X) dissemination in this region. In 2022, we tested the presence of tet(X) in 618 E. coli isolates collected from diverse sources, including patients, pig-related samples, chicken-related samples, and vegetables in Yangzhou, China. The antimicrobial susceptibility of tet(X)-positive E. coli isolates was conducted using the agar dilution method or the broth microdilution method. Whole genome sequencing was performed on tet(X)-positive strains using Illumina and Oxford Nanopore platforms. Four isolates from pig or pork samples carried tet(X4) and exhibited resistance to multiple antimicrobial agents, including tigecycline. They were classified as ST542, ST10, ST761, and ST48, respectively. The tet(X4) gene was located on IncFIA8-IncHI1/ST17 (n=2), IncFIA18-IncFIB(K)-IncX1 (n=1), and IncX1 (n=1) plasmids, respectively. These tet(X4)-carrying plasmids exhibited high similarity to other tet(X4)-bearing plasmids with the same incompatible types found in diverse sources in China. They shared related genetic environments of tet(X4) associated with ISCR2, as observed in the first identified tet(X4)-bearing plasmid p47EC. In conclusion, although a low prevalence (0.65%) of tet(X) in E. coli strains was observed in this study, the horizontal transfer of tet(X4) among E. coli isolates mediated by pandemic plasmids and the mobile element ISCR2 raises great concerns. Thus, heightened surveillance and immediate action are imperative to curb this clinically significant resistance gene and preserve the efficacy of tigecycline.

Structural Variations and Rearrangements in Bacterial Type II Toxin-Antitoxin Systems.

Bacteria encode a wide range of survival and immunity systems, including CRISPR-Cas, restriction-modification systems, and toxin-antitoxin systems involved in defence against bacteriophages, as well as survival during challenging growth conditions or exposure to antibiotics. Toxin-antitoxin (TA) systems are small two- or three-gene cassettes consisting of a metabolic regulator (the "toxin") and its associated antidote (the "antitoxin"), which also often functions as a transcriptional regulator. TA systems are widespread in the genomes of pathogens but are also present in commensal bacterial species and on plasmids. For mobile elements such as plasmids, TA systems play a role in maintenance, and increasing evidence now points to roles of chromosomal toxin-antitoxin systems in anti-phage defence. Moreover, the widespread occurrence of toxin-antitoxin systems in the genomes of pathogens has been suggested to relate to survival during host infection as well as in persistence during antibiotic treatment. Upon repeated exposure to antibiotics, TA systems have been shown to acquire point mutations as well as more dramatic rearrangements such as in-frame deletions with potential relevance for bacterial survival and pathogenesis. In this review, we present an overview of the known functional and structural consequences of mutations and rearrangements arising in bacterial toxin-antitoxin systems and discuss their relevance for survival and persistence of pathogenic species.

Production of Double-Stranded RNA in Planta by a Potato Mop-Top Virus (PMTV)-Based Vector for Inducing Gene Silencing.

RNA silencing (also known as gene silencing) is an evolutionary conserved mechanism that is involved in regulating gene expression, suppressing mobile elements, and defensing virus infection. RNA silencing is triggered by double-stranded RNA via Dicer or Dicer-like riboendonucleases. DsRNAs are also the replication intermediates of all RNA viruses; as a result, plant RNA viruses are ideal candidates to induce RNA silencing. A large body of plant viruses have been modified into vectors for RNA silencing in varied plant species. Here, we described a simple, time-saving, and operable system for gene function and genetic breeding study of potato and Nicotiana benthamiana using a potato mop-top (MPTV)-based vector.

Parallel Evolution of Transcription Factors in Basal Metazoans.

Transcription factors (TFs) play a pivotal role as regulators of gene expression, orchestrating the formation and maintenance of diverse animal body plans and innovations. However, the precise contributions of TFs and the underlying mechanisms driving the origin of basal metazoan body plans, particularly in ctenophores, remain elusive. Here, we present a comprehensive catalog of TFs in 2 ctenophore species, Pleurobrachia bachei and Mnemiopsis leidyi, revealing 428 and 418 TFs in their respective genomes. In contrast, morphologically simpler metazoans have a reduced TF representation compared to ctenophores, cnidarians, and bilaterians: the sponge Amphimedon encodes 277 TFs, and the placozoan Trichoplax adhaerens encodes 274 TFs. The emergence of complex ctenophore tissues and organs coincides with significant lineage-specific diversification of the zinc finger C2H2 (ZF-C2H2) and homeobox superfamilies of TFs. Notable, the lineages leading to Amphimedon and Trichoplax exhibit independent expansions of leucine zipper (BZIP) TFs. Some lineage-specific TFs may have evolved through the domestication of mobile elements, thereby supporting alternative mechanisms of parallel TF evolution and body plan diversification across the Metazoa.

Independent and combined effects of microplastics pollution and drought on soil bacterial community

Global terrestrial ecosystems are simultaneously threatened by multiple environmental pressures, with microplastics (MPs) pollution and drought possibly being the most pressing, both of which may have unanticipated effects on soil organisms. Here, we investigated the responses of diversity, composition and functions of soil bacterial community to MPs pollution (including two MPs types: polyethylene (PE) and polylactic acid (PLA); two MPs sizes: < 20 μm and <300 μm) and drought in microcosms. We found that only 20 μm PLA MPs significantly decreased soil bacterial diversity by 17.4 % and altered soil bacterial community composition, while PE MPs and 300 μm PLA MPs had no significant effects. The copiotrophic bacteria (i.e., Proteobacteria and Firmicutes) were enriched in the 20 μm PLA MPs pollution soils due to the enhanced dissolved organic carbon contents. Moreover, our results showed that the 20 μm PLA MPs also affected the potential phenotypes and functions of soil bacterial community, increasing the potentially pathogenic, stress-tolerant, containing mobile elements and forming biofilms phenotypes, and promoting membrane transport and signal transduction pathways. These results suggested that the effects of MPs on soil bacterial community varied depending on MPs types and sizes. However, drought significantly increased soil bacterial diversity by 10.3 % and affected soil bacterial community composition in the 20 μm PLA MPs pollution soils. We also found that drought inhibited the levels of potentially pathogenic, containing mobile elements and forming biofilms phenotypes in the 20 μm PLA MPs pollution soils. Taken together, these findings reveal that drought may alleviate the adverse effects of MPs pollution on soil bacterial community, which enhances our understanding of the interactive effects of multiple global change factors on agroecosystem functions.

Pathogenic Factors and Recent Study on the Rapid Detection of Shiga Toxin-Producing Escherichia coli (STEC).

This comprehensive review delves into the pathogenicity and detection of Shiga Toxin-Producing Escherichia coli (STEC), shedding light on its various genetic and clinical manifestations. STEC originating from E. coli acquires pathogenicity through mobility and genetic elements. The pathogenicity of STEC is explored in terms of clinical progression, complications, and key toxins such as Shiga toxin (Stx). Stx1 and Stx2 are two distinct Stx types exhibiting different toxicities, with Stx2 often associated with severe diseases. This review also delves into Subtilase cytotoxin, an additional cytotoxin produced by some STEC strains. Pathogenic mechanisms of STEC, such as attaching and effacing intestinal lesions, are discussed, with a focus on roles of genetic factors. Plasmids in STEC can confer unique pathogenicity. Hybridization with other pathogenic E. coli can create more lethal pathogens. This review covers a range of detection methods, ranging from DNA amplification to antigen detection techniques, emphasizing the need for innovative approaches to improve the sensitivity and speed of STEC diagnosis. In conclusion, understanding diverse aspects of STEC pathogenicity and exploring enhanced diagnostic methods are critical to addressing this foodborne pathogen effectively. Pathology of Shiga toxin toxicity. STEC-derived Shiga toxin consists of one A subunit and five B subunits. Pathological symptoms of the disease can progress to HUS within two weeks after the onset of diarrhea. Shiga toxin intoxication is also associated with many complications, such as neurological and cardiac complications. This figure was reconstructed based on data from Bruyand et al.

Genesis and supergene weathering of tetrahedrite-(Hg) in meta-carbonate rocks: Bearing on differential mobility of priority pollutant metals

The Cu-Sb-Hg mineralization of San Giuliano Terme (Monti Pisani, Tuscany, Italy) is characterized by the widespread occurrence of deeply altered tetrahedrite-(Hg) hosted within joints and faults in the Liassic “Calcari ceroidi” Formation. Through a multi-technique approach (optical and scanning electron microscopy, electron microprobe analysis, single-crystal and powder X-ray diffraction, micro-Raman spectroscopy, X-ray fluorescence, fluid inclusion analysis), tetrahedrite-(Hg) and its alteration products have been characterized and data about its genesis and successive supergene weathering have been collected. Tetrahedrite-(Hg) from San Giuliano Terme has the empirical formula Cu9.92Ag0.02(Hg1.64Fe0.30Zn0.04)Σ1.98(Sb3.53As0.56)Σ4.09S12.95, and is found with scarce gangue minerals represented by calcite, baryte, and very rare fluorite. The mineralization formed from hydrothermal fluids with moderately high salinity (∼17.5 wt% NaClequiv.) of dominantly metamorphic origin at T ∼ 285 °C. Tetrahedrite-(Hg) is usually fully replaced by a mixture of cinnabar, roméite-group minerals, malachite, and rarely azurite. Based on the modal abundance of the mineralogical constituents and their micro-textures, four stages of supergene weathering of tetrahedrite-(Hg) have been recognized. The alteration stages reflect the progressive ingression of meteoric water into the system, with consequent oxidation of tetrahedrite-(Hg) and the introduction of Ca2+, HCO3– and H2O, as well as the progressive removal of S, Sb, and Cu. The relative proportions of the supergene minerals in the four alteration stages can be taken as a proxy for the mobility of the main chemical constituents of tetrahedrite-(Hg), three of which (Hg, Sb, and Cu) are priority pollutant metals. Mercury was found to be the least mobile element in the reconstructed geochemical process. In fact, the widespread precipitation of cinnabar in the space formerly occupied by tetrahedrite-(Hg) hinders the dispersion of Hg in the environment, sequestering it in a solid matrix.

FosA11, a novel chromosomal-encoded fosfomycin resistance gene identified in Providencia rettgeri.

This study investigated resistance genes corresponding to the fosfomycin resistance phenotype in clinical isolate Providencia rettgeri W986, as well as characterizing the enzymatic activity of FosA11 and the genetic environment. Antimicrobial susceptibility testing was performed using the agar microdilution method based on the Clinical and Laboratory Standards Institute guidelines. The whole genomic sequence of Providencia rettgeri W986 was obtained using Illumina sequencing and the PacBio platform. The fosA-11 gene was amplified by PCR and cloned into the pUCP20 vector. The recombinant strain pCold1-fosA11-BL21 was expressed to extract the target protein, and absorbance photometry was applied for enzymatic parameter determination. Minimal inhibitory concentration (MIC) tests showed that W986 conferred fosfomycin resistance and was inhibited by phosphonoformate, thereby indicating the presence of a FosA protein. A novel resistance gene designated as fosA11 was identified by whole-genome sequencing and bioinformatics analysis, and it shared 54.41%-64.23% amino acid identity with known FosA proteins. Cloning fosA11 into Escherichia coli obtained a significant increase (32-fold) in the MIC with fosfomycin. Determination of the enzyme kinetics showed that FosA11 had a high catalytic effect on fosfomycin, with Km = 18 ± 4 and Kcat = 56.1 ± 3.2. We also found that fosA11 was located on the chromosome, but the difference in the GC content between the chromosome and fosA11 was dubious, and thus further investigation is required. In this study, we identified and characterized a novel fosfomycin inactivation enzyme called FosA11. The origin and prevalence of the fosA11 gene in other bacteria require further investigation.IMPORTANCEFosfomycin is an effective antimicrobial agent against Enterobacterales strains. However, the resistance rate of fosfomycin is increasing year by year. Therefore, it is necessary to study the deep molecular mechanism of bacterial resistance to fosfomycin. We identified a novel chromosomal fosfomycin glutathione S-transferase, FosA11 from Providencia rettgeri, which shares a very low identity (54.41%-64.23%) with the previously known FosA and exhibits highly efficient catalytic ability against fosfomycin. Analysis of the genetic context and origin of fosA11 displays that the gene and its surrounding environments are widely conserved in Providencia and no mobile elements are discovered, implying that FosA11 may be broadly important in the natural resistance to fosfomycin of Providencia species.

Агроэкологическая характеристика черноземов Каменной степи: влияние растительных сообществ и распашки

Changes in soil carbon stocks have a significant impact on atmospheric CO2 concentrations and the global carbon balance. Despite the proven effectiveness of agroforestry in erosion control and prevention of soil fertility loss, there are many controversial data suggesting that the impact of afforestation on Chernozem soils should be further investigated. The Kamennaya Steppe site (arable land surrounded by shelterbelt forests) is a reference site for monitoring studies at the Voronezh Carbon Test Site, where the carbon balance of agro-ecosystems is being studied and the ecological role of shelterbelt forests in changing soil properties and carbon sequestration is being evaluated. The study was focused on the evaluation of agro-ecological characteristics and the impact of tillage on Chernozems of Kamennaya Steppe under different vegetation types. The study of the chemical properties of chernozems was carried out using classical chemical methods; the analysis of heavy metals was carried out using the voltampermetric method. Comprehensive agro-ecological evaluation showed that the studied Vorony-Calcic Chernozems had a high content of humus, which reached 7-8% in the upper horizons, enriched with mineral nutrition elements, and had favorable physical and chemical properties. Forest and grassland vegetation contribute to enrichment of the soil with organic residues, while tillage and mineralization of organic matter on arable land led to a decrease in humus content. Data analysis suggested that the study area did not suffer from contamination. Furthermore, it was found that the organic matter of the studied chernozems was able to bind the studied metals and retain them in an unavailable state. This phenomenon was supported by rather high correlations between humus and total heavy metal content (r = 0.946 for Pb and r = 0.975 for Cd at p &lt; 0.00001). It should be emphasized that shelterbelt forests could act as a biogeochemical barrier to the lateral migration of heavy metals. Cadmium is a rather mobile element potentially capable to migrate to adjacent environments. Therefore, regular monitoring of the agro-ecological condition of the Chernozems of the Kamennaya Steppe is required.

Insights into the roles of biochar pores toward alleviating antibiotic resistance genes accumulation in biofiltration systems

Biofiltration systems would harbor and spread various antibiotic resistance genes (ARGs) when treating antibiotic micro-pollution, constituting a potential ecological risk. This study aimed to investigate the effects of biochar pores on ARG emergence and related microbial response mechanisms in bench-scale biofiltration systems. Results showed that biochar pores effectively reduced the absolute copies of the corresponding ARGs sul1 and sul2 by 54.1% by lowering the sorbed-SMX's bioavailability compared to non-porous anthracite. An investigation of antimicrobial resistomes revealed a considerable decrease in the abundance and diversity of ARGs and mobile gene elements. Metagenomic and metaproteomic analysis demonstrated that biochar pores induced the changeover of microbial defense strategy against SMX from blocking SMX uptake by EPS absorbing to SMX biotransformation. Microbial SOS response, antibiotic efflux pump, EPS secretion, and biofilm formation were decreased. Functions related to SMX biotransformation, such as sadABC-mediated transformation, xenobiotics degradation, and metabolism, were significantly promoted.

Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain

Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.