Mobile Elements Research Articles

GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.

Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles andFR profiles, and identified 14636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.

From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs.

Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE-1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause-effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non-coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non-coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.

Emergence of the mobile RND-type efflux pump gene cluster tmexCD1-toprJ1 in Klebsiella pneumoniae clinical isolates in Japan.

Tigecycline is an antimicrobial agent with a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. However, mobile tigecycline resistance gene clusters, such as tnfxB-tmexCD-toprJ, have spread globally. The prevalence of tigecycline-resistant Enterobacterales in clinical settings in Japan is unknown. To investigate the tnfxB-tmexCD-toprJ gene cluster in the genome sequences of Enterobacterales clinical isolates in Japan. We investigated the tnfxB-tmexCD-toprJ cluster from the genome sequences of 5143 Enterobacterales isolates collected from 175 hospitals around Japan between 2019 and 2020 as part of a national genomic surveillance program for antimicrobial-resistant bacteria. The tnfxB1-tmexCD1-toprJ1 cluster was detected in two Klebsiella pneumoniae isolates in 2019. One isolate possessed a 299.4 kb IncFIB(K) plasmid, pJBBGAAF19431, and the other possessed a 224.9 kb IncHI1B/IncFIB(K) hybrid plasmid, pJBEAACG19501, co-carrying multiple antimicrobial resistance genes, including extended-spectrum β-lactamase genes, blaOXA-1 and blaCTX-M-27, respectively, along with tnfxB1-tmexCD1-toprJ1. The genetic context of the tnfxB1-tmexCD1-toprJ1-surrounding structure on pJBBGAAF19431 was similar to that of a K. pneumoniae plasmid pHNAH8I-1 from a chicken in China in 2017, and the cluster was embedded in an apparently intact mobile DNA element: strand-biased circularizing integrative element. The tnfxB1-tmexCD1-toprJ1 on pJBEAACG19501 was embedded in a Tn3 family transposon related to TnAs1. The plasmid pJBEAACG19501 was highly similar to that of K. pneumoniae, isolated from humans in China in 2021. tmexCD-toprJ was present in Japan as of 2019. Even in Japan, where the clinical use of tigecycline is significantly rare, tmexCD-toprJ-harbouring multidrug-resistant Enterobacterales is a public health threat and requires continuous monitoring.

Epigenetic control of T-DNA during transgenesis and pathogenesis.

Mobile elements known as T-DNAs are transferred from pathogenic Agrobacterium to plants and reprogram the host cell to form hairy roots or tumors. Disarmed non-oncogenic T-DNAs are extensively used to deliver transgenes in plant genetic engineering. Such T-DNAs were the first known targets of RNA silencing mechanisms, which detect foreign RNA in plant cells and produce small RNAs that induce transcript degradation. These T-DNAs can also be transcriptionally silenced by the deposition of epigenetic marks such as DNA methylation and the dimethylation of lysine 9 (H3K9me2) in plants. Here, we review the targeting and the roles of RNA silencing and DNA methylation on T-DNAs in transgenic plants as well as during pathogenesis. In addition, we discuss the crosstalk between T-DNAs and genome-wide changes in DNA methylation during pathogenesis. We also cover recently discovered regulatory phenomena, such as T-DNA suppression and RNA silencing-independent and epigenetic-independent mechanisms that can silence T-DNAs. Finally, we discuss the implications of findings on T-DNA silencing for the improvement of plant genetic engineering.

Variable orthogonality of serine integrase interactions within the ϕC31 family

Serine integrases are phage- (or mobile element-) encoded enzymes that catalyse site-specific recombination reactions between a short DNA sequence on the phage genome (attP) and a corresponding host genome sequence (attB), thereby integrating the phage DNA into the host genome. Each integrase has its unique pair of attP and attB sites, a feature that allows them to be used as orthogonal tools for genome modification applications. In the presence of a second protein, the Recombination Directionality Factor (RDF), integrase catalyses the reverse excisive reaction, generating new recombination sites, attR and attL. In addition to promoting attR x attL reaction, the RDF inhibits attP x attB recombination. This feature makes the directionality of integrase reactions programmable, allowing them to be useful for building synthetic biology devices. In this report, we describe the degree of orthogonality of both integrative and excisive reactions for three related integrases (ϕC31, ϕBT1, and TG1) and their RDFs. Among these, TG1 integrase is the most active, showing near complete recombination in both attP x attB and attR x attL reactions, and the most directional in the presence of its RDF. Our findings show that there is varying orthogonality among these three integrases – RDF pairs. ϕC31 integrase was the least selective, with all three RDFs activating it for attR x attL recombination. Similarly, ϕC31 RDF was the least effective among the three RDFs in promoting the excisive activities of the integrases, including its cognate ϕC31 integrase. ϕBT1 and TG1 RDFs were noticeably more effective than ϕC31 RDF at inhibiting attP x attB recombination by their respective integrases, making them more suitable for building reversible genetic switches. AlphaFold-Multimer predicts very similar structural interactions between each cognate integrase – RDF pair. The binding surface on the RDF is much more conserved than the binding surface on the integrase, an indication that specificity is determined more by the integrase than the RDF. Overall, the observed weak integrase/RDF orthogonality across the three enzymes emphasizes the need for identifying and characterizing more integrase – RDF pairs. Additionally, the ability of a particular integrase’s preferred reaction direction to be controlled to varying degrees by non-cognate RDFs provides a path to tunable, non-binary genetic switches.

Geochemical signatures of forearc serpentinites from oceanic to continental subduction

In subduction systems, the forearc (FA) serpentinized mantle plays a key role as a reservoir for fluid-mobile elements, especially those prone to early mobilisation from the slab. FA serpentinites therefore provide an indication of the fluid characteristics that have been steamed out of the slab, and allow better quantification of elemental recycling and fluid flow. FA serpentinites outcropping along the Indus Suture Zone are formed by hydration of mantle peridotites by fluids derived from the Indian slab, providing a geochemical record of fluid-rock interactions during the India-Eurasia convergence. Systematic trace and multi-isotope (Sr and Pb) analyses of serpentinites from three major sites, namely Shergol-Tingdo, Kargil and Tso Morari, along the Indus Suture Zone in Ladakh (NW Himalaya) show that these rocks record a major change in the origin of metasomatic agents, from oceanic to continental subduction. The Shergol-Tingdo and Kargil FA serpentinites, formed under low temperature and pressure conditions, are characterised by high B enrichment and As and Sb depletion, high alkali/U ratios and relatively unradiogenic Sr and Pb isotope ratios. These geochemical characteristics are identical to those reported for modern oceanic subduction zones (e.g., Mariana forearc) and are consistent with input by fluids derived from subducted oceanic crust. In contrast, FA serpentinites from the Tso Morari ultra-high pressure unit show enrichment in fluid mobile elements such as As, Sb and U, low alkali/U ratios and radiogenic Sr and Pb isotopic compositions. These features suggest a change in the metasomatizing agent with a strong influence from subducted continental material. Consistent with this scenario, the Sr-Pb isotopic composition of the Kargil FA serpentinites can be reproduced by mixing between an Indian MORB-depleted mantle source and fluids derived from dewatering of blueschist facies oceanic metasediments, whereas in the case of Tso Morari a fluid end-member derived from various eclogitic continental metasediments is required. We propose that the observed geochemical signature of the Indus Suture Zone FA serpentinites can be used to reconstruct the geochemical exchanges between the slab and the overlying mantle from intra-oceanic to continental subduction. This successful systematic approach could be applied to other collisional contexts

Identification of an ArgR-controlled promoter within the outermost region of the IS10R mobile element.

Mobile genetic elements are small DNA fragments that can relocate within the genome, causing either gene inactivation or enhanced gene expression. Our research identified a new functional promoter and mRNA translation region within the IS10R element, which is part of the widely distributed Tn10 transposon. We found that the global regulators ArgR and IHF control the activity of this promoter. Additionally, insertion of this mini-Tn10 derivative into the barA gene resulted in the expression of a truncated but constitutive active form of the BarA sensor kinase. Overall, our work sheds light on how mobile genetic elements could impact the physiology and virulence of opportunistic pathogenic bacteria.

Genetic profile of carbapenem-resistant <i>Acinetobacter baumannii</i> strains

The purpose of the research: the molecular genetic characteristic ofA. baumanniicarbapenem-resistant strains, including clonal affiliation, resistome and virulome pattern analysis, description of genetic environment resistance determinants, comparative genetic analysis, and assessment of phylogenetic relationships are presented in the work. The studiedA. baumanniistrains belonged to sequence types ST2Pas/ST2062.2063Oxf(n = 5) and ST78Pas/ST1757Oxf(n = 2). The nucleotide sequences of the studiedA. baumanniiST2Pas/ST2062.2063Oxfstrains were grouped into a single cluster according to phylogenetic analysis. And the sequences of theA. baumanniiST78Pas/ST1757Oxfstrains were combined with the nucleotide sequence of theA. baumanniiAbCTX5 strain, isolated in France in 2015. The presence of intrinsic (OXA-51-like) and acquired carbapenemases genes was shown inA. baumanniistrains. In particular,blaOXA-23are identified in members of ST2Pas/ST2062.2063Oxf, and inA. baumanniiST78Pas/ST1757Oxfstrains —blaOXA-72as part of the plasmid DNA. TheA. baumanniiST78Passtrains possessed additional extended-spectrum beta-lactamase genes. Тhe CTX-M-115 cephalosporinase gene are present in both strains, and theA. baumanniistrain NNAb_2023.3 has theblaCARB-16gene. MostA. baumanniistrains are characterized by the presence of acquired genes for enzymatic modification of macrolides(mph(E), msr(E)), chloramphenicols(catB8), aminoglycosides(aadA, aph(3'')-Ib, aph(6)-Id, aac(6')-Ib, aph(3')-Ia, armA). A comparative analysis showed that inA. baumanniiST2Pas/ST2062.2063Oxfstrains the resistance determinants to macrolides and aminoglycosides are located in the Tn6279-like transposon, and the aminoglycosidases genesaph(3'')-Ib, aph(6)-Idare associated with theIS91-like mobile element. InA. baumanniiST78Pas/ST1757Oxfstrains, resistance genes to aminoglycosides, macrolides, sulfonamides, and beta-lactamase genes are grouped in a region from 60 to 80 Kb long between theglmSandhutCgenes. The presence of mutations in thegyrAandparCgenes associated with resistance to fluoroquinolones were characterized in allA. baumanniistrains. Thus, new knowledge about the genetic profile of carbapenem-resistantA. baumanniistrains representing epidemically significant international clonal lineage has been obtained.

Molecular Characterization of Enterococcus faecium Clinical Isolates Harbouring erm (T) from an Italian Hospital.

The presence of erm(T) gene conferring resistance to macrolides, lincosamides and streptogramin B (MLSB), was screened in 296 enterococci collected from clinical samples in a central Italy hospital and seven Enterococcus faecium isolates resulted positive to erm(T) by PCR. All isolates were resistant to erythromycin, tetracycline, ciprofloxacin and ampicillin but susceptible to vancomycin and chloramphenicol. Whole Genome Sequencing analysis revealed that in five E. faecium isolates, all belonging to the sequence type ST80 included in the clonal complex CC17 responsible of nosocomial infections, erm (T) gene was chromosome-located, in different genetic contexts. In E. faecium 735,236, erm (T) was on a 4,159-bp region flanked by two IS1216 and inserted at the 3' end of the mp gene. In E. faecium 711,448 and 739,437, erm (T) was found in a 4,463-bp region identical to that detected in E. faecium 735,236 except for 319bp. In E. faecium 713,729 and 757,415, erm (T) was on a 7,038-bp region flanked by IS1251 and ISEfm2 transposases and encompassed between the genes encoding a recombinase and three hypothetical proteins. erm(T)-carrying minicircles were detected in all isolates by inverse PCR assays demonstrating that erm(T) was included in mobile elements. However, in conjugation assays by filter mating, the erm(T) transferability was unsuccessful. Although macrolides are not used to treat enterococcal infections, the resistance is nonetheless widespread. These antibiotics are critically important in human medicine, but only few studies focused on erm (T)-harbouring clinical enterococci. The emergence of erm (T)-mediated erythromycin resistance among enterococci, potentially transferable to other nosocomial pathogens, should be constantly monitored.

Insertion sequence elements and unique symmetrical genomic regions mediate chromosomal inversions in Streptococcus pyogenes.

Chromosomal inversions are a phenomenon in many bacterial species, often across the axis of replication. Inversions have been shown to alter gene expression, changing persistence of colonisation and infection following environmental stresses. In Streptococcus pyogenes, inversions have been reported. However, frequency and molecular markers of inversions have not been systematically examined. Here, 249 complete S.pyogenes genomes were analysed using a pangenomic core gene synteny framework to identify sequences associated with inversions. 47% of genomes (118/249) contained at least one inversion, from 23 unique inversion locations. Chromosomal locations enabling inversions were usually associated with mobile elements (insertion sequences n=9 and prophages n=7). Two insertion sequences, IS1548 and IS1239, accounted for>80% of insertion sequences and were the only insertion sequences associated with inversions. The most observed inversion location (n=104 genomes, 88% of genomes with an inversion) occurs between two conserved regions encoding rRNAs, tRNAsand sigma factor genes. The regions are symmetrically placed around the origin of replication forming a unique chromosomal structure inS. pyogenes, relative to other streptococci. Cataloging of thechromosomal location and frequency of inversions can direct dissection of phenotypic changes following chromosomal inversions. The framework used here can be transferred to other bacterial species to characterise chromosomal inversions.

Columnar jointing in Paleoproterozoic carbon-bearing rocks (Onega Basin, NW Russia): implications for carbon migration in sedimentary rocks

ABSTRACT Columnar jointing occurs commonly in igneous rocks and rarely in sedimentary rocks. We report the results of combined field and petrological studies, Raman spectroscopy and column geometry analysis of columnar jointing in Paleoproterozoic carbon-bearing rocks, Eastern Fennoscandian Shield, NW Russia. The columnar rocks occur near the contact with the saucer-shaped dolerite sill emplaced in the unconsolidated organic rich sediments. Columnar jointing aureole (1 to 7 m) and column architecture strongly depends on the contact morphology. Columnar jointing is caused by the contraction of organic-rich sediments due to generation and further release of gas and oil rich fluid. The results of integrated studies indicate that fluidization driving the jointing is associated with not only the dehydration, but also with the mobilization of gas and oil rich fluid due to the thermal maturation of organic matter. Columnar jointing is associated with intensive fluid circulation and devolatilization evidenced by the numerous veins, globules, and vugs filled with migrated carbonaceous matter and secondary minerals in the columnar rocks as well as high vesicularity of dolerites near the contact. The redistribution of the mobile elements (K, Rb, LREE) along with the significant enrichment of S near the contact also indicates the intensive fluid circulation. The study contributes to understanding of mechanism of columnar jointing in sedimentary rocks and formation the fracture networks in organic-rich sediments.

Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools.

The evolutionary arms race between bacteria and phages led to the emergence of bacterial immune systems whose diversity and dynamics remain poorly understood. Here we use comparative genomics to describe a widespread genetic element, defined by the presence of the Gamma-Mobile-Trio (GMT) proteins, that serves as a reservoir of offensive and defensive tools. We demonstrate, using Vibrio parahaemolyticus as a model, that GMT-containing genomic islands are active mobile elements. Furthermore, we show that GMT islands' cargoes contain various anti-phage defence systems, antibacterial type VI secretion system (T6SS) effectors and antibiotic-resistance genes. We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy. Our findings underscore the need to broaden the concept of 'defence islands' to include defensive and offensive tools, as both share the same mobile elements for dissemination.

Psychometric testing of the continence and mobility in older adults knowledge quiz

AbstractWhat are the psychometric properties of the Continence and Mobility in Older Adults Knowledge Quiz? Our previous research revealed gaps in practicing and student nurses' knowledge of mobility and continence in older people. To address this gap, we developed a self‐directed e‐learning module on continence and mobility to enhance student nurses knowledge. The module provided education about continence, mobility, and the links between them. Since we were unable to locate a continence and mobility measure that captured both lower urinary track symptoms and elements of mobility, we developed a continence and mobility knowledge quiz. For researchers and educators to be able to use this quiz with confidence, psychometric testing of our continence and mobility knowledge quiz was required. When caring for older people, two geriatric challenges—continence and mobility—are often linked and viewed as indicators of frailty. Functional changes related to continence and/or mobility can indicate an acute illness in older persons and, if left untreated, can result in permanent changes managing continence needs. Continence care is often viewed negatively and is not prioritized by nurses. We employed stages in development of the Continence and Mobility Knowledge Quiz. In stage one, we developed 18 item true/false items from the literature with the guidance of a continence expert. In stage two, we tested the Quiz with nursing students from three universities in Canada. In stage three, (the current stage) we assessed the validity of the scale using a factor analysis and a reliability analysis (via standardized Cronbach's alpha). From our sample of 420, factor analysis indicated a two‐factor model (as suggested by Kaiser's rule), explained 22% of the variation in responses to the assessment items. We recommend removing item 7 as it does not contribute to the internal consistency of the tool. Cronbach's alpha after removing 7 is 0.65, indicating satisfactory reliability. To our knowledge, this is the first validated tool for measuring nurse knowledge about continence and mobility that addresses both a range of lower urinary tract symptoms and elements of mobility in older adults.

Complete Genome Sequence and Probiotic Characterization of Lactobacillus delbrueckii subsp. Indicus DC-3 Isolated from Traditional Indigenous Fermented Milk.

In this study, Lactobacillus delbrueckii subsp. indicus DC-3 was isolated from Indian traditional indigenous fermented milk Dahi and identified using whole genome sequencing. The safety of the strain was evaluated using genetic and phenotypic analyses, such as the presence of virulence factors, mobile and insertion elements, plasmids, antibiotic resistance, etc. Besides this, the strain was comprehensively investigated for in vitro probiotic traits, biofilm formation, antibacterials, and exopolysaccharide (EPS) production. In results, the strain showed a single circular chromosome (3,145,837bp) with a GC content of 56.73%, a higher number of accessory and unique genes, an open pan-genome, and the absence of mobile and insertion elements, plasmids, virulence, and transmissible antibiotic resistance genes. The strain was capable of surviving in gastric juice (83% viability at 3h) and intestinal juice (71% viability at 6h) and showed 42.5% autoaggregation, adhesion to mucin, 8.7% adhesion to xylene, and 8.3% adhesion to Caco-2 cells. The γ-hemolytic nature, usual antibiotic susceptibility profile, and negative results for mucin and gelatin degradation ensure the safety of the strain. The strain produced 10.5g/L of D-lactic acid and hydrogen peroxide, capable of inhibiting and co-aggregating Escherichia coli MTCC 1687, Proteus mirabilis MTCC 425, and Candida albicans ATCC 14,053. In addition, the strain showed 90mg/L EPS (48h) and biofilm formation. In conclusion, this study demonstrates that L. delbrueckii subsp. indicus DC-3 is unique and different than previously reported L. delbrueckii subsp. indicus strains and is a safe potential probiotic candidate.

Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance.

The acquisition of multidrug resistance by pathogenic bacteria is a potentially incipient pandemic. Horizontal transfer of DNA from mobile integrative conjugative elements (ICEs) provides an important way to introduce genes that confer antibiotic (Ab)-resistance in recipient cells. Sizable numbers of SXT/R391 ICEs encode a hypermutagenic Rum DNA polymerase (Rum pol), which has significant homology with Escherichia coli pol V. Here, we show that even under tight transcriptional and post-transcriptional regulation imposed by host bacteria and the R391 ICE itself, Rum pol rapidly accelerates development of multidrug resistance (CIPR, RifR, AmpR) in E. coli in response to SOS-inducing Ab and non-Ab external stressors bleomycin (BLM), ciprofloxacin (CIP) and UV radiation. The impact of Rum pol on the rate of acquisition of drug resistance appears to surpass potential contributions from other cellular processes. We have shown that RecA protein plays a central role in controlling the ability of Rum pol to accelerate antibiotic resistance. A single amino acid substitution in RecA, M197D, acts as a 'Master Regulator' that effectively eliminates the Rum pol-induced Ab resistance. We suggest that Rum pol should be considered as one of the major factors driving development of de novo Ab resistance in pathogens carrying SXT/R391 ICEs.

A unified framework to analyze transposable element insertion polymorphisms using graph genomes

Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.

Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements.

Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the genera Limosilactobacillus, Pseudosulfitobacter or Staphylococcus. Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.

The Distribution of Acme Gene and MRSA Related Virulence Genes in Staphylococcus Aureus Strains from Nigeria

Background: Arginine Catabolic Mobile Element (acme) is a Staphylococcal genomic island that enhances fitness and ability of bacteria cells to colonize on mucous membrane and skin. It is stongly associated with the epidemic and virulent S. aureus USA 300. This study determined the distribution of acme and Methicillin Resistant Staphyllococus Aureus (MRSA)-related genes in S. aureus isolated from patients in five tertiary hospitals in Nigeria. Methods: A total of 51 S. aureus isolates from the clinical specimens submitted to laboratories in five tertiary hospitals in Nigeria were used in this study. Phenotypic and genotypic identifications of the S. aureus were performed. Antibiotic Susceptibility Test (AST) was carried out to determine the susceptibility pattern of the isolates using various antibiotics discs. Minimum Inhibitory Concentration (MIC) was used to determine the degree of resistance of the isolates to methicillin and vancomycin. Polymerase Chain Reaction (PCR) was used to screen for the presence of mecA, acme sae, sarA, PVL, α-psm and norB genes using specific primers. The SCCmec type was determined for all the MRSA isolates using polymerase chain reaction. Results: The MIC for mecA negative strains was ≤4 µg/ml, while the MIC for mecA positive was 8 µg/ml. mecA gene was detected in 35 (68.6%) of 51 strains of S. aureus. The prevalence of sae, sarA, mecA, acme, PVL, α-psm and norB gene were estimated to be 70.6%, 68.6%, 68.6%, 29.4%, 5.1%, 39.2% and 33.3% respectively. There was an association between the distribution of mecA+ and norB+ strains (P = 0.034) and the hospitals (P =0.008) where the isolates were obtained from, whereas there was no association between acme positive strains and the hospitals (P = 0.669) from which the isolates were obtained from. Also, there was no association between mecA, norB, acme with the sex, age and hospital admission status (P>0.05). Furthermore, there was an association between PVL gene and the two geographical regions (South-Western and North-Western, Nigeria) (χ2 = 7.77; p < 0.05). The SCCmec typing showed that 21 (60.0%) out of the 35 MRSA used in this study carried the SCCmec type elements such as type I, II, III and VIII which were all the characteristic of HA-MRSA while the remaining 14 (40%) carried the SCCmec type elements such as type IV, V, VI and VII which were all characteristic of CA-MRSA. Thus the overall prevalence of HA-MRSA and CA-MRSA in this study was 60.0% and 40.0%, respectively. Conclusion: The prevalence of acme and α-psm genes in S. aureus are high and this is a novel discovery in Nigeria which has opened a new era in the transmission and fitness of circulating MRSA in causing infection in the community at large. The study concluded that there is high prevalence of HA-MRSA in South-Western, Nigeria and high prevalence of CA-MRSA in the North-Western, Nigeria.

RAD51 Paralogs and RAD51 Paralog Complexes BCDX2 and CX3 Interact with BRCA2.

Homologous recombination (HR) is an important mechanism for repairing DNA double-strand breaks (DSBs) and preserving genome integrity. Pathogenic mutations in the HR proteins BRCA2 and the RAD51 paralogs predispose individuals to breast, ovarian, pancreatic, and prostate cancer. The RAD51 paralogs: RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3 form two complexes RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2) and RAD51C-XRCC3 (CX3). Similar to BRCA2, loss of RAD51 paralog functions in mammalian cells lead to chromosomal abnormalities, growth defects, disrupted RAD51 foci formation, and PARP inhibitor sensitivity. Despite significant effort over the past three decades, the specific molecular functions of the human RAD51 paralogs have remained elusive due to technical challenges such as low protein expression in human cell lines and instability of the purified proteins. Recent studies have determined the molecular structures of the BCDX2 and CX3 complexes dramatically enhancing our understanding of these challenging proteins. Using multiple approaches, we demonstrate that the RAD51 paralogs interact with BRCA2 at two distinct interaction hubs located in the BRC repeats and the DNA binding domain. We confirm, using a yeast 3-hybrid approach, that human RAD51 paralogs interact directly with BRC repeats one and two (BRC1-2) of BRCA2. Because of the dynamic nature of the RAD51B C-terminal domain (CTD), identified in the recently solved cryo-EM structures, we focused on elucidating the interaction with RAD51B. We determined that BRCA2 interacts with the CTD of RAD51B and not the N-terminal domain (NTD) that is involved in stacking interactions with RAD51C and RAD51D. Furthermore, the interaction with RAD51B is dependent upon an FxxA motif located on a surface exposed region of the CTD. Our study has identified novel interactions between the RAD51 paralogs and BRCA2 and further demonstrated that a previously unrecognized FxxA motif located within a mobile element of RAD51B is critical for the interaction.

Surface exclusion of IncC conjugative plasmids and their relatives.

The phenomenon of exclusion allows conjugative plasmids to selectively impede the entry of identical or related elements into their host cell to prevent the resulting instability. Entry exclusion blocks DNA translocation into the recipient cell, whereas surface exclusion destabilizes the mating pair. IncC conjugative plasmids largely contribute to the dissemination of antibiotic-resistance genes in Gammaproteobacteria. IncC plasmids are known to exert exclusion against their relatives, including IncC and IncA plasmids, yet the entry exclusion factor eexC alone does not account for the totality of the exclusion phenotype. In this study, a transposon-directed insertion sequencing approach identified sfx as necessary and sufficient for the remaining exclusion phenotype. Sfx is an exclusion factor unrelated to the ones described to date. A cell fractionation assay localized Sfx in the outer membrane. Reverse transcription PCR and beta-galactosidase experiments showed that sfx is expressed constitutively at a higher level than eexC. A search in Gammaproteobacteria genomes identified Sfx homologs encoded by IncC, IncA and related, untyped conjugative plasmids and an uncharacterized family of integrative and mobilizable elements that likely rely on IncC plasmids for their mobility. Mating assays demonstrated that sfx is not required in the donor for exclusion, ruling out Sfx as the exclusion target. Instead, complementation assays revealed that the putative adhesin TraN in the donor mediates the specificity of surface exclusion. Mating assays with TraN homologs from related untyped plasmids from Aeromonas spp. and Photobacterium damselae identified two surface exclusion groups, with each Sfx being specific of TraN homologs from the same group. Together, these results allow us to better understand the apparent incompatibility between IncA and IncC plasmids and to propose a mechanistic model for surface exclusion mediated by Sfx in IncC plasmids and related elements, with implications for the rampant dissemination of antibiotic resistance.