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Journal of Molecular Biology Apr 2023Mobile genetic elements (MGEs) such as bacteriophages and their host prokaryotes are trapped in an eternal battle against each other. To cope with foreign infection,... (Review)
Review
Mobile genetic elements (MGEs) such as bacteriophages and their host prokaryotes are trapped in an eternal battle against each other. To cope with foreign infection, bacteria and archaea have evolved multiple immune strategies, out of which CRISPR-Cas system is up to now the only discovered adaptive system in prokaryotes. Despite the fact that CRISPR-Cas system provides powerful and delicate protection against MGEs, MGEs have also evolved anti-CRISPR proteins (Acrs) to counteract the CRISPR-Cas immune defenses. To date, 46 families of Acrs targeting type I CRISPR-Cas system have been characterized, out of which structure information of 21 families have provided insights on their inhibition strategies. Here, we review the non-canonical inhibition strategies adopted by Acrs targeting type I CRISPR-Cas systems based on their structure information by incorporating the most recent advances in this field, and discuss our current understanding and future perspectives. The delicate interplay between type I CRISPR-Cas systems and their Acrs provides us with important insights into the ongoing fierce arms race between prokaryotic hosts and their predators.
Topics: Archaea; Bacteria; Bacteriophages; CRISPR-Cas Systems; Evolution, Molecular; Interspersed Repetitive Sequences; Viral Proteins; Protein Conformation
PubMed: 36754343
DOI: 10.1016/j.jmb.2023.167996 -
Journal of Contaminant Hydrology May 2022The fate and removal efficiency of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in livestock wastewater by microbial fuel cell (MFC) was...
The fate and removal efficiency of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in livestock wastewater by microbial fuel cell (MFC) was evaluated by High-throughput quantitative PCR. The results showed that 137 ARGs and 9 MGEs were detected in untreated livestock wastewater. The ARG number of macrolide-lincosamide-streptogramin group B (MLSB), tetracycline and sulfonamide were relatively higher. Throughout the treatment process, the number and abundance of ARGs and MGEs significantly decreased. The relative abundance of tetracycline, sulfonamide and chloramphenicol resistance genes showed the most obvious decreasing trend, and the relative abundance of MGEs decreased by 75% (from 0.012 copies/16S rRNA copies to 0.003 copies/16S rRNA copies). However, the absolute abundance of beta-lactamase resistance genes slightly increased. The operation process of MFC produces selective pressure on microorganisms, and Actinobacteria were predominant and had the ability to decompose antibiotics. The COD removal rate and TN removal rate of livestock wastewater were 67.81% and 62.09%, and the maximum power density and coulomb efficiency (CE) reached 11.49% and 38.40% respectively. This study demonstrated that although the removal of COD and TN by MFC was limited, MFC was quite effective in reducing the risk of antibiotic toxicity and horizontal gene transfer.
Topics: Animals; Anti-Bacterial Agents; Bioelectric Energy Sources; Drug Resistance, Microbial; Genes, Bacterial; Interspersed Repetitive Sequences; Livestock; RNA, Ribosomal, 16S; Sulfonamides; Tetracycline; Wastewater
PubMed: 35247696
DOI: 10.1016/j.jconhyd.2022.103981 -
The Brazilian Journal of Infectious... 2020Carbapenem resistance in members of order Enterobacterales is a growing public health problem causing high mortality in developing and industrialized countries. Its... (Review)
Review
INTRODUCTION
Carbapenem resistance in members of order Enterobacterales is a growing public health problem causing high mortality in developing and industrialized countries. Its emergence and rapid propagation worldwide was due to both intercontinental spread of pandemic strains and horizontal dissemination via mobile genetic elements (MGE) such as plasmids and transposons.
OBJECTIVE
To describe MGE carrying carbapenem resistance genes in Enterobacterales which have been reported in South America.
SEARCH STRATEGY AND SELECTION CRITERIA
A search of the literature in English or Spanish published until 2019 in PubMed, Google Scholar, LILACS and SciELO databases was performed for studies of MGE in Enterobacterales reported in South American countries.
RESULTS
Seven South American countries reported MGE related to carbapenemases. Carbapenemase-producing Klebsiella pneumoniae belonging to clonal complex 258 were the most prevalent pathogens reported; others carbapenemase-producing Enterobacterales such as Escherichia coli, Serratia marcescens, and Providencia rettgeri also have been reported. The MGE implicated in the spread of the most prevalent carbapenemase genes are Tn4401 and non-Tn4401 elements for bla and ISAba125 for bla, located in different plasmid incompatibility groups, i.e. L/M, A/C, FII and bacterial clones.
CONCLUSION
This review indicates that, like in other parts of the world, the most commonly reported carbapenemases in Enterobacterales from South America are being disseminated through clones, plasmids, and transposons which have been previously reported in other parts of the world.
Topics: Bacterial Proteins; Enterobacteriaceae; Interspersed Repetitive Sequences; Klebsiella pneumoniae; Plasmids; South America; beta-Lactamases
PubMed: 32325019
DOI: 10.1016/j.bjid.2020.03.002 -
Genome Biology Jul 2020Mobile elements are a major source of structural variants in the human genome, and some mobile elements can regulate gene expression and transcript splicing. However,...
BACKGROUND
Mobile elements are a major source of structural variants in the human genome, and some mobile elements can regulate gene expression and transcript splicing. However, the impact of polymorphic mobile element insertions (pMEIs) on gene expression and splicing in diverse human tissues has not been thoroughly studied. The multi-tissue gene expression and whole genome sequencing data generated by the Genotype-Tissue Expression (GTEx) project provide a great opportunity to systematically evaluate the role of pMEIs in regulating gene expression in human tissues.
RESULTS
Using the GTEx whole genome sequencing data, we identify 20,545 high-quality pMEIs from 639 individuals. Coupling pMEI genotypes with gene expression profiles, we identify pMEI-associated expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) in 48 tissues. Using joint analyses of pMEIs and other genomic variants, pMEIs are predicted to be the potential causal variant for 3522 eQTLs and 3717 sQTLs. The pMEI-associated eQTLs and sQTLs show a high level of tissue specificity, and these pMEIs are enriched in the proximity of affected genes and in regulatory elements. Using reporter assays, we confirm that several pMEIs associated with eQTLs and sQTLs can alter gene expression levels and isoform proportions, respectively.
CONCLUSION
Overall, our study shows that pMEIs are associated with thousands of gene expression and splicing variations, indicating that pMEIs could have a significant role in regulating tissue-specific gene expression and transcript splicing. Detailed mechanisms for the role of pMEIs in gene regulation in different tissues will be an important direction for future studies.
Topics: Alternative Splicing; Datasets as Topic; Gene Expression; Humans; Interspersed Repetitive Sequences; Quantitative Trait Loci
PubMed: 32718348
DOI: 10.1186/s13059-020-02101-4 -
Microbial Drug Resistance (Larchmont,... Aug 2022The study describes the first isolation of multidrug-resistant (MDR) ST16, ST131 (Esc), and subsp. steigerwaltii ST93 ( complex [ECC]) in Sri Lanka. Eight MDR strains...
Antimicrobial Resistance Genes, Virulence Genes, and Associated Mobile Genetic Elements of Eight Multidrug-Resistant Isolated from Hospital-Acquired Urinary Tract Infections in Sri Lanka.
The study describes the first isolation of multidrug-resistant (MDR) ST16, ST131 (Esc), and subsp. steigerwaltii ST93 ( complex [ECC]) in Sri Lanka. Eight MDR strains of uropathogenic Enterobacterales isolated from hospital acquired urinary tract infections (UTIs) were analyzed using genomic sequencing and comparative genomics. Isolates carried multiple carbapenemase, AmpC, and ESBL (extended-spectrum β-lactamase) genes. ECC manifested both and . The strains harbored fimbrial genes that facilitate pathogenesis of UTI. Several extraintestinal pathogenic associated virulence genes were identified in Esc. The efflux pump gene, , and the T6SS gene cluster were detected in ECC. Many antimicrobial resistance (AMR) and virulence genes were identified associated with mobile genetic elements. ISEcp1 flanked upstream of . The carbapenemase genes were carried on ColKP3 plasmids and were associated with ISEcp1. In Esc, the AMR gene and virulence gene were found on an IncF plasmid replicon. In the AMR genes and tetB present on IncR plasmid replicons and were associated with the insertion sequence IS6100. In Kp5, and coexisted and were flanked by ISEcl. AMR gene clusters, conferring resistance to multiple antimicrobial classes, flanked by mobile elements were identified in seven isolates.
Topics: Anti-Bacterial Agents; Cross Infection; Drug Resistance, Multiple, Bacterial; Enterobacter; Escherichia coli; Humans; Interspersed Repetitive Sequences; Klebsiella pneumoniae; Microbial Sensitivity Tests; Sri Lanka; Urinary Tract Infections; Virulence; beta-Lactamases
PubMed: 35972764
DOI: 10.1089/mdr.2022.0003 -
Journal of Hazardous Materials Jun 2024Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and...
Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.
Topics: Rivers; Microplastics; Anti-Bacterial Agents; Water Pollutants, Chemical; Bacteria; Water Microbiology; Interspersed Repetitive Sequences; Genes, Bacterial; Drug Resistance, Bacterial; Disinfectants; Microbiota; Drug Resistance, Microbial
PubMed: 38678707
DOI: 10.1016/j.jhazmat.2024.134353 -
The Journal of Eukaryotic Microbiology Sep 2022Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While... (Review)
Review
Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered "junk" DNA (i.e., deleterious or at best neutral), more recent studies reveal the potential adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single-celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co-opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer (LGT) from bacteria, which introduces genetic diversity and, in several cases, may drive ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic materials and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non-Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance.
Topics: Ciliophora; DNA Transposable Elements; Epigenesis, Genetic; Evolution, Molecular; Genome; Humans; Interspersed Repetitive Sequences
PubMed: 35100457
DOI: 10.1111/jeu.12891 -
Nucleic Acids Research Jan 2022Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the...
Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).
Topics: Animals; Base Sequence; DNA Transposable Elements; Databases, Nucleic Acid; Genome; Humans; Internet; Plants; Repetitive Sequences, Nucleic Acid; Retroelements; Sequence Analysis, DNA; User-Computer Interface
PubMed: 34850956
DOI: 10.1093/nar/gkab1089 -
PloS One 2020Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant...
Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32-3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5'-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.
Topics: Animals; Base Sequence; CHO Cells; Cell Line, Tumor; Cricetinae; Cricetulus; Gene Expression Regulation; Gene Silencing; Genome, Human; Green Fluorescent Proteins; Humans; In Situ Hybridization, Fluorescence; Matrix Attachment Regions; Plasmids; Repetitive Sequences, Nucleic Acid; Replication Origin; Retroelements; Transcriptional Activation
PubMed: 32579599
DOI: 10.1371/journal.pone.0235127 -
Microbiology Spectrum Dec 2021Pseudomonas aeruginosa may become multidrug-resistant (MDR) due to multiple inherited and acquired resistance mechanisms. The human gastrointestinal tract is known as a...
Pseudomonas aeruginosa may become multidrug-resistant (MDR) due to multiple inherited and acquired resistance mechanisms. The human gastrointestinal tract is known as a reservoir of P. aeruginosa and its resistance genes. In this study, we collected 76 intestinal carbapenem-resistant P. aeruginosa (CRPA) strains from clinical inpatients admitted to our hospital from 2014 to 2019, together with their medical data. We aim to analyze the clinical risk factors associated with CRPA infection and its molecular features. We found that the prevalence of CRPA in P. aeruginosa strains was 41.3% (95% confidence interval [CI], 34.1 to 48.8%). We also identified four variables associated with intestinal CRPA positivity, prior antibiotic exposure to aminoglycosides or carbapenems, underlying diabetes mellitus, and extraintestinal P. aeruginosa isolation. is the only detected carbapenemase gene, accounting for 21.1% of CRPA strains. The genetic environment showed that the gene was flanked immediately by IS and IS and several other mobile elements further upstream or downstream. Four sequence types (STs) were identified, with ST463 as the dominant sequence type. In conclusion, screening for P. aeruginosa colonization upon hospital admission could reduce the risk of P. aeruginosa infection and spread of CRPA in the hospital. Pseudomonas aeruginosa may become multidrug-resistant (MDR) due to multiple inherited and acquired resistance mechanisms. The human gastrointestinal tract is known as a reservoir of P. aeruginosa and its resistance genes. Risk factor analysis and molecular epidemiology are critical for preventing their potential dissemination. Here, we identified four risk factors associated with intestinal CRPA-prior antibiotic exposure to aminoglycosides or carbapenems, underlying diabetes mellitus, and extraintestinal P. aeruginosa isolation. Further, we found similar genetic environments with several mobile elements surrounding the gene, a carbapenemase gene only detected in intestinal CRPA strains in this study. These findings are of significant public health importance, as the information will facilitate the control of the emergence and spread of CRPA.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Carbapenems; China; Cross Infection; Drug Resistance, Multiple, Bacterial; Gastrointestinal Microbiome; Genome, Bacterial; Humans; Interspersed Repetitive Sequences; Intestines; Microbial Sensitivity Tests; Middle Aged; Molecular Epidemiology; Prevalence; Pseudomonas Infections; Pseudomonas aeruginosa; beta-Lactamases
PubMed: 34817230
DOI: 10.1128/Spectrum.01344-21