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PloS One 2021Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our...
Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins-Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.
Topics: Anaerobiosis; Bioreactors; Dairying; Drug Resistance, Microbial; Genes, Bacterial; Interspersed Repetitive Sequences; Least-Squares Analysis; Manure; Nonlinear Dynamics; RNA, Ribosomal, 16S
PubMed: 34432793
DOI: 10.1371/journal.pone.0254836 -
FEMS Microbiology Reviews May 2015CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key... (Review)
Review
CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences acquired from invading mobile genomes is transcribed as a precursor crRNA (pre-crRNA) molecule. This pre-crRNA undergoes one or two maturation steps to generate the mature crRNAs that guide CRISPR-associated (Cas) protein(s) to cognate invading genomes for their destruction. Different types of CRISPR-Cas systems have evolved distinct crRNA biogenesis pathways that implicate highly sophisticated processing mechanisms. In Types I and III CRISPR-Cas systems, a specific endoribonuclease of the Cas6 family, either standalone or in a complex with other Cas proteins, cleaves the pre-crRNA within the repeat regions. In Type II systems, the trans-acting small RNA (tracrRNA) base pairs with each repeat of the pre-crRNA to form a dual-RNA that is cleaved by the housekeeping RNase III in the presence of the protein Cas9. In this review, we present a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the three CRISPR-Cas types.
Topics: Archaea; Bacteria; Clustered Regularly Interspaced Short Palindromic Repeats; Interspersed Repetitive Sequences; RNA; Ribonucleases
PubMed: 25994611
DOI: 10.1093/femsre/fuv023 -
Current Opinion in Microbiology Oct 2005Amoebozoa represent one of the earliest branches from the last common ancestor of all eukaryotes and contain some of the most dangerous human pathogens. Two amoebozoan... (Comparative Study)
Comparative Study Review
Amoebozoa represent one of the earliest branches from the last common ancestor of all eukaryotes and contain some of the most dangerous human pathogens. Two amoebozoan genomes -- from the model organism Dictyostelium discoideum and the human pathogen Entamoeba histolytica -- have been published this year. Owing to their high A+T content, both genomes were difficult to sequence. In addition to nine amoebozoan expressed sequence tag projects, efforts are underway for comparative sequencing of four additional Entamoeba species. The completed genome sequences of D. discoideum and E. histolytica revealed unusual telomere structures, a high percentage of repetitive elements and a remarkably high gene content that is close to the one of Drosophila melanogaster. Finally, both organisms are brilliant examples of the influence of the lifestyle of an organism on its genome.
Topics: Adaptation, Biological; Animals; Dictyostelium; Entamoeba histolytica; Gene Transfer, Horizontal; Genes, Protozoan; Genome, Protozoan; Genomics; Humans; Interspersed Repetitive Sequences; Telomere
PubMed: 16125444
DOI: 10.1016/j.mib.2005.08.009 -
PLoS Genetics Feb 2022Most bacterial genomes contain horizontally acquired and transmissible mobile genetic elements, including temperate bacteriophages and integrative and conjugative...
Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage.
Most bacterial genomes contain horizontally acquired and transmissible mobile genetic elements, including temperate bacteriophages and integrative and conjugative elements. Little is known about how these elements interact and co-evolved as parts of their host genomes. In many cases, it is not known what advantages, if any, these elements provide to their bacterial hosts. Most strains of Bacillus subtilis contain the temperate phage SPß and the integrative and conjugative element ICEBs1. Here we show that the presence of ICEBs1 in cells protects populations of B. subtilis from predation by SPß, likely providing selective pressure for the maintenance of ICEBs1 in B. subtilis. A single gene in ICEBs1 (yddK, now called spbK for SPß killing) was both necessary and sufficient for this protection. spbK inhibited production of SPß, during both activation of a lysogen and following de novo infection. We found that expression spbK, together with the SPß gene yonE constitutes an abortive infection system that leads to cell death. spbK encodes a TIR (Toll-interleukin-1 receptor)-domain protein with similarity to some plant antiviral proteins and animal innate immune signaling proteins. We postulate that many uncharacterized cargo genes in ICEs may confer selective advantage to cells by protecting against other mobile elements.
Topics: Animals; Bacteriophages; Conjugation, Genetic; DNA, Bacterial; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Predatory Behavior
PubMed: 35157704
DOI: 10.1371/journal.pgen.1010065 -
Plasmid Sep 2018Multi-antibiotic resistant (MAR) bacteria cost billions in medical care and tens of thousands of lives annually but perennial calls to limit agricultural and other... (Review)
Review
Multi-antibiotic resistant (MAR) bacteria cost billions in medical care and tens of thousands of lives annually but perennial calls to limit agricultural and other misuse of antibiotics and to fund antibiotic discovery have not slowed this MAR deluge. Since mobile genetic elements (MGEs) stitch single antibiotic resistance genes into clinically significant MAR arrays, it is high time to focus on how MGEs generate MAR and how disabling them could ameliorate the MAR problem. However, to consider only antibiotics as the drivers of MAR is to miss the significant impact of exposure to non-antibiotic toxic chemicals, specifically metals, on the persistence and spread of MAR. Toxic metals were among the earliest discovered targets of plasmid-encoded resistance genes. Recent genomic epidemiology clearly demonstrated the co-prevalence of metal resistances and antibiotic multi-resistance, uniquely in humans and domestic animals. Metal resistances exploit the same, ancient "transportation infrastructure" of plasmids, transposons, and integrons that spread the antibiotic resistance genes and will continue to do so even if all antibiotic misuse were stopped today and new antibiotics were flowing from the pipeline monthly. In a key experiment with primates, continuous oral exposure to mercury (Hg) released from widely used dental amalgam fillings co-selected for MAR bacteria in the oral and fecal commensal microbiomes and, most importantly, when amalgams were replaced with non-metal fillings, MAR bacteria declined dramatically. Could that also be happening on the larger public health scale as use of amalgam restorations is curtailed or banned in many countries? This commentary covers salient past and recent findings of key metal-antibiotic resistance associations and proposes that the shift from phenotyping to genotyping in surveillance of resistance loci will allow a test of whether declining exposure to this leading source of Hg is accompanied by a decline in MAR compared to countries where amalgam is still used. If this hypothesis is correct, the limited success of antibiotic stewardship practices may be because MAR is also being driven by continuous, daily exposure to Hg, a non-antibiotic toxicant widely used in humans.
Topics: Antimicrobial Stewardship; Bacteria; Dental Amalgam; Drug Resistance, Multiple, Bacterial; Humans; Interspersed Repetitive Sequences; Mercury; Metals; Plasmids
PubMed: 30193909
DOI: 10.1016/j.plasmid.2018.08.003 -
Microbiology Spectrum Dec 2014Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely... (Review)
Review
Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.
Topics: Bacteria; Drug Resistance, Bacterial; Evolution, Molecular; Gene Transfer, Horizontal; Genetic Variation; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 26104437
DOI: 10.1128/microbiolspec.MDNA3-0008-2014 -
Clinical Microbiology and Infection :... Jul 2012Tetracycline resistance genes are common in the human oral cavity. However, a complete understanding of tetracycline resistance and the vectors responsible for spread of... (Review)
Review
Tetracycline resistance genes are common in the human oral cavity. However, a complete understanding of tetracycline resistance and the vectors responsible for spread of resistance requires that we understand the contribution of organisms that cannot be cultivated in the laboratory. To do this, metagenomic approaches have been applied and this has allowed the isolation of novel tetracycline resistance genes and mobile genetic elements.
Topics: Genes, Bacterial; Humans; Interspersed Repetitive Sequences; Metagenome; Mouth; Tetracycline Resistance
PubMed: 22647052
DOI: 10.1111/j.1469-0691.2012.03858.x -
Briefings in Functional Genomics &... Mar 2006Recently a number of groups have introduced computational methods for the detection of A-to-I RNA editing sites. These approaches have resulted in finding thousands of... (Comparative Study)
Comparative Study Review
Recently a number of groups have introduced computational methods for the detection of A-to-I RNA editing sites. These approaches have resulted in finding thousands of editing sites within the genomic repeats, as well as a few novel genetic recoding sites. We review these recent advancements, emphasizing the principles underlying the various methods used. Possible directions for extending these methods are discussed.
Topics: Algorithms; Animals; Computational Biology; Humans; Interspersed Repetitive Sequences; RNA Editing; Sequence Analysis, RNA
PubMed: 16769677
DOI: 10.1093/bfgp/ell014 -
Current Biology : CB Jan 2004The discovery of Sfi1p as a novel binding partner for the Ca2+-binding protein centrin has provided new insight into the dynamic behavior of centrosomes. Sfi1 binds to... (Review)
Review
The discovery of Sfi1p as a novel binding partner for the Ca2+-binding protein centrin has provided new insight into the dynamic behavior of centrosomes. Sfi1 binds to multiple centrin molecules along a series of internal repeats, and the complex forms Ca2+-sensitive contractile fibers that function to reorient centrioles and alter centrosome structure.
Topics: Calcium; Calcium-Binding Proteins; Cell Cycle Proteins; Centrosome; Chromosomal Proteins, Non-Histone; Contractile Proteins; Eukaryota; Interspersed Repetitive Sequences; Models, Biological; Repressor Proteins; Saccharomyces cerevisiae Proteins; Yeasts
PubMed: 14711432
DOI: 10.1016/j.cub.2003.12.019 -
Nature Reviews. Genetics Aug 2001'Selfish genetic elements', such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are common features of eukaryotes.... (Review)
Review
'Selfish genetic elements', such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are common features of eukaryotes. However, their importance in the evolution of eukaryotic genomes is still controversial. In this review, we discuss these diverse elements and their potential importance in the evolution of genetic systems, adaptation, and the extinction and birth of species.
Topics: Animals; Chromosome Segregation; DNA Replication; DNA Restriction Enzymes; Eukaryotic Cells; Evolution, Molecular; Humans; Interspersed Repetitive Sequences
PubMed: 11483984
DOI: 10.1038/35084545