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Annual Review of Virology Nov 2015The phage-inducible chromosomal islands (PICIs) are a family of highly mobile genetic elements that contribute substantively to horizontal gene transfer, host... (Review)
Review
The phage-inducible chromosomal islands (PICIs) are a family of highly mobile genetic elements that contribute substantively to horizontal gene transfer, host adaptation, and virulence. Initially identified in Staphylococcus aureus, these elements are now thought to occur widely in gram-positive bacteria. They are molecular parasites that exploit certain temperate phages as helpers, using a variety of elegant strategies to manipulate the phage life cycle and promote their own spread, both intra- and intergenerically. At the same time, these PICI-encoded mechanisms severely interfere with helper phage reproduction, thereby enhancing survival of the bacterial population. In this review we discuss the genetics and the life cycle of these elements, with special emphasis on how they interact and interfere with the helper phage machinery for their own benefit. We also analyze the role that these elements play in driving bacterial and viral evolution.
Topics: Bacteria; Bacteriophages; Genomic Islands; Interspersed Repetitive Sequences
PubMed: 26958912
DOI: 10.1146/annurev-virology-031413-085446 -
Parasitology Feb 2008Draft genome sequences for Schistosoma mansoni and Schistosoma japonicum are now available. However, the identity and importance of most schistosome genes have yet to be... (Review)
Review
Draft genome sequences for Schistosoma mansoni and Schistosoma japonicum are now available. However, the identity and importance of most schistosome genes have yet to be determined. Recently, progress has been made towards the genetic manipulation and transgenesis of schistosomes. Both loss-of-function and gain-of-function approaches appear to be feasible in schistosomes based on findings described in the past 5 years. This review focuses on reports of schistosome transgenesis, specifically those dealing with the transformation of schistosomes with exogenous mobile genetic elements and/or their endogenous relatives for the genetic manipulation of schistosomes. Transgenesis mediated by mobile genetic elements offers a potentially tractable route to introduce foreign genes to schistosomes, a means to determine the importance of schistosome genes, including those that could be targeted in novel interventions and the potential to undertake large-scale forward genetics by insertional mutagenesis.
Topics: Animals; Animals, Genetically Modified; DNA Transposable Elements; Genetic Engineering; Interspersed Repetitive Sequences; Retroviridae; Schistosoma; Transduction, Genetic
PubMed: 17991304
DOI: 10.1017/S0031182007003824 -
PLoS Genetics Jun 2017One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal...
One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element.
Topics: Chromosome Inversion; Evolution, Molecular; Genome, Archaeal; Integrases; Interspersed Repetitive Sequences; Plasmids; Recombination, Genetic; Thermococcales
PubMed: 28628615
DOI: 10.1371/journal.pgen.1006847 -
Microbiology Spectrum Jan 2018Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been...
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Drug Resistance, Multiple, Bacterial; Evolution, Molecular; Gene Transfer, Horizontal; Genetic Speciation; Genome, Bacterial; Interspersed Repetitive Sequences; Virulence
PubMed: 29350130
DOI: 10.1128/microbiolspec.MTBP-0006-2016 -
Applied and Environmental Microbiology Jan 2019Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene...
Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifying sp. strains and searched for mobile genetic elements that contain denitrification genes. All sp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase gene was located on large replicons (549 to 941 kbp). Genome sequencing showed that strains that had similar sequences also shared similar gene arrangements, especially between the TSH58, Sp7, and Sp245 strains. In addition to the high similarity between gene clusters among the three strains, a composite transposon structure was identified in the genome of strain TSH58, which contains the gene cluster and the novel IS family insertion sequences (IS and IS). The gene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing the gene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely related sp. denitrifiers. The evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses of sp. denitrifiers, we identified denitrification genes, including and , located on a mobile genetic element in the genome of sp. strain TSH58. The was actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.
Topics: Azospirillum; DNA Transposable Elements; DNA, Bacterial; Denitrification; Gene Transfer, Horizontal; Genes, Bacterial; Interspersed Repetitive Sequences; Nitrite Reductases; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S
PubMed: 30413471
DOI: 10.1128/AEM.02474-18 -
Research in Microbiology May 2015Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes... (Review)
Review
Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes transfer of antibiotic resistance and other factors that allow the organism to survive challenging environments, modulation of toxin gene expression, transfer of the toxin genes themselves and the conversion of non-toxigenic strains to toxin producers. Mobile genetic elements have also been adapted by investigators to probe the biology of the organism and the various ways in which these have been used are reviewed.
Topics: Adaptation, Biological; Bacterial Toxins; Clostridioides difficile; Gene Transfer, Horizontal; Genome, Bacterial; Interspersed Repetitive Sequences
PubMed: 25576774
DOI: 10.1016/j.resmic.2014.12.005 -
International Journal of Medical... Apr 2004The growing knowledge of genetic diversity and whole genome organization in bacteria shows that pathogenicity islands (PAIs) represent a subtype of a more general... (Review)
Review
The growing knowledge of genetic diversity and whole genome organization in bacteria shows that pathogenicity islands (PAIs) represent a subtype of a more general genetic element, termed genomic island (GEI), which is widespread among pathogenic and non-pathogenic microbes. These findings mirror the importance of horizontal gene transfer, genome reduction and recombination events as fundamental mechanisms involved in evolution of bacterial variants. GEIs are part of the flexible gene pool and carry selfish genes, but also determinants which may be beneficial under certain conditions thus increasing bacterial fitness and consequently their survival or transmission. In this review, we focus on the role of mobile genetic elements that may also contain toxin-encoding genes for genome variability and evolution of bacteria.
Topics: Bacterial Toxins; Enterobacteriaceae; Enterobacteriaceae Infections; Gene Transfer, Horizontal; Genetic Variation; Genome, Bacterial; Interspersed Repetitive Sequences; Repetitive Sequences, Nucleic Acid; Virulence
PubMed: 15149018
DOI: 10.1078/1438-4221-00290 -
Microbes and Infection May 2016Pathogenicity islands (PAIs) are regions of the chromosome of pathogenic bacteria that harbor virulence genes, which were probably acquired by lateral gene transfer.... (Review)
Review
Pathogenicity islands (PAIs) are regions of the chromosome of pathogenic bacteria that harbor virulence genes, which were probably acquired by lateral gene transfer. Several PAIs can excise from the bacterial chromosome by site-specific recombination and in this review have been denominated "excisable PAIs". Here, the characteristic of some of the excisable PAIs from Salmonella enterica and the possible role and impact of the excision process on bacterial virulence is discussed. Understanding the role of PAI excision could provide important insights relative to the emergence, evolution and virulence of pathogenic enterobacteria.
Topics: Animals; Disease Models, Animal; Genomic Islands; Humans; Interspersed Repetitive Sequences; Recombination, Genetic; Salmonella Infections; Salmonella enterica; Virulence
PubMed: 26939722
DOI: 10.1016/j.micinf.2016.02.001 -
Microbiology Spectrum Dec 2014Two related tyrosine recombinases, XerC and XerD, are encoded in the genome of most bacteria where they serve to resolve dimers of circular chromosomes by the addition... (Review)
Review
Two related tyrosine recombinases, XerC and XerD, are encoded in the genome of most bacteria where they serve to resolve dimers of circular chromosomes by the addition of a crossover at a specific site, dif. From a structural and biochemical point of view they belong to the Cre resolvase family of tyrosine recombinases. Correspondingly, they are exploited for the resolution of multimers of numerous plasmids. In addition, they are exploited by mobile DNA elements to integrate into the genome of their host. Exploitation of Xer is likely to be advantageous to mobile elements because the conservation of the Xer recombinases and of the sequence of their chromosomal target should permit a quite easy extension of their host range. However, it requires means to overcome the cellular mechanisms that normally restrict recombination to dif sites harbored by a chromosome dimer and, in the case of integrative mobile elements, to convert dedicated tyrosine resolvases into integrases.
Topics: Integrases; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 26104463
DOI: 10.1128/microbiolspec.MDNA3-0056-2014 -
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