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Advances in Microbial Physiology 2014Clostridium difficile infection (CDI) is now recognised as the main cause of healthcare associated diarrhoea. Over the recent years there has been a change in the... (Review)
Review
Clostridium difficile infection (CDI) is now recognised as the main cause of healthcare associated diarrhoea. Over the recent years there has been a change in the epidemiology of CDI with certain related strains dominating infection. These strains have been termed hyper-virulent and have successfully spread across the globe. Many C. difficile strains have had their genomes completely sequenced allowing researchers to build up a very detailed picture of the contribution of horizontal gene transfer to the adaptive potential, through the acquisition of mobile DNA, of this organism. Here, we review and discuss the contribution of mobile genetic elements to the biology of this clinically important pathogen.
Topics: Bacteriophages; Clostridioides difficile; Clostridium Infections; DNA Transposable Elements; Diarrhea; Gene Transfer, Horizontal; Genome, Bacterial; Humans; Interspersed Repetitive Sequences; Introns; Virulence
PubMed: 25476764
DOI: 10.1016/bs.ampbs.2014.08.002 -
Current Opinion in Genetics &... Dec 2015Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of... (Review)
Review
Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.
Topics: DNA, Plant; Evolution, Molecular; Gene Expression Regulation, Plant; Genetic Variation; Genome Size; Genome, Plant; Interspersed Repetitive Sequences; Magnoliopsida; Phylogeny
PubMed: 26605684
DOI: 10.1016/j.gde.2015.10.006 -
Current Opinion in Microbiology Aug 2017Integrative and conjugative elements (ICEs) are nearly ubiquitous in microbial genomes and influence their evolution by providing adaptive functions to their host and by... (Review)
Review
Integrative and conjugative elements (ICEs) are nearly ubiquitous in microbial genomes and influence their evolution by providing adaptive functions to their host and by enhancing genome plasticity and diversification. For a long-time, it has been assumed that by integrating into the chromosome of their host, these self-transmissible elements were passively inherited in subsequent generations. Recent findings point to a much more complex story that includes multiple strategies used by ICEs to leverage maintenance in cell populations such as transient replication, active partition of the excised circular intermediate or disassembly into multiple parts scattered in the chromosome. Here I review these diverse mechanisms of stabilization in the general context of ICEs belonging to diverse families.
Topics: Genomic Instability; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 28482230
DOI: 10.1016/j.mib.2017.03.014 -
Current Genetics Dec 2020Bacteria and other prokaryotes evolve primarily through rapid changes in their gene content by quickly losing and gaining genes whenever an ecological opportunity... (Review)
Review
Bacteria and other prokaryotes evolve primarily through rapid changes in their gene content by quickly losing and gaining genes whenever an ecological opportunity emerges. As gene loss and horizontal gene transfer (HGT) appear to be the most common events across the prokaryotic tree of life, we need to think beyond gradual sequence evolution if we wish to understand the microbial world. Especially genes that reside on mobile genetic elements (MGEs) may spread much more rapidly through a microbial population than genes that reside on the bacterial chromosome. This raises the question: why are some genes associated with MGEs, while others are not? Here, I briefly review a recently proposed class of genes for which we have coined the term "rescuable genes". The fitness effect of carrying these genes is so small, either constantly or on average, that they are prone to be lost from a microbial population. I argue that HGT, even when costly to the individual cells, may play an important role in maintaining these rescuable genes in microbial communities.
Topics: Bacteria; Chromosomes, Bacterial; Evolution, Molecular; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Prokaryotic Cells
PubMed: 32880674
DOI: 10.1007/s00294-020-01104-9 -
Current Opinion in Microbiology Aug 2017Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be... (Review)
Review
Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be selfish parasites, group I and group II introns and inteins can be triggered by environmental cues to splice and/or to mobilize. These cues include stressors such as oxidizing agents, reactive oxygen and nitrogen species, starvation, temperature, osmolarity and DNA damage. Their sensitivity to these stimuli leads to a carefully choreographed dance between the mobile element and its host that is in tune with the cellular environment. This responsiveness to a changing milieu provides strong evidence that these diverse, self-splicing mobile elements have adapted to react to prevailing conditions, to the potential advantage of both the element and its host.
Topics: Adaptation, Biological; Environmental Exposure; Gene Expression Regulation; Inteins; Interspersed Repetitive Sequences; Introns; RNA Splicing
PubMed: 28482231
DOI: 10.1016/j.mib.2017.04.003 -
Biology of Reproduction May 2012Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the... (Review)
Review
Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing.
Topics: Animals; DNA Methylation; DNA Transposable Elements; Eukaryotic Cells; Gene Expression Regulation, Developmental; Germ Cells; Heterochromatin; Interspersed Repetitive Sequences; Male; RNA Interference; RNA, Small Interfering; Repetitive Sequences, Nucleic Acid
PubMed: 22357546
DOI: 10.1095/biolreprod.111.095463 -
Cellular and Molecular Life Sciences :... Sep 2010Bacteria such as Staphylococcus aureus are successful as commensal organisms or pathogens in part because they adapt rapidly to selective pressures imparted by the human... (Review)
Review
Bacteria such as Staphylococcus aureus are successful as commensal organisms or pathogens in part because they adapt rapidly to selective pressures imparted by the human host. Mobile genetic elements (MGEs) play a central role in this adaptation process and are a means to transfer genetic information (DNA) among and within bacterial species. Importantly, MGEs encode putative virulence factors and molecules that confer resistance to antibiotics, including the gene that confers resistance to beta-lactam antibiotics in methicillin-resistant S. aureus (MRSA). Inasmuch as MRSA infections are a significant problem worldwide and continue to emerge in epidemic waves, there has been significant effort to improve diagnostic assays and to develop new antimicrobial agents for treatment of disease. Our understanding of S. aureus MGEs and the molecules they encode has played an important role toward these ends and has provided detailed insight into the evolution of antimicrobial resistance mechanisms and virulence.
Topics: Drug Resistance, Bacterial; Genomic Islands; Humans; Interspersed Repetitive Sequences; Staphylococcus aureus
PubMed: 20668911
DOI: 10.1007/s00018-010-0389-4 -
Mutation Research Mar 2007Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers.... (Review)
Review
Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.
Topics: Alu Elements; Animals; Cattle; Chickens; DNA; Forensic Genetics; Genetic Markers; Humans; Interspersed Repetitive Sequences; Meat; Polymorphism, Genetic; Retroelements; Sequence Analysis, DNA; Sex Characteristics; Short Interspersed Nucleotide Elements; Species Specificity
PubMed: 17161440
DOI: 10.1016/j.mrfmmm.2006.11.019 -
The Journal of Clinical Endocrinology... Feb 2011During meiosis I, the recombination frequency in the pseudoautosomal region on Xp and Yp (PAR1) in males is very high. As a result, mutated genes located within the PAR1...
CONTEXT
During meiosis I, the recombination frequency in the pseudoautosomal region on Xp and Yp (PAR1) in males is very high. As a result, mutated genes located within the PAR1 region can be transferred from the Y-chromosome to the X-chromosome and vice versa.
PATIENTS
Here we describe three families with SHOX abnormalities resulting in Leri-Weill dyschondrosteosis or Langer mesomelic dysplasia.
RESULTS
In about half of the segregations investigated, a transfer of the SHOX abnormality to the alternate sex chromosome was demonstrated.
CONCLUSIONS
Patients with an abnormality of the SHOX gene should receive genetic counseling as to the likelihood that they may transmit the mutation or deletion to a son as well as to a daughter.
Topics: Adult; Arm; Body Height; Child; Chromosome Disorders; Chromosomes, Human, X; Chromosomes, Human, Y; Exons; Family; Female; Growth Disorders; Hand; Homeodomain Proteins; Humans; In Situ Hybridization, Fluorescence; Interspersed Repetitive Sequences; Karyotyping; Male; Nucleic Acid Amplification Techniques; Osteochondrodysplasias; Pedigree; Pregnancy; Radiography; Short Stature Homeobox Protein; Wrist
PubMed: 21068148
DOI: 10.1210/jc.2010-1505 -
Plasmid May 2015Antibiotic resistance is a major concern for society because it threatens the effective prevention of infectious diseases. While some bacterial strains display intrinsic... (Review)
Review
Antibiotic resistance is a major concern for society because it threatens the effective prevention of infectious diseases. While some bacterial strains display intrinsic resistance, others achieve antibiotic resistance by mutation, by the recombination of foreign DNA into the chromosome or by horizontal gene acquisition. In many cases, these three mechanisms operate together. Several mobile genetic elements (MGEs) have been reported to mobilize different types of resistance genes and despite sharing common features, they are often considered and studied separately. Bacteriophages and phage-related particles have recently been highlighted as MGEs that transfer antibiotic resistance. This review focuses on phages, phage-related elements and on composite MGEs (phages-MGEs) involved in antibiotic resistance mobility. We review common features of these elements, rather than differences, and provide a broad overview of the antibiotic resistance transfer mechanisms observed in nature, which is a necessary first step to controlling them.
Topics: Anti-Bacterial Agents; Bacteria; Bacteriophages; Drug Resistance, Bacterial; Environmental Microbiology; Gene Transfer, Horizontal; Interspersed Repetitive Sequences
PubMed: 25597519
DOI: 10.1016/j.plasmid.2015.01.001