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Biological Psychiatry Sep 2019
Topics: Genome; Humans; Interspersed Repetitive Sequences; Mental Disorders
PubMed: 31416517
DOI: 10.1016/j.biopsych.2019.07.003 -
Psychiatria Danubina Dec 2009Variation in the human genome may explain genetic contributions to complex traits and common diseases. (Review)
Review
OBJECTIVES
Variation in the human genome may explain genetic contributions to complex traits and common diseases.
FINDINGS
Until recently, single nucleotide polymorphisms were thought to be the most prevalent form of interindividual genetic variation. However, structural genomic rearrangements such as deletions, duplications, and inversions lead to variation in gene copy number and contribute even more to genomic diversity. Other sources of genomic variation include noncoding genes, pseudogenes, and mobile genetic elements (transposons).
CONCLUSIONS
Genome dynamics, including changes in gene number and position as well as epigenetic modifications of coding and noncoding sequences, can affect regulation of gene expression and may contribute to the variability of complex phenotypes.
Topics: Chromosome Deletion; Chromosome Inversion; DNA Copy Number Variations; DNA Transposable Elements; Epigenesis, Genetic; Gene Duplication; Gene Expression Regulation; Genetic Variation; Genome, Human; Genomic Structural Variation; Humans; Interspersed Repetitive Sequences; Introns; Mental Disorders; Phenotype; Polymorphism, Single Nucleotide; Pseudogenes; RNA, Untranslated
PubMed: 19935494
DOI: No ID Found -
BMC Genomics Apr 2018Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to... (Comparative Study)
Comparative Study
BACKGROUND
Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin.
RESULTS
To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax. The mitochondrial genomes were similar in terms of their general architecture, gene content and presence of a large repeat region. However, gene order was poorly conserved. Characteristic features of cryptophyte mtDNAs included large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. The cryptophyte mitochondrial genomes retain almost all genes found in many other eukaryotes including the nad, sdh, cox, cob, and atp genes, with the exception of sdh2 and atp3. In addition, gene cluster analysis showed that cryptophytes possess a gene order closely resembling the jakobid flagellates Jakoba and Reclinomonas. Interestingly, the cox1 gene of R. salina, T. amphioxeia, and Storeatula species was found to contain group II introns encoding a reverse transcriptase protein, as did the cob gene of Storeatula species CCMP1868.
CONCLUSIONS
These newly sequenced genomes increase the breadth of data available from algae and will aid in the identification of general trends in mitochondrial genome evolution. While most of the genomes were highly conserved, extensive gene arrangements have shuffled gene order, perhaps due to genome rearrangements associated with hairpin-containing mobile genetic elements, tRNAs with palindromic sequences, and tandem repeat sequences. The cox1 and cob gene sequences suggest that introns have recently been acquired during cryptophyte evolution. Comparison of phylogenetic trees based on plastid and mitochondrial genome data sets underscore the different evolutionary histories of the host and endosymbiont components of present-day cryptophytes.
Topics: Cryptophyta; Gene Rearrangement; Genome, Mitochondrial; Genomics; Interspersed Repetitive Sequences; Phylogeny
PubMed: 29678149
DOI: 10.1186/s12864-018-4626-9 -
Journal of Bacteriology Oct 2021Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via... (Review)
Review
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
Topics: Biological Evolution; CRISPR-Cas Systems; Enterococcus faecalis; Enterococcus faecium; Interspersed Repetitive Sequences
PubMed: 34370561
DOI: 10.1128/JB.00177-21 -
Current Opinion in Virology Dec 2018Among the virus world, Giant viruses (GVs) compose one of the most successful eukaryovirus families. By contrast with other eukaryoviruses, GV genomes contain a wide... (Review)
Review
Among the virus world, Giant viruses (GVs) compose one of the most successful eukaryovirus families. By contrast with other eukaryoviruses, GV genomes contain a wide array of mobile genetic elements (MGEs) that encompass diverse, mostly prokaryotic-like, transposable element families, introns, inteins, restriction-modification systems and enigmatic classes of mobile elements having little similarities with known families. Interestingly, several of these MGEs may be beneficial to the GVs, fulfilling two kinds of functions: (1) degrading host or competing virus/virophage DNA and (2) promoting viral genome integration, dissemination and excision into the host genomes. By providing fitness advantages to the virus in which they reside, these MGEs compose a kind of molecular symbiotic association in which both partners benefit from the presence of each other's. Thus, protective effects provided by some of these MGEs may have generated an arm race between competing GVs in order to encode the most diverse arsenal of anti-viral weapons, explaining the unusual abundance of MGEs in GV genomes by a kind of ratchet effect.
Topics: Eukaryota; Evolution, Molecular; Genes, Viral; Giant Viruses; Host-Parasite Interactions; Interspersed Repetitive Sequences
PubMed: 30114664
DOI: 10.1016/j.coviro.2018.07.013 -
Heredity Jan 2011Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally.... (Review)
Review
Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes.
Topics: Bacteria; Gene Transfer, Horizontal; Genome, Bacterial; Interspersed Repetitive Sequences; Plasmids
PubMed: 20332804
DOI: 10.1038/hdy.2010.24 -
Methods in Molecular Biology (Clifton,... 2012The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of... (Review)
Review
The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of mobile genetic elements (MGEs). Bacterial and archaeal genomes are mosaics of vertically and horizontally transmitted DNA segments. This generates reticulate relationships between members of the prokaryotic world that are better represented by networks than by "classical" phylogenetic trees. In this review we summarize the nature and activities of MGEs, and the problems that presently limit their analysis on a large scale. We propose routes to improve their annotation in the flow of genomic and metagenomic sequences that currently exist and those that become available. We describe network analysis of evolutionary relationships among some MGE categories and sketch out possible developments of this type of approach to get more insight into the role of the mobilome in bacterial adaptation and evolution.
Topics: Bacteriophages; Conjugation, Genetic; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Archaeal; Genome, Bacterial; Homologous Recombination; Interspersed Repetitive Sequences; Molecular Sequence Annotation; Systems Biology; Transformation, Bacterial
PubMed: 22144148
DOI: 10.1007/978-1-61779-361-5_4 -
Applied and Environmental Microbiology May 2018The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene cassettes. Wastewater treatment plants (WWTPs)...
The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance genes; however, knowledge about the impacts of wastewater treatment on integrons and their gene cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding gene cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron gene cassettes, whereas class 3 integron gene cassettes exhibited highest diversity in activated sludge. Most of the gene cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance genes were highly prevalent in class 1 integron gene cassettes, while class 3 integrons mainly carried beta-lactam resistance gene cassettes. A core class 1 integron resistance gene cassette pool persisted during wastewater treatment, implying that these resistance genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance genes within both class 1 and 3 integrons. Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and genes spreading into environments. Integrons are important genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their gene cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze gene cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their gene cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated gene cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments.
Topics: Bacteria; China; Cities; Drug Resistance, Bacterial; Genetic Variation; Integrons; Interspersed Repetitive Sequences; Waste Disposal, Fluid; Wastewater
PubMed: 29475864
DOI: 10.1128/AEM.02766-17 -
Current Opinion in Microbiology Aug 2017A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1... (Review)
Review
A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the Cas1-Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers.
Topics: Adaptation, Biological; Archaea; Bacteria; CRISPR-Cas Systems; Interspersed Repetitive Sequences
PubMed: 28472712
DOI: 10.1016/j.mib.2017.04.004 -
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