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Trends in Microbiology May 2016The SOS response is an essential process for responding to DNA damage in bacteria. The expression of SOS genes is under the control of LexA, a global transcription... (Review)
Review
The SOS response is an essential process for responding to DNA damage in bacteria. The expression of SOS genes is under the control of LexA, a global transcription factor that undergoes self-cleavage during stress to allow the expression of DNA repair functions and delay cell division until the damage is rectified. LexA also regulates genes that are not part of this cell rescue program, and the induction of bacteriophages, the movement of pathogenicity islands, and the expression of virulence factors and bacteriocins are all controlled by this important transcription factor. Recently it has emerged that when regulating the expression of genes from mobile genetic elements (MGEs), LexA often does so in concert with a corepressor. This accessory regulator can either be a host-encoded global transcription factor, which responds to various metabolic changes, or a factor that is encoded for by the MGE itself. Thus, the coupling of LexA-mediated regulation to a secondary transcription factor not only detaches LexA from its primary SOS role, but also fine-tunes gene expression from the MGE, enabling it to respond to multiple stresses. Here we discuss the mechanisms of such coordinated regulation and its implications for cells carrying such MGEs.
Topics: Bacterial Proteins; Bacteriophages; DNA Damage; Interspersed Repetitive Sequences; Regulon; SOS Response, Genetics; Serine Endopeptidases; Transcription, Genetic
PubMed: 26970840
DOI: 10.1016/j.tim.2016.02.009 -
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 -
Microbiology (Reading, England) Jul 2015Integrons are genetic elements that contain a site-specific recombination system able to capture, express and exchange gene cassettes. Mobile integrons are widespread... (Review)
Review
Integrons are genetic elements that contain a site-specific recombination system able to capture, express and exchange gene cassettes. Mobile integrons are widespread and often confer resistance to multiple antibiotics, due to the expression of the arrays of gene cassettes they carry. Although >300 cassette arrays have been described, < 10 array compositions prevail in the reports related to class 1 integrons. These common arrays are found in a broad variety of hosts and environments, highlighting the high level of horizontal dissemination of these elements amongst bacterial populations and species. Clonal expansion also contributes to the current prevalence and inter-regional spread of integron-carrying bacterial species. Here, we review the dissemination pattern of common cassette arrays with a focus on the bacterial species, the geographical dispersal pattern and the environments in which they reside. Conserved arrays of gene cassettes are found in at least 74 countries and 72 species present in different environments. The factors governing the further spread and population dynamics of these cassette arrays remain to be determined.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Bacterial Infections; Disease Transmission, Infectious; Drug Resistance, Bacterial; Environmental Microbiology; Gene Transfer, Horizontal; Global Health; Humans; Integrons; Interspersed Repetitive Sequences
PubMed: 25901001
DOI: 10.1099/mic.0.000099 -
Bioscience, Biotechnology, and... May 2017Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different... (Review)
Review
Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different environments is reviewed, in particular, behavior of the plasmid pCAR1, a carbazole-degradative plasmid isolated from Pseudomonas resinovorans CA10. pCAR1 belongs to incompatibility P-7 group and is self-transmissible among different bacteria. Comparisons of changes in the transcriptome of different host strains caused by carrying pCAR1 revealed common responses in the hosts and host-specific responses. Monitoring the survival of the host and transfer of the plasmid in artificial and natural environmental samples revealed several environmental factors, including cations and water content, which changed the behavior of both the host and its plasmid. Single-cell level analysis to detect the transconjugants of different plasmids successfully determined the transfer range of the plasmids. Three nucleoid-associated proteins encoded on pCAR1 are important factors affecting its genetic stability, maintenance, and transfer.
Topics: Carbazoles; Genomics; Host Specificity; Interspersed Repetitive Sequences; Plasmids
PubMed: 28077029
DOI: 10.1080/09168451.2016.1270743 -
Molecular Biology and Evolution Jun 2020Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse...
Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.
Topics: Evolution, Molecular; Hydrothermal Vents; Integrases; Interspersed Repetitive Sequences; Pseudogenes; Thermococcus
PubMed: 32068866
DOI: 10.1093/molbev/msaa041 -
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 -
Nature Dec 2023Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in...
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
Topics: Humans; Alleles; Australia; Australian Aboriginal and Torres Strait Islander Peoples; Datasets as Topic; DNA Copy Number Variations; Genetic Loci; Genetics, Medical; Genomic Structural Variation; Genomics; INDEL Mutation; Interspersed Repetitive Sequences; Microsatellite Repeats; Genome, Human
PubMed: 38093003
DOI: 10.1038/s41586-023-06842-7 -
Current Opinion in Microbiology Jun 2023Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with... (Review)
Review
Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.
Topics: Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Bacteria; Biological Evolution; Microbiota
PubMed: 36863168
DOI: 10.1016/j.mib.2023.102282 -
ELife Mar 2021Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial...
Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICE, an integrative and conjugative element of , provides to its host cells. Activation of ICE conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICE-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICE gene, (formerly ), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICE to increase host fitness, thereby increasing propagation of the element.
Topics: Bacillus subtilis; DNA, Bacterial; Gene Transfer, Horizontal; Genetic Fitness; Host Microbial Interactions; Interspersed Repetitive Sequences
PubMed: 33655883
DOI: 10.7554/eLife.65924 -
BioEssays : News and Reviews in... Feb 2023Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages...
Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception - a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
Topics: Bacteria; DNA Transposable Elements; Genome, Bacterial; Interspersed Repetitive Sequences
PubMed: 36456469
DOI: 10.1002/bies.202200085