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Cell Reports Jul 2023Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and... (Review)
Review
Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature and differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding of the abundance and diversity of prokaryotic immune systems has greatly expanded. These defense systems can degrade the invading genetic material, inhibit genome replication, or trigger abortive infection, leading to population protection. In this review, we highlight these strategies, focusing on the most recent discoveries. The study of prokaryotic defenses not only sheds light on microbial evolution but also uncovers novel enzymatic activities with promising biotechnological applications.
Topics: Prokaryotic Cells; Plasmids; Bacteriophages; Genome; Interspersed Repetitive Sequences
PubMed: 37347666
DOI: 10.1016/j.celrep.2023.112672 -
Philosophical Transactions of the Royal... Oct 2022Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned... (Review)
Review
Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell-MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
Topics: Biological Evolution; Gene Transfer, Horizontal; Interspersed Repetitive Sequences
PubMed: 35989606
DOI: 10.1098/rstb.2021.0234 -
Genes Mar 2023Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other... (Review)
Review
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
Topics: Bacteria; Myxococcales; Biological Evolution; Genome; Interspersed Repetitive Sequences
PubMed: 36980919
DOI: 10.3390/genes14030648 -
Genes Feb 2020Cas3 has essential functions in CRISPR immunity but its other activities and roles, in vitro and in cells, are less widely known. We offer a concise review of the latest... (Review)
Review
Cas3 has essential functions in CRISPR immunity but its other activities and roles, in vitro and in cells, are less widely known. We offer a concise review of the latest understanding and questions arising from studies of Cas3 mechanism during CRISPR immunity, and highlight recent attempts at using Cas3 for genetic editing. We then spotlight involvement of Cas3 in other aspects of cell biology, for which understanding is lacking-these focus on CRISPR systems as regulators of cellular processes in addition to defense against mobile genetic elements.
Topics: Clustered Regularly Interspaced Short Palindromic Repeats; DNA Helicases; Gene Editing; Interspersed Repetitive Sequences; Models, Molecular; Protein Conformation
PubMed: 32085454
DOI: 10.3390/genes11020208 -
Current Opinion in Microbiology Aug 2017Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of... (Review)
Review
Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea that this mode of HGT may be pervasive in natural bacterial populations.
Topics: Bacteria; Bacteriophages; Conjugation, Genetic; DNA, Viral; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 28551392
DOI: 10.1016/j.mib.2017.04.009 -
Clinical Chemistry and Laboratory... Jun 2000Bacteria can transfer genetic information to provide themselves with protection against most antibiotics. The acquisition of resistance gene arrays involves genetic... (Review)
Review
Bacteria can transfer genetic information to provide themselves with protection against most antibiotics. The acquisition of resistance gene arrays involves genetic mobile elements like plasmids and transposons. Another class of genetic structures, termed integrons, have been described and contain one or more gene cassettes located at a specific site. Integrons are defined by an intl gene encoding an integrase, a recombination site attl and a strong promoter. At least six classes of integrons have been determined according to their intl gene. Classes 1, 2 and 3 are the most studied and are largely implicated in the dissemination of antibiotic resistance. A gene cassette includes an open reading frame and, at the 3'-end, a recombination site attC. Integration or excision of cassettes occur by a site-specific recombination mechanism catalyzed by the integrase. However, insertion can occur, albeit rarely, at non-specific sites leading to a stable situation for the cassette. Cassettes are transcribed from the common promoter located in the 5'-conserved segment and expression of distal genes is reduced by the presence of upstream cassettes. Most gene cassettes encode antibiotic resistant determinants but antiseptic resistant genes have also been described. Integrons seem to have a major role in the spread of multidrug resistance in gram-negative bacteria but integrons in gram-positive bacteria were described recently. Moreover, the finding of super-integrons with gene-cassettes coding for other determinants (biochemical functions, virulence factors) in Vibrio isolates dating from 1888 suggests the likely implication of this multicomponent cassette-integron system in bacterial genome evolution before the antibiotic era and to a greater extent than initially believed.
Topics: Animals; Drug Resistance, Microbial; Genome, Bacterial; Humans; Interspersed Repetitive Sequences
PubMed: 10987194
DOI: 10.1515/CCLM.2000.070 -
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 -
Nature Biotechnology Apr 2003
Topics: Cell Nucleus; Chloroplasts; DNA, Chloroplast; Gene Expression Regulation, Plant; Interspersed Repetitive Sequences; Recombination, Genetic; Nicotiana; Transgenes
PubMed: 12665821
DOI: 10.1038/nbt0403-374 -
Trends in Genetics : TIG Oct 2005DNA primases are essential for the initiation of DNA replication and progression of the replication fork. Recent phylogenetic analyses coupled with biochemical and... (Comparative Study)
Comparative Study Review
DNA primases are essential for the initiation of DNA replication and progression of the replication fork. Recent phylogenetic analyses coupled with biochemical and structural studies have revealed that the arrangement of catalytic residues within the archaeal and eukaryotic primase has significant similarity to those of the Pol X family of DNA-repair polymerases. Furthermore, two additional groups of enzymes, the ligase/primase of the bacterial nonhomologous end-joining machinery and a putative replicase from an archaeal plasmid have shown striking functional and structural similarities to the core primase. The promiscuous nature of the archaeal primases suggests that these proteins might have additional roles in DNA repair in the archaea.
Topics: Catalytic Domain; DNA Primase; DNA Repair; DNA-Directed DNA Polymerase; Evolution, Molecular; Interspersed Repetitive Sequences; Models, Molecular
PubMed: 16095750
DOI: 10.1016/j.tig.2005.07.010 -
BioEssays : News and Reviews in... Nov 2015It is tempting to invoke organismal selection as perpetually optimizing the function of any given gene. However, natural selection can drive genic functional change... (Review)
Review
It is tempting to invoke organismal selection as perpetually optimizing the function of any given gene. However, natural selection can drive genic functional change without improvement of biochemical activity, even to the extinction of gene activity. Detrimental mutations can creep in owing to linkage with other selectively favored loci. Selection can promote functional degradation, irrespective of genetic drift, when adaptation occurs by loss of gene function. Even stabilizing selection on a trait can lead to divergence of the underlying molecular constituents. Selfish genetic elements can also proliferate independent of any functional benefits to the host genome. Here we review the logic and evidence for these diverse processes acting in genome evolution. This collection of distinct evolutionary phenomena - while operating through easily understandable mechanisms - all contribute to the seemingly counterintuitive notion that maintenance or improvement of a gene's biochemical function sometimes do not determine its evolutionary fate.
Topics: Adaptation, Physiological; Animals; Biological Evolution; Brassica; Caenorhabditis; Evolution, Molecular; Gene Frequency; Genetic Drift; Interspersed Repetitive Sequences; Models, Genetic; Selection, Genetic
PubMed: 26411745
DOI: 10.1002/bies.201500083