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Trends in Microbiology Jan 2020In this opinion article we highlight links between the H-NS nucleoid-associated protein, variable DNA topology, the regulation of CRISPR-cas locus expression, CRISPR-Cas... (Review)
Review
In this opinion article we highlight links between the H-NS nucleoid-associated protein, variable DNA topology, the regulation of CRISPR-cas locus expression, CRISPR-Cas activity, and the recruitment of novel genetic information by the CRISPR array. We propose that the requirement that the invading mobile genetic element be negatively supercoiled limits effective CRISPR action to a window in the bacterial growth cycle when DNA topology is optimal, and that this same window is used for the efficient integration of new spacer sequences at the CRISPR array. H-NS silences CRISPR promoters, and we propose that antagonists of H-NS, such as the LeuO transcription factor, provide a basis for a stochastic genetic switch that acts at random in each cell in the bacterial population. In addition, we wish to propose a mechanism by which mobile genetic elements can suppress CRISPR-cas transcription using H-NS homologues. Although the individual components of this network are known, we propose a new model in which they are integrated and linked to the physiological state of the bacterium. The model provides a basis for cell-to-cell variation in the expression and performance of CRISPR systems in bacterial populations.
Topics: Bacteria; Bacterial Physiological Phenomena; Bacterial Proteins; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Immunity; Integration Host Factors; Interspersed Repetitive Sequences; Promoter Regions, Genetic; Transcription Factors; Transcriptome
PubMed: 31519332
DOI: 10.1016/j.tim.2019.08.004 -
Current Opinion in Genetics &... Jun 2023The organization of the genome into euchromatin and heterochromatin has been known for almost 100 years [1]. More than 50% of mammalian genomes contain repetitive... (Review)
Review
The organization of the genome into euchromatin and heterochromatin has been known for almost 100 years [1]. More than 50% of mammalian genomes contain repetitive sequences [2,3]. Recently, a functional link between the genome and its folding has been identified [4,5]. Homotypic clustering of long interspersed nuclear element 1 (LINE1 or L1) and B1/Alu retrotransposons forms grossly exclusive nuclear domains that characterize and predict heterochromatin and euchromatin, respectively. The spatial segregation of L1 and B1/Alu-rich compartments is conserved in mammalian cells and can be rebuilt during the cell cycle and established de novo in early embryogenesis. Inhibition of L1 RNA drastically weakened homotypic repeat contacts and compartmental segregation, indicating that L1 plays a more significant role than just being a compartmental marker. This simple and inclusive genetic coding model of L1 and B1/Alu in shaping the macroscopic structure of the genome provides a plausible explanation for the remarkable conservation and robustness of its folding in mammalian cells. It also proposes a conserved core structure on which subsequent dynamic regulation takes place.
Topics: Animals; Heterochromatin; Euchromatin; Repetitive Sequences, Nucleic Acid; Long Interspersed Nucleotide Elements; Retroelements; Alu Elements; Mammals
PubMed: 37229928
DOI: 10.1016/j.gde.2023.102049 -
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 -
Microbiology Spectrum Apr 2015The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid... (Review)
Review
The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".
Topics: Adaptation, Biological; Attachment Sites, Microbiological; Gene Rearrangement; Gene Transfer, Horizontal; Gram-Negative Bacteria; Integrons; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 26104695
DOI: 10.1128/microbiolspec.MDNA3-0019-2014 -
Methods in Molecular Biology (Clifton,... 2018Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes....
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects. The mechanisms catalyzing DNA breakage and coordinating the "random" assembly of genomic fragments are actively being investigated. Recently, retrotransposons-a type of "jumping gene"-have been implicated as one means to generate double-stranded DNA breaks during chromothripsis and as sequences which can contribute to the final configuration of the derived chromosomes. In this methods chapter, I discuss how to apply available bioinformatic tools and the hallmarks of retrotransposon mobilization to breakpoint junctions to assess the role for active and inactive retrotransposon sequences in chromothriptic events.
Topics: Alu Elements; Chromothripsis; Genome, Human; Homologous Recombination; Humans; Long Interspersed Nucleotide Elements; Mutagenesis, Insertional; Retroelements; Sequence Deletion; Sequence Inversion
PubMed: 29564824
DOI: 10.1007/978-1-4939-7780-2_11 -
Annual Review of Food Science and... Feb 2017Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and... (Review)
Review
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
Topics: Bacteria; Bacterial Vaccines; Bacteriophages; CRISPR-Cas Systems; Food Industry; Food Microbiology; Gene Editing; Genes, Bacterial; Interspersed Repetitive Sequences; Probiotics
PubMed: 28245154
DOI: 10.1146/annurev-food-072816-024723 -
Microbial Pathogenesis Mar 2018Regarded as a common genetic element responsible for horizontal gene transfer and wide spread of antimicrobial resistance among a large variety of bacteria, integrons... (Review)
Review
Regarded as a common genetic element responsible for horizontal gene transfer and wide spread of antimicrobial resistance among a large variety of bacteria, integrons are commonly distributed and considered as a determinant in the acquisition and evolution of virulence and antibiotic resistance. To date, the surveillances of integrons have been widely conducted in clinic, community even husbandry. For exact and accurate integron screening, as well as resistant cassettes, reliable monitoring methods is need. Current methods applied on integron screening are mainly conducted by the screening of integrases, followed by the detection of various gene cassettes inserted into integrons. PCR and PCR-related methods (such as RFLP) are mainly employed under such circumstances. Matured LAMP and Sequencing technology have lowered cost and dramatically increased throughput in integron screening and possessed the advantages in similarity analysis of mutated resistant cassettes. This review focused on the classification and characterization of integrons, antimicrobial resistance of integron and genotyping methods for integrons. In methodology, PCR, LAMP and Sequencing technology were mainly introduced for the screening of various classes' integrons and the detection of resistant gene cassettes. Staphylococcus, Pseudomonas and Enterococcus were selected as typical integron-positive clinical and environmental pathogens screened with three methods mentioned above. With the surveillance of the occurrence of integron and resistance gene cassettes conducted in South China, the review also summarized the occurrence, pathogenicity and virulence mediated by integrons.
Topics: Bacterial Infections; China; Drug Resistance, Bacterial; Enterococcus; Gene Transfer, Horizontal; Genotyping Techniques; High-Throughput Nucleotide Sequencing; Humans; Integrons; Interspersed Repetitive Sequences; Pseudomonas; Staphylococcus; Virulence
PubMed: 29306009
DOI: 10.1016/j.micpath.2017.12.073 -
Molecular Biology Reports Aug 2014Among the bacteria groups, most of them are known to be beneficial to human being whereas only a minority is being recognized as harmful. The pathogenicity of bacteria... (Review)
Review
Among the bacteria groups, most of them are known to be beneficial to human being whereas only a minority is being recognized as harmful. The pathogenicity of bacteria is due, in part, to their rapid adaptation in the presence of selective pressures exerted by the human host. In addition, through their genomes, bacteria are subject to mutations, various rearrangements or horizontal gene transfer among and/or within bacterial species. Bacteria's essential metabolic functions are generally encoding by the core genes. Apart of the core genes, there are several number of mobile genetic elements (MGE) acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. These MGE namely bacteriophages, transposons, plasmids, and pathogenicity islands represent about 15% Staphylococcus aureus genomes. The acquisition of most of the MGE is made by horizontal genomic islands (GEI), recognized as discrete DNA segments between closely related strains, transfer. The GEI contributes to the wide spread of microorganisms with an important effect on their genome plasticity and evolution. The GEI are also involve in the antibiotics resistance and virulence genes dissemination. In this review, we summarize the mobile genetic elements of S. aureus.
Topics: Bacteriophages; Chromosomes, Bacterial; DNA Transposable Elements; Gene Transfer, Horizontal; Genomic Islands; Humans; Interspersed Repetitive Sequences; Staphylococcus aureus
PubMed: 24728610
DOI: 10.1007/s11033-014-3367-3 -
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 -
Helicobacter Sep 2016The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of... (Review)
Review
The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.
Topics: Evolution, Molecular; Genes, Bacterial; Genome, Bacterial; Helicobacter pylori; Humans; Interspersed Repetitive Sequences; Sequence Analysis, DNA; Transcriptome
PubMed: 27531533
DOI: 10.1111/hel.12334