scholarly journals Discovering complete quasispecies in bacterial genomes

2017 ◽  
Author(s):  
Frederic Bertels ◽  
Chaitanya S. Gokhale ◽  
Arne Traulsen
Keyword(s):  
Natural Populations ◽  
Mobile Genetic Elements ◽  
Small Range ◽  
Mutational Load ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Genetic Elements ◽  
Quasispecies Model ◽  
A Genome ◽  
Almost All

ABSTRACTMobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs within a genome are an evolving populations because they replicate and mutate. We know the exact composition of this population and the sequence of each member of a REPIN population, in contrast to most other biological populations. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to ten different REPIN populations from ten different bacterial strains and estimate duplication rates. We find that our estimated duplication rates range from about 5 × 10−9to 37 × 10−9duplications per generation per genome. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size and we also see an example of competition between two REPIN populations.

scholarly journals Similarity in the Structure of tetD-Carrying Mobile Genetic Elements in Bacterial Strains of Different Genera Isolated from Cultured Yellowtail

2016 ◽  
Vol 21 (3) ◽  
pp. 183-186 ◽  
Author(s):  
MANABU FURUSHITA ◽  
HIROSHI AKAGI ◽  
AZUSA KANEOKA ◽  
TOSHIMICHI MAEDA ◽  
TSUBASA FUKUDA ◽  
...  
Keyword(s):  
Mobile Genetic Elements ◽  
Bacterial Strains ◽  
Genetic Elements

scholarly journals High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages inClostridioides difficile

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Julian R. Garneau ◽  
Ognjen Sekulovic ◽  
Bruno Dupuy ◽  
Olga Soutourina ◽  
Marc Monot ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mobile Genetic Elements ◽  
Large Chromosome ◽  
Comparative Genomic ◽  
Content Type ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
A Genome ◽  
Depth Analysis ◽  
High Prevalence

ABSTRACTClostridioides difficile(formerlyClostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified inC. difficileso far, with a genome of 131 kbp. It shares morphological and genomic similarity with other large siphophages, like phage 949, infectingLactococcus lactis, and phage c-st, infectingClostridium botulinum. A PhageTerm analysis indicated the presence of 378-bp direct terminal repeats at the phiCD211 genome termini. Among striking features of phiCD211, the presence of several transposase and integrase genes suggests past recombination events with other mobile genetic elements. Several gene products potentially influence the bacterial lifestyle and fitness, including a putative AcrB/AcrD/AcrF multidrug resistance protein, an EzrA septation ring formation regulator, and a spore protease. We also identified a CRISPR locus and acas3gene. We screened 2,584C. difficilegenomes available and detected 149 prophages sharing ≥80% nucleotide identity with phiCD211 (5% prevalence). Overall, phiCD211-like phages were detected inC. difficilestrains corresponding to 21 different multilocus sequence type groups, showing their high prevalence. Comparative genomic analyses revealed the existence of several clusters of highly similar phiCD211-like phages. Of note, large chromosome inversions were observed in some members, as well as multiple gene insertions and module exchanges. This highlights the great plasticity and gene coding potential of the phiCD211/phiCDIF1296T genome. Our analyses also suggest active evolution involving recombination with other mobile genetic elements.IMPORTANCEClostridioides difficileis a clinically important pathogen representing a serious threat to human health. Our hypothesis is that genetic differences between strains caused by the presence of integrated prophages could explain the apparent differences observed in the virulence of differentC. difficilestrains. In this study, we provide a full characterization of phiCD211, also known as phiCDIF1296T, the largest phage known to infectC. difficileso far. Screening 2,584C. difficilegenomes revealed the presence of highly similar phiCD211-like phages in 5% of the strains analyzed, showing their high prevalence. Multiple-genome comparisons suggest that evolution of the phiCD211-like phage community is dynamic, and some members have acquired genes that could influence bacterial biology and fitness. Our study further supports the relevance of studying phages inC. difficileto better understand the epidemiology of this clinically important human pathogen.

scholarly journals Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

2021 ◽  
Author(s):  
Ezequiel G Mogro ◽  
Nicolás M Ambrosis ◽  
Mauricio J Lozano
Keyword(s):  
Insertion Sequence ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Genome Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
A Genome ◽  
Phenotypic Variations ◽  
Genome Assemblies ◽  
Straightforward Approach

Abstract Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

scholarly journals Mobile genetic element insertions drive antibiotic resistance across pathogens

2019 ◽  
Author(s):  
Matthew G. Durrant ◽  
Michelle M. Li ◽  
Ben Siranosian ◽  
Ami S. Bhatt
Keyword(s):  
Antibiotic Resistance ◽  
De Novo ◽  
Bacterial Species ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Genetic Elements ◽  
Element Insertion ◽  
A Genome ◽  
Mobile Element Insertion

AbstractMobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate ade novoapproach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on ‘split-read’ alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenicEscherichia coli. In summary, by applying ade novoapproach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.

scholarly journals Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses

2021 ◽  
Author(s):  
Fatima Aysha Hussain ◽  
Javier Dubert ◽  
Joseph Elsherbini ◽  
Mikayla Murphy ◽  
David VanInsberghe ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Bacterial Genome ◽  
Mobile Genetic Elements ◽  
Bacterial Strains ◽  
Genomic Features ◽  
Genetic Elements ◽  
Flexible Genome ◽  
In The Wild ◽  
Putative Phage ◽  
Resistance To Viruses

AbstractAlthough it is generally accepted that viruses (phages) drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. Here we show that the arms race between phages and their hosts is mediated by large and highly diverse mobile genetic elements. These phage-defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection afforded by multiple elements is cumulative, and a single bacterial genome can harbor as many as 18 putative phage-defense elements. Overall, elements account for 90% of the flexible genome amongst closely related strains. The rapid turnover of these elements demonstrates that phage resistance is unlinked from other genomic features and that resistance to phage therapy might be as easily acquired as antibiotic resistance.

scholarly journals How important is CRISPR-Cas for protecting natural populations of bacteria against infections by mobile genetic elements?

2020 ◽  
Author(s):  
Edze Westra ◽  
Bruce Levin
Keyword(s):  
Computer Simulation ◽  
Immune System ◽  
Natural Populations ◽  
Adaptive Immune System ◽  
Simulation Models ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Adaptive Immune ◽  
Computer Simulation Models

AbstractArticles on CRISPR commonly open with some variant of the phrase ‘these short-palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements’. There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes, and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea and the mobile genetic elements that infect them.SignificanceThere is no question about the importance and utility of CRISPR-Cas for editing and modifying genomes. On the other hand, the mechanisms responsible for the evolution and maintenance of these systems and the magnitude of their importance to the ecology and evolution of bacteria, archaea and their infectious DNAs, are not at all clear. With the aid of heuristic mathematical – computer simulation models and reviews of the existing literature, we raise questions that have to be answered to elucidate the contribution of selection – mediated by phage and plasmids – to the evolution and maintenance of this adaptive immune system and its consequences for the ecology and evolution of prokaryotes and their viruses and plasmids.

scholarly journals DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10674
Author(s):  
Oxana Khapilina ◽  
Olesya Raiser ◽  
Alevtina Danilova ◽  
Vladislav Shevtsov ◽  
Ainur Turzhanova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Biological Diversity ◽  
Vegetative Reproduction ◽  
Natural Populations ◽  
Mobile Genetic Elements ◽  
Ice Age ◽  
Conservation Strategy ◽  
Relict Species ◽  
Genetic Elements

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

scholarly journals Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

2019 ◽  
Author(s):  
Aude Bernheim ◽  
David Bikard ◽  
Marie Touchon ◽  
Eduardo P C Rocha
Keyword(s):  
Mobile Genetic Elements ◽  
Type I ◽  
Large Set ◽  
Bacterial Genomes ◽  
Epistatic Interactions ◽  
Unique Type ◽  
Genetic Elements ◽  
Multiple Copies ◽  
In Trans ◽  
Genomic Locations

Abstract Prokaryotes use CRISPR–Cas systems for adaptive immunity, but the reasons for the frequent existence of multiple CRISPRs and cas clusters remain poorly understood. Here, we analysed the joint distribution of CRISPR and cas genes in a large set of fully sequenced bacterial genomes and their mobile genetic elements. Our analysis suggests few negative and many positive epistatic interactions between Cas subtypes. The latter often result in complex genetic organizations, where a locus has a single adaptation module and diverse interference mechanisms that might provide more effective immunity. We typed CRISPRs that could not be unambiguously associated with a cas cluster and found that such complex loci tend to have unique type I repeats in multiple CRISPRs. Many chromosomal CRISPRs lack a neighboring Cas system and they often have repeats compatible with the Cas systems encoded in trans. Phages and 25 000 prophages were almost devoid of CRISPR–Cas systems, whereas 3% of plasmids had CRISPR–Cas systems or isolated CRISPRs. The latter were often compatible with the chromosomal cas clusters, suggesting that plasmids can co-opt the latter. These results highlight the importance of interactions between CRISPRs and cas present in multiple copies and in distinct genomic locations in the function and evolution of bacterial immunity.

scholarly journals It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements

2020 ◽  
Vol 117 (45) ◽  
pp. 27777-27785
Author(s):  
Edze R. Westra ◽  
Bruce R. Levin
Keyword(s):  
A Priori ◽  
Natural Populations ◽  
Adaptive Immune System ◽  
Simulation Models ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Adaptive Immune ◽  
Different Types ◽  
Computer Simulation Models

Articles on CRISPR commonly open with some variant of the phrase “these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements.” There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical–computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus

2020 ◽  
Vol 76 (1) ◽  
pp. 48-54
Author(s):  
Javier Eduardo Fernandez ◽  
Vincent Perreten ◽  
Sybille Schwendener
Keyword(s):  
Resistance Genes ◽  
Resistance Mechanism ◽  
Mobile Genetic Elements ◽  
Bioinformatic Analysis ◽  
Membered Ring ◽  
Macrolide Resistance ◽  
The Novel ◽  
Bacterial Strains ◽  
Chloramphenicol Resistance ◽  
Genetic Elements

Abstract Objectives To analyse macrolide resistance in a Macrococcus canis strain isolated from a dog with an ear infection, and determine whether the resistance mechanism is also present in other bacteria, and associated with mobile genetic elements. Methods The whole genome of M. canis Epi0082 was sequenced using PacBio and Illumina technologies. Novel macrolide resistance determinants were identified through bioinformatic analysis, and functionality was demonstrated by expression in Staphylococcus aureus. Mobile genetic elements containing the novel genes were analysed in silico for strain Epi0082 as well as in other bacterial strains deposited in GenBank. Results M. canis Epi0082 contained a 3212 bp operon with the novel macrolide resistance genes mef(F) and msr(G) encoding a efflux protein and an ABC-F ribosomal protection protein, respectively. Cloning in S. aureus confirmed that both genes individually confer resistance to the 14- and 15-membered ring macrolides erythromycin and azithromycin, but not the 16-membered ring macrolide tylosin. A reduced susceptibility to the streptogramin B pristinamycin IA was additionally observed when msr(G) was expressed in S. aureus under erythromycin induction. Epi0082 carried the mef(F)–msr(G) operon together with the chloramphenicol resistance gene fexB in a novel 39 302 bp plasmid pMiCAN82a. The mef(F)–msr(G) operon was also found in macrolide-resistant Macrococcus caseolyticus strains in the GenBank database, but was situated in the chromosome as part of a novel 13 820 bp or 13 894 bp transposon Tn6776. Conclusions The identification of mef(F) and msr(G) on different mobile genetic elements in Macrococcus species indicates that these genes hold potential for further dissemination of resistance to the clinically important macrolides in the bacterial population.

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