scholarly journals Evolution of Staphylococcus aureus by Large Chromosomal Replacements

2004 ◽  
Vol 186 (4) ◽  
pp. 1060-1064 ◽  
Author(s):  
D. Ashley Robinson ◽  
Mark C. Enright
Keyword(s):  
Staphylococcus Aureus ◽  
Natural Populations ◽  
Mobile Genetic Elements ◽  
Conjugative Transfer ◽  
Bacterial Evolution ◽  
Genetic Elements ◽  
Unique Structure ◽  
Large Size ◽  
Order Of Magnitude

ABSTRACT Conjugative transfer and replacement of hundreds of kilobases of a bacterial chromosome can occur in vitro, but replacements in nature are either an order of magnitude smaller or involve the movement of mobile genetic elements. We discovered that two lineages of Staphylococcus aureus, including a pandemic methicillin-resistant lineage, were founded by single chromosomal replacements of at least ∼244 and ∼557 kb representing ∼10 and ∼20% of the chromosome, respectively, without the obvious involvement of mobile genetic elements. The replacements are unprecedented in natural populations of bacteria because of their large size and unique structure and may have a dramatic impact on bacterial evolution.

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 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.

scholarly journals Mobile genetic elements: in silico,in vitro,in vivo

2016 ◽  
Vol 25 (5) ◽  
pp. 1027-1031 ◽  
Author(s):  
Irina R. Arkhipova ◽  
Phoebe A. Rice
Keyword(s):  
In Silico ◽  
Mobile Genetic Elements ◽  
Genetic Elements

scholarly journals Cas3 Protein—A Review of a Multi-Tasking Machine

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 208 ◽  
Author(s):  
Liu He ◽  
Michael St. John James ◽  
Marin Radovcic ◽  
Ivana Ivancic-Bace ◽  
Edward L. Bolt
Keyword(s):  
Cell Biology ◽  
Protein A ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Cellular Processes ◽  
Concise Review ◽  
In Cells

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.

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 Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

2021 ◽  
Author(s):  
Eugen Pfeifer ◽  
Jorge A Moura de Sousa ◽  
Marie Touchon ◽  
Eduardo P C Rocha
Keyword(s):  
Mobile Genetic Elements ◽  
Bacterial Evolution ◽  
Bacterial Phyla ◽  
Genetic Organization ◽  
Plasmid Gene ◽  
Genetic Elements ◽  
Accessory Genes ◽  
Number Distribution ◽  
Sizeable Fraction ◽  
Large Groups

Abstract Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage–plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage–plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage–plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage–plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage–plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage–plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

scholarly journals Non-canonical Staphylococcus aureus pathogenicity island repression

2021 ◽  
Author(s):  
Laura Miguel-Romero ◽  
Mohammed Alqasmi ◽  
Julio Bacarizo ◽  
Jason A. Tan ◽  
Richard J. Cogdell ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Virulence Factors ◽  
Pathogenicity Island ◽  
Mobile Genetic Elements ◽  
Life Cycles ◽  
Genetic Elements ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Induction System

ABSTRACTMobile genetic elements (MGEs) control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here we describe an unprecedented repression-derepression mechanism involved in the transfer of the Staphylococcus aureus pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetrameric conformation, never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterise a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.SignificanceWhile most repressors controlling the transfer of mobile genetic elements are dimers, we demonstrate here that the Staphylococcal pathogenicity island 1 (SaPI1) is repressed by two tetramers, which have a novel structural fold in their body that has never been seen before in other proteins. Moreover, by solving the structure of the SaPI1 repressor in complex with its inducing protein Sri, we have demonstrated that Sri forces the SaPI1 repressor to adopt a conformation that is incompatible with DNA binding, explaining how SaPI1 is induced. Finally, our results demonstrate that this repression system is not exclusive of the SaPIs but widespread in nature. Our studies provide important insights understanding how SaPIs spread in nature.

scholarly journals Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from California, USA

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Samantha J. Hau ◽  
Darrell O. Bayles ◽  
David P. Alt ◽  
Tracy L. Nicholson
Keyword(s):  
Staphylococcus Aureus ◽  
Draft Genome ◽  
Mobile Genetic Elements ◽  
Sequence Type ◽  
Genome Sequences ◽  
Content Type ◽  
Genetic Elements

ABSTRACT Staphylococcus aureus is part of the human epithelial microbiota; however, it is also a pathogen. The acquisition of mobile genetic elements plays a role in the virulence of S. aureus isolates and contributes to treatment failures. This report details the draft genome sequences of 14 clinical S. aureus isolates.

scholarly journals Complete Genome Sequences of Two Staphylococcus aureus Sequence Type 5 Isolates from California, USA

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Samantha J. Hau ◽  
Darrell O. Bayles ◽  
David P. Alt ◽  
Tracy L. Nicholson
Keyword(s):  
Staphylococcus Aureus ◽  
Complete Genome ◽  
Mobile Genetic Elements ◽  
Sequence Type ◽  
Human Diseases ◽  
Genome Sequences ◽  
Content Type ◽  
Genetic Elements

ABSTRACT Staphylococcus aureus causes a variety of human diseases ranging in severity. The pathogenicity of S. aureus can be partially attributed to the acquisition of mobile genetic elements. In this report, we provide two complete genome sequences from human clinical S. aureus isolates.

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