Metagenomic Insight into Sulfonamide-Induced Variation in Antibiotic Resistome of Soil Associated with Taxonomy, Mobile Genetic Elements (MGEs), and Function

We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution.

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Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein

mBio ◽

10.1128/mbio.01751-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 31

Author(s):

April Pawluk ◽

Megha Shah ◽

Marios Mejdani ◽

Charles Calmettes ◽

Trevor F. Moraes ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Transcriptional Repressor ◽

Mobile Genetic Elements ◽

Type I ◽

Genetic Studies ◽

Genetic Elements ◽

Crispr System ◽

Mechanistic Insight ◽

Resistance To Invasion ◽

Insight Into

ABSTRACT CRISPR (clustered regularly interspaced short palindromic repeat)-Cas adaptive immune systems are prevalent defense mechanisms in bacteria and archaea. They provide sequence-specific detection and neutralization of foreign nucleic acids such as bacteriophages and plasmids. One mechanism by which phages and other mobile genetic elements are able to overcome the CRISPR-Cas system is through the expression of anti-CRISPR proteins. Over 20 different families of anti-CRISPR proteins have been described, each of which inhibits a particular type of CRISPR-Cas system. In this work, we determined the structure of type I-E anti-CRISPR protein AcrE1 by X-ray crystallography. We show that AcrE1 binds to the CRISPR-associated helicase/nuclease Cas3 and that the C-terminal region of the anti-CRISPR protein is important for its inhibitory activity. We further show that AcrE1 can convert the endogenous type I-E CRISPR system into a programmable transcriptional repressor. IMPORTANCE The CRISPR-Cas immune system provides bacteria with resistance to invasion by potentially harmful viruses, plasmids, and other foreign mobile genetic elements. This study presents the first structural and mechanistic insight into a phage-encoded protein that inactivates the type I-E CRISPR-Cas system in Pseudomonas aeruginosa. The interaction of this anti-CRISPR protein with the CRISPR-associated helicase/nuclease proteins Cas3 shuts down the CRISPR-Cas system and protects phages carrying this gene from destruction. This interaction also allows the repurposing of the endogenous type I-E CRISPR system into a programmable transcriptional repressor, providing a new biotechnological tool for genetic studies of bacteria encoding this type I-E CRISPR-Cas system. IMPORTANCE The CRISPR-Cas immune system provides bacteria with resistance to invasion by potentially harmful viruses, plasmids, and other foreign mobile genetic elements. This study presents the first structural and mechanistic insight into a phage-encoded protein that inactivates the type I-E CRISPR-Cas system in Pseudomonas aeruginosa. The interaction of this anti-CRISPR protein with the CRISPR-associated helicase/nuclease proteins Cas3 shuts down the CRISPR-Cas system and protects phages carrying this gene from destruction. This interaction also allows the repurposing of the endogenous type I-E CRISPR system into a programmable transcriptional repressor, providing a new biotechnological tool for genetic studies of bacteria encoding this type I-E CRISPR-Cas system.

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CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

Nucleic Acids Research ◽

10.1093/nar/gkab859 ◽

2021 ◽

Author(s):

Rafael Pinilla-Redondo ◽

Jakob Russel ◽

David Mayo-Muñoz ◽

Shiraz A Shah ◽

Roger A Garrett ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Comprehensive Analysis ◽

Immune Protection ◽

Genetic Elements ◽

And Function

Abstract Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences highlight the genetic independence of plasmids and suggest a major role for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.

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Evolution and function of mobile genetic elements and DNA methyltransferases in extraintestinal pathogenic Escherichia coli

10.14264/uql.2019.128 ◽

2019 ◽

Author(s):

Melinda Ashcroft

Keyword(s):

Escherichia Coli ◽

Mobile Genetic Elements ◽

Dna Methyltransferases ◽

Genetic Elements ◽

Pathogenic Escherichia Coli ◽

And Function

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Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

Biology ◽

10.3390/biology10090896 ◽

2021 ◽

Vol 10 (9) ◽

pp. 896

Author(s):

Ilektra-Chara Giassa ◽

Panagiotis Alexiou

Keyword(s):

Machine Learning ◽

Chromatin Modification ◽

Mobile Genetic Elements ◽

Learning Approaches ◽

Sequencing Data ◽

Methylation Analysis ◽

Developmental Defects ◽

Genetic Elements ◽

Bisulfite Sequencing Data ◽

And Function

Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease, and drug resistance. Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.

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CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

10.1101/2021.06.04.447074 ◽

2021 ◽

Author(s):

Rafael Pinilla-Redondo ◽

Jakob Russel ◽

David Mayo-Muñoz ◽

Shiraz A Shah ◽

Roger A Garrett ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Comprehensive Analysis ◽

Immune Protection ◽

Genetic Elements ◽

And Function

Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet, a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is markedly distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences dominate across the diversity of CRISPR-Cas subtypes and host taxa, highlighting the genetic independence of plasmids and suggesting a major role of CRISPR-Cas for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.

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A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

Journal of Bacteriology ◽

10.1128/jb.06244-11 ◽

2011 ◽

Vol 194 (2) ◽

pp. 376-394 ◽

Cited By ~ 89

Author(s):

J. J. Gillespie ◽

V. Joardar ◽

K. P. Williams ◽

T. Driscoll ◽

J. B. Hostetler ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Obligate Intracellular ◽

Genetic Elements ◽

Insight Into

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AcrIIA22 is a novel anti-CRISPR that impairs SpyCas9 activity by relieving DNA torsion of target plasmids

10.1101/2020.09.28.317578 ◽

2020 ◽

Author(s):

Kevin J. Forsberg ◽

Danica T. Schmidtke ◽

Rachel Werther ◽

Deanna Hausman ◽

Barry L. Stoddard ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Nucleic Acid Binding ◽

Human Gut ◽

X Ray ◽

Genetic Elements ◽

Defense Systems ◽

Nucleic Acid Binding Proteins ◽

Genomic Regions ◽

Insight Into ◽

Negative Supercoils

AbstractTo overcome CRISPR-Cas defense systems, many phages and mobile genetic elements encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all mechanistically characterized Acrs directly bind their cognate Cas protein to inactivate CRISPR immunity. Here, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of Clostridial bacteria and their prophages from the human gut microbiome. Uncovered in a functional metagenomic selection, AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic-acid binding proteins. This homology helped us deduce that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids, rendering them less susceptible to SpyCas9, which is highly dependent on negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and mobile genetic elements.

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Structure and function of neural networks in the retina

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102213 ◽

1988 ◽

Vol 46 ◽

pp. 26-27

Author(s):

Peter Sterling

Keyword(s):

Ganglion Cells ◽

Three Dimensional ◽

Structure And Function ◽

Synaptic Connections ◽

Visual Axis ◽

One Dimensional ◽

Cat Retina ◽

Ultrathin Sections ◽

And Function ◽

Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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