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

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.

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

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.

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

Biology ◽  
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.

scholarly journals Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

PLoS ONE ◽  
2019 ◽  
Vol 14 (12) ◽  
pp. e0223680 ◽  
Author(s):  
Xiaofang Jiang ◽  
Andrew Brantley Hall ◽  
Ramnik J. Xavier ◽  
Eric J. Alm
Keyword(s):  
Gut Microbiome ◽  
Mobile Genetic Elements ◽  
Comprehensive Analysis ◽  
Gene Pools ◽  
Genetic Elements

scholarly journals Comprehensive analysis of mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

2017 ◽  
Author(s):  
Xiaofang Jiang ◽  
Andrew Brantley Hall ◽  
Ramnik J. Xavier ◽  
Eric Alm
Keyword(s):  
Antibiotic Resistance ◽  
Human Health ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Comprehensive Analysis ◽  
Gene Pools ◽  
Genetic Elements

AbstractMobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method called Split Read Insertion Detection (SRID) that enables the identification of the exact mobilizable unit of MGEs. Leveraging the SRID method, we curated a database of 5600 putative MGEs encompassing seven MGE classes called ImmeDB (Intestinal microbiome mobile element database) (https://immedb.mit.edu/). We observed that many MGEs carry genes that confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Additionally, we observed that horizontal transfer of MGEs is extensive within phyla but rare across phyla. Taken together, our findings support a phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future fundamental and translational studies on the gut microbiome and MGE communities.

ISSR-PCR markers and mobile genetic elements in horse (Equus caballus) genome

2014 ◽  
pp. 42-57 ◽  
Author(s):  
N.V. Bardukov ◽  
◽  
A.V. Feofilov ◽  
T.T. Glazko ◽  
V.I. Glazko ◽  
...  
Keyword(s):  
Equus Caballus ◽  
Mobile Genetic Elements ◽  
Pcr Markers ◽  
Genetic Elements ◽  
Issr Pcr
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