Hierarchical length and sequence preferences establish a single major piRNA 3'-end

PIWI-interacting RNAs (piRNAs) guard germline genomes against the deleterious action of retroviruses and other mobile genetic elements. How piRNAs faithfully discriminate between self and non-self to restrict all mobile elements while sparing essential genes remains a key outstanding question in genome biology. PiRNAs use extensive base-pairing to recognize their targets and variable 3'ends could change the specificity and efficacy of piRNA silencing. Here, we identify conserved rules that ensure the generation of a single major piRNA 3'end in flies and mice. Our data suggest that the PIWI proteins initially define a short interval on pre-piRNAs that grants access to the ZUC-processor complex. Within this Goldilocks zone, the preference of the ZUC-processor to cut in front of a Uridine determines the ultimate processing site. We observe a mouse-specific roadblock that relocates the Goldilocks zone and generates an opportunity for consecutive trimming by PNLDC1. Our data reveal a conserved hierarchy between length and sequence preferences that controls the piRNA sequence space. The unanticipated precision of 3'end formation bolsters the emerging understanding that the functional piRNA sequence space is tightly controlled to ensure effective defense.

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Mobile genetic element insertions drive antibiotic resistance across pathogens

10.1101/527788 ◽

2019 ◽

Cited By ~ 1

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.

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Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements

Microbiology ◽

10.1099/mic.0.030486-0 ◽

2009 ◽

Vol 155 (9) ◽

pp. 2962-2977 ◽

Cited By ~ 33

Author(s):

Timothy Sampson ◽

Gregory W. Broussard ◽

Laura J. Marinelli ◽

Deborah Jacobs-Sera ◽

Mondira Ray ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Analysis ◽

Mycobacterium Smegmatis ◽

Active Form ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

Comparative Genome Analysis ◽

Coding Region ◽

Comparative Genome ◽

Genetic Elements

Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41 901 bp, 42 289 bp and 41 441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.

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FtsK translocation permits discrimination between an endogenous and an imported Xer/dif recombination complex

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1523178113 ◽

2016 ◽

Vol 113 (28) ◽

pp. 7882-7887 ◽

Cited By ~ 13

Author(s):

Florian Fournes ◽

Estelles Crozat ◽

Carine Pages ◽

Catherine Tardin ◽

Laurence Salomé ◽

...

Keyword(s):

Chromosome Segregation ◽

Genomic Island ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

The Other ◽

Central Question ◽

Genetic Transmission ◽

Genetic Elements ◽

Daughter Cells ◽

Dna Translocase

In bacteria, the FtsK/Xer/dif (chromosome dimer resolution site) system is essential for faithful vertical genetic transmission, ensuring the resolution of chromosome dimers during their segregation to daughter cells. This system is also targeted by mobile genetic elements that integrate into chromosomal dif sites. A central question is thus how Xer/dif recombination is tuned to both act in chromosome segregation and stably maintain mobile elements. To explore this question, we focused on pathogenic Neisseria species harboring a genomic island in their dif sites. We show that the FtsK DNA translocase acts differentially at the recombination sites flanking the genomic island. It stops at one Xer/dif complex, activating recombination, but it does not stop on the other site, thus dismantling it. FtsK translocation thus permits cis discrimination between an endogenous and an imported Xer/dif recombination complex.

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Diverse mobile genetic elements support the persistence of Listeria monocytogenes on dairy farms

10.1101/2021.03.15.435412 ◽

2021 ◽

Author(s):

Hanna Castro ◽

Francois Douillard ◽

Hannu Korkeala ◽

Miia Lindström

Keyword(s):

Listeria Monocytogenes ◽

Resistance Genes ◽

Dairy Farms ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

Modification System ◽

Genetic Elements ◽

Restriction Modification System ◽

Biocide Resistance ◽

Potential Reservoir

Listeria monocytogenes is a food-borne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements of Listeria inhabiting dairy farms. We found that prophages and other mobile elements were significantly more numerous among persistent than sporadically occurring strains. We identified a remarkable diversity of mobile elements among farm isolates, including a novel group of plasmids infecting hypervirulent subtypes of L. monocytogenes and occasionally carrying biocide resistance determinants bcrABC or qacH. Resistance genes against bacitracin, arsenic and cadmium were significantly more prevalent among persistent than sporadic strains. Several of the mobile elements in Listeria were identical to the mobile elements of Enterococci, indicative of recent transfer between these genera. Finally, we demonstrated that the CRISPR-cas IIa system and a type II restriction-modification system were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements harbouring resistance genes against antimicrobials, biocides, and heavy metals.

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Discovery of widespread type I and type V CRISPR-Cas inhibitors

Science ◽

10.1126/science.aau5174 ◽

2018 ◽

Vol 362 (6411) ◽

pp. 240-242 ◽

Cited By ~ 99

Author(s):

Nicole D. Marino ◽

Jenny Y. Zhang ◽

Adair L. Borges ◽

Alexander A. Sousa ◽

Lina M. Leon ◽

...

Keyword(s):

Immune Function ◽

Broad Spectrum ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

Human Cells ◽

Type I ◽

Type Ii ◽

Genetic Elements ◽

Type V

Bacterial CRISPR-Cas systems protect their host from bacteriophages and other mobile genetic elements. Mobile elements, in turn, encode various anti-CRISPR (Acr) proteins to inhibit the immune function of CRISPR-Cas. To date, Acr proteins have been discovered for type I (subtypes I-D, I-E, and I-F) and type II (II-A and II-C) but not other CRISPR systems. Here, we report the discovery of 12 acr genes, including inhibitors of type V-A and I-C CRISPR systems. AcrVA1 inhibits a broad spectrum of Cas12a (Cpf1) orthologs—including MbCas12a, Mb3Cas12a, AsCas12a, and LbCas12a—when assayed in human cells. The acr genes reported here provide useful biotechnological tools and mark the discovery of acr loci in many bacteria and phages.

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Experimental approaches to tracking mobile genetic elements in microbial communities

FEMS Microbiology Reviews ◽

10.1093/femsre/fuaa025 ◽

2020 ◽

Vol 44 (5) ◽

pp. 606-630 ◽

Cited By ~ 1

Author(s):

Christina C Saak ◽

Cong B Dinh ◽

Rachel J Dutton

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Microbial Communities ◽

Mobile Genetic Elements ◽

Mobile Elements ◽

Microbial Evolution ◽

Fermented Food ◽

Chromosome Conformation ◽

Genetic Elements ◽

Experimental Approaches

ABSTRACT Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.

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