Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?

Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called “cellular defense systems,” whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.

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Many defense systems in microbial genomes, but which is defending whom from what?

10.32942/osf.io/zuh4c ◽

2021 ◽

Author(s):

Eduardo P. C. Rocha ◽

David Bikard

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Arms Race ◽

Significant Fraction ◽

Bacterial Genomes ◽

Microbial Genomes ◽

Genetic Elements ◽

Cellular Defense ◽

Defense Systems ◽

Intragenomic Conflict

Prokaryotes have numerous mobile genetic elements (MGE) that mediate horizontal gene transfer between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control or inactivate them. Surprisingly, many phages, conjugative plasmids, and their parasites, phage satellites or mobilizable plasmids, encode defense systems homologous to those of bacteria. They constitute a significant fraction of the systems found in bacterial genomes. As components of MGEs, they have presumably evolved to provide them, not the cell, adaptive functions that may be defensive, offensive, or both. This sheds new light on the role, effect, and fate of the so called “cellular defense systems”, whereby they are not merely microbial defensive weapons in a two-partner arms race, but tools of intragenomic conflict between multiple genetic elements with divergent interests. It also raises many intriguing questions.

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Disentangling the effects of selection and loss bias on gene dynamics

10.1101/139725 ◽

2017 ◽

Cited By ~ 2

Author(s):

Jaime Iranzo ◽

José A. Cuesta ◽

Susanna Manrubia ◽

Mikhail I. Katsnelson ◽

Eugene V. Koonin

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Size ◽

Mobile Genetic Elements ◽

Loss Ratio ◽

Effective Population ◽

Strong Selection ◽

Genetic Elements ◽

Defense Systems ◽

Parasite Defense

ABSTRACTWe combine mathematical modelling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most non-parasitic genes is low albeit positive, compatible with the observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in anti-parasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction-modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not the duplication to loss ratio, correlates with genome size, potentially explaining the increased abundance of neutral and costly elements in larger genomes.SIGNIFICANCEEvolution of microbes is dominated by horizontal gene transfer and the incessant host-parasite arms race that promotes the evolution of diverse anti-parasite defense systems. The evolutionary factors governing these processes are complex and difficult to disentangle but the rapidly growing genome databases provide ample material for testing evolutionary models. Rigorous mathematical modeling of evolutionary processes, combined with computer simulation and comparative genomics, allowed us to elucidate the evolutionary regimes of different classes of microbial genes. Only genes involved in key informational and metabolic pathways are subject to strong selection whereas most of the others are effectively neutral or even burdensome. Mobile genetic elements and defense systems are costly, supporting the understanding that their evolution is governed by the same factors.

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Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

10.1101/2020.05.22.110304 ◽

2020 ◽

Cited By ~ 2

Author(s):

Rafael Pinilla-Redondo ◽

Saadlee Shehreen ◽

Nicole D. Marino ◽

Robert D. Fagerlund ◽

Chris M. Brown ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Gene Clustering ◽

Type I ◽

Defense Gene ◽

Genetic Elements ◽

Defense Systems ◽

Prokaryotic Genomes ◽

New Type ◽

Genomic Regions ◽

Potential Exploitation

AbstractMany prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements within Enterobacteriaceae and Pseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5) and assayed against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas), revealing the type I-F and/or I-E acr genes and a new aca (aca9). We find that acr genes not only associate with other acr genes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be “anti-defense islands”, reminiscent of the clustered arrangement of “defense islands” in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation of acr loci neighborhoods for identifying new anti-defense systems.

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Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome

10.1101/2021.04.16.440249 ◽

2021 ◽

Author(s):

Stephany Flores Ramos ◽

Silvio D. Brugger ◽

Isabel Fernández Escapa ◽

Chelsey A Skeete ◽

Sean L Cotton ◽

...

Keyword(s):

Human Microbiome ◽

Genomic Stability ◽

Gene Clusters ◽

Mobile Genetic Elements ◽

Phylogenomic Analysis ◽

Hotspot Analysis ◽

Systematic Analysis ◽

Chromosomal Structure ◽

Genetic Elements ◽

Defense Systems

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites including one RM system hotspot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms.

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Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements

Nature Communications ◽

10.1038/s41467-020-19415-3 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Rafael Pinilla-Redondo ◽

Saadlee Shehreen ◽

Nicole D. Marino ◽

Robert D. Fagerlund ◽

Chris M. Brown ◽

...

Keyword(s):

Immune Evasion ◽

Mobile Genetic Elements ◽

Gene Clustering ◽

Type I ◽

Defense Gene ◽

Genetic Elements ◽

Defense Systems ◽

Evasion Strategy ◽

Genes Encoding ◽

Potential Exploitation

Abstract Many prokaryotes employ CRISPR–Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I–F (Pseudomonas, Pectobacterium, and Serratia), I–E (Pseudomonas and Serratia), and I–C (Pseudomonas). We uncover 11 type I–F and/or I–E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.

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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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Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

mBio ◽

10.1128/mbio.02938-21 ◽

2021 ◽

Author(s):

Sean Benler ◽

Guilhem Faure ◽

Han Altae-Tran ◽

Sergey Shmakov ◽

Feng Zheng ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Defense Systems

Transposons are major vehicles of horizontal gene transfer that, in addition to genes directly involved in transposition, carry cargo genes. However, characterization of these genes is hampered by the difficulty of identification of transposon boundaries.

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Recruitment of CRISPR-Cas systems by Tn7-like transposons

10.1101/154229 ◽

2017 ◽

Author(s):

Joseph E. Peters ◽

Kira S. Makarova ◽

Sergey Shmakov ◽

Eugene V. Koonin

Keyword(s):

Phylogenetic Analysis ◽

Host Defense ◽

Mobile Genetic Elements ◽

Comparative Genomic ◽

Type I ◽

Genetic Elements ◽

Defense Systems ◽

Crispr Array ◽

Target Binding ◽

Chromosomal Sequences

AbstractA survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain ‘minimal’ type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f and cas6f genes, and a short CRISPR array. Additionally, several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas systems. This gene composition of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-crRNA processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Here we present phylogenetic analysis demonstrating that evolution of the CRISPR-Cas containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We further show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences, and in some cases, chromosomal sequences adjacent to the transposon. A hypothesis is proposed that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. This scenario fits the “guns for hire” concept whereby mobile genetic elements can capture host defense systems and repurpose them for different stages in the life cycle of the element.ImportanceCRISPR-Cas is an adaptive immunity system that protects bacteria and archaea from mobile genetic elements. We present comparative genomic and phylogenetic analysis of degenerate CRISPR-Cas variants associated with distinct families of transposable elements and develop the hypothesis that such repurposed defense systems contribute to the transposable element propagation by facilitating transposition into specific sites. Such recruitment of defense systems by mobile elements supports the “guns for hire” concept under which the same enzymatic machineries can be alternately employed for transposon proliferation or host defense.

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