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López-Beltrán A, Botelho J, Iranzo J. Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome. THE ISME JOURNAL 2024; 18:wrae134. [PMID: 39023219 PMCID: PMC11307328 DOI: 10.1093/ismejo/wrae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/07/2024] [Accepted: 07/17/2024] [Indexed: 07/20/2024]
Abstract
Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.
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Affiliation(s)
- Adrián López-Beltrán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Parque Científico y Tecnológico UPM, Campus de Montegancedo, 28223, Madrid, Spain
| | - João Botelho
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Parque Científico y Tecnológico UPM, Campus de Montegancedo, 28223, Madrid, Spain
| | - Jaime Iranzo
- Centro de Astrobiología (CAB), CSIC-INTA, Ctra. de Torrejón a Ajalvir Km 4, 28850, Torrejón de Ardoz, Madrid, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Campus Río Ebro, 50018, Zaragoza, Spain
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2
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Pavlova YS, Paez-Espino D, Morozov AY, Belalov IS. Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling. PLoS Comput Biol 2021; 17:e1008841. [PMID: 33770071 PMCID: PMC8026048 DOI: 10.1371/journal.pcbi.1008841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 04/07/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.
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Affiliation(s)
- Yekaterina S. Pavlova
- Mathematics Department, Palomar College, San Marcos, California, United States of America
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
- Mammoth BioSciences, South San Francisco, California, United States of America
| | - Andrew Yu. Morozov
- School of Mathematics and Actuarial Science, University of Leicester, Leicester, United Kingdom
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ilya S. Belalov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
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3
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Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium. Microorganisms 2020; 8:microorganisms8050720. [PMID: 32408568 PMCID: PMC7284854 DOI: 10.3390/microorganisms8050720] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.
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Brandt K, Nethery MA, O'Flaherty S, Barrangou R. Genomic characterization of Lactobacillus fermentum DSM 20052. BMC Genomics 2020; 21:328. [PMID: 32349666 PMCID: PMC7191730 DOI: 10.1186/s12864-020-6740-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/16/2020] [Indexed: 12/11/2022] Open
Abstract
Background Lactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of select strains that may provide human health benefits. Here, we genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species. Results We determined the polished whole genome sequence of this type strain and compared it to 37 available genome sequences within this species. Results reveal genetic diversity across nine clades, with variable content encompassing mobile genetic elements, CRISPR-Cas immune systems and genomic islands, as well as numerous genome rearrangements. Interestingly, we determined a high frequency of occurrence of diverse Type I, II, and III CRISPR-Cas systems in 72% of the genomes, with a high level of strain hypervariability. Conclusions These findings provide a basis for the genetic characterization of L. fermentum strains of scientific and commercial interest. Furthermore, our study enables genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest.
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Affiliation(s)
- Katelyn Brandt
- Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Matthew A Nethery
- Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rodolphe Barrangou
- Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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Type I-F CRISPR-Cas Distribution and Array Dynamics in Legionella pneumophila. G3-GENES GENOMES GENETICS 2020; 10:1039-1050. [PMID: 31937548 PMCID: PMC7056967 DOI: 10.1534/g3.119.400813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In bacteria and archaea, several distinct types of CRISPR-Cas systems provide adaptive immunity through broadly similar mechanisms: short nucleic acid sequences derived from foreign DNA, known as spacers, engage in complementary base pairing with invasive genetic elements setting the stage for nucleases to degrade the target DNA. A hallmark of type I CRISPR-Cas systems is their ability to acquire spacers in response to both new and previously encountered invaders (naïve and primed acquisition, respectively). Our phylogenetic analyses of 43 L. pneumophila type I-F CRISPR-Cas systems and their resident genomes suggest that many of these systems have been horizontally acquired. These systems are frequently encoded on plasmids and can co-occur with nearly identical chromosomal loci. We show that two such co-occurring systems are highly protective and undergo efficient primed acquisition in the lab. Furthermore, we observe that targeting by one system’s array can prime spacer acquisition in the other. Lastly, we provide experimental and genomic evidence for a model in which primed acquisition can efficiently replenish a depleted type I CRISPR array following a mass spacer deletion event.
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Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature 2020; 578:425-431. [PMID: 32051592 PMCID: PMC7162821 DOI: 10.1038/s41586-020-2007-4] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
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Affiliation(s)
- Basem Al-Shayeb
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lin-Xing Chen
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Fred Ward
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Audra Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Matthew R Olm
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan
| | - Christine He
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Brandon Brooks
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alex Thomas
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adi Lavy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Christine Sun
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | | | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Allison Sharrar
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Alexander L Jaffe
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Tara C Nelson
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rose Kantor
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ray Keren
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Katherine R Lane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ibrahim F Farag
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Kari Finstad
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Ronald Amundson
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Karthik Anantharaman
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Alexander J Probst
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Mary E Power
- Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kelly Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sue Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Lesley Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
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Bernheim A, Bikard D, Touchon M, Rocha EPC. Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. Nucleic Acids Res 2020; 48:748-760. [PMID: 31745554 PMCID: PMC7145637 DOI: 10.1093/nar/gkz1091] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes use CRISPR-Cas systems for adaptive immunity, but the reasons for the frequent existence of multiple CRISPRs and cas clusters remain poorly understood. Here, we analysed the joint distribution of CRISPR and cas genes in a large set of fully sequenced bacterial genomes and their mobile genetic elements. Our analysis suggests few negative and many positive epistatic interactions between Cas subtypes. The latter often result in complex genetic organizations, where a locus has a single adaptation module and diverse interference mechanisms that might provide more effective immunity. We typed CRISPRs that could not be unambiguously associated with a cas cluster and found that such complex loci tend to have unique type I repeats in multiple CRISPRs. Many chromosomal CRISPRs lack a neighboring Cas system and they often have repeats compatible with the Cas systems encoded in trans. Phages and 25 000 prophages were almost devoid of CRISPR-Cas systems, whereas 3% of plasmids had CRISPR-Cas systems or isolated CRISPRs. The latter were often compatible with the chromosomal cas clusters, suggesting that plasmids can co-opt the latter. These results highlight the importance of interactions between CRISPRs and cas present in multiple copies and in distinct genomic locations in the function and evolution of bacterial immunity.
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Affiliation(s)
- Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
- Synthetic Biology Group, Institut Pasteur, 25–28 rue Dr. Roux, Paris 75015, France
- AgroParisTech, F-75005 Paris, France
- Ecole doctorale Frontières du vivant, Université Paris Diderot, Université Sorbonne Paris Cité, 75013 Paris, France
| | - David Bikard
- Synthetic Biology Group, Institut Pasteur, 25–28 rue Dr. Roux, Paris 75015, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
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Scrascia M, D'Addabbo P, Roberto R, Porcelli F, Oliva M, Calia C, Dionisi AM, Pazzani C. Characterization of CRISPR-Cas Systems in Serratia marcescens Isolated from Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Curculionidae). Microorganisms 2019; 7:microorganisms7090368. [PMID: 31546915 PMCID: PMC6780938 DOI: 10.3390/microorganisms7090368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
The CRISPR-Cas adaptive immune system has been attracting increasing scientific interest for biological functions and biotechnological applications. Data on the Serratia marcescens system are scarce. Here, we report a comprehensive characterisation of CRISPR-Cas systems identified in S. marcescens strains isolated as secondary symbionts of Rhynchophorus ferrugineus, also known as Red Palm Weevil (RPW), one of the most invasive pests of major cultivated palms. Whole genome sequencing was performed on four strains (S1, S5, S8, and S13), which were isolated from the reproductive apparatus of RPWs. Subtypes I-F and I-E were harboured by S5 and S8, respectively. No CRISPR-Cas system was detected in S1 or S13. Two CRISPR arrays (4 and 51 spacers) were detected in S5 and three arrays (11, 31, and 30 spacers) were detected in S8. The CRISPR-Cas systems were located in the genomic region spanning from ybhR to phnP, as if this were the only region where CRISPR-Cas loci were acquired. This was confirmed by analyzing the S. marcescens complete genomes available in the NCBI database. This region defines a genomic hotspot for horizontally acquired genes and/or CRISPR-Cas systems. This study also supplies the first identification of subtype I-E in S. marcescens.
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Affiliation(s)
- Maria Scrascia
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Pietro D'Addabbo
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Roberta Roberto
- Department of Plants, Food, and Soil Sciences, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Francesco Porcelli
- Department of Plants, Food, and Soil Sciences, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Marta Oliva
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Carla Calia
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Anna Maria Dionisi
- Department of Infectious diseases, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Carlo Pazzani
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
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Crawley AB, Henriksen JR, Barrangou R. CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. CRISPR J 2019. [PMID: 31021201 DOI: 10.1089/crispr.2017.0022.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.
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Affiliation(s)
- Alexandra B Crawley
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
| | | | - Rodolphe Barrangou
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
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10
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Crawley AB, Henriksen ED, Stout E, Brandt K, Barrangou R. Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli. Sci Rep 2018; 8:11544. [PMID: 30068963 PMCID: PMC6070500 DOI: 10.1038/s41598-018-29746-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/09/2018] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems provide immunity against phages and plasmids in bacteria and archaea. Despite the popularity of CRISPR-Cas9 based genome editing, few endogenous systems have been characterized to date. Here, we sampled 1,262 publically available lactobacilli genomes found them to be enriched with CRISPR-Cas adaptive immunity. While CRISPR-Cas is ubiquitous in some Lactobacillus species, CRISPR-Cas content varies at the strain level in most Lactobacillus species. We identified that Type II is the most abundant type across the genus, with II-A being the most dominant sub-type. We found that many Type II-A systems are actively transcribed, and encode spacers that efficiently provide resistance against plasmid uptake. Analysis of various CRISPR transcripts revealed that guide sequences are highly diverse in terms of crRNA and tracrRNA length and structure. Interference assays revealed highly diverse target PAM sequences. Lastly, we show that these systems can be readily repurposed for self-targeting by expressing an engineered single guide RNA. Our results reveal that Type II-A systems in lactobacilli are naturally active in their native host in terms of expression and efficiently targeting invasive and genomic DNA. Together, these systems increase the possible Cas9 targeting space and provide multiplexing potential in native hosts and heterologous genome editing purpose.
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Affiliation(s)
- Alexandra B Crawley
- North Carolina State University Functional Genomics, Raleigh, NC, 27695, USA
| | - Emily D Henriksen
- North Carolina State University Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, 27695, USA
| | - Emily Stout
- North Carolina State University Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, 27695, USA
| | - Katelyn Brandt
- North Carolina State University Functional Genomics, Raleigh, NC, 27695, USA
| | - Rodolphe Barrangou
- North Carolina State University Functional Genomics, Raleigh, NC, 27695, USA.
- North Carolina State University Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, 27695, USA.
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11
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Crawley AB, Henriksen JR, Barrangou R. CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. CRISPR J 2018; 1:171-181. [PMID: 31021201 PMCID: PMC6636876 DOI: 10.1089/crispr.2017.0022] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.
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Affiliation(s)
- Alexandra B Crawley
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
| | | | - Rodolphe Barrangou
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
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