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Chintakovid N, Singkhamanan K, Yaikhan T, Nokchan N, Wonglapsuwan M, Jitpakdee J, Kantachote D, Surachat K. Probiogenomic analysis of Lactiplantibacillus plantarum SPS109: A potential GABA-producing and cholesterol-lowering probiotic strain. Heliyon 2024; 10:e33823. [PMID: 39044985 PMCID: PMC11263657 DOI: 10.1016/j.heliyon.2024.e33823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
Lactiplantibacillus plantarum SPS109, an isolated strain of lactic acid bacteria (LAB) from fermented foods, showed remarkable potential as a probiotic with dual capabilities in γ-aminobutyric acid (GABA) production and cholesterol reduction. This study employs genomic and comparative analyses to search into the strain's genetic profile, safety features, and probiotic attributes. The safety assessment reveals the absence of virulence factors and antimicrobial resistance genes, while the genome uncovers bacteriocin-related elements, including sactipeptides and a cluster for putative plantaricins, strengthening its ability to combat diverse pathogens. Pangenome analysis revealed unique bacteriocin-related genes, specifically lcnD and bcrA, distinguishing SPS109 from four other L. plantarum strains producing GABA. In addition, genomic study emphasizes SPS109 strain distinctive features, two GABA-related genes responsible for GABA production and a bile tolerance gene (cbh) crucial for cholesterol reduction. Additionally, the analysis highlights several genes of potential probiotic properties, including stress tolerance, vitamin production, and antioxidant activity. In summary, L. plantarum SPS109 emerges as a promising probiotic candidate with versatile applications in the food and beverage industries, supported by its unique genomic features and safety profile.
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Affiliation(s)
- Nutwadee Chintakovid
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Thunchanok Yaikhan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Natakorn Nokchan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jirayu Jitpakdee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
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Cunha-Ferreira IC, Vizzotto CS, Freitas MAM, Peixoto J, Carvalho LS, Tótola MR, Thompson FL, Krüger RH. Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil. Braz J Microbiol 2024; 55:1099-1115. [PMID: 38605254 PMCID: PMC11153394 DOI: 10.1007/s42770-024-01324-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).
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Affiliation(s)
- I C Cunha-Ferreira
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - C S Vizzotto
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, University of Brasília (UNB), Brasília, Brazil
| | - M A M Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J Peixoto
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - L S Carvalho
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - M R Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | - F L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R H Krüger
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil.
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3
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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4
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Allemailem KS. Recent Advances in Understanding the Molecular Mechanisms of Multidrug Resistance and Novel Approaches of CRISPR/Cas9-Based Genome-Editing to Combat This Health Emergency. Int J Nanomedicine 2024; 19:1125-1143. [PMID: 38344439 PMCID: PMC10859101 DOI: 10.2147/ijn.s453566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The rapid spread of multidrug resistance (MDR), due to abusive use of antibiotics has led to global health emergency, causing substantial morbidity and mortality. Bacteria attain MDR by different means such as antibiotic modification/degradation, target protection/modification/bypass, and enhanced efflux mechanisms. The classical approaches of counteracting MDR bacteria are expensive and time-consuming, thus, it is highly significant to understand the molecular mechanisms of this resistance to curb the problem from core level. The revolutionary approach of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated sequence 9 (CRISPR/Cas9), considered as a next-generation genome-editing tool presents an innovative opportunity to precisely target and edit bacterial genome to alter their MDR strategy. Different bacteria possessing antibiotic resistance genes such as mecA, ermB, ramR, tetA, mqrB and blaKPC that have been targeted by CRISPR/Cas9 to re-sensitize these pathogens against antibiotics, such as methicillin, erythromycin, tigecycline, colistin and carbapenem, respectively. The CRISPR/Cas9 from S. pyogenes is the most widely studied genome-editing tool, consisting of a Cas9 DNA endonuclease associated with tracrRNA and crRNA, which can be systematically coupled as sgRNA. The targeting strategies of CRISPR/Cas9 to bacterial cells is mediated through phage, plasmids, vesicles and nanoparticles. However, the targeting approaches of this genome-editing tool to specific bacteria is a challenging task and still remains at a very preliminary stage due to numerous obstacles awaiting to be solved. This review elaborates some recent updates about the molecular mechanisms of antibiotic resistance and the innovative role of CRISPR/Cas9 system in modulating these resistance mechanisms. Furthermore, the delivery approaches of this genome-editing system in bacterial cells are discussed. In addition, some challenges and future prospects are also described.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah51452, Saudi Arabia
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Wimmer F, Englert F, Wandera KG, Alkhnbashi O, Collins S, Backofen R, Beisel C. Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation. Nucleic Acids Res 2024; 52:769-783. [PMID: 38015466 PMCID: PMC10810201 DOI: 10.1093/nar/gkad1097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host's genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. We show that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. When expressed in Escherichia coli, each Cascade complex binds its PAM-flanked DNA target to block transcription, while the addition of Cas3 paired with genome targeting induces cell killing. While exploring how X. albilineans survives self-targeting, we predicted putative anti-CRISPR proteins (Acrs) encoded within the bacterium's genome. Screening of identified candidates with cell-free transcription-translation systems and in E. coli revealed two Acrs, which we named AcrIC11 and AcrIF12Xal, that inhibit the activity of Cas3 but not Cascade of the respective system. While AcrF12Xal is homologous to AcrIF12, AcrIC11 shares sequence and structural homology with the anti-restriction protein KlcA. These findings help explain tolerance of self-targeting through two CRISPR-Cas systems and expand the known suite of DNA degradation-inhibiting Acrs.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Intelligent Secure Systems (IRC-ISS), King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
| | - Scott P Collins
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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6
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Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. THE ISME JOURNAL 2024; 18:wrae005. [PMID: 38366192 PMCID: PMC10910852 DOI: 10.1093/ismejo/wrae005] [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: 12/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Abstract
CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Ling Deng
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
| | - Philippe Horvath
- IFF Danisco, Health & Biosciences, Dangé-Saint-Romain 86220, France
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dennis S Nielsen
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, Jouy-en-Josas 78350, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
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Sawhney SS, Vargas RC, Wallace MA, Muenks CE, Lubbers BV, Fritz SA, Burnham CAD, Dantas G. Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms. Nat Commun 2023; 14:7065. [PMID: 37923729 PMCID: PMC10624692 DOI: 10.1038/s41467-023-42694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Staphylococcus pseudintermedius is historically understood as a prevalent commensal and pathogen of dogs, though modern clinical diagnostics reveal an expanded host-range that includes humans. It remains unclear whether differentiation across S. pseudintermedius populations is driven primarily by niche-type or host-species. We sequenced 501 diagnostic and commensal isolates from a hospital, veterinary diagnostic laboratory, and within households in the American Midwest, and performed a comparative genomics investigation contrasting human diagnostic, animal diagnostic, human colonizing, pet colonizing, and household-surface S. pseudintermedius isolates. Though indistinguishable by core and accessory gene architecture, diagnostic isolates harbor more encoded and phenotypic resistance, whereas colonizing and surface isolates harbor similar CRISPR defense systems likely reflective of common household phage exposures. Furthermore, household isolates that persist through anti-staphylococcal decolonization report elevated rates of base-changing mutations in - and parallel evolution of - defense genes, as well as reductions in oxacillin and trimethoprim-sulfamethoxazole susceptibility. Together we report parallel niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation.
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Affiliation(s)
- Sanjam S Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meghan A Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol E Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Lubbers
- Department of Clinical Sciences, Kansas State University, Manhattan, KS, USA
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Reysenbach AL, Terns MP. CRISPR-influenced symbiosis. Nat Microbiol 2023; 8:1611-1612. [PMID: 37580593 PMCID: PMC10791070 DOI: 10.1038/s41564-023-01445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
CRISPR systems canonically confer microorganisms with protection against invading viral DNA, plasmids and mobile genetic elements, however a multi-omics investigation of deep subsurface archaeal communities suggests that archaeal CRISPR systems might target other archaeal parasites or force a transition from parasitism to mutualism.
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Affiliation(s)
- Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA.
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Athens, GA, USA.
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9
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Huo W, Price VJ, Sharifi A, Zhang MQ, Palmer KL. Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid. Appl Environ Microbiol 2023; 89:e0012423. [PMID: 37278656 PMCID: PMC10304774 DOI: 10.1128/aem.00124-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged that are replete with mobile genetic elements (MGEs). Non-MDR E. faecalis strains frequently possess CRISPR-Cas systems, which reduce the frequency of MGE acquisition. We demonstrated in previous studies that E. faecalis populations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-type E. faecalis populations but not E. faecalis populations that lacked the cas9 gene. Our results indicate that E. faecalis CRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer. IMPORTANCE Enterococcus faecalis is a leading cause of hospital-acquired infections and disseminator of antibiotic resistance plasmids among Gram-positive bacteria. We have previously shown that E. faecalis strains with an active CRISPR-Cas system can prevent plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. However, CRISPR-Cas is not a perfect barrier. In this study, we observed populations of E. faecalis with transient coexistence of CRISPR-Cas and one of its plasmid targets. Our experimental data demonstrate that antibiotic selection results in compromised E. faecalis CRISPR-Cas function, thereby facilitating the acquisition of additional resistance plasmids by E. faecalis.
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Affiliation(s)
- Wenwen Huo
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Valerie J. Price
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Ardalan Sharifi
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Michael Q. Zhang
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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10
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Parra-Sánchez Á, Antequera-Zambrano L, Martínez-Navarrete G, Zorrilla-Muñoz V, Paz JL, Alvarado YJ, González-Paz L, Fernández E. Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes. Genes (Basel) 2023; 14:1337. [PMID: 37510242 PMCID: PMC10379622 DOI: 10.3390/genes14071337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR.
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Affiliation(s)
- Ángel Parra-Sánchez
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
| | - Laura Antequera-Zambrano
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
| | - Gema Martínez-Navarrete
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
| | - Vanessa Zorrilla-Muñoz
- Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
- University Institute on Gender Studies, University Carlos III of Madrid, Getafe, 28903 Madrid, Spain
| | - José Luis Paz
- Academic Department of Inorganic Chemistry, Faculty of Chemistry and Chemical Engineering, National University of San Marcos, Lima 15081, Peru
| | - Ysaias J Alvarado
- Laboratory of Theoretical and Experimental Biophysical Chemistry (LQBTE), Center for Molecular Biomedicine (CBM), Venezuelan Institute for Scientific Research (IVIC), Maracaibo 4001, Venezuela
| | - Lenin González-Paz
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
- Laboratory of Biocomputing (LB), Center for Molecular Biomedicine (CBM), Venezuelan Institute for Scientific Research (IVIC), Maracaibo 4001, Venezuela
| | - Eduardo Fernández
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
- Biomedical Research Network Center (CIBER-BBN), 28029 Madrid, Spain
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11
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Poulalier-Delavelle M, Baker JP, Millard J, Winzer K, Minton NP. Endogenous CRISPR/Cas systems for genome engineering in the acetogens Acetobacterium woodii and Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1213236. [PMID: 37425362 PMCID: PMC10328091 DOI: 10.3389/fbioe.2023.1213236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Acetogenic bacteria can play a major role in achieving Net Zero through their ability to convert CO2 into industrially relevant chemicals and fuels. Full exploitation of this potential will be reliant on effective metabolic engineering tools, such as those based on the Streptococcus pyogenes CRISPR/Cas9 system. However, attempts to introduce cas9-containing vectors into Acetobacterium woodii were unsuccessful, most likely as a consequence of Cas9 nuclease toxicity and the presence of a recognition site for an endogenous A. woodii restriction-modification (R-M) system in the cas9 gene. As an alternative, this study aims to facilitate the exploitation of CRISPR/Cas endogenous systems as genome engineering tools. Accordingly, a Python script was developed to automate the prediction of protospacer adjacent motif (PAM) sequences and used to identify PAM candidates of the A. woodii Type I-B CRISPR/Cas system. The identified PAMs and the native leader sequence were characterized in vivo by interference assay and RT-qPCR, respectively. Expression of synthetic CRISPR arrays, consisting of the native leader sequence, direct repeats, and adequate spacer, along with an editing template for homologous recombination, successfully led to the creation of 300 bp and 354 bp in-frame deletions of pyrE and pheA, respectively. To further validate the method, a 3.2 kb deletion of hsdR1 was also generated, as well as the knock-in of the fluorescence-activating and absorption-shifting tag (FAST) reporter gene at the pheA locus. Homology arm length, cell density, and the amount of DNA used for transformation were found to significantly impact editing efficiencies. The devised workflow was subsequently applied to the Type I-B CRISPR/Cas system of Clostridium autoethanogenum, enabling the generation of a 561 bp in-frame deletion of pyrE with 100% editing efficiency. This is the first report of genome engineering of both A. woodii and C. autoethanogenum using their endogenous CRISPR/Cas systems.
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Affiliation(s)
| | | | | | | | - Nigel P. Minton
- *Correspondence: Margaux Poulalier-Delavelle, ; Nigel P. Minton,
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12
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Webb EA, Held NA, Zhao Y, Graham ED, Conover AE, Semones J, Lee MD, Feng Y, Fu FX, Saito MA, Hutchins DA. Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades. ISME COMMUNICATIONS 2023; 3:15. [PMID: 36823453 PMCID: PMC9950141 DOI: 10.1038/s43705-023-00214-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/13/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.
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Affiliation(s)
- Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Environmental Systems Science, ETH, Zurich, Switzerland
| | - Yiming Zhao
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Elaina D Graham
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Asa E Conover
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jake Semones
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | - Yuanyuan Feng
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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13
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Malla RR, Middela K. CRISPR-Based Approaches for Cancer Immunotherapy. Crit Rev Oncog 2023; 28:1-14. [PMID: 38050977 DOI: 10.1615/critrevoncog.2023048723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) technology is a powerful gene editing tool that has the potential to revolutionize cancer treatment. It allows for precise and efficient editing of specific genes that drive cancer growth and progression. CRISPR-based approaches gene knock-out, which deletes specific genes or sequences of DNA within a cancer cell, and gene knock-in, which inserts new sequences of DNA into a cancer cell to identify potential targets for cancer therapy. Further, genome-wide CRISPR-Cas9-based screens identify specific markers for diagnosis of cancers. Recently, immunotherapy has become a highly efficient strategy for the treatment of cancer. The use of CRISPR in cancer immunotherapy is focused on enhancing the function of T cells, making them more effective at attacking cancer cells and inactivating the immune evasion mechanisms of cancer cells. It has the potential to generate CAR-T cells, which are T cells that have been genetically engineered to target and attack cancer cells specifically. This review uncovers the latest developments in CRISPR-based gene editing strategies and delivery of their components in cancer cells. In addition, the applications of CRISPR in cancer immune therapy are discussed. Overall, this review helps to explore the potential of CRISPR-based strategies in cancer immune therapy in clinical settings.
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Affiliation(s)
- Rama Rao Malla
- Cancer Biology Laboratory, Department of Biochemistry and Bioinformatics, School of Science, Gandhi Institute of Technology and Management (GITAM) (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India; Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
| | - Keerthana Middela
- Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
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14
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Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications. Arch Microbiol 2022; 204:703. [DOI: 10.1007/s00203-022-03312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 10/29/2022] [Indexed: 11/14/2022]
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15
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Lam TJ, Mortensen K, Ye Y. Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population. BMC Genomics 2022; 23:573. [PMID: 35953824 PMCID: PMC9367070 DOI: 10.1186/s12864-022-08770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Background CRISPR-Cas (clustered regularly interspaced short palindromic repeats—CRISPR-associated proteins) systems are adaptive immune systems commonly found in prokaryotes that provide sequence-specific defense against invading mobile genetic elements (MGEs). The memory of these immunological encounters are stored in CRISPR arrays, where spacer sequences record the identity and history of past invaders. Analyzing such CRISPR arrays provide insights into the dynamics of CRISPR-Cas systems and the adaptation of their host bacteria to rapidly changing environments such as the human gut. Results In this study, we utilized 601 publicly available Bacteroides fragilis genome isolates from 12 healthy individuals, 6 of which include longitudinal observations, and 222 available B. fragilis reference genomes to update the understanding of B. fragilis CRISPR-Cas dynamics and their differential activities. Analysis of longitudinal genomic data showed that some CRISPR array structures remained relatively stable over time whereas others involved radical spacer acquisition during some periods, and diverse CRISPR arrays (associated with multiple isolates) co-existed in the same individuals with some persisted over time. Furthermore, features of CRISPR adaptation, evolution, and microdynamics were highlighted through an analysis of host-MGE network, such as modules of multiple MGEs and hosts, reflecting complex interactions between B. fragilis and its invaders mediated through the CRISPR-Cas systems. Conclusions We made available of all annotated CRISPR-Cas systems and their target MGEs, and their interaction network as a web resource at https://omics.informatics.indiana.edu/CRISPRone/Bfragilis. We anticipate it will become an important resource for studying of B. fragilis, its CRISPR-Cas systems, and its interaction with mobile genetic elements providing insights into evolutionary dynamics that may shape the species virulence and lead to its pathogenicity. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08770-8).
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Affiliation(s)
- Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Kate Mortensen
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA.
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16
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Chabas H, Müller V, Bonhoeffer S, Regoes RR. Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems. PLoS Comput Biol 2022; 18:e1010329. [PMID: 35881633 PMCID: PMC9355216 DOI: 10.1371/journal.pcbi.1010329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/05/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Bacteria have adaptive immunity against viruses (phages) in the form of CRISPR-Cas immune systems. Currently, 6 types of CRISPR-Cas systems are known and the molecular study of three of these has revealed important molecular differences. It is unknown if and how these molecular differences change the outcome of phage infection and the evolutionary pressure the CRISPR-Cas systems faces. To determine the importance of these molecular differences, we model a phage outbreak entering a population defending exclusively with a type I/II or a type III CRISPR-Cas system. We show that for type III CRISPR-Cas systems, rapid phage extinction is driven by the probability to acquire at least one resistance spacer. However, for type I/II CRISPR-Cas systems, rapid phage extinction is characterized by an a threshold-like behaviour: any acquisition probability below this threshold leads to phage survival whereas any acquisition probability above it, results in phage extinction. We also show that in the absence of autoimmunity, high acquisition rates evolve. However, when CRISPR-Cas systems are prone to autoimmunity, intermediate levels of acquisition are optimal during a phage outbreak. As we predict an optimal probability of spacer acquisition 2 factors of magnitude above the one that has been measured, we discuss the origin of such a discrepancy. Finally, we show that in a biologically relevant parameter range, a type III CRISPR-Cas system can outcompete a type I/II CRISPR-Cas system with a slightly higher probability of acquisition. CRISPR-Cas systems are adaptive immune systems that use a complex 3-step molecular mechanism to defend prokaryotes against phages. Viral infections of populations defending themselves with CRISPR-Cas can result in rapid phage extinction or in medium-term phage maintenance. To investigate what controls the fate of the phage population, we use mathematical modeling of type I/II and type III CRISPR-Cas systems, and show that two parameters control the epidemiological short-term outcome: the type of CRISPR-Cas systems and CRISPR-Cas probability of resistance acquisition. Furthermore, the latter impacts host fitness. From this, we derive that 1) for both types, CRISPR-Cas acquisition probability is a key predictor of the efficiency and of the cost of a CRISPR-Cas system, 2) during an outbreak, there is an optimal probability of resistance acquisition balancing the cost of autoimmunity and immune efficiency and 3) type I/II CRISPR-Cas systems are likely to evolve higher acquisition probability than type III.
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Affiliation(s)
- Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
- * E-mail:
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | | | - Roland R. Regoes
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
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17
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Zaayman M, Wheatley RM. Fitness costs of CRISPR-Cas systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849532 DOI: 10.1099/mic.0.001209] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.
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18
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Nath A, Bhattacharjee R, Nandi A, Sinha A, Kar S, Manoharan N, Mitra S, Mojumdar A, Panda PK, Patro S, Dutt A, Ahuja R, Verma SK, Suar M. Phage delivered CRISPR-Cas system to combat multidrug-resistant pathogens in gut microbiome. Biomed Pharmacother 2022; 151:113122. [PMID: 35594718 DOI: 10.1016/j.biopha.2022.113122] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022] Open
Abstract
The Host-microbiome interactions that exist inside the gut microbiota operate in a synergistic and abnormal manner. Additionally, the normal homeostasis and functioning of gut microbiota are frequently disrupted by the intervention of Multi-Drug Resistant (MDR) pathogens. CRISPR-Cas (CRISPR-associated protein with clustered regularly interspersed short palindromic repeats) recognized as a prokaryotic immune system has emerged as an effective genome-editing tool to edit and delete specific microbial genes for the expulsion of bacteria through bactericidal action. In this review, we demonstrate many functioning CRISPR-Cas systems against the anti-microbial resistance of multiple pathogens, which infiltrate the gastrointestinal tract. Moreover, we discuss the advancement in the development of a phage-delivered CRISPR-Cas system for killing a gut MDR pathogen. We also discuss a combinatorial approach to use bacteriophage as a delivery system for the CRISPR-Cas gene for targeting a pathogenic community in the gut microbiome to resensitize the drug sensitivity. Finally, we discuss engineered phage as a plausible potential option for the CRISPR-Cas system for pathogenic killing and improvement of the efficacy of the system.
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Affiliation(s)
- Arijit Nath
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Rahul Bhattacharjee
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Adrija Sinha
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Sulagna Kar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | | | - Shirsajit Mitra
- KaviKrishna Laboratory, Indian Institute of Technology, Guwahati, Assam, India
| | - Abhik Mojumdar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Swadheena Patro
- KIIT School of Dental Sciences, KIIT University. Bhubaneswar 751024, Odisha
| | - Ateet Dutt
- Instituto de Investigaciones en Materiales, UNAM, CDMX, Mexico
| | - Rajeev Ahuja
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Suresh K Verma
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India.
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19
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Huang CJ, Adler BA, Doudna JA. A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression. Mol Cell 2022; 82:2148-2160.e4. [PMID: 35659325 DOI: 10.1016/j.molcel.2022.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/14/2022] [Accepted: 04/14/2022] [Indexed: 12/26/2022]
Abstract
Used widely for genome editing, CRISPR-Cas enzymes provide RNA-guided immunity to microbes by targeting foreign nucleic acids for cleavage. We show here that the native activity of CRISPR-Cas12c protects bacteria from phage infection by binding to DNA targets without cleaving them, revealing that antiviral interference can be accomplished without chemical attack on the invader or general metabolic disruption in the host. Biochemical experiments demonstrate that Cas12c is a site-specific ribonuclease capable of generating mature CRISPR RNAs (crRNAs) from precursor transcripts. Furthermore, we find that crRNA maturation is essential for Cas12c-mediated DNA targeting. These crRNAs direct double-stranded DNA binding by Cas12c using a mechanism that precludes DNA cutting. Nevertheless, Cas12c represses transcription and can defend bacteria against lytic bacteriophage infection when targeting an essential phage gene. Together, these results show that Cas12c employs targeted DNA binding to provide antiviral immunity in bacteria, providing a native DNase-free pathway for transient antiviral immunity.
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Affiliation(s)
- Carolyn J Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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20
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Koskella B, Hernandez CA, Wheatley RM. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annu Rev Virol 2022; 9:57-78. [PMID: 35584889 DOI: 10.1146/annurev-virology-091919-075914] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA;
| | - Catherine A Hernandez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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21
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Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. Nat Microbiol 2022; 7:530-541. [PMID: 35314780 PMCID: PMC7612570 DOI: 10.1038/s41564-022-01074-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/01/2022] [Indexed: 11/08/2022]
Abstract
CRISPR-Cas systems store fragments of foreign DNA called spacers as immunological recordings used to combat future infections. Of the many spacers stored in a CRISPR array, the newest spacers are known to be prioritized for immune defense. However, the underlying mechanism remains unclear. Here we show that the leader region upstream of CRISPR arrays in CRISPR-Cas9 systems enhances CRISPR RNA (crRNA) processing from the newest spacer, prioritizing defense against the matching invader. Using the CRISPR-Cas9 system from Streptococcus pyogenes as a model, we found that the transcribed leader interacts with the conserved repeats bordering the newest spacer. The resulting interaction promotes tracrRNA hybridization with the second repeat, accelerating crRNA processing. Accordingly, disrupting this structure reduces the abundance of the associated crRNA and immune defense against targeted plasmids and bacteriophages. Beyond the S. pyogenes system, bioinformatics analyses revealed that leader-repeat structures appear across CRISPR-Cas9 systems. CRISPR-Cas systems thus possess an RNA-based mechanism to prioritize defense against the most recently encountered invaders.
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22
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Lan XR, Liu ZL, Niu DK. Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C. Front Microbiol 2022; 13:773114. [PMID: 35300480 DOI: 10.3389/fmicb.2022.773114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. We observed an abrupt increase of bacterial CRISPR-Cas abundance at around 45°C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45°C. From the literature, we noticed that the diversities of cellular predators (like protozoa, nematodes, and myxobacteria) have a steep decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45°C and almost disappears above 60°C. We propose that viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority at higher temperatures. In temperature ranges where the abundance of cellular predators does not change with temperature, the growth temperatures of bacteria would not significantly affect their CRISPR-Cas contents. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.
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Affiliation(s)
- Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhi-Ling Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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23
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Wimmer F, Mougiakos I, Englert F, Beisel CL. Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Mol Cell 2022; 82:1210-1224.e6. [PMID: 35216669 DOI: 10.1016/j.molcel.2022.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/30/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
CRISPR-Cas biology and technologies have been largely shaped to date by the characterization and use of single-effector nucleases. By contrast, multi-subunit effectors dominate natural systems, represent emerging technologies, and were recently associated with RNA-guided DNA transposition. This disconnect stems from the challenge of working with multiple protein subunits in vitro and in vivo. Here, we apply cell-free transcription-translation (TXTL) systems to radically accelerate the characterization of multi-subunit CRISPR effectors and transposons. Numerous DNA constructs can be combined in one TXTL reaction, yielding defined biomolecular readouts in hours. Using TXTL, we mined phylogenetically diverse I-E effectors, interrogated extensively self-targeting I-C and I-F systems, and elucidated targeting rules for I-B and I-F CRISPR transposons using only DNA-binding components. We further recapitulated DNA transposition in TXTL, which helped reveal a distinct branch of I-B CRISPR transposons. These capabilities will facilitate the study and exploitation of the broad yet underexplored diversity of CRISPR-Cas systems and transposons.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Ioannis Mougiakos
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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Wentz TG, Tremblay BJM, Bradshaw M, Doxey AC, Sharma SK, Sauer JD, Pellett S. Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. Front Microbiol 2022; 12:787726. [PMID: 35222299 PMCID: PMC8865420 DOI: 10.3389/fmicb.2021.787726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/27/2021] [Indexed: 12/28/2022] Open
Abstract
Most strains of proteolytic group I Clostridium botulinum (G1 C. botulinum) and some strains of Clostridium sporogenes possess genes encoding botulinum neurotoxin (BoNT), a potent neuroparalytic agent. Within G1 C. botulinum, conserved bont gene clusters of three major toxin serotypes (bont/A/B/F) can be found on conjugative plasmids and/or within chromosomal pathogenicity islands. CRISPR-Cas systems enable site-specific targeting of previously encountered mobile genetic elements (MGE) such as plasmids and bacteriophage through the creation of a spacer library complementary to protospacers within the MGEs. To examine whether endogenous CRISPR-Cas systems restrict the transfer of bont gene clusters across strains we conducted a bioinformatic analysis profiling endogenous CRISPR-Cas systems from 241 G1 C. botulinum and C. sporogenes strains. Approximately 6,200 CRISPR spacers were identified across the strains and Type I-B, III-A/B/D cas genes and CRISPR array features were identified in 83% of the strains. Mapping the predicted spacers against the masked strain and RefSeq plasmid dataset identified 56,000 spacer-protospacer matches. While spacers mapped heavily to targets within bont(+) plasmids, no protospacers were identified within the bont gene clusters. These results indicate the toxin is not a direct target of CRISPR-Cas but the plasmids predominantly responsible for its mobilization are. Finally, while the presence of a CRISPR-Cas system did not reliably indicate the presence or absence of a bont gene cluster, comparative genomics across strains indicates they often occupy the same hypervariable loci common to both species, potentially suggesting similar mechanisms are involved in the acquisition and curation of both genomic features.
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Affiliation(s)
- Travis G. Wentz
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, United States,Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States,Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | | | - Marite Bradshaw
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Shashi K. Sharma
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States,*Correspondence: Sabine Pellett,
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25
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Lee H, Sashital DG. Creating memories: molecular mechanisms of CRISPR adaptation. Trends Biochem Sci 2022; 47:464-476. [DOI: 10.1016/j.tibs.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
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Solayappan M, Azlan A, Khor KZ, Yik MY, Khan M, Yusoff NM, Moses EJ. Utilization of CRISPR-Mediated Tools for Studying Functional Genomics in Hematological Malignancies: An Overview on the Current Perspectives, Challenges, and Clinical Implications. Front Genet 2022; 12:767298. [PMID: 35154242 PMCID: PMC8834884 DOI: 10.3389/fgene.2021.767298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Hematological malignancies (HM) are a group of neoplastic diseases that are usually heterogenous in nature due to the complex underlying genetic aberrations in which collaborating mutations enable cells to evade checkpoints that normally safeguard it against DNA damage and other disruptions of healthy cell growth. Research regarding chromosomal structural rearrangements and alterations, gene mutations, and functionality are currently being carried out to understand the genomics of these abnormalities. It is also becoming more evident that cross talk between the functional changes in transcription and proteins gives the characteristics of the disease although specific mutations may induce unique phenotypes. Functional genomics is vital in this aspect as it measures the complete genetic change in cancerous cells and seeks to integrate the dynamic changes in these networks to elucidate various cancer phenotypes. The advent of CRISPR technology has indeed provided a superfluity of benefits to mankind, as this versatile technology enables DNA editing in the genome. The CRISPR-Cas9 system is a precise genome editing tool, and it has revolutionized methodologies in the field of hematology. Currently, there are various CRISPR systems that are used to perform robust site-specific gene editing to study HM. Furthermore, experimental approaches that are based on CRISPR technology have created promising tools for developing effective hematological therapeutics. Therefore, this review will focus on diverse applications of CRISPR-based gene-editing tools in HM and its potential future trajectory. Collectively, this review will demonstrate the key roles of different CRISPR systems that are being used in HM, and the literature will be a representation of a critical step toward further understanding the biology of HM and the development of potential therapeutic approaches.
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Affiliation(s)
- Maheswaran Solayappan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Malaysia
| | - Adam Azlan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Kang Zi Khor
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Mot Yee Yik
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Matiullah Khan
- Department of Pathology, Faculty of Medicine, AIMST University, Bedong, Malaysia
| | - Narazah Mohd Yusoff
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Emmanuel Jairaj Moses
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
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Mizuki H, Shimoyama Y, Ishikawa T, Sasaki M. A genomic sequence of the type II-A clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system in Mycoplasma salivarium strain ATCC 29803. J Oral Microbiol 2022; 14:2008153. [PMID: 34992734 PMCID: PMC8725752 DOI: 10.1080/20002297.2021.2008153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems are RNA-mediated adaptive immune systems that actagainst invading genetic elements such as phages or plasmids. CRISPR/Cas systems exist in nearly half of bacteria. Mycoplasma salivarium is a commensal species of the oropharynx. The American Type Culture Collection maintains five M. salivarium strains: ATCC 14277, 23064, 23557, 29803, and 33130. The genome sequence of ATCC 23064 revealed that it has an incomplete CRISPR/Cas system. However, the genome sequences of the remaining strains have not been analyzed. Methods We performed polymerase chain reaction-amplicon sequencing and de novo genome sequencing to evaluate the presence of the CRISPR/Cas system in four strains. Results Only ATCC 29803 possessed cas1, cas2, cas9, and csn2 genes, a CRISPR array, and tracrRNA. The sequences of most components were identical between the CRISPR/Cas systems of ATCC 29803 and ATCC 23064, whereas the spacer sequences and a region of the cas9 gene were different. Unlike the CRISPR/Cas system of ATCC 23064, the cas9 gene of ATCC 29803 was not disrupted by the presence of stop codons. Conclusion ATCC 29803 possesses genomic components required to express the type II-A CRISPR/Cas system, which potentially functions as an RNA-guided endonuclease.
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Affiliation(s)
- Harumi Mizuki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Yu Shimoyama
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Taichi Ishikawa
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
| | - Minoru Sasaki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, Shiwa-gun, Japan
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28
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Sharma SK, Gupta OP, Pathaw N, Sharma D, Maibam A, Sharma P, Sanasam J, Karkute SG, Kumar S, Bhattacharjee B. CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security. Front Nutr 2022; 8:751512. [PMID: 34977113 PMCID: PMC8716883 DOI: 10.3389/fnut.2021.751512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/31/2021] [Indexed: 12/14/2022] Open
Abstract
Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.
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Affiliation(s)
| | - Om Prakash Gupta
- Division of Quality & Basic Science, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeta Pathaw
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Albert Maibam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Parul Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jyotsana Sanasam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Suhas Gorakh Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Sandeep Kumar
- Department of Plant Pathology, Odisha University of Agriculture & Technology, Bhubaneswar, India
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29
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Egorova A, Mikhaylova Y, Saenko S, Tyumentseva M, Tyumentsev A, Karbyshev K, Chernyshkov A, Manzeniuk I, Akimkin V, Shelenkov A. Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates. Microorganisms 2021; 10:89. [PMID: 35056538 PMCID: PMC8781764 DOI: 10.3390/microorganisms10010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/19/2022] Open
Abstract
Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018-2020, and long-read (MinION) WGS of five more representative isolates. We sought to determine whether foodborne S. Infantis have acquired new characteristics, traits, and dynamics in MDR growth in recent years. All sequenced isolates belonged to the sequence type ST32 and more than the half of isolates was characterized by six similar antimicrobial susceptibility profiles, most of which corresponded well with the antimicrobial resistance determinants to aminoglycosides, sulphonamides, tetracycline, and chloramphenicol revealed in silico. Some of the isolates were characterized by the presence of several types of plasmids simultaneously. Plasmid typing using WGS revealed Col440I, ColpVC, ColRNAI, IncFIB, IncFII, IncX1, IncHI2, IncHI2A, and IncN replicons. The identified virulence genes for 45 whole genomes of S. Infantis were similar and included 129 genes encoding structural components of the cell, factors responsible for successful invasion of the host, and secreted products. These data will be a valuable contribution to further comparative genomics of S. Infantis circulating in Russia, as well as to epidemiological surveillance of foodborne Salmonella isolates and investigations of Salmonella outbreaks.
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Affiliation(s)
- Anna Egorova
- Central Research Institute of Epidemiology, Novogireevskaya str., 3a, 111123 Moscow, Russia; (Y.M.); (S.S.); (M.T.); (A.T.); (K.K.); (A.C.); (I.M.); (V.A.); (A.S.)
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30
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Abstract
CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a trans-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances.
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Affiliation(s)
- Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany;
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany;
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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31
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Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Robledo PA, Ferreira E, Rosselló-Móra R. Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain. Syst Appl Microbiol 2021; 44:126277. [PMID: 34788687 DOI: 10.1016/j.syapm.2021.126277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Pedro A Robledo
- Delegation of Geological and Mining Institute of Spain (IGME-CSIC) in Balearic Islands, Palma de Mallorca, Spain
| | | | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
- Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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Ratner HK, Weiss DS. crRNA complementarity shifts endogenous CRISPR-Cas systems between transcriptional repression and DNA defense. RNA Biol 2021; 18:1560-1573. [PMID: 33733999 PMCID: PMC8583161 DOI: 10.1080/15476286.2021.1878335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that recognize and cleave nucleic acid targets using small RNAs called CRISPR RNAs (crRNAs) to guide Cas protein(s). There is increasing evidence for the broader endogenous roles of these systems. The CRISPR-Cas9 system of Francisella novicida also represses endogenous transcription using a non-canonical small RNA (scaRNA). We examined whether the crRNAs of the native F. novicida CRISPR-Cas systems, Cas12a and Cas9, can guide transcriptional repression. Both systems repressed mRNA transcript levels when crRNA-target complementarity was limited, and led to target cleavage with extended complementarity. Using these parameters we engineered the CRISPR array of Cas12a to guide the transcriptional repression of a new and endogenous target. Since the majority of crRNA targets remain unidentified, this work suggests that a re-analysis of crRNAs for endogenous targets with limited complementarity could reveal new, diverse regulatory roles for CRISPR-Cas systems in prokaryotic biology.
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Affiliation(s)
- Hannah K. Ratner
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - David S. Weiss
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria. Appl Microbiol Biotechnol 2021; 105:8805-8822. [PMID: 34716462 DOI: 10.1007/s00253-021-11659-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.
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35
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Tyumentseva M, Mikhaylova Y, Prelovskaya A, Karbyshev K, Tyumentsev A, Petrova L, Mironova A, Zamyatin M, Shelenkov A, Akimkin V. CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. Antibiotics (Basel) 2021; 10:antibiotics10111301. [PMID: 34827239 PMCID: PMC8615150 DOI: 10.3390/antibiotics10111301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is a member of the ESKAPE opportunistic pathogen group, which includes six species of the most dangerous microbes. This pathogen is characterized by the rapid acquisition of antimicrobial resistance, thus causing major healthcare concerns. This study presents a comprehensive analysis of clinical P. aeruginosa isolates based on whole-genome sequencing data. The isolate collection studied was characterized by a variety of clonal lineages with a domination of high-risk epidemic clones and different CRISPR/Cas element patterns. This is the first report on the coexistence of two and even three different types of CRISPR/Cas systems simultaneously in Russian clinical strains of P. aeruginosa. The data include molecular typing and genotypic antibiotic resistance determination, as well as the phylogenetic analysis of the full-length cas gene and anti-CRISPR genes sequences, predicted prophage sequences, and conducted a detailed CRISPR array analysis. The differences between the isolates carrying different types and quantities of CRISPR/Cas systems were investigated. The pattern of virulence factors in P. aeruginosa isolates lacking putative CRISPR/Cas systems significantly differed from that of samples with single or multiple putative CRISPR/Cas systems. We found significant correlations between the numbers of prophage sequences, antibiotic resistance genes, and virulence genes in P. aeruginosa isolates with different patterns of CRISPR/Cas-elements. We believe that the data presented will contribute to further investigations in the field of bacterial pathoadaptability, including antimicrobial resistance and the role of CRISPR/Cas systems in the plasticity of the P. aeruginosa genome.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Anna Prelovskaya
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Konstantin Karbyshev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Aleksandr Tyumentsev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Lyudmila Petrova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Anna Mironova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Mikhail Zamyatin
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
- Correspondence: or
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
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36
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Correlation between type IIIA CRISPR-Cas system and SCCmec in Staphylococcus epidermidis. Arch Microbiol 2021; 203:6275-6286. [PMID: 34668031 DOI: 10.1007/s00203-021-02595-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/25/2022]
Abstract
A subculture of S.epidermidis strain ATCC35984 that is amenable to genetically manipulate was occasionally found in our laboratory. This mutant exhibited susceptibility to methicillin in contrast to its parent strain. To unveil the underlying mechanism, whole-genome sequencing of the mutant was performed. A comparative analysis revealed that a large DNA fragment encompassing the CRISPR-Cas system, type I R-M system and the SCCmec element was deleted from the mutant. The large chromosomal deletion associated with CRISPR-Cas system was also observed to occur spontaneously in S. epidermidis in another independent laboratory, or artificially induced by introducing engineering crRNAs in other bacterial species. These findings imply the CRISPR-Cas systems can affect bacterial genome remodeling through deletion of the integrated MGEs (mobile genetic elements). Further bioinformatics analysis identified a higher carriage rate of SCCmec element in the S. epidermidis strains harboring the CRISPR-Cas system. MLST typing and phylogenetic analysis of those CRIPSR-Cas-positive S. epidermidis strains revealed multiple origins. In addition, distinct types of SCCmec carried in those strains suggested that acquisition of this MGE originated from multiple independent recombination events. Intriguingly, CRISPR-Cas systems are found to be always located in the vicinity of orfX gene among staphylococci. Allelic analysis of CRISPR loci flanking cas genes disclosed that the loci distal to the orfX gene are considerably stable and conserved, which probably serve as recombination hotspot between CRISPR-Cas system and phage or plasmid. Therefore, the findings generally support the notion that incomplete immune protection of CRISPR-Cas system can promote dissemination of its neighboring SCCmec element.
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Vink JNA, Baijens JHL, Brouns SJJ. PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. Genome Biol 2021; 22:281. [PMID: 34593010 PMCID: PMC8482600 DOI: 10.1186/s13059-021-02495-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. RESULTS By using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders. CONCLUSIONS This study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Jan H L Baijens
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
- Kavli Institute of Nanoscience, Delft, The Netherlands.
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38
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Le Gratiet T, Le Marechal C, Devaere M, Chemaly M, Woudstra C. Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato. Front Microbiol 2021; 12:711413. [PMID: 34589070 PMCID: PMC8473940 DOI: 10.3389/fmicb.2021.711413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I-IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.
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Affiliation(s)
- Thibault Le Gratiet
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
- UFR of Life Sciences and Environment, University of Rennes, Rennes, France
| | - Caroline Le Marechal
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marie Devaere
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marianne Chemaly
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Cédric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Badel C, Da Cunha V, Oberto J. Archaeal tyrosine recombinases. FEMS Microbiol Rev 2021; 45:fuab004. [PMID: 33524101 PMCID: PMC8371274 DOI: 10.1093/femsre/fuab004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
The integration of mobile genetic elements into their host chromosome influences the immediate fate of cellular organisms and gradually shapes their evolution. Site-specific recombinases catalyzing this integration have been extensively characterized both in bacteria and eukarya. More recently, a number of reports provided the in-depth characterization of archaeal tyrosine recombinases and highlighted new particular features not observed in the other two domains. In addition to being active in extreme environments, archaeal integrases catalyze reactions beyond site-specific recombination. Some of these integrases can catalyze low-sequence specificity recombination reactions with the same outcome as homologous recombination events generating deep rearrangements of their host genome. A large proportion of archaeal integrases are termed suicidal due to the presence of a specific recombination target within their own gene. The paradoxical maintenance of integrases that disrupt their gene upon integration implies novel mechanisms for their evolution. In this review, we assess the diversity of the archaeal tyrosine recombinases using a phylogenomic analysis based on an exhaustive similarity network. We outline the biochemical, ecological and evolutionary properties of these enzymes in the context of the families we identified and emphasize similarities and differences between archaeal recombinases and their bacterial and eukaryal counterparts.
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Affiliation(s)
- Catherine Badel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jacques Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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40
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Abstract
CRISPR transposons (CASTs) represent unique mobile genetic elements that co-opted CRISPR-Cas immune systems for RNA-guided DNA transposition. However, CAST-encoded CRISPR arrays rarely match the CAST's chromosomal location. A recent publication in Cell helps resolve this paradox by revealing CRISPR-array-independent mechanisms of chromosomal homing unique to different CAST types.
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Affiliation(s)
- Ioannis Mougiakos
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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41
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Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.
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42
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Steinum TM, Turgay E, Yardımcı RE, Småge SB, Karataş S. Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping. J Appl Microbiol 2021; 131:1848-1857. [PMID: 33905598 DOI: 10.1111/jam.15116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 11/27/2022]
Abstract
AIMS We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST). METHODS AND RESULTS Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Twenty-three completed/draft genomes were also downloaded from the NCBI database and analysed. MLST of Turkish isolates was achieved with a well-established 7-gene scheme. Tenacibaculum maritimum genomes carry a structurally complete but partially defective class II CRISPRcas locus due to known amino acid substitutions in encoded Cas9 proteins. Our spacer identification suggests that the host range of bacteriophage P2559Y and Vibrio phage nt-1 include T. maritimum and that the most recurrent infection recorded by isolates has been with Tenacibaculum phage PTm5. Thirty-eight isolates with this CRISPRcas locus belonged to 25 spoligotypes and to 24 sequence types by MLST, respectively. According to MLST, T. maritimum isolates from Turkey are most related to previously defined sequence types ST3, ST40 and ST41 isolates from Spain, Malta and France. CONCLUSIONS The evaluated spoligotyping offers discriminatory power comparable to MLST. SIGNIFICANCE AND IMPACT OF THE STUDY Spoligotyping has potential as a quick, easy and cheap tool for subtyping of T. maritimum isolates.
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Affiliation(s)
- T M Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - E Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - R E Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | | | - S Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
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43
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Zink IA, Fouqueau T, Tarrason Risa G, Werner F, Baum B, Bläsi U, Schleper C. Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic Sulfolobales and the evasion of lethal gene silencing. RNA Biol 2021; 18:421-434. [PMID: 32957821 PMCID: PMC7951960 DOI: 10.1080/15476286.2020.1813411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/22/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPR type III systems, which are abundantly found in archaea, recognize and degrade RNA in their specific response to invading nucleic acids. Therefore, these systems can be harnessed for gene knockdown technologies even in hyperthermophilic archaea to study essential genes. We show here the broader usability of this posttranscriptional silencing technology by expanding the application to further essential genes and systematically analysing and comparing silencing thresholds and escape mutants. Synthetic guide RNAs expressed from miniCRISPR cassettes were used to silence genes involved in cell division (cdvA), transcription (rpo8), and RNA metabolism (smAP2) of the two crenarchaeal model organisms Saccharolobus solfataricus and Sulfolobus acidocaldarius. Results were systematically analysed together with those obtained from earlier experiments of cell wall biogenesis (slaB) and translation (aif5A). Comparison of over 100 individual transformants revealed gene-specific silencing maxima ranging between 40 and 75%, which induced specific knockdown phenotypes leading to growth retardation. Exceedance of this threshold by strong miniCRISPR constructs was not tolerated and led to specific mutation of the silencing miniCRISPR array and phenotypical reversion of cultures. In two thirds of sequenced reverted cultures, the targeting spacers were found to be precisely excised from the miniCRISPR array, indicating a still hypothetical, but highly active recombination system acting on the dynamics of CRISPR spacer arrays. Our results indicate that CRISPR type III - based silencing is a broadly applicable tool to study in vivo functions of essential genes in Sulfolobales which underlies a specific mechanism to avoid malignant silencing overdose.
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Affiliation(s)
- Isabelle Anna Zink
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thomas Fouqueau
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Gabriel Tarrason Risa
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Finn Werner
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Buzz Baum
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Udo Bläsi
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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44
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Newsom S, Parameshwaran HP, Martin L, Rajan R. The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies. Front Cell Infect Microbiol 2021; 10:619763. [PMID: 33585286 PMCID: PMC7876343 DOI: 10.3389/fcimb.2020.619763] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.
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Affiliation(s)
- Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Lindsie Martin
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
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45
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Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C. Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe 2021; 29:94-106.e4. [PMID: 33217332 PMCID: PMC7813156 DOI: 10.1016/j.chom.2020.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 10/26/2020] [Indexed: 01/13/2023]
Abstract
Many bacteria resist invasive DNA by incorporating sequences into CRISPR loci, which enable sequence-specific degradation. CRISPR systems have been well studied from isolate genomes, but culture-independent metagenomics provide a new window into their diversity. We profiled CRISPR loci and cas genes in the body-wide human microbiome using 2,355 metagenomes, yielding functional and taxonomic profiles for 2.9 million spacers by aligning the spacer content to each sample's metagenome and corresponding gene families. Spacer and repeat profiles agree qualitatively with those from isolate genomes but expand their diversity by approximately 13-fold, with the highest spacer load present in the oral microbiome. The taxonomy of spacer sequences parallels that of their source community, with functional targets enriched for viral elements. When coupled with cas gene systems, CRISPR-Cas subtypes are highly site and taxon specific. Our analysis provides a comprehensive collection of natural CRISPR-cas loci and targets in the human microbiome.
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Affiliation(s)
- Philipp C Münch
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany; Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.
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46
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Abstract
Bacteriophages encode diverse anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas immunity during infection of their bacterial hosts. Although detailed mechanisms have been characterized for multiple Acr proteins, an understanding of their role in phage infection biology is just emerging. Here, we review recent work in this area and propose a framework of "phage autonomy" to evaluate CRISPR-immune evasion strategies. During phage infection, Acr proteins are deployed by a tightly regulated "fast on-fast off" transcriptional burst, which is necessary, but insufficient, for CRISPR-Cas inactivation. Instead of a single phage shutting down CRISPR-Cas immunity, a community of acr-carrying phages cooperate to suppress bacterial immunity, displaying low phage autonomy. Enzymatic Acr proteins with novel mechanisms have been recently revealed and are predicted to enhance phage autonomy, while phage DNA protective measures offer the highest phage autonomy observed. These varied Acr mechanisms and strengths also have unexpected impacts on the bacterial populations and competing phages.
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Affiliation(s)
- Yuping Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94403, USA; Innovative Genomics Institute, Berkeley, CA, USA.
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47
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Nobrega FL, Walinga H, Dutilh BE, Brouns SJJ. Prophages are associated with extensive CRISPR-Cas auto-immunity. Nucleic Acids Res 2020; 48:12074-12084. [PMID: 33219687 PMCID: PMC7708048 DOI: 10.1093/nar/gkaa1071] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS has been suggested to reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a regulatory mechanism for gene expression. Here we investigated the incidence, distribution, and evasion of STS in over 100 000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of escape from the potentially deleterious effects of STS by other mechanisms such as anti-CRISPR proteins and CRISPR target mutations. We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects as mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages.
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Affiliation(s)
- Franklin L Nobrega
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Hielke Walinga
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
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48
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Fage C, Lemire N, Moineau S. Delivery of CRISPR-Cas systems using phage-based vectors. Curr Opin Biotechnol 2020; 68:174-180. [PMID: 33360715 DOI: 10.1016/j.copbio.2020.11.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
Antimicrobial resistance has spread quickly on a worldwide scale, reducing therapeutic options for bacterial infections. CRISPR-Cas is an adaptive immune system found in many prokaryotes that can be designed to target bacterial genomes, leading to cell death. Repurposing the CRISPR-Cas system as a therapeutic strategy offers an attractive way to overcome antimicrobial resistance. However, this strategy requires efficient vectors for the CRISPR-Cas system to reach the bacterial genomes. Engineered phages offer an attractive option as cargo delivery vectors. In this review, we discuss the production of phage-based vectors and the relevance of using repurposed CRISPR-Cas systems as antimicrobials. We also discuss recent progress in phage engineering that can potentially overcome the limitations and increase the efficiency of CRISPR-Cas delivery.
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Affiliation(s)
- Clément Fage
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
| | - Nicolas Lemire
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada.
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49
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Abstract
Here we review data suggestive of a role for RNA-binding proteins in vertebrate immunity. We focus on the products of genes found in the class III region of the Major Histocompatibility Complex. Six of these genes, DDX39B (aka BAT1), DXO, LSM2, NELFE, PRRC2A (aka BAT2), and SKIV2L, encode RNA-binding proteins with clear roles in post-transcriptional gene regulation and RNA surveillance. These genes are likely to have important functions in immunity and are associated with autoimmune diseases.
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Affiliation(s)
- Geraldine Schott
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Biochemistry and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Programme in Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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Abstract
CRISPR-Cas systems, widespread in bacteria and archaea, are mainly responsible for adaptive cellular immunity against exogenous DNA (plasmid and phage). However, the latest research shows their involvement in other functions, such as gene expression regulation, DNA repair and virulence. In recent years, they have undergone intensive research as convenient tools for genomic editing, with Cas9 being the most commonly used nuclease. Gene editing may be of interest in biotechnology, medicine (treatment of inherited disorders, cancer, etc.), and in the development of model systems for various genetic diseases. The dCas9 system, based on a modified Cas9 devoid of nuclease activity, called CRISPRi, is widely used to control gene expression in bacteria for new drug biotargets validation and is also promising for therapy of genetic diseases. In addition to direct use for genomic editing in medicine, CRISPR-Cas can also be used in diagnostics, for microorganisms’ genotyping, controlling the spread of drug resistance, or even directly as “smart” antibiotics. This review focuses on the main applications of CRISPR-Cas in medicine, and challenges and perspectives of these approaches.
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