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Wu Y, Zhang J, Wang B, Zhang Y, Li H, Liu Y, Yin J, He D, Luo H, Gan F, Tang B, Tang XF. Dissecting the Arginine and Lysine Biosynthetic Pathways and Their Relationship in Haloarchaeon Natrinema gari J7-2 via Endogenous CRISPR-Cas System-Based Genome Editing. Microbiol Spectr 2023; 11:e0028823. [PMID: 37347159 PMCID: PMC10433800 DOI: 10.1128/spectrum.00288-23] [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: 01/19/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
The evolutionary relationship between arginine and lysine biosynthetic pathways has been well established in bacteria and hyperthermophilic archaea but remains largely unknown in haloarchaea. Here, the endogenous CRISPR-Cas system was harnessed to edit arginine and lysine biosynthesis-related genes in the haloarchaeon Natrinema gari J7-2. The ΔargW, ΔargX, ΔargB, and ΔargD mutant strains display an arginine auxotrophic phenotype, while the ΔdapB mutant shows a lysine auxotrophic phenotype, suggesting that strain J7-2 utilizes the ArgW-mediated pathway and the diaminopimelate (DAP) pathway to synthesize arginine and lysine, respectively. Unlike the ArgD in Escherichia coli acting as a bifunctional aminotransferase in both the arginine biosynthesis pathway and the DAP pathway, the ArgD in strain J7-2 participates only in arginine biosynthesis. Meanwhile, in strain J7-2, the function of argB cannot be compensated for by its evolutionary counterpart ask in the DAP pathway. Moreover, strain J7-2 cannot utilize α-aminoadipate (AAA) to synthesize lysine via the ArgW-mediated pathway, in contrast to hyperthermophilic archaea that employ a bifunctional LysW-mediated pathway to synthesize arginine (or ornithine) and lysine from glutamate and AAA, respectively. Additionally, the replacement of a 5-amino-acid signature motif responsible for substrate specificity of strain J7-2 ArgX with that of its hyperthermophilic archaeal homologs cannot endow the ΔdapB mutant with the ability to biosynthesize lysine from AAA. The in vitro analysis shows that strain J7-2 ArgX acts on glutamate rather than AAA. These results suggest that the arginine and lysine biosynthetic pathways of strain J7-2 are highly specialized during evolution. IMPORTANCE Due to their roles in amino acid metabolism and close evolutionary relationship, arginine and lysine biosynthetic pathways represent interesting models for probing functional specialization of metabolic routes. The current knowledge with respect to arginine and lysine biosynthesis is limited for haloarchaea compared to that for bacteria and hyperthermophilic archaea. Our results demonstrate that the haloarchaeon Natrinema gari J7-2 employs the ArgW-mediated pathway and the DAP pathway for arginine and lysine biosynthesis, respectively, and the two pathways are functionally independent of each other; meanwhile, ArgX is a key determinant of substrate specificity of the ArgW-mediated pathway in strain J7-2. This study provides new clues about haloarchaeal amino acid metabolism and confirms the convenience and efficiency of endogenous CRISPR-Cas system-based genome editing in haloarchaea.
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Affiliation(s)
- Yi Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jia Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bingxue Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanyan Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huai Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan He
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hongyi Luo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
| | - Xiao-Feng Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
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van der Does C, Braun F, Ren H, Albers SV. Putative nucleotide-based second messengers in archaea. MICROLIFE 2023; 4:uqad027. [PMID: 37305433 PMCID: PMC10249747 DOI: 10.1093/femsml/uqad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/07/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.
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Affiliation(s)
- Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hongcheng Ren
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
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Yoshida-Takashima Y, Takaki Y, Yoshida M, Zhang Y, Nunoura T, Takai K. Genomic insights into phage-host interaction in the deep-sea chemolithoautotrophic Campylobacterota, Nitratiruptor. ISME COMMUNICATIONS 2022; 2:108. [PMID: 37938718 PMCID: PMC9723563 DOI: 10.1038/s43705-022-00194-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
The genus Nitratiruptor represents one of the most numerically abundant chemolithoautotrophic Campylobacterota populations in the mixing zones of habitats between hydrothermal fluids and ambient seawater in deep-sea hydrothermal environments. We isolated and characterized four novel temperate phages (NrS-2, NrS-3, NrS-4, and NrS-5) having a siphoviral morphology, infecting Nitratiruptor strains from the Hatoma Knoll hydrothermal field in the southern-Okinawa Trough, Japan, and conducted comparative genomic analyses among Nitratiruptor strains and their phages. The Nitratiruptor temperate phages shared many potential core genes (e.g., integrase, Cro, two structural proteins, lysozyme, and MazG) with each other despite their diverse morphological and genetic features. Some homologs of coding sequences (CDSs) of the temperate phages were dispersed throughout the non-prophage regions of the Nitratiruptor genomes. In addition, several regions of the phage genome sequences matched to spacer sequences within clustered regularly interspaced short palindromic repeats (CRISPR) in Nitratiruptor genomes. Moreover, a restriction-modification system found in a temperate phage affected an epigenetic feature of its host. These results strongly suggested a coevolution of temperate phages and their host genomes via the acquisition of temperate phages, the CRISPR systems, the nucleotide substitution, and the epigenetic regulation during multiple phage infections in the deep-sea environments.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mitsuhiro Yoshida
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yi Zhang
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Schwarz TS, Schreiber SS, Marchfelder A. CRISPR Interference as a Tool to Repress Gene Expression in Haloferax volcanii. Methods Mol Biol 2022; 2522:57-85. [PMID: 36125743 DOI: 10.1007/978-1-0716-2445-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To date, a plethora of tools for molecular biology have been developed on the basis of the CRISPR-Cas system. Almost all use the class 2 systems since here the setup is the simplest with only one protein and one guide RNA, allowing for easy transfer to and expression in other organisms. However, the CRISPR-Cas components harnessed for applications are derived from mesophilic bacteria and are not optimal for use in extremophilic archaea.Here, we describe the application of an endogenous CRISPR-Cas system as a tool for silencing gene expression in a halophilic archaeon. Haloferax volcanii has a CRISPR-Cas system of subtype I-B, which can be easily used to repress the transcription of endogenous genes, allowing to study the effects of their depletion. This article gives a step-by-step introduction on how to use the implemented system for any gene of interest in Haloferax volcanii. The concept of CRISPRi described here for Haloferax can be transferred to any other archaeon, that is genetically tractable and has an endogenous CRISPR-Cas I systems.
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Abstract
Transcriptional regulators that integrate cellular and environmental signals to control cell division are well known in bacteria and eukaryotes, but their existence is poorly understood in archaea. We identified a conserved gene (cdrS) that encodes a small protein and is highly transcribed in the model archaeon Haloferax volcanii. The cdrS gene could not be deleted, but CRISPR interference (CRISPRi)-mediated repression of the cdrS gene caused slow growth and cell division defects and changed the expression of multiple genes and their products associated with cell division, protein degradation, and metabolism. Consistent with this complex regulatory network, overexpression of cdrS inhibited cell division, whereas overexpression of the operon encoding both CdrS and a tubulin-like cell division protein (FtsZ2) stimulated division. Chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) identified 18 DNA-binding sites of the CdrS protein, including one upstream of the promoter for a cell division gene, ftsZ1, and another upstream of the essential gene dacZ, encoding diadenylate cyclase involved in c-di-AMP signaling, which is implicated in the regulation of cell division. These findings suggest that CdrS is a transcription factor that plays a central role in a regulatory network coordinating metabolism and cell division. IMPORTANCE Cell division is a central mechanism of life and is essential for growth and development. Members of the Bacteria and Eukarya have different mechanisms for cell division, which have been studied in detail. In contrast, cell division in members of the Archaea is still understudied, and its regulation is poorly understood. Interestingly, different cell division machineries appear in members of the Archaea, with the Euryarchaeota using a cell division apparatus based on the tubulin-like cytoskeletal protein FtsZ, as in bacteria. Here, we identify the small protein CdrS as essential for survival and a central regulator of cell division in the euryarchaeon Haloferax volcanii. CdrS also appears to coordinate other cellular pathways, including synthesis of signaling molecules and protein degradation. Our results show that CdrS plays a sophisticated role in cell division, including regulation of numerous associated genes. These findings are expected to initiate investigations into conditional regulation of division in archaea.
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Butiuc-Keul A, Farkas A, Carpa R, Iordache D. CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes. Microb Physiol 2021; 32:2-17. [PMID: 34192695 DOI: 10.1159/000516643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.
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Affiliation(s)
- Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Anca Farkas
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Rahela Carpa
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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Märkle P, Maier LK, Maaß S, Hirschfeld C, Bartel J, Becher D, Voß B, Marchfelder A. A Small RNA Is Linking CRISPR-Cas and Zinc Transport. Front Mol Biosci 2021; 8:640440. [PMID: 34055875 PMCID: PMC8155600 DOI: 10.3389/fmolb.2021.640440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon Haloferax volcanii, a plethora of sRNAs have been identified; however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from Haloferax volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, and the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild-type Haloferax cells and the deletion mutant revealed upregulation of six genes in the deletion strain, showing that this sRNA has a clearly defined function. Three of the six upregulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, and ZnuC1) suggesting the involvement of s479 in the regulation of zinc transport. Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. Furthermore, electrophoretic mobility shift assays demonstrate a direct interaction of s479 with the target znuC1 mRNA. Proteome comparison of wild-type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. Interestingly, s479 is not only encoded next to CRISPR-cas genes, but the mature s479 contains a crRNA-like 5' handle, and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. Together, this might suggest that the CRISPR-Cas system is involved in s479 function.
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Affiliation(s)
- Pascal Märkle
- Department of Biology II, Ulm University, Ulm, Germany
| | | | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Björn Voß
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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Zink IA, Wimmer E, Schleper C. Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales. Biomolecules 2020; 10:E1523. [PMID: 33172134 PMCID: PMC7694759 DOI: 10.3390/biom10111523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.
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Zheng Y, Li J, Wang B, Han J, Hao Y, Wang S, Ma X, Yang S, Ma L, Yi L, Peng W. Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering. Front Bioeng Biotechnol 2020; 8:62. [PMID: 32195227 PMCID: PMC7064716 DOI: 10.3389/fbioe.2020.00062] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022] Open
Abstract
Establishment of production platforms through prokaryotic engineering in microbial organisms would be one of the most efficient means for chemicals, protein, and biofuels production. Despite the fact that CRISPR (clustered regularly interspaced short palindromic repeats)–based technologies have readily emerged as powerful and versatile tools for genetic manipulations, their applications are generally limited in prokaryotes, possibly owing to the large size and severe cytotoxicity of the heterogeneous Cas (CRISPR-associated) effector. Nevertheless, the rich natural occurrence of CRISPR-Cas systems in many bacteria and most archaea holds great potential for endogenous CRISPR-based prokaryotic engineering. The endogenous CRISPR-Cas systems, with type I systems that constitute the most abundant and diverse group, would be repurposed as genetic manipulation tools once they are identified and characterized as functional in their native hosts. This article reviews the major progress made in understanding the mechanisms of invading DNA immunity by type I CRISPR-Cas and summarizes the practical applications of endogenous type I CRISPR-based toolkits for prokaryotic engineering.
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Affiliation(s)
- Yanli Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Baiyang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jiamei Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yile Hao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiangdong Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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Tian Y, Liu RR, Xian WD, Xiong M, Xiao M, Li WJ. A novel thermal Cas12b from a hot spring bacterium with high target mismatch tolerance and robust DNA cleavage efficiency. Int J Biol Macromol 2020; 147:376-384. [DOI: 10.1016/j.ijbiomac.2020.01.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/30/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022]
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Behler J, Hess WR. Approaches to study CRISPR RNA biogenesis and the key players involved. Methods 2020; 172:12-26. [PMID: 31325492 DOI: 10.1016/j.ymeth.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins provide an inheritable and adaptive immune system against phages and foreign genetic elements in many bacteria and archaea. The three stages of CRISPR-Cas immunity comprise adaptation, CRISPR RNA (crRNA) biogenesis and interference. The maturation of the pre-crRNA into mature crRNAs, short guide RNAs that target invading nucleic acids, is crucial for the functionality of CRISPR-Cas defense systems. Mature crRNAs assemble with Cas proteins into the ribonucleoprotein (RNP) effector complex and guide the Cas nucleases to the cognate foreign DNA or RNA target. Experimental approaches to characterize these crRNAs, the specific steps toward their maturation and the involved factors, include RNA-seq analyses, enzyme assays, methods such as cryo-electron microscopy, the crystallization of proteins, or UV-induced protein-RNA crosslinking coupled to mass spectrometry analysis. Complex and multiple interactions exist between CRISPR-cas-encoded specific riboendonucleases such as Cas6, Cas5d and Csf5, endonucleases with dual functions in maturation and interference such as the enzymes of the Cas12 and Cas13 families, and nucleases belonging to the cell's degradosome such as RNase E, PNPase and RNase J, both in the maturation as well as in interference. The results of these studies have yielded a picture of unprecedented diversity of sequences, enzymes and biochemical mechanisms.
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Affiliation(s)
- Juliane Behler
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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12
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Stachler AE, Schwarz TS, Schreiber S, Marchfelder A. CRISPRi as an efficient tool for gene repression in archaea. Methods 2020; 172:76-85. [DOI: 10.1016/j.ymeth.2019.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 11/30/2022] Open
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Milicevic O, Repac J, Bozic B, Djordjevic M, Djordjevic M. A Simple Criterion for Inferring CRISPR Array Direction. Front Microbiol 2019; 10:2054. [PMID: 31551987 PMCID: PMC6737040 DOI: 10.3389/fmicb.2019.02054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022] Open
Abstract
Inferring transcriptional direction (orientation) of the CRISPR array is essential for many applications, including systematically investigating non-canonical CRISPR/Cas functions. The standard method, CRISPRDirection (embedded within CRISPRCasFinder), fails to predict the orientation (ND predictions) for ∼37% of the classified CRISPR arrays (>2200 loci); this goes up to >70% for the II-B subtype where non-canonical functions were first experimentally discovered. Alternatively, Potential Orientation (also embedded within CRISPRCasFinder), has a much smaller frequency of ND predictions but might have significantly lower accuracy. We propose a novel simple criterion, where the CRISPR array direction is assigned according to the direction of its associated cas genes (Cas Orientation). We systematically assess the performance of the three methods (Cas Orientation, CRISPRDirection, and Potential Orientation) across all CRISPR/Cas subtypes, by a mutual crosscheck of their predictions, and by comparing them to the experimental dataset. Interestingly, CRISPRDirection agrees much better with Cas Orientation than with Potential Orientation, despite CRISPRDirection and Potential Orientation being mutually related – Potential Orientation corresponding to one of six (heterogeneous) predictors employed by CRISPRDirection – and being unrelated to Cas Orientation. We find that Cas Orientation has much higher accuracy compared to Potential Orientation and comparable accuracy to CRISPRDirection – while accurately assigning an orientation to ∼95% of the CRISPR arrays that are non-determined by CRISPRDirection. Cas Orientation is, at the same time, simple to employ, requiring only (routine for prokaryotes) the prediction of the associated protein coding gene direction.
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Affiliation(s)
- Ognjen Milicevic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Multidisciplinary Ph.D. Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Jelena Repac
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | - Bojan Bozic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | | | - Marko Djordjevic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
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14
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Jain I, Minakhin L, Mekler V, Sitnik V, Rubanova N, Severinov K, Semenova E. Defining the seed sequence of the Cas12b CRISPR-Cas effector complex. RNA Biol 2019; 16:413-422. [PMID: 30022698 PMCID: PMC6546406 DOI: 10.1080/15476286.2018.1495492] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/12/2018] [Indexed: 12/14/2022] Open
Abstract
Target binding by CRISPR-Cas ribonucleoprotein effectors is initiated by the recognition of double-stranded PAM motifs by the Cas protein moiety followed by destabilization, localized melting, and interrogation of the target by the guide part of CRISPR RNA moiety. The latter process depends on seed sequences, parts of the target that must be strictly complementary to CRISPR RNA guide. Mismatches between the target and CRISPR RNA guide outside the seed have minor effects on target binding, thus contributing to off-target activity of CRISPR-Cas effectors. Here, we define the seed sequence of the Type V Cas12b effector from Bacillus thermoamylovorans. While the Cas12b seed is just five bases long, in contrast to all other effectors characterized to date, the nucleotide base at the site of target cleavage makes a very strong contribution to target binding. The generality of this additional requirement was confirmed during analysis of target recognition by Cas12b effector from Alicyclobacillus acidoterrestris. Thus, while the short seed may contribute to Cas12b promiscuity, the additional specificity determinant at the site of cleavage may have a compensatory effect making Cas12b suitable for specialized genome editing applications.
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Affiliation(s)
- Ishita Jain
- Department of Rutgers University, Rutgers The State University of New Jersey, Waksman Institute of Microbiology, Piscataway, NJ, USA
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Skolkovo, Russia
| | - Leonid Minakhin
- Department of Rutgers University, Rutgers The State University of New Jersey, Waksman Institute of Microbiology, Piscataway, NJ, USA
| | - Vladimir Mekler
- Department of Rutgers University, Rutgers The State University of New Jersey, Waksman Institute of Microbiology, Piscataway, NJ, USA
| | - Vasily Sitnik
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Skolkovo, Russia
| | - Natalia Rubanova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Skolkovo, Russia
| | - Konstantin Severinov
- Department of Rutgers University, Rutgers The State University of New Jersey, Waksman Institute of Microbiology, Piscataway, NJ, USA
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Skolkovo, Russia
| | - Ekaterina Semenova
- Department of Rutgers University, Rutgers The State University of New Jersey, Waksman Institute of Microbiology, Piscataway, NJ, USA
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15
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Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nat Microbiol 2018; 4:177-186. [PMID: 30478289 PMCID: PMC6298592 DOI: 10.1038/s41564-018-0302-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids, based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other's CRISPR-Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR-Cas systems in microbial speciation.
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16
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Abstract
CRISPR-Cas systems are a highly effective immune mechanism for prokaryotes, providing defense against invading foreign DNA. By definition, all CRISPR-Cas systems have short repeats interspersing their spacers. These repeats play a key role in preventing cleavage of self DNA and in the integration of new spacers. Here we focus on the phenomenon of repeat modularity, namely the unexpectedly high degree of repeat conservation across different systems within a genome or between different species. We hypothesize that modularity can be beneficial for CRISPR-Cas containing organisms, because it facilitates horizontal acquisition of 'pre-immunized' CRISPR arrays and allows the utilization of spacers acquired by one system for use by other systems within the same cell.
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Affiliation(s)
- Yael Yair
- a School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel
| | - Uri Gophna
- a School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv , Israel
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17
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Maikova A, Severinov K, Soutourina O. New Insights Into Functions and Possible Applications of Clostridium difficile CRISPR-Cas System. Front Microbiol 2018; 9:1740. [PMID: 30108577 PMCID: PMC6079278 DOI: 10.3389/fmicb.2018.01740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/12/2018] [Indexed: 12/26/2022] Open
Abstract
Over the last decades the enteric bacterium Clostridium difficile (novel name Clostridioides difficile) - has emerged as an important human nosocomial pathogen. It is a leading cause of hospital-acquired diarrhea and represents a major challenge for healthcare providers. Many aspects of C. difficile pathogenesis and its evolution remain poorly understood. Efficient defense systems against phages and other genetic elements could have contributed to the success of this enteropathogen in the phage-rich gut communities. Recent studies demonstrated the presence of an active CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) subtype I-B system in C. difficile. In this mini-review, we will discuss the recent advances in characterization of original features of the C. difficile CRISPR-Cas system in laboratory and clinical strains, as well as interesting perspectives for our understanding of this defense system function and regulation in this important enteropathogen. This knowledge will pave the way for the development of promising biotechnological and therapeutic tools in the future. Possible applications for the C. difficile strain monitoring and genotyping, as well as for CRISPR-based genome editing and antimicrobials are also discussed.
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Affiliation(s)
- Anna Maikova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Microbiology, Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Konstantin Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Olga Soutourina
- Microbiology, Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Institut Pasteur, Paris, France
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18
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Affiliation(s)
- Xu Zhang
- MOE Lab of Bioinformatics; School of Life Sciences; Tsinghua University; Beijing 100084 China
- Center for Synthetic and Systems Biology; Tsinghua University; Beijing 100084 China
| | - Yina Lin
- MOE Lab of Bioinformatics; School of Life Sciences; Tsinghua University; Beijing 100084 China
- Center for Synthetic and Systems Biology; Tsinghua University; Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences; Tsinghua University; Beijing 100084 China
| | - Guo-Qiang Chen
- MOE Lab of Bioinformatics; School of Life Sciences; Tsinghua University; Beijing 100084 China
- Center for Synthetic and Systems Biology; Tsinghua University; Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences; Tsinghua University; Beijing 100084 China
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19
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Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol 2018; 16:469-480. [PMID: 29649958 PMCID: PMC6546412 DOI: 10.1080/15476286.2018.1460994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Invading genetic elements pose a constant threat to prokaryotic survival, requiring an effective defence. Eleven years ago, the arsenal of known defence mechanisms was expanded by the discovery of the CRISPR-Cas system. Although CRISPR-Cas is present in the majority of archaea, research often focuses on bacterial models. Here, we provide a perspective based on insights gained studying CRISPR-Cas system I-B of the archaeon Haloferax volcanii. The system relies on more than 50 different crRNAs, whose stability and maintenance critically depend on the proteins Cas5 and Cas7, which bind the crRNA and form the Cascade complex. The interference machinery requires a seed sequence and can interact with multiple PAM sequences. H. volcanii stands out as the first example of an organism that can tolerate autoimmunity via the CRISPR-Cas system while maintaining a constitutively active system. In addition, the H. volcanii system was successfully developed into a tool for gene regulation.
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Affiliation(s)
| | | | | | | | | | - Karina A Haas
- a Biology II, Ulm University , Ulm , Germany.,b Microbiology and Biotechnology, Ulm University , Ulm , Germany
| | | | - Omer S Alkhnbashi
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany
| | - Kundan Sharma
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,f Ludwig Institute for Cancer Research, University of Oxford , Oxford , United Kingdom
| | - Henning Urlaub
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,g Institute for Clinical Chemistry, University Medical Center Göttingen , Robert Koch Straße 10, Göttingen , Germany
| | - Rolf Backofen
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany.,d Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg , Germany
| | - Uri Gophna
- h School of Molecular Cell Biology & Biotechnology, George S. Wise, Faculty of Life Sciences, Tel Aviv University , Tel Aviv , Israel
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20
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Stachler AE, Turgeman-Grott I, Shtifman-Segal E, Allers T, Marchfelder A, Gophna U. High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon. Nucleic Acids Res 2017; 45:5208-5216. [PMID: 28334774 PMCID: PMC5435918 DOI: 10.1093/nar/gkx150] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems allow bacteria and archaea to acquire sequence-specific immunity against selfish genetic elements such as viruses and plasmids, by specific degradation of invader DNA or RNA. However, this involves the risk of autoimmunity if immune memory against host DNA is mistakenly acquired. Such autoimmunity has been shown to be highly toxic in several bacteria and is believed to be one of the major costs of maintaining these defense systems. Here we generated an experimental system in which a non-essential gene, required for pigment production and the reddish colony color, is targeted by the CRISPR-Cas I-B system of the halophilic archaeon Haloferax volcanii. We show that under native conditions, where both the self-targeting and native crRNAs are expressed, self-targeting by CRISPR-Cas causes no reduction in transformation efficiency of the plasmid encoding the self-targeting crRNA. Furthermore, under such conditions, no effect on organismal growth rate or loss of the reddish colony phenotype due to mutations in the targeted region could be observed. In contrast, in cells deleted for the pre-crRNA processing gene cas6, where only the self-targeting crRNA exists as mature crRNA, self-targeting leads to moderate toxicity and the emergence of deletion mutants. Sequencing of the deletions caused by CRISPR-Cas self targeting indicated DNA repair via microhomology-mediated end joining.
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Affiliation(s)
| | - Israela Turgeman-Grott
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978-01, Israel
| | - Ella Shtifman-Segal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978-01, Israel
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | | | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978-01, Israel
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21
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Zhang Q, Ye Y. Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics 2017; 18:92. [PMID: 28166719 PMCID: PMC5294841 DOI: 10.1186/s12859-017-1512-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023] Open
Abstract
Background The CRISPR–Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR–Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. Results Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don’t contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. Conclusion This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR–Cas systems. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1512-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quan Zhang
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave, Bloomington, IN, 47405, USA.
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22
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Moller AG, Liang C. Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics. PeerJ 2017; 5:e2844. [PMID: 28097058 PMCID: PMC5228507 DOI: 10.7717/peerj.2844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/29/2016] [Indexed: 01/12/2023] Open
Abstract
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.
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Affiliation(s)
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, United States
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23
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Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PMG, Duggin IG, Cavicchioli R. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function. Sci Rep 2016; 6:34639. [PMID: 27708407 PMCID: PMC5052560 DOI: 10.1038/srep34639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/16/2016] [Indexed: 01/04/2023] Open
Abstract
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J C Walsh
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - M Ji
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - P M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - I G Duggin
- The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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24
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Mousaei M, Deng L, She Q, Garrett RA. Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus. RNA Biol 2016; 13:1166-1173. [PMID: 27618562 DOI: 10.1080/15476286.2016.1229735] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The stringency of crRNA-protospacer DNA base pair matching required for effective CRISPR-Cas interference is relatively low in crenarchaeal Sulfolobus species in contrast to that required in some bacteria. To understand its biological significance we studied crRNA-protospacer interactions in Sulfolobus islandicus REY15A which carries multiple, and functionally diverse, interference complexes. A range of mismatches were introduced into a vector-borne protospacer that was identical to spacer 1 of CRISPR locus 2, with a cognate CCN PAM sequence. Two important crRNA annealing regions were identified on the 39 bp protospacer, a strong primary site centered on nucleotides 3 - 7 and a weaker secondary site at nucleotides 21 - 25. Multiple mismatches introduced into remaining protospacer regions did not seriously impair interference. Extending the study to different protospacers demonstrated that the efficacy of the secondary site was greatest for protospacers with higher G+C contents. In addition, the interference effects were assigned specifically to the type I-A dsDNA-targeting module by repeating the experiments with mutated protospacer constructs that were transformed into an S. islandicus mutant lacking type III-Bα and III-Bβ interference gene cassettes, which showed similar interference levels to those of the wild-type strain. Parallels are drawn to the involvement of 2 annealing sites for microRNAs on some eukaryal mRNAs which provide enhanced binding capacity and specificity. A biological rationale for the relatively low crRNA-protospacer base pairing stringency among the Sulfolobales is considered.
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Affiliation(s)
- Marzieh Mousaei
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Ling Deng
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Qunxin She
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Roger A Garrett
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
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25
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Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex. Extremophiles 2016; 21:95-107. [PMID: 27582008 DOI: 10.1007/s00792-016-0871-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/16/2016] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas immune systems defend prokaryotes against viruses and plasmids. CRISPR RNAs (crRNAs) associate with various CRISPR-associated (Cas) protein modules to form structurally and functionally diverse (Type I-VI) crRNP immune effector complexes. Previously, we identified three, co-existing effector complexes in Pyrococcus furiosus -Type I-A (Csa), Type I-G (Cst), and Type III-B (Cmr)-and demonstrated that each complex functions in vivo to eliminate invader DNA. Here, we reconstitute functional Cst crRNP complexes in vitro from recombinant Cas proteins and synthetic crRNAs and investigate mechanisms of crRNP assembly and invader DNA recognition and destruction. All four known Cst-affiliated Cas proteins (Cas5t, Cst1, Cst2, and Cas3) are required for activity, but each subunit plays a distinct role. Cas5t and Cst2 comprise a minimal set of proteins that selectively interact with crRNA. Further addition of Cst1, enables the four subunit crRNP (Cas5t, Cst1, Cst2, crRNA) to specifically bind complementary, double-stranded DNA targets and to recruit the Cas3 effector nuclease, which catalyzes cleavages at specific sites within the displaced, non-target DNA strand. Our results indicate that Type I-G crRNPs selectively bind target DNA in a crRNA and, protospacer adjacent motif dependent manner to recruit a dedicated Cas3 nuclease for invader DNA destruction.
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26
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Babski J, Haas KA, Näther-Schindler D, Pfeiffer F, Förstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A, Soppa J. Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). BMC Genomics 2016; 17:629. [PMID: 27519343 PMCID: PMC4983044 DOI: 10.1186/s12864-016-2920-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/07/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii. RESULTS Three independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5'-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 % of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 %) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 %) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 % of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs). CONCLUSION This study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated.
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Affiliation(s)
- Julia Babski
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | | | - Daniela Näther-Schindler
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, MaxPlanckInstitute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Konrad U. Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany
| | - Matthias Hammelmann
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | - Rolf Hilker
- Bioinformatik und Systembiologie, University of Gießen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Anke Becker
- LOEWE-Center for Synthetic Microbiology, Hans-Meerwein-Str., 35032 Marburg, Germany
| | - Cynthia M. Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany
| | | | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
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Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 2016; 44:5872-82. [PMID: 27216815 PMCID: PMC4937334 DOI: 10.1093/nar/gkw469] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 12/26/2022] Open
Abstract
Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The Cas protein-CRISPR RNA interaction sites within this complex were identified via mass spectrometry. Additional Cas proteins, commonly described as large and small subunits, that are present in all other investigated Cascade structures, were not detected. We introduced this minimal Type I system in Escherichia coli and show that it provides heterologous protection against lambda phage. The absence of a large subunit suggests that the length of the crRNA might not be fixed and recombinant Cascade complexes with drastically shortened and elongated crRNAs were engineered. Size-exclusion chromatography and small-angle X-ray scattering analyses revealed that the number of Cas7fv backbone subunits is adjusted in these shortened and extended Cascade variants. Larger Cascade complexes can still confer immunity against lambda phage infection in E. coli. Minimized Type I CRISPR-Cas systems expand our understanding of the evolution of Cascade assembly and diversity. Their adjustable crRNA length opens the possibility for customizing target DNA specificity.
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Affiliation(s)
- Daniel Gleditzsch
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Kundan Sharma
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany
| | - Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany
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Stachler AE, Marchfelder A. Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System. J Biol Chem 2016; 291:15226-42. [PMID: 27226589 PMCID: PMC4946936 DOI: 10.1074/jbc.m116.724062] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is used by bacteria and archaea to fend off foreign genetic elements. Since its discovery it has been developed into numerous applications like genome editing and regulation of transcription in eukaryotes and bacteria. For archaea currently no tools for transcriptional repression exist. Because molecular biology analyses in archaea become more and more widespread such a tool is vital for investigating the biological function of essential genes in archaea. Here we use the model archaeon Haloferax volcanii to demonstrate that its endogenous CRISPR-Cas system I-B can be harnessed to repress gene expression in archaea. Deletion of cas3 and cas6b genes results in efficient repression of transcription. crRNAs targeting the promoter region reduced transcript levels down to 8%. crRNAs targeting the reading frame have only slight impact on transcription. crRNAs that target the coding strand repress expression only down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%. Repression of an essential gene results in reduction of transcription levels down to 22%. Targeting efficiencies can be enhanced by expressing a catalytically inactive Cas3 mutant. Genes can be targeted on plasmids or on the chromosome, they can be monocistronic or part of a polycistronic operon.
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Affiliation(s)
| | - Anita Marchfelder
- From the Department of Biology II, Ulm University, 89069 Ulm, Germany
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29
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Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K. Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Front Microbiol 2016; 7:398. [PMID: 27064693 PMCID: PMC4814470 DOI: 10.3389/fmicb.2016.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.
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Affiliation(s)
- Anna Lopatina
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia
| | - Sofia Medvedeva
- Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
| | - Sergey Shmakov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology Skolkovo, Russia
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University Moscow, Russia
| | - Vjacheslav Krylenkov
- Department of Botany, Saint-Petersburg State University Saint-Petersburg, Russia
| | - Konstantin Severinov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
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Elmore J, Deighan T, Westpheling J, Terns RM, Terns MP. DNA targeting by the type I-G and type I-A CRISPR-Cas systems of Pyrococcus furiosus. Nucleic Acids Res 2015; 43:10353-63. [PMID: 26519471 PMCID: PMC4666368 DOI: 10.1093/nar/gkv1140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/16/2015] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems silence plasmids and viruses in prokaryotes. CRISPR–Cas effector complexes contain CRISPR RNAs (crRNAs) that include sequences captured from invaders and direct CRISPR-associated (Cas) proteins to destroy corresponding invader nucleic acids. Pyrococcus furiosus (Pfu) harbors three CRISPR–Cas immune systems: a Cst (Type I-G) system with an associated Cmr (Type III-B) module at one locus, and a partial Csa (Type I-A) module (lacking known invader sequence acquisition and crRNA processing genes) at another locus. The Pfu Cmr complex cleaves complementary target RNAs, and Csa systems have been shown to target DNA, while the mechanism by which Cst complexes silence invaders is unknown. In this study, we investigated the function of the Cst as well as Csa system in Pfu strains harboring a single CRISPR–Cas system. Plasmid transformation assays revealed that the Cst and Csa systems both function by DNA silencing and utilize similar flanking sequence information (PAMs) to identify invader DNA. Silencing by each system specifically requires its associated Cas3 nuclease. crRNAs from the 7 shared CRISPR loci in Pfu are processed for use by all 3 effector complexes, and Northern analysis revealed that individual effector complexes dictate the profile of mature crRNA species that is generated.
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Affiliation(s)
- Joshua Elmore
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Trace Deighan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Jan Westpheling
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA Department of Genetics, University of Georgia, Athens, GA 30602, USA Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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31
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Dwarakanath S, Brenzinger S, Gleditzsch D, Plagens A, Klingl A, Thormann K, Randau L. Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens. Nucleic Acids Res 2015; 43:8913-23. [PMID: 26350210 PMCID: PMC4605320 DOI: 10.1093/nar/gkv882] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/26/2022] Open
Abstract
Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs.
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Affiliation(s)
- Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Susanne Brenzinger
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Daniel Gleditzsch
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - André Plagens
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I, Biocentre LMU Munich, Großhaderner Str. 2-4, Planegg-Martinsried D-82152, Germany
| | - Kai Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany LOEWE Center for Synthetic Microbiology (Synmikro), Marburg, Hessen D-35043, Germany
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33
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Abstract
Clostridium difficile is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen, C. difficile must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in C. difficile reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic C. difficile strain. Through genome sequencing and host range analysis of several new C. difficile phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both C. difficile strains. We further demonstrate that C. difficile Cas proteins are capable of interference in a heterologous host, Escherichia coli. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites. Clostridium difficile is the major cause of nosocomial infections associated with antibiotic therapy worldwide. To survive in bacteriophage-rich gut communities, enteropathogens must develop efficient systems for defense against foreign DNA elements. CRISPR-Cas systems have recently taken center stage among various anti-invader bacterial defense systems. We provide experimental evidence for the function of the C. difficile CRISPR system against plasmid DNA and bacteriophages. These data demonstrate the original features of active C. difficile CRISPR system and bring important insights into the interactions of this major enteropathogen with foreign DNA invaders during its infection cycle.
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Tschitschko B, Williams TJ, Allen MA, Páez-Espino D, Kyrpides N, Zhong L, Raftery MJ, Cavicchioli R. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME JOURNAL 2015; 9:2094-107. [PMID: 26125682 DOI: 10.1038/ismej.2015.110] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/15/2015] [Accepted: 05/19/2015] [Indexed: 01/21/2023]
Abstract
Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions-interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host-virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics.
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Affiliation(s)
- Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | | | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CVC, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. RNA (NEW YORK, N.Y.) 2015; 21:1147-58. [PMID: 25904135 PMCID: PMC4436667 DOI: 10.1261/rna.049130.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5' ends (8-nt repeat-derived 5' tag sequences) but heterogeneous 3' ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3' end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
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Affiliation(s)
- Sonali Majumdar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Neil T Pfister
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Mark Compton
- Department of Poultry Science, University of Georgia, Athens, Georgia 30602, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Claiborne V C Glover
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA Department of Genetics, University of Georgia, Athens, Georgia 30602, USA Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) systems provide bacteria and archaea with adaptive immunity to repel invasive genetic elements. Type I systems use 'cascade' [CRISPR-associated (Cas) complex for antiviral defence] ribonucleoprotein complexes to target invader DNA, by base pairing CRISPR RNA (crRNA) to protospacers. Cascade identifies PAMs (protospacer adjacent motifs) on invader DNA, triggering R-loop formation and subsequent DNA degradation by Cas3. Cas8 is a candidate PAM recognition factor in some cascades. We analysed Cas8 homologues from type IB CRISPR systems in archaea Haloferax volcanii (Hvo) and Methanothermobacter thermautotrophicus (Mth). Cas8 was essential for CRISPR interference in Hvo and purified Mth Cas8 protein responded to PAM sequence when binding to nucleic acids. Cas8 interacted physically with Cas5-Cas7-crRNA complex, stimulating binding to PAM containing substrates. Mutation of conserved Cas8 amino acid residues abolished interference in vivo and altered catalytic activity of Cas8 protein in vitro. This is experimental evidence that Cas8 is important for targeting Cascade to invader DNA.
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Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 2015; 117:119-28. [PMID: 25868999 DOI: 10.1016/j.biochi.2015.03.025] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 12/26/2022]
Abstract
Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus-host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues.
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Affiliation(s)
- Devashish Rath
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Lina Amlinger
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Archana Rath
- Department of Biotechnology, University of Mumbai, Mumbai 400098, India
| | - Magnus Lundgren
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
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Abstract
ABSTRACT
Horizontal gene transfer drives the evolution of bacterial genomes, including the adaptation to changing environmental conditions. Exogenous DNA can enter a bacterial cell through transformation (free DNA or plasmids) or through the transfer of mobile genetic elements by conjugation (plasmids) and transduction (bacteriophages). Favorable genes can be acquired, but undesirable traits can also be inadvertently acquired through these processes. Bacteria have systems, such as clustered regularly interspaced short palindromic repeat CRISPR–associated genes (CRISPR-Cas), that can cleave foreign nucleic acid molecules. In this review, we discuss recent advances in understanding CRISPR-Cas system activity against mobile genetic element transfer through transformation and conjugation. We also highlight how CRISPR-Cas systems influence bacterial evolution and how CRISPR-Cas components affect plasmid replication.
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Maier LK, Dyall-Smith M, Marchfelder A. The Adaptive Immune System of Haloferax volcanii. Life (Basel) 2015; 5:521-37. [PMID: 25692903 PMCID: PMC4390866 DOI: 10.3390/life5010521] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/03/2015] [Indexed: 11/30/2022] Open
Abstract
To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this prokaryotic defence system is present in 90% of archaeal and 40% of bacterial species, and enables foreign intruders to be eliminated in a sequence-specific manner. There are three major types (I–III) and at least 14 subtypes of this system, with only some of the subtypes having been analysed in detail, and many aspects of the defence reaction remaining to be elucidated. Few archaeal examples have so far been analysed. Here we summarize the characteristics of the CRISPR-Cas system of Haloferax volcanii, an extremely halophilic archaeon originally isolated from the Dead Sea. It carries a single CRISPR-Cas system of type I-B, with a Cascade like complex composed of Cas proteins Cas5, Cas6b and Cas7. Cas6b is essential for CRISPR RNA (crRNA) maturation but is otherwise not required for the defence reaction. A systematic search revealed that six protospacer adjacent motif (PAM) sequences are recognised by the Haloferax defence system. For successful invader recognition, a non-contiguous seed sequence of 10 base-pairs between the crRNA and the invader is required.
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Affiliation(s)
| | - Mike Dyall-Smith
- School of Biomedical Sciences, Charles Sturt University, 2650 NSW, Australia.
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Peng W, Feng M, Feng X, Liang YX, She Q. An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Nucleic Acids Res 2015; 43:406-17. [PMID: 25505143 PMCID: PMC4288192 DOI: 10.1093/nar/gku1302] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/30/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide a small RNA-based mechanism to defend against invasive genetic elements in archaea and bacteria. To investigate the in vivo mechanism of RNA interference by two type III-B systems (Cmr-α and Cmr-β) in Sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-CRISPR (AC) locus with a single spacer. After pAC plasmids were introduced into different strains, Northern analyses confirmed that mature crRNAs were produced from the plasmid-borne CRISPR loci, which then guided gene silencing to target gene expression. Spacer mutagenesis identified a trinucleotide sequence in the 3'-region of crRNA that was crucial for RNA interference. Studying mutants lacking Cmr-α or Cmr-β system showed that each Cmr complex exhibited RNA interference. Strikingly, these analyses further revealed that the two Cmr systems displayed distinctive interference features. Whereas Cmr-β complexes targeted transcripts and could be recycled in RNA cleavage, Cmr-α complexes probably targeted nascent RNA transcripts and remained associated with the substrate. Moreover, Cmr-β exhibited much stronger RNA cleavage activity than Cmr-α. Since we previously showed that S. islandicus Cmr-α mediated transcription-dependent DNA interference, the Cmr-α constitutes the first CRISPR system exhibiting dual targeting of RNA and DNA.
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Affiliation(s)
- Wenfang Peng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xu Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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Heidrich N, Dugar G, Vogel J, Sharma CM. Investigating CRISPR RNA Biogenesis and Function Using RNA-seq. Methods Mol Biol 2015; 1311:1-21. [PMID: 25981463 DOI: 10.1007/978-1-4939-2687-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The development of deep sequencing technology has greatly facilitated transcriptome analyses of both prokaryotes and eukaryotes. RNA-sequencing (RNA-seq), which is based on massively parallel sequencing of cDNAs, has been used to annotate transcript boundaries and revealed widespread antisense transcription as well as a wealth of novel noncoding transcripts in many bacteria. Moreover, RNA-seq is nowadays widely used for gene expression profiling and about to replace hybridization-based approaches such as microarrays. RNA-seq has also informed about the biogenesis and function of CRISPR RNAs (crRNAs) of different types of bacterial RNA-based CRISPR-Cas immune systems. Here we describe several studies that employed RNA-seq for crRNA analyses, with a particular focus on a differential RNA-seq (dRNA-seq) approach, which can distinguish between primary and processed transcripts and allows for a genome-wide annotation of transcriptional start sites. This approach helped to identify a new crRNA biogenesis pathway of Type II CRISPR-Cas systems that involves a trans-encoded small RNA, tracrRNA, and the host factor RNase III.
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Affiliation(s)
- Nadja Heidrich
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2/Bau D15, 97080, Würzburg, Germany
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Maier LK, Stachler AE, Saunders SJ, Backofen R, Marchfelder A. An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. J Biol Chem 2014; 290:4192-201. [PMID: 25512373 PMCID: PMC4326828 DOI: 10.1074/jbc.m114.617506] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3′ handle are still active in triggering an interference reaction. The complete 3′ handle could be removed without loss of activity. However, manipulations of the 5′ handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference.
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Affiliation(s)
| | | | - Sita J Saunders
- the Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, and
| | - Rolf Backofen
- the Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, and the BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, Albert-Ludwigs-University Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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Staals RHJ, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJR, Nogales E, Doudna JA, Shinkai A, van der Oost J. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol Cell 2014; 56:518-30. [PMID: 25457165 PMCID: PMC4342149 DOI: 10.1016/j.molcel.2014.10.005] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/27/2014] [Accepted: 10/02/2014] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1-Csm5) with an uneven stoichiometry and a single crRNA of variable size (35-53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence.
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Affiliation(s)
- Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands.
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - David W Taylor
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jack E Kornfeld
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Nirajan Neupane
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Koen Varossieau
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | | | | | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Saitama 351-0198, Japan
| | | | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, 37075 Göttingen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands
| | - Eva Nogales
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720-3200, USA
| | - Jennifer A Doudna
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720-3200, USA
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN, Kanagawa 230-0045, Japan
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands.
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Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system. Biochem Soc Trans 2014; 41:1444-8. [PMID: 24256235 DOI: 10.1042/bst20130098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Uptake of foreign mobile genetic elements is often detrimental and can result in cell death. For protection against invasion, prokaryotes have developed several defence mechanisms, which take effect at all stages of infection; an example is the recently discovered CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) immune system. This defence system directly degrades invading genetic material and is present in almost all archaea and many bacteria. Current data indicate a large variety of mechanistic molecular approaches. Although almost all archaea carry this defence weapon, only a few archaeal systems have been fully characterized. In the present paper, we summarize the prerequisites for the detection and degradation of invaders in the halophilic archaeon Haloferax volcanii. H. volcanii encodes a subtype I-B CRISPR-Cas system and the defence can be triggered by a plasmid-based invader. Six different target-interference motifs are recognized by the Haloferax defence and a 9-nt non-contiguous seed sequence is essential. The repeat sequence has the potential to fold into a minimal stem-loop structure, which is conserved in haloarchaea and might be recognized by the Cas6 endoribonuclease during the processing of CRISPR loci into mature crRNA (CRISPR RNA). Individual crRNA species were present in very different concentrations according to an RNA-Seq analysis and many were unable to trigger a successful defence reaction. Recognition of the plasmid invader does not depend on its copy number, but instead results indicate a dependency on the type of origin present on the plasmid.
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Li M, Wang R, Xiang H. Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation. Nucleic Acids Res 2014; 42:7226-35. [PMID: 24803673 PMCID: PMC4066796 DOI: 10.1093/nar/gku389] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The prokaryotic immune system CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) adapts to foreign invaders by acquiring their short deoxyribonucleic acid (DNA) fragments as spacers, which guide subsequent interference to foreign nucleic acids based on sequence matching. The adaptation mechanism avoiding acquiring ‘self’ DNA fragments is poorly understood. In Haloarcula hispanica, we previously showed that CRISPR adaptation requires being primed by a pre-existing spacer partially matching the invader DNA. Here, we further demonstrate that flanking a fully-matched target sequence, a functional PAM (protospacer adjacent motif) is still required to prime adaptation. Interestingly, interference utilizes only four PAM sequences, whereas adaptation-priming tolerates as many as 23 PAM sequences. This relaxed PAM selectivity explains how adaptation-priming maximizes its tolerance of PAM mutations (that escape interference) while avoiding mis-targeting the spacer DNA within CRISPR locus. We propose that the primed adaptation, which hitches and cooperates with the interference pathway, distinguishes target from non-target by CRISPR ribonucleic acid guidance and PAM recognition.
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Affiliation(s)
- Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Molecular mechanisms of CRISPR-mediated microbial immunity. Cell Mol Life Sci 2014; 71:449-65. [PMID: 23959171 PMCID: PMC3890593 DOI: 10.1007/s00018-013-1438-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/21/2013] [Accepted: 07/24/2013] [Indexed: 12/15/2022]
Abstract
Bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. Thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. Not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. Phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. The antagonistic interaction between bacteria and rapidly diversifying viruses promotes the evolution and dissemination of bacteriophage-resistance mechanisms in bacteria. Recently, an adaptive microbial immune system, named clustered regularly interspaced short palindromic repeats (CRISPR) and which provides acquired immunity against viruses and plasmids, has been identified. Unlike the restriction–modification anti-phage barrier that subjects to cleavage any foreign DNA lacking a protective methyl-tag in the target site, the CRISPR–Cas systems are invader-specific, adaptive, and heritable. In this review, we focus on the molecular mechanisms of interference/immunity provided by different CRISPR–Cas systems.
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Biswas A, Fineran PC, Brown CM. Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. ACTA ACUST UNITED AC 2014; 30:1805-13. [PMID: 24578404 DOI: 10.1093/bioinformatics/btu114] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MOTIVATION CRISPR RNAs (crRNAs) are a type of small non-coding RNA that form a key part of an acquired immune system in prokaryotes. Specific prediction methods find crRNA-encoding loci in nearly half of sequenced bacterial, and three quarters of archaeal, species. These Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays consist of repeat elements alternating with specific spacers. Generally one strand is transcribed, producing long pre-crRNAs, which are processed to short crRNAs that base pair with invading nucleic acids to facilitate their destruction. No current software for the discovery of CRISPR loci predicts the direction of crRNA transcription. RESULTS We have developed an algorithm that accurately predicts the strand of the resulting crRNAs. The method uses as input CRISPR repeat predictions. CRISPRDirection uses parameters that are calculated from the CRISPR repeat predictions and flanking sequences, which are combined by weighted voting. The prediction may use prior coding sequence annotation but this is not required. CRISPRDirection correctly predicted the orientation of 94% of a reference set of arrays. AVAILABILITY AND IMPLEMENTATION The Perl source code is freely available from http://bioanalysis.otago.ac.nz/CRISPRDirection.
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Affiliation(s)
- Ambarish Biswas
- Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New ZealandDepartment of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand
| | - Chris M Brown
- Department of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New ZealandDepartment of Biochemistry, Department of Microbiology and Immunology and Genetics Otago, University of Otago, Dunedin 9054, New Zealand
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Künne T, Swarts DC, Brouns SJJ. Planting the seed: target recognition of short guide RNAs. Trends Microbiol 2014; 22:74-83. [PMID: 24440013 DOI: 10.1016/j.tim.2013.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/06/2013] [Accepted: 12/11/2013] [Indexed: 12/23/2022]
Abstract
Small guide RNAs play important roles in cellular processes such as regulation of gene expression and host defense against invading nucleic acids. The mode of action of small RNAs relies on protein-assisted base pairing of the guide RNA with target mRNA or DNA to interfere with their transcription, translation, or replication. Several unrelated classes of small noncoding RNAs have been identified including eukaryotic RNA silencing-associated small RNAs, prokaryotic small regulatory RNAs (sRNAs), and prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats) RNAs (crRNAs). All three groups identify their target sequence by base pairing after finding it in a pool of millions of other nucleotide sequences in the cell. In this complicated target search process, a region of 6-12 nucleotides (nt) of the small RNA termed the 'seed' plays a critical role. We review the concept of seed sequences and discuss its importance for initial target recognition and interference.
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Affiliation(s)
- Tim Künne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Daan C Swarts
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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Brendel J, Stoll B, Lange SJ, Sharma K, Lenz C, Stachler AE, Maier LK, Richter H, Nickel L, Schmitz RA, Randau L, Allers T, Urlaub H, Backofen R, Marchfelder A. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii. J Biol Chem 2014; 289:7164-7177. [PMID: 24459147 PMCID: PMC3945376 DOI: 10.1074/jbc.m113.508184] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.
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Affiliation(s)
- Jutta Brendel
- Department of Biology II, Ulm University, 89069 Ulm, Germany
| | - Britta Stoll
- Department of Biology II, Ulm University, 89069 Ulm, Germany
| | - Sita J Lange
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Kundan Sharma
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christof Lenz
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | | | | | - Hagen Richter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Lisa Nickel
- Institute for General Microbiology, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany; Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg, 79110 Freiburg, Germany
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