1
|
Xu PX, Ren HY, Zhao N, Jin XJ, Wen BH, Qin T. Distribution characteristics of the Legionella CRISPR-Cas system and its regulatory mechanism underpinning phenotypic function. Infect Immun 2024; 92:e0022923. [PMID: 38099659 PMCID: PMC10790817 DOI: 10.1128/iai.00229-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/10/2023] [Indexed: 01/17/2024] Open
Abstract
Legionella is a common intracellular parasitic bacterium that infects humans via the respiratory tract, causing Legionnaires' disease, with fever and pneumonia as the main symptoms. The emergence of highly virulent and azithromycin-resistant Legionella pneumophila is a major challenge in clinical anti-infective therapy. The CRISPR-Cas acquired immune system provides immune defense against foreign nucleic acids and regulates strain biological functions. However, the distribution of the CRISPR-Cas system in Legionella and how it regulates gene expression in L. pneumophila remain unclear. Herein, we assessed 915 Legionella whole-genome sequences to determine the distribution characteristics of the CRISPR-Cas system and constructed gene deletion mutants to explore the regulation of the system based on growth ability in vitro, antibiotic sensitivity, and intracellular proliferation of L. pneumophila. The CRISPR-Cas system in Legionella was predominantly Type II-B and was mainly concentrated in the genome of L. pneumophila ST1 strains. The Type II-B CRISPR-Cas system showed no effect on the strain's growth ability in vitro but significantly reduced resistance to azithromycin and decreased proliferation ability due to regulation of the lpeAB efflux pump and the Dot/Icm type IV secretion system. Thus, the Type II-B CRISPR-Cas system plays a crucial role in regulating the virulence of L. pneumophila. This expands our understanding of drug resistance and pathogenicity in Legionella, provides a scientific basis for the prevention of Legionnaires' disease outbreaks and the rational use of clinical drugs, and facilitates effective treatment of Legionnaires' disease.
Collapse
Affiliation(s)
- Pei-Xing Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong-Yu Ren
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao-Jing Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bo-Hai Wen
- Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tian Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
2
|
Shaibullah S, Shuhaimi N, Ker DS, Mohd-Sharif N, Ho KL, Teh AH, Waterman J, Tang TH, Wong RR, Nathan S, Mohamed R, Ng MJ, Fung SY, Jonet MA, Firdaus-Raih M, Ng CL. Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family. Commun Biol 2023; 6:920. [PMID: 37684342 PMCID: PMC10491678 DOI: 10.1038/s42003-023-05265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na+ and K+) is crucial for nuclease activity. An active site with a unique D11(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D11(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2.
Collapse
Affiliation(s)
- Sofiyah Shaibullah
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Nurshahirah Shuhaimi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - De-Sheng Ker
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Nurhikmah Mohd-Sharif
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Rui-Rui Wong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana, BBN, Nilai, 71800, Negeri Sembilan, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Rahmah Mohamed
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Min Jia Ng
- Medicinal Mushroom Research Group (MMRG), Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shin-Yee Fung
- Medicinal Mushroom Research Group (MMRG), Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia (NIBM), Jalan Bangi, Kajang, 43000, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia.
| |
Collapse
|
3
|
Campbell JA, Cianciotto NP. Legionella pneumophila Cas2 Promotes the Expression of Small Heat Shock Protein C2 That Is Required for Thermal Tolerance and Optimal Intracellular Infection. Infect Immun 2022; 90:e0036922. [PMID: 36073935 PMCID: PMC9584283 DOI: 10.1128/iai.00369-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Previously, we demonstrated that Cas2 encoded within the CRISPR-Cas locus of Legionella pneumophila strain 130b promotes the ability of the Legionella pathogen to infect amoebal hosts. Given that L. pneumophila Cas2 has RNase activity, we posited that the cytoplasmic protein is regulating the expression of another Legionella gene(s) that fosters intracellular infection. Proteomics revealed 10 proteins at diminished levels in the cas2 mutant, and reverse transcription-quantitative (qRT-PCR) confirmed the reduced expression of a gene encoding putative small heat shock protein C2 (HspC2), among several others. As predicted, the gene was expressed more highly at 37°C to 50°C than that at 30°C, and an hspC2 mutant, but not its complemented derivative, displayed ~100-fold reduced CFU following heat shock at 55°C. Compatible with the effect of Cas2 on hspC2 expression, strains lacking Cas2 also had impaired thermal tolerance. The hspC2 mutant, like the cas2 mutant before it, was greatly impaired for infection of Acanthamoeba castellanii, a frequent host for legionellae in waters. HspC2 and Cas2 were not required for entry into these host cells but promoted the replicative phase of intracellular infection. Finally, the hspC2 mutant exhibited an additional defect during the infection of macrophages, which are the primary host for legionellae during lung infection. In summary, hspC2 is upregulated by the presence of Cas2, and HspC2 uniquely promotes both L. pneumophila extracellular survival at high temperatures and infection of amoebal and human host cells. To our knowledge, these findings also represent the first genetic proof linking Cas2 to thermotolerance, expanding the repertoire of noncanonical functions associated with CRISPR-Cas proteins.
Collapse
Affiliation(s)
- Jackson A. Campbell
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| |
Collapse
|
4
|
Anand V, Prabhakaran HS, Gogoi P, Kanaujia SP, Kumar M. Structural and functional characterization of Cas2 of CRISPR-Cas subtype I-C lacking the CRISPR component. Front Mol Biosci 2022; 9:988569. [PMID: 36172044 PMCID: PMC9510766 DOI: 10.3389/fmolb.2022.988569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
The genome of pathogenic Leptospira interrogans serovars (Copenhageni and Lai) are predicted to have CRISPR-Cas of subtypes I-B and I-C. Cas2, one of the core Cas proteins, has a crucial role in adaptive defense against foreign nucleic acids. However, subtype I-C lacks the CRISPR element at its loci essential for RNA-mediated adaptive immunity against foreign nucleic acids. The reason for sustaining the expense of cas genes are unknown in the absence of a CRISPR array. Thus, Cas2C was chosen as a representative Cas protein from two well-studied serovars of Leptospira to address whether it is functional. In this study, the recombinant Cas2C of Leptospira serovars Copenhageni (rLinCas2C, 12 kDa) and Lai (rLinCas2C_Lai, 8.6 kDa) were overexpressed and purified. Due to natural frameshift mutation in the cas2c gene of serovar Lai, rLinCas2C_Lai was overexpressed and purified as a partially translated protein. Nevertheless, the recombinant Cas2C from each serovar exhibited metal-dependent DNase and metal-independent RNase activities. The crystal structure of rLinCas2C obtained at the resolution of 2.60 Å revealed the protein is in apostate conformation and contains N- (1–71 amino acids) and C-terminal (72–90 amino acids) regions, with the former possessing a ferredoxin fold. Substitution of the conserved residues (Tyr7, Asp8, Arg33, and Phe39) with alanine and deletion of Loop L2 resulted in compromised DNase activity. On the other hand, a moderate reduction in RNase activity was evident only in selective rLinCas2C mutants. Overall, in the absence of an array, the observed catalytic activity of Cas2C may be required for biological processes distinct from the CRISPR-Cas-associated function.
Collapse
Affiliation(s)
| | | | | | | | - Manish Kumar
- *Correspondence: Shankar Prasad Kanaujia, ; Manish Kumar,
| |
Collapse
|
5
|
Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
Collapse
Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
| |
Collapse
|
6
|
Dixit B, Anand V, Hussain MS, Kumar M. The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100040. [PMID: 34841331 PMCID: PMC8610317 DOI: 10.1016/j.crmicr.2021.100040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the adaptation module in many variants of the CRISPR-Cas system in prokaryotes against the invading genetic elements. Cas4 is recognized as a DNA exonuclease that contains a RecB nuclease domain and a Fe-S cluster-binding module. In Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130, the cas4 gene is functionally transcribed as an active component of the CRISPR-Cas I-B system. Investigation of nuclease activity of Cas4 (LinCas4) of the L. interrogans illustrated divalent-metal cofactor (Mn2+ or Mg2+) dependent endonuclease activity on the DNA substrate. In agreement, mutation of the selective metal interacting residues (Asp74 and Glu87) curtails the DNA cleavage activity in LinCas4. Computational modeling shows metal-ion interacting residues (Asp74 and Glu87) in the LinCas4 to be a part of the RecB motifs II and III, the same as other Cas4 orthologs. The mutation of a potential DNA interacting residue in the LinCas4 (LinCas4Y132A) or one of the four cysteine residues (LinCas4C18A) involved in coordinating the 4Fe-4S cluster did not perturb its DNase activity. Iron chelation assay of the purified LinCas4 demonstrated it in the apostate conformation. Reconstitution of the Fe-S cluster in the LinCas4 under in vitro condition displayed its coordination with four iron atoms per LinCas4 monomer and was confirmed by the UV and CD spectroscopy studies.
Collapse
Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vineet Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Md. Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| |
Collapse
|
7
|
Wang Y, Mao T, Li Y, Xiao W, Liang X, Duan G, Yang H. Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci. Front Microbiol 2021; 12:736565. [PMID: 34751223 PMCID: PMC8571024 DOI: 10.3389/fmicb.2021.736565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus (S. aureus), which is one of the most important species of Staphylococci, poses a great threat to public health. Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune platform to combat foreign mobile genetic elements (MGEs) such as plasmids and phages. The aim of this study is to describe the distribution and structure of CRISPR-Cas system in S. aureus, and to explore the relationship between CRISPR and horizontal gene transfer (HGT). Here, we analyzed 67 confirmed CRISPR loci and 15 companion Cas proteins in 52 strains of Staphylococci with bioinformatics methods. Comparing with the orphan CRISPR loci in Staphylococci, the strains harboring complete CRISPR-Cas systems contained multiple CRISPR loci, direct repeat sequences (DR) forming stable RNA secondary structures with lower minimum free energy (MFE), and variable spacers with detectable protospacers. In S. aureus, unlike the orphan CRISPRs away from Staphylococcal cassette chromosome mec (SCCmec), the complete CRISPR-Cas systems were in J1 region of SCCmec. In addition, we found a conserved motif 5'-TTCTCGT-3' that may protect their downstream sequences from DNA interference. In general, orphan CRISPR locus in S. aureus differed greatly from the structural characteristics of the CRISPR-Cas system. Collectively, our results provided new insight into the diversity and characterization of the CRISPR-Cas system in S. aureus.
Collapse
Affiliation(s)
- Ying Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Tingting Mao
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinxia Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Wenwei Xiao
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xuan Liang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
8
|
Bourne CR. Bacterial Growth Mindset: Structural Plasticity in Defense Systems. Structure 2021; 29:97-98. [PMID: 33545061 DOI: 10.1016/j.str.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this issue of Structure, Bertelsen et al. determine the three-dimensional structures of the Haemophilus influenzae VapD toxin, a Cas-2 homolog, with and without its cognate neutralizing antitoxin, VapX, that together comprise a toxin-antitoxin system. These reveal a unique stoichiometry, with two VapD toxins neutralized simultaneously by one VapX antitoxin.
Collapse
Affiliation(s)
- Christina R Bourne
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, OK 73019, USA.
| |
Collapse
|
9
|
Quan FS, Kong HH, Lee HA, Chu KB, Moon EK. Identification of differentially expressed Legionella genes during its intracellular growth in Acanthamoeba. Heliyon 2020; 6:e05238. [PMID: 33088972 PMCID: PMC7566939 DOI: 10.1016/j.heliyon.2020.e05238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/01/2020] [Accepted: 10/08/2020] [Indexed: 11/28/2022] Open
Abstract
Legionella grows intracellularly in free-living amoeba as well as in mammalian macrophages. Until now, the overall gene expression pattern of intracellular Legionella in Acanthamoeba was not fully explained. Intracellular bacteria are capable of not only altering the gene expression of its host, but it can also regulate the expression of its own genes for survival. In this study, differentially expressed Legionella genes within Acanthamoeba during the 24 h intracellular growth period were investigated for comparative analysis. RNA sequencing analysis revealed 3,003 genes from the intracellular Legionella. Among them, 115 genes were upregulated and 1,676 genes were downregulated more than 2 fold compared to the free Legionella. Gene ontology (GO) analysis revealed the suppression of multiple genes within the intracellular Legionella, which were categorized under 'ATP binding' and 'DNA binding' in the molecular function domain. Gene expression of alkylhydroperoxidase, an enzyme involved in virulence and anti-oxidative stress response, was strongly enhanced 24 h post-intracellular growth. Amino acid ABC transporter substrate-binding protein that utilizes energy generation was also highly expressed. Genes associated with alkylhydroperoxidase, glucose pathway, and Dot/Icm type IV secretion system were shown to be differentially expressed. These results contribute to a better understanding of the survival strategies of intracellular Legionella within Acanthamoeba.
Collapse
Affiliation(s)
- Fu-Shi Quan
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Republic of Korea.,Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Hae-Ahm Lee
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Ki-Back Chu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| |
Collapse
|
10
|
Abstract
Porphyromonas gingivalis is a key pathogen of periodontitis, a polymicrobial disease characterized by a chronic inflammation that destroys the tissues supporting the teeth. Thus, understanding the virulence potential of P. gingivalis is essential to maintaining a healthy oral microbiome. In nonoral organisms, CRISPR-Cas systems have been shown to modulate a variety of microbial processes, including protection from exogenous nucleic acids, and, more recently, have been implicated in bacterial virulence. Previously, our clinical findings identified activation of the CRISPR-Cas system in patient samples at the transition to disease; however, the mechanism of contribution to disease remained unknown. The importance of the present study resides in that it is becoming increasingly clear that CRISPR-associated proteins have broader functions than initially thought and that those functions now include their role in the virulence of periodontal pathogens. Studying a P. gingivaliscas3 mutant, we demonstrate that at least one of the CRISPR-Cas systems is involved in the regulation of virulence during infection. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system is a unique genomic entity that provides prokaryotic cells with adaptive and heritable immunity. Initial studies identified CRISPRs as central elements used by bacteria to protect against foreign nucleic acids; however, emerging evidence points to CRISPR involvement in bacterial virulence. The present study aimed to identify the participation of one CRISPR-Cas protein, Cas3, in the virulence of the oral pathogen Porphyromonas gingivalis, an organism highly associated with periodontitis. Our results show that compared to the wild type, a mutant with a deletion of the Cas3 gene, an essential nuclease part of the class 1 type I CRISPR-Cas system, increased the virulence of P. gingivalis. In vitro infection modeling revealed only mildly enhanced production of proinflammatory cytokines by THP-1 cells when infected with the mutant strain. Dual transcriptome sequencing (RNA-seq) analysis of infected THP-1 cells showed an increase in expression of genes associated with pathogenesis in response to Δcas3 mutant infection, with the target of Cas3 activities in neutrophil chemotaxis and gene silencing. The importance of cas3 in controlling virulence was corroborated in a Galleria mellonella infection model, where the presence of the Δcas3 mutant resulted in a statistically significant increase in mortality of G. mellonella. A time-series analysis of transcription patterning during infection showed that G. mellonella elicited very different immune responses to the wild-type and the Δcas3 mutant strains and revealed a rearrangement of association in coexpression networks. Together, these observations show for the first time that Cas3 plays a significant role in regulating the virulence of P. gingivalis. IMPORTANCEPorphyromonas gingivalis is a key pathogen of periodontitis, a polymicrobial disease characterized by a chronic inflammation that destroys the tissues supporting the teeth. Thus, understanding the virulence potential of P. gingivalis is essential to maintaining a healthy oral microbiome. In nonoral organisms, CRISPR-Cas systems have been shown to modulate a variety of microbial processes, including protection from exogenous nucleic acids, and, more recently, have been implicated in bacterial virulence. Previously, our clinical findings identified activation of the CRISPR-Cas system in patient samples at the transition to disease; however, the mechanism of contribution to disease remained unknown. The importance of the present study resides in that it is becoming increasingly clear that CRISPR-associated proteins have broader functions than initially thought and that those functions now include their role in the virulence of periodontal pathogens. Studying a P. gingivaliscas3 mutant, we demonstrate that at least one of the CRISPR-Cas systems is involved in the regulation of virulence during infection.
Collapse
|
11
|
Abstract
CRISPR research began over 30 years ago with the incidental discovery of an unusual nucleotide arrangement in the Escherichia coli genome. It took 20 years to find the main function of CRISPR-Cas systems as an adaptive defence mechanism against invading nucleic acids, and our knowledge of their biology has steadily increased ever since. In parallel, the number of applications derived from CRISPR-Cas systems has risen spectacularly. The CRISPR-based genome editing tool is arguably the most exciting application in both basic and applied research. Lately, CRISPR-Cas research has partially shifted to the least understood aspect of its biology: the ability of CRISPR-Cas systems to acquire new immunities during the so-called adaptation step. To date, the most efficient natural system to readily acquire new spacers is the type II-A system of the gram-positive dairy bacterium Streptococcus thermophilus. The discovery of additional systems able to acquire new spacers will hopefully draw more attention to this step of CRISPR-Cas biology. This review focuses on the breakthroughs that have helped to unravel the adaptation phase and on questions that remain to be answered.
Collapse
Affiliation(s)
- Cas Mosterd
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Xiao G, Yi Y, Che R, Zhang Q, Imran M, Khan A, Yan J, Lin X. Characterization of CRISPR-Cas systems in Leptospira reveals potential application of CRISPR in genotyping of Leptospira interrogans. APMIS 2019; 127:202-216. [PMID: 30908774 DOI: 10.1111/apm.12935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat-CRISPR-associated gene (CRISPR-Cas) systems can help bacteria against invading mobile genetic elements. In this study, the occurrence and diversity of CRISPR-Cas systems in 41 genomes of Leptospira strains were investigated. Three subtypes (subtype I-B, subtype I-C and subtype I-E) of CRISPR-Cas systems were identified in both pathogenic and intermediate Leptospira species but not in saprophytic species. Noteworthy, the majority of pathogenic species harbor two different types of CRISPR-Cas systems (subtype I-B and subtype I-E). Furthermore, Cas2 protein of subtype I-C in L. interrogans exhibited a metal-dependent DNase activity in a nonspecific manner. CRISPR spacers in subtype I-B are highly conserved within the same serovars and hypervariable across different serovars of L. interrogans. Based on the subtype I-B CRISPR arrays, the serotypes of different L. interrogans strains were easily identified. Investigation of the origin of CRISPR spacers showed that 192 spacers (23.5%) matched to mobile genetic elements, indicating CRISPR-Cas systems may play an important role in the defense of foreign invading DNA.
Collapse
Affiliation(s)
- Guohui Xiao
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Yusi Yi
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Rongbo Che
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qinchao Zhang
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Muhammad Imran
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Abidullah Khan
- Department of Burns, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xu'ai Lin
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
14
|
Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli. Molecules 2019; 24:molecules24040784. [PMID: 30795631 PMCID: PMC6413058 DOI: 10.3390/molecules24040784] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas is an adaptive bacterial immune system, whose CRISPR array can actively change in response to viral infections. However, Type I-E CRISPR/Cas in E. coli (an established model system), appears not to exhibit such active adaptation, which suggests that it might have functions other than immune response. Through computational analysis, we address the involvement of the system in non-canonical functions. To assess targets of CRISPR spacers, we align them against both E. coli genome and an exhaustive (~230) set of E. coli viruses. We systematically investigate the obtained alignments, such as hit distribution with respect to genome annotation, propensity to target mRNA, the target functional enrichment, conservation of CRISPR spacers and putative targets in related bacterial genomes. We find that CRISPR spacers have a statistically highly significant tendency to target i) host compared to phage genomes, ii) one of the two DNA strands, iii) genomic dsDNA rather than mRNA, iv) transcriptionally active regions, and v) sequences (cis-regulatory elements) with slower turn-over rate compared to CRISPR spacers (trans-factors). The results suggest that the Type I-E CRISPR/Cas system has a major role in transcription regulation of endogenous genes, with a potential to rapidly rewire these regulatory interactions, with targets being selected through naïve adaptation.
Collapse
|
15
|
Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
Collapse
|
16
|
Koonin EV. CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology. BIOLOGY & PHILOSOPHY 2019; 34:9. [PMID: 30930513 PMCID: PMC6404382 DOI: 10.1007/s10539-018-9658-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and (re)acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, "altruistic" shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements (MGE) to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools.
Collapse
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 USA
| |
Collapse
|
17
|
Delafont V, Rodier MH, Maisonneuve E, Cateau E. Vermamoeba vermiformis: a Free-Living Amoeba of Interest. MICROBIAL ECOLOGY 2018; 76:991-1001. [PMID: 29737382 DOI: 10.1007/s00248-018-1199-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/30/2018] [Indexed: 05/22/2023]
Abstract
Free-living amoebae are protists that are widely distributed in the environment including water, soil, and air. Although the amoebae of the genus Acanthamoeba are still the most studied, other species, such as Vermamoeba vermiformis (formerly Hartmannella vermiformis), are the subject of increased interest. Found in natural or man-made aquatic environments, V. vermiformis can support the multiplication of other microorganisms and is able to harbor and potentially protect pathogenic bacteria or viruses. This feature is to be noted because of the presence of this thermotolerant amoeba in hospital water networks. As a consequence, this protist could be implicated in health concerns and be indirectly responsible for healthcare-related infections. This review highlights, among others, the consequences of V. vermiformis relationships with other microorganisms and shows that this free-living amoeba species is therefore of interest for public health.
Collapse
Affiliation(s)
- Vincent Delafont
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe Microbiologie de l'Eau, Université de Poitiers, 1 rue Georges Bonnet, 86022, Poitiers Cedex, France
| | - Marie-Helene Rodier
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe Microbiologie de l'Eau, Université de Poitiers, 1 rue Georges Bonnet, 86022, Poitiers Cedex, France
- Laboratoire de parasitologie et mycologie, CHU La Milètrie, 86021, Poitiers Cedex, France
| | - Elodie Maisonneuve
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe Microbiologie de l'Eau, Université de Poitiers, 1 rue Georges Bonnet, 86022, Poitiers Cedex, France
| | - Estelle Cateau
- Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe Microbiologie de l'Eau, Université de Poitiers, 1 rue Georges Bonnet, 86022, Poitiers Cedex, France.
- Laboratoire de parasitologie et mycologie, CHU La Milètrie, 86021, Poitiers Cedex, France.
| |
Collapse
|
18
|
Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M. In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. Front Genet 2018; 9:474. [PMID: 30386377 PMCID: PMC6199352 DOI: 10.3389/fgene.2018.00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023] Open
Abstract
In addition to its well-established defense function, CRISPR/Cas can also exhibit crucial non-canonical activity through endogenous gene expression regulation, which was found to mainly affect bacterial virulence. These non-canonical functions depend on scaRNA, which is a small RNA encoded outside of CRISPR array, that is typically flanked by a transcription start site (TSS) and a terminator, and is in part complementary to another small CRISPR/Cas-associated RNA (tracrRNAs). Identification of scaRNAs is however largely complicated by the scarcity of RNA-Seq data across different bacteria, so that they were identified only in a relatively rare CRISPR/Cas subtype (IIB), and the possibility of finding them in other Type II systems is currently unclear. This study presents the first effort toward systematic detection of small CRISPR/Cas-associated regulatory RNAs, where obtained predictions can guide future experiments. The core of our approach is ab initio detection of small RNAs from bacterial genome, which is based on jointly predicting transcription signals - TSS and terminators - and homology to CRISPR array repeat. Particularly, we employ our improved approach for detecting bacterial TSS, since accurate TSS detection is the main limiting factor for accurate small RNA prediction. We also explore how our predictions match to available RNA-Seq data and analyze their conservation across related bacterial species. In Type IIB systems, our predictions are consistent with experimental data, and we systematically identify scaRNAs throughout this subtype. Furthermore, we identify scaRNA:tracrRNA pairs in a number of IIA/IIC systems, where the appearance of scaRNAs co-occurs with the strains being pathogenic. RNA-Seq and conservation analysis show that our method is well suited for predicting CRISPR/Cas-associated small RNAs. We also find possible existence of a modified mechanism of CRISPR-associated small RNA action, which, interestingly, closely resembles the setup employed in biotechnological applications. Overall, our findings indicate that scaRNA:tracrRNA pairs are present in all subtypes of Type II systems, and point to an underlying connection with bacterial virulence. In addition to formulating these hypotheses, careful manual curation that we performed, makes an important first step toward fully automated predictor of CRISPR/Cas-associated small RNAs, which will allow their large scale analysis across diverse bacterial genomes.
Collapse
Affiliation(s)
- Jelena Guzina
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Wei-Hua Chen
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Tamara Stankovic
- Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | | | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
19
|
Faure G, Makarova KS, Koonin EV. CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity. J Mol Biol 2018; 431:3-20. [PMID: 30193985 DOI: 10.1016/j.jmb.2018.08.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/26/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that functions by incorporating fragments of foreign DNA into CRISPR arrays. The arrays containing spacers derived from foreign DNA are transcribed, and the transcripts are processed to generate spacer-containing mature CRISPR-RNAs that are employed as guides to specifically recognize and cleave the DNA or RNA of the cognate parasitic genetic elements. The CRISPR-Cas systems show remarkable complexity and diversity of molecular organization and appear to be involved in various cellular functions that are distinct from, even if connected to, adaptive immunity. In this review, we discuss some of such functional links of CRISPR-Cas systems including their effect on horizontal gene transfer that can be either inhibitory or stimulatory, connections between CRISPR-Cas and DNA repair systems as well as programmed cell death and signal transduction mechanisms, and potential role of CRISPR-Cas in transposon integration and plasmid maintenance. The interplay between the primary function of CRISPR-Cas as an adaptive immunity mechanism and these other roles defines the richness of the biological effects of these systems and affects their spread among bacteria and archaea.
Collapse
Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
20
|
Hille F, Richter H, Wong SP, Bratovič M, Ressel S, Charpentier E. The Biology of CRISPR-Cas: Backward and Forward. Cell 2018. [DOI: 10.1016/j.cell.2017.11.032] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
21
|
Jeong M, Kim I, Kim G, Ka D, Kim NK, Bae E, Ryu KS, Suh JY. Solution structure and dynamics of Xanthomonas albilineans
Cas2 provide mechanistic insight on nuclease activity. FEBS Lett 2018; 592:147-155. [DOI: 10.1002/1873-3468.12942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 09/30/2017] [Accepted: 12/10/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Migyeong Jeong
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Iktae Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Gowoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Donghyun Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Nak-Kyun Kim
- Advanced Analysis Center; Korea Institute of Science and Technology; Seoul Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team; Korea Basic Science Institute; Ochang Chungbuk Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
- Institute for Biomedical Sciences; Shinshu University; Nagano Japan
| |
Collapse
|
22
|
Arslan-Aydoğdu EÖ, Kimiran A. An investigation of virulence factors of Legionella pneumophila environmental isolates. Braz J Microbiol 2017; 49:189-199. [PMID: 29037504 PMCID: PMC5790574 DOI: 10.1016/j.bjm.2017.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Nine Legionella pneumophila strains isolated from cooling towers and a standard strain (L. pneumophila serogroup 1, ATCC 33152, Philadelphia 1) were analyzed and compared in terms of motility, flagella structure, ability to form biofilms, enzymatic activities (hemolysin, nucleases, protease, phospholipase A, phospholipase C, acid phosphatase, alkaline phosphatase and lipase), hemagglutination capabilities, and pathogenicity in various host cells (Acanthamoeba castellanii ATCC 30234, mouse peritoneal macrophages and human peripheral monocytes). All the isolates of bacteria appeared to be motile and polar-flagellated and possessed the type-IV fimbria. Upon the evaluation of virulence factors, isolate 4 was found to be the most pathogenic strain, while 6 out of the 9 isolates (the isolates 1, 2, 3, 4, 5, and 7) were more virulent than the ATCC 33152 strain. The different bacterial strains exhibited differences in properties such as adhesion, penetration and reproduction in the hosts, and preferred host type. To our knowledge, this is the first study to compare the virulence of environmental L. pneumophila strains isolated in Turkey, and it provides important information relevant for understanding the epidemiology of L. pneumophila.
Collapse
Affiliation(s)
| | - Ayten Kimiran
- Istanbul University, Faculty of Science, Department of Biology, Istanbul, Turkey
| |
Collapse
|
23
|
CRISPR-Cas adaptive immunity and the three Rs. Biosci Rep 2017; 37:BSR20160297. [PMID: 28674106 PMCID: PMC5518543 DOI: 10.1042/bsr20160297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
In this summary, we focus on fundamental biology of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas (CRISPR-associated proteins) adaptive immunity in bacteria. Emphasis is placed on emerging information about functional interplay between Cas proteins and proteins that remodel DNA during homologous recombination (HR), DNA replication or DNA repair. We highlight how replication forks may act as ‘trigger points’ for CRISPR adaptation events, and the potential for cascade-interference complexes to act as precise roadblocks in DNA replication by an invader MGE (mobile genetic element), without the need for DNA double-strand breaks.
Collapse
|
24
|
Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
Collapse
|
25
|
Abstract
Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| |
Collapse
|
26
|
Abstract
Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.
Collapse
Affiliation(s)
- Hannah K Ratner
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - Timothy R Sampson
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - David S Weiss
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329
| |
Collapse
|
27
|
Koonin EV, Zhang F. Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices. Bioessays 2016; 39:1-9. [DOI: 10.1002/bies.201600186] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information; National Library of Medicine; Bethesda MD USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard; Cambridge MA USA
- Department of Health Sciences and Technology; Massachusetts Institute of Technology; Cambridge MA USA
- McGovern Institute for Brain Research at MIT; Cambridge MA USA
- Departments of Brain and Cognitive Science and Biological Engineering; Cambridge MA USA
| |
Collapse
|
28
|
Westra ER, Dowling AJ, Broniewski JM, van Houte S. Evolution and Ecology of CRISPR. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032428] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edze R. Westra
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Andrea J. Dowling
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Jenny M. Broniewski
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Stineke van Houte
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| |
Collapse
|
29
|
Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
Collapse
Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
30
|
Khodr A, Kay E, Gomez-Valero L, Ginevra C, Doublet P, Buchrieser C, Jarraud S. Molecular epidemiology, phylogeny and evolution of Legionella. INFECTION GENETICS AND EVOLUTION 2016; 43:108-22. [PMID: 27180896 DOI: 10.1016/j.meegid.2016.04.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022]
Abstract
Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles.
Collapse
Affiliation(s)
- A Khodr
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, France; CNRS, UMR 3525, 28, Rue du Dr Roux, 75724 Paris, France
| | - E Kay
- CIRI, International Center for Infectiology Research, Inserm, U1111, CNRS, UMR 5308, Université Lyon 1, École Normale Supérieure de Lyon, Lyon F-69008, France
| | - L Gomez-Valero
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, France; CNRS, UMR 3525, 28, Rue du Dr Roux, 75724 Paris, France
| | - C Ginevra
- CIRI, International Center for Infectiology Research, Inserm, U1111, CNRS, UMR 5308, Université Lyon 1, École Normale Supérieure de Lyon, Lyon F-69008, France; French National Reference Center of Legionella, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - P Doublet
- CIRI, International Center for Infectiology Research, Inserm, U1111, CNRS, UMR 5308, Université Lyon 1, École Normale Supérieure de Lyon, Lyon F-69008, France
| | - C Buchrieser
- Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires, France; CNRS, UMR 3525, 28, Rue du Dr Roux, 75724 Paris, France
| | - S Jarraud
- CIRI, International Center for Infectiology Research, Inserm, U1111, CNRS, UMR 5308, Université Lyon 1, École Normale Supérieure de Lyon, Lyon F-69008, France; French National Reference Center of Legionella, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| |
Collapse
|
31
|
Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW. Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. Cell Microbiol 2016; 18:1319-38. [PMID: 26936325 PMCID: PMC5071653 DOI: 10.1111/cmi.12586] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 02/25/2016] [Indexed: 01/04/2023]
Abstract
Clustered regularly interspaced short palindromic repeats with CRISPR‐associated gene (CRISPR‐Cas) systems are widely recognized as critical genome defense systems that protect microbes from external threats such as bacteriophage infection. Several isolates of the intracellular pathogen Legionella pneumophila possess multiple CRISPR‐Cas systems (type I‐C, type I‐F and type II‐B), yet the targets of these systems remain unknown. With the recent observation that at least one of these systems (II‐B) plays a non‐canonical role in supporting intracellular replication, the possibility remained that these systems are vestigial genome defense systems co‐opted for other purposes. Our data indicate that this is not the case. Using an established plasmid transformation assay, we demonstrate that type I‐C, I‐F and II‐B CRISPR‐Cas provide protection against spacer targets. We observe efficient laboratory acquisition of new spacers under ‘priming’ conditions, in which initially incomplete target elimination leads to the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify the first known target of L. pneumophila CRISPR‐Cas: a 30 kb episome of unknown function whose interbacterial transfer is guarded against by CRISPR‐Cas. We provide evidence that the element can subvert CRISPR‐Cas by mutating its targeted sequences – but that primed spacer acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial fitness, this element drives a host specialization event – with improved fitness in Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These observations add to a growing body of evidence that host range restriction can serve as an existential threat to L. pneumophila in the wild.
Collapse
Affiliation(s)
- Chitong Rao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Carmen Pelaz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jessica Wasserscheid
- The McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Joseph Bondy-Denomy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ken Dewar
- The McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexander W Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Public Health Ontario, Toronto, Ontario, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
32
|
Dixit B, Ghosh KK, Fernandes G, Kumar P, Gogoi P, Kumar M. Dual nuclease activity of a Cas2 protein in CRISPR-Cas subtype I-B ofLeptospira interrogans. FEBS Lett 2016; 590:1002-16. [DOI: 10.1002/1873-3468.12124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/20/2016] [Accepted: 03/03/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Karukriti Kaushik Ghosh
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Gary Fernandes
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Pankaj Kumar
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Manish Kumar
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| |
Collapse
|
33
|
I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope. Curr Opin Infect Dis 2016; 28:267-74. [PMID: 25887612 DOI: 10.1097/qco.0000000000000154] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE OF REVIEW CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids that adapt as new environmental threats arise. There are emerging examples of CRISPR-Cas functions in bacterial physiology beyond their role in adaptive immunity. This highlights the poorly understood, but potentially common, moonlighting functions of these abundant systems. We propose that these noncanonical CRISPR-Cas activities have evolved to respond to stresses at the cell envelope. RECENT FINDINGS Here, we discuss recent literature describing the impact of the extracellular environment on the regulation of CRISPR-Cas systems, and the influence of CRISPR-Cas activity on bacterial physiology. These described noncanonical CRISPR-Cas functions allow the bacterial cell to respond to the extracellular environment, primarily through changes in envelope physiology. SUMMARY This review discusses the expanding noncanonical functions of CRISPR-Cas systems, including their roles in virulence, focusing mainly on their relationship to the cell envelope. We first examine the effects of the extracellular environment on regulation of CRISPR-Cas components, and then discuss the impact of CRISPR-Cas systems on bacterial physiology, concentrating on their roles in influencing interactions with the environment including host organisms.
Collapse
|
34
|
Mendes JS, Santiago ADS, Toledo MAS, Rosselli-Murai LK, Favaro MTP, Santos CA, Horta MAC, Crucello A, Beloti LL, Romero F, Tasic L, de Souza AA, de Souza AP. VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity. PLoS One 2015; 10:e0145765. [PMID: 26694028 PMCID: PMC4687846 DOI: 10.1371/journal.pone.0145765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.
Collapse
Affiliation(s)
- Juliano S. Mendes
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - André da S. Santiago
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Marcelo A. S. Toledo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Luciana K. Rosselli-Murai
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Marianna T. P. Favaro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Clelton A. Santos
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Maria Augusta C. Horta
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Aline Crucello
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Lilian L. Beloti
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
| | - Fabian Romero
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-970
| | - Ljubica Tasic
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-970
| | | | - Anete P. de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil, CEP 13083-875
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, SP, Brazil, CEP 13083-862
| |
Collapse
|
35
|
Subtyping of the Legionella pneumophila “Ulm” outbreak strain using the CRISPR–Cas system. Int J Med Microbiol 2015; 305:828-37. [DOI: 10.1016/j.ijmm.2015.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/13/2015] [Accepted: 08/04/2015] [Indexed: 12/24/2022] Open
|
36
|
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Cell 2015; 163:840-53. [PMID: 26478180 DOI: 10.1016/j.cell.2015.10.008] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 12/26/2022]
Abstract
Bacteria acquire memory of viral invaders by incorporating invasive DNA sequence elements into the host CRISPR locus, generating a new spacer within the CRISPR array. We report on the structures of Cas1-Cas2-dual-forked DNA complexes in an effort toward understanding how the protospacer is sampled prior to insertion into the CRISPR locus. Our study reveals a protospacer DNA comprising a 23-bp duplex bracketed by tyrosine residues, together with anchored flanking 3' overhang segments. The PAM-complementary sequence in the 3' overhang is recognized by the Cas1a catalytic subunits in a base-specific manner, and subsequent cleavage at positions 5 nt from the duplex boundary generates a 33-nt DNA intermediate that is incorporated into the CRISPR array via a cut-and-paste mechanism. Upon protospacer binding, Cas1-Cas2 undergoes a significant conformational change, generating a flat surface conducive to proper protospacer recognition. Here, our study provides important structure-based mechanistic insights into PAM-dependent spacer acquisition.
Collapse
|