1
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Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [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: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
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Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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2
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Im J, Kim S, Park S, Wang SX, Lee JR. Evaluation of restriction and Cas endonuclease kinetics using matrix-insensitive magnetic biosensors. Biosens Bioelectron 2024; 249:116017. [PMID: 38262299 PMCID: PMC10867820 DOI: 10.1016/j.bios.2024.116017] [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: 11/13/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
The enzymatic actions of endonucleases in vivo can be altered due to bound substrates and differences in local environments, including enzyme concentration, pH, salinity, ionic strength, and temperature. Thus, accurate estimation of enzymatic reactions in vivo using matrix-dependent methods in solution can be challenging. Here, we report a matrix-insensitive magnetic biosensing platform that enables the measurement of endonuclease activity under different conditions with varying pH, salinity, ionic strength, and temperature. Using biosensor arrays and orthogonal pairs of oligonucleotides, we quantitatively characterized the enzymatic activity of EcoRI under different buffer conditions and in the presence of inhibitors. To mimic a more physiological environment, we monitored the sequence-dependent star activity of EcoRI under unconventional conditions. Furthermore, enzymatic activity was measured in cell culture media, saliva, and serum. Last, we estimated the effective cleavage rates of Cas12a on anchored single-strand DNAs using this platform, which more closely resembles in vivo settings. This platform will facilitate precise characterization of restriction and Cas endonucleases under various conditions.
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Affiliation(s)
- Jisoo Im
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Songeun Kim
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Suhyeon Park
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Shan X Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea; Graduate Program in Smart Factory, Ewha Womans University, Seoul, 03760, Republic of Korea.
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3
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Neill P, Crist N, McGorty R, Robertson-Anderson R. Enzymatic cleaving of entangled DNA rings drives scale-dependent rheological trajectories. SOFT MATTER 2024; 20:2750-2766. [PMID: 38440846 DOI: 10.1039/d3sm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate multi-site restriction endonucleases into dense DNA solutions to linearize and fragment circular DNA molecules. We pair optical tweezers microrheology with differential dynamic microscopy and single-molecule tracking to measure the linear and nonlinear viscoelastic response and transport properties of entangled DNA solutions over a wide range of spatiotemporal scales throughout the course of enzymatic digestion. We show that, at short timescales, relative to the relaxation timescales of the polymers, digestion of these 'topologically-active' fluids initially causes an increase in elasticity and relaxation times followed by a gradual decrease. Conversely, for long timescales, linear viscoelastic moduli exhibit signatures of increasing elasticity. DNA diffusion, likewise, becomes increasingly slowed, in direct opposition to the short-time behavior. We hypothesize that this scale-dependent rheology arises from the population of small DNA fragments, which increases as digestion proceeds, driving self-association of larger fragments via depletion interactions, giving rise to slow relaxation modes of clusters of entangled chains, interspersed among shorter unentangled fragments. While these slow modes likely dominate at long times, they are presumably frozen out in the short-time limit, which instead probes the faster relaxation modes of the unentangled population.
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Affiliation(s)
- Philip Neill
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Natalie Crist
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Ryan McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Rae Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
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4
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Baudrier L, Benamozig O, Langley J, Chopra S, Kalashnikova T, Benaoudia S, Singh G, Mahoney DJ, Wright NAM, Billon P. One-pot DTECT enables rapid and efficient capture of genetic signatures for precision genome editing and clinical diagnostics. CELL REPORTS METHODS 2024; 4:100698. [PMID: 38301655 PMCID: PMC10921016 DOI: 10.1016/j.crmeth.2024.100698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/05/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
The detection of genomic sequences and their alterations is crucial for basic research and clinical diagnostics. However, current methodologies are costly and time-consuming and require outsourcing sample preparation, processing, and analysis to genomic companies. Here, we establish One-pot DTECT, a platform that expedites the detection of genetic signatures, only requiring a short incubation of a PCR product in an optimized one-pot mixture. One-pot DTECT enables qualitative, quantitative, and visual detection of biologically relevant variants, such as cancer mutations, and nucleotide changes introduced by prime editing and base editing into cancer cells and human primary T cells. Notably, One-pot DTECT achieves quantification accuracy for targeted genetic signatures comparable with Sanger and next-generation sequencing. Furthermore, its effectiveness as a diagnostic platform is demonstrated by successfully detecting sickle cell variants in blood and saliva samples. Altogether, One-pot DTECT offers an efficient, versatile, adaptable, and cost-effective alternative to traditional methods for detecting genomic signatures.
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Affiliation(s)
- Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Jethro Langley
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Sanchit Chopra
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Tatiana Kalashnikova
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Sacha Benaoudia
- Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Gurpreet Singh
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Douglas J Mahoney
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Snyder Institute for Chronic Disease, Calgary, AB, Canada; Department of Microbiology, Immunology and Infectious Disease, Calgary, AB, Canada
| | - Nicola A M Wright
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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5
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Zimmerman EH, Ramsey EL, Hunter KE, Villadelgado SM, Phillips CM, Shipman RT, Forsyth MH. The Helicobacter pylori methylome is acid-responsive due to regulation by the two-component system ArsRS and the type I DNA methyltransferase HsdM1 (HP0463). J Bacteriol 2024; 206:e0030923. [PMID: 38179929 PMCID: PMC10810217 DOI: 10.1128/jb.00309-23] [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: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5'-TCAm6AVN6TGY-3' and 3'-AGTN6GAm6ACA-5'. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. IMPORTANCE This study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR~P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.
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Affiliation(s)
| | - Erin L. Ramsey
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | | | | | - Ryan T. Shipman
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Mark H. Forsyth
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
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6
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Zhang Y, Takaki Y, Yoshida-Takashima Y, Hiraoka S, Kurosawa K, Nunoura T, Takai K. A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems. mSystems 2023; 8:e0081723. [PMID: 37843256 PMCID: PMC10734518 DOI: 10.1128/msystems.00817-23] [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: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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7
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Kottenhahn P, Philipps G, Bunk B, Spröer C, Jennewein S. The Restriction-Modification Systems of Clostridium carboxidivorans P7. Microorganisms 2023; 11:2962. [PMID: 38138106 PMCID: PMC10745947 DOI: 10.3390/microorganisms11122962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Clostridium carboxidivorans P7 (DSM 15243) is a bacterium that converts syngas (a mixture of CO, H2, and CO2) into hexanol. An optimized and scaled-up industrial process could therefore provide a renewable source of fuels and chemicals while consuming industry waste gases. However, the genetic engineering of this bacterium is hindered by its multiple restriction-modification (RM) systems: the genome of C. carboxidivorans encodes at least ten restriction enzymes and eight methyltransferases (MTases). To gain insight into the complex RM systems of C. carboxidivorans, we analyzed genomic methylation patterns using single-molecule real-time (SMRT) sequencing and bisulfite sequencing. We identified six methylated sequence motifs. To match the methylation sites to the predicted MTases of C. carboxidivorans, we expressed them individually in Escherichia coli for functional characterization. Recognition motifs were identified for all three Type I MTases (CAYNNNNNCTGC/GCAGNNNNNRTG, CCANNNNNNNNTCG/CGANNNNNNNNTGG and GCANNNNNNNTNNCG/CGNNANNNNNNNTGC), two Type II MTases (GATAAT and CRAAAAR), and a single Type III MTase (GAAAT). However, no methylated recognition motif was found for one of the three Type II enzymes. One recognition motif that was methylated in C. carboxidivorans but not in E. coli (AGAAGC) was matched to the remaining Type III MTase through a process of elimination. Understanding these enzymes and the corresponding recognition sites will facilitate the development of genetic tools for C. carboxidivorans that can accelerate the industrial exploitation of this strain.
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Affiliation(s)
- Patrick Kottenhahn
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 52074 Aachen, Germany
- Department of Biology, RWTH Aachen University, 52074 Aachen, Germany
| | - Gabriele Philipps
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 52074 Aachen, Germany
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Culture Collection for Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Culture Collection for Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Stefan Jennewein
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 52074 Aachen, Germany
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8
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Mandal SC, Chakrabarti J. In-silicon studies on hydration in EcoRI-cognate DNA complex. Biophys Chem 2023; 303:107121. [PMID: 37837721 DOI: 10.1016/j.bpc.2023.107121] [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] [Received: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023]
Abstract
Restriction endonucleases (REs) cleave DNA at specific site in presence of Mg2+ ion. Experiments further emphasize the role of hydration in metal ion specificity and sequence specificity of DNA cleavage. However, the relation between hydration and specificity has not been understood till date. This leads us to study via all-atom molecular dynamics (MD) simulations how the hydration around the scissile phosphate group changes in presence of Mg2+ and Ca2+ and depend on the DNA sequence. We observe the least number of hydrogen bonds around the scissile phosphate group in presence of Mg2+ ion. We further find that the hydrogen bonds decrease at the scissile phosphate on mutating one base pair in the cleavage region of the DNA in Mg2+ loaded EcoRI-DNA complex. We also perform steered MD simulations and observe that the rate of decrease of fraction of hydrogen bonds is slower in the mutated complex than the unmutated complex.
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Affiliation(s)
- Sasthi Charan Mandal
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India..
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9
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Marfai J, McGorty RJ, Robertson-Anderson RM. Cooperative Rheological State-Switching of Enzymatically-Driven Composites of Circular DNA And Dextran. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305824. [PMID: 37500570 DOI: 10.1002/adma.202305824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, composites of circular DNA and dextran are pushed out-of-equilibrium via enzymatic digestion of DNA rings to linear fragments. These time-resolved rheology measurements reveal discrete state-switching, with composites undergoing abrupt transitions between dissipative and elastic-like states. The gating time and lifetime of the elastic-like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non-monotonically depend on the DNA fraction. These results are modeled using sigmoidal two-state functions to show that bulk state-switching can arise from continuous molecular-level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. This platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound-healing to self-repairing infrastructure.
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Affiliation(s)
- Juexin Marfai
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, 92110, USA
| | - Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, 92110, USA
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10
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Huang R, Shu B. Editorial: Enzyme-based theranostics. Front Bioeng Biotechnol 2023; 11:1280647. [PMID: 37711447 PMCID: PMC10497944 DOI: 10.3389/fbioe.2023.1280647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Ru Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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11
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Sorida M, Bonasio R. An efficient cloning method to expand vector and restriction site compatibility of Golden Gate Assembly. CELL REPORTS METHODS 2023; 3:100564. [PMID: 37671021 PMCID: PMC10475842 DOI: 10.1016/j.crmeth.2023.100564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023]
Abstract
Golden Gate Assembly is an efficient and rapid cloning method but requires dedicated vectors. Here, we modified Golden Gate to expand its compatibility to a broader range of destination vectors while maintaining its strengths. Our Expanded Golden Gate (ExGG) assembly adds to the insert(s) type IIS restriction sites that generate protruding ends compatible with traditional type IIP sites on the recipient vector. The ligated product cannot be cleaved again, owing to a single-base change near the junction. This allows the reaction to proceed in a single tube without an intermediate purification step. ExGG can be used to introduce multiple fragments into a vector simultaneously, including shorter fragments (<100 bp) and fragments with shared sequences, which can be difficult to assemble with other fast cloning strategies. Thus, ExGG extends the convenience of Golden Gate to a much larger space of pre-existing vectors designed for conventional cloning.
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Affiliation(s)
- Masato Sorida
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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12
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Ailloud F, Gottschall W, Suerbaum S. Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori. Commun Biol 2023; 6:839. [PMID: 37573385 PMCID: PMC10423294 DOI: 10.1038/s42003-023-05218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023] Open
Abstract
The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation implied that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection may shape both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.
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Affiliation(s)
- Florent Ailloud
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Wilhelm Gottschall
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sebastian Suerbaum
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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13
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Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL. Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI. Nucleic Acids Res 2023; 51:4467-4487. [PMID: 36987874 PMCID: PMC10201449 DOI: 10.1093/nar/gkad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
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Affiliation(s)
- Madison A Kennedy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
| | | | - Caleigh M Azumaya
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Minyong Chen
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
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14
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Huang D, Yuan MM, Chen J, Zheng X, Wong D, Alvarez PJJ, Yu P. The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes. ISME COMMUNICATIONS 2023; 3:46. [PMID: 37142716 PMCID: PMC10160068 DOI: 10.1038/s43705-023-00249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoxuan Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongsheng Wong
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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15
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Lu X, Huang F, Cheng R, Zhu B. A Unique m6A-Dependent Restriction Endonuclease from an Archaeal Virus. Microbiol Spectr 2023:e0426222. [PMID: 36946751 PMCID: PMC10101028 DOI: 10.1128/spectrum.04262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Prokaryotes possess numerous diverse defense systems to resist viral infections, while some viruses have also evolved antiviral defense systems to exclude other viruses in cases of multiple infections. Here, we report the first virus-derived modification-dependent restriction endonuclease (HHPV4I) from the archaeal virus HHPV4 (Haloarcula hispanica pleomorphic virus 4). HHPV4I contains an SRA domain, a winged helix (wH) domain, and an HNH domain; recognizes the Gm6ATC site; and specifically binds to Gm6ATC site-containing DNA. Both the wH domain and the HNH domain are responsible for DNA binding. Unlike the well-known m6A-specific restriction enzyme DpnI, HHPV4I only efficiently cleaves DNA with a fully methylated Gm6ATC site and cleaves DNA both upstream and downstream of the Gm6ATC sites on both DNA strands. Furthermore, HHPV4I preferentially cleaves DNA between VR bases (V = A/G/C, R = A/G) 4 to 20 nt away from the Gm6ATC site. Thus, the cleavage pattern of HHPV4I is distinct from those of all of the presently characterized restriction endonucleases. Mutations in the wH domain of HHPV4I do not alter m6A-dependent endonuclease activity, but they decrease recognition sequence specificity, thus expanding the cleaving capacity to more m6A-containing DNA sequences. The wH domain provides a target for searching, developing, and engineering novel m6A-dependent endonucleases. IMPORTANCE Many modification-dependent restriction endonucleases (MDREs) were identified in prokaryotes and recognized modified cytosine bases, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and glucosyl-5-hydroxymethylcytosine (g5hmC). The first virus-derived MDRE (HHPV4I) from the archaeal virus HHPV4 was identified in this study. The viral MDRE suggested a new strategy employed by the virus to exclude other viruses in the case of multiple replications. HHPV4I is a novel N6-methyladenine (m6A)-dependent restriction endonuclease, while the cleavage pattern of HHPV4I is distinct from the well-known m6A-dependent restriction endonuclease DpnI. HHPV4I recognizes Gm6ATC sites and cleaves DNA both upstream and downstream of the Gm6ATC sites on both DNA strands. It preferentially cleaves DNA between VR bases (V = A/G/C, R = A/G) 4 to 20 nt away from the Gm6ATC sites. Furthermore, mutations in the HHPV4I wH domain can alter the sequence specificity without impeding the m6A-dependent DNA cleavage activity, providing a target for engineering more m6A-dependent endonucleases with different sequence specificities.
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Affiliation(s)
- Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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16
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Gulati P, Singh A, Goel M, Saha S. The extremophile Picrophilus torridus carries a DNA adenine methylase M.PtoI that is part of a Type I restriction-modification system. Front Microbiol 2023; 14:1126750. [PMID: 37007530 PMCID: PMC10050889 DOI: 10.3389/fmicb.2023.1126750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
DNA methylation events mediated by orphan methyltransferases modulate various cellular processes like replication, repair and transcription. Bacteria and archaea also harbor DNA methyltransferases that are part of restriction-modification systems, which serve to protect the host genome from being cleaved by the cognate restriction enzyme. While DNA methylation has been exhaustively investigated in bacteria it remains poorly understood in archaea. Picrophilus torridus is a euryarchaeon that can thrive under conditions of extremely low pH (0.7), and thus far no reports have been published regarding DNA methylation in this extremophile. This study reports the first experimentation examining DNA methylation in P. torridus. We find the genome to carry methylated adenine (m6A) but not methylated cytosine (m5C) residues. The m6A modification is absent at GATC sites, indicating the absence of an active Dam methylase even though the dam gene has been annotated in the genome sequence. Two other methylases have also been annotated in the P. torridus genome sequence. One of these is a part of a Type I restriction-modification system. Considering that all Type I modification methylases characterized to date target adenine residues, the modification methylase of this Type I system has been examined. The genes encoding the S subunit (that is responsible for DNA recognition) and M subunit (that is responsible for DNA methylation) have been cloned and the recombinant protein purified from E.coli, and regions involved in M-S interactions have been identified. The M.PtoI enzyme harbors all the motifs that typify Type I modification methylases, and displays robust adenine methylation in in vitro assays under a variety of conditions. Interestingly, magnesium is essential for enzyme activity. The enzyme displays substrate inhibition at higher concentrations of AdoMet. Mutational analyses reveal that Motif I plays a role in AdoMet binding, and Motif IV is critical for methylation activity. The data presented here lays the foundation for further research in the area of DNA methylation and restriction-modification research in this most unusual microorganism.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
- *Correspondence: Swati Saha, ;
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17
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Casselli T, Tourand Y, Gura K, Stevenson B, Zückert WR, Brissette CA. Endogenous Linear Plasmids lp28-4 and lp25 Are Required for Infectivity and Restriction Protection in the Lyme Disease Spirochete Borrelia mayonii. Infect Immun 2023; 91:e0006123. [PMID: 36853005 PMCID: PMC10016076 DOI: 10.1128/iai.00061-23] [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: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Borrelia mayonii is a newly recognized causative agent of Lyme disease in the Upper Midwestern United States, with distinct clinical presentations compared to classical Lyme disease caused by other Lyme Borrelia species. However, little is known about the B. mayonii genetic determinants required for establishing infection or perpetuating disease in mammals. Extrachromosomal plasmids in Borrelia species often encode proteins necessary for infection and pathogenesis, and spontaneous loss of these plasmids can lead to the identification of virulence determinant genes. Here, we describe infection of Lyme disease-susceptible C3H mice with B. mayonii, and show bacterial dissemination and persistence in peripheral tissues. Loss of endogenous plasmids, including lp28-4, lp25, and lp36 correlated with reduced infectivity in mice. The apparent requirement for lp28-4 during murine infection suggests the presence of a novel virulence determinant, as this plasmid does not encode homologs of any known virulence determinant. We also describe transformation and stable maintenance of a self-replicating shuttle vector in B. mayonii, and show that loss of either lp25 or lp28-4 correlated with increased transformation competency. Finally, we demonstrate that linear plasmids lp25 and lp28-4 each encode functional restriction modification systems with distinct but partially overlapping target modification sequences, which likely accounts for the observed decrease in transformation efficiency when those plasmids are present. Taken together, this study describes a role for endogenous plasmids in mammalian infection and restriction protection in the Lyme disease spirochete Borrelia mayonii.
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Affiliation(s)
- Timothy Casselli
- Department of Biological Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Yvonne Tourand
- Department of Biological Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Kaitlyn Gura
- Department of Biological Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, School of Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Wolfram R. Zückert
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Catherine A. Brissette
- Department of Biological Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
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18
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Bizic M, Brad T, Ionescu D, Barbu-Tudoran L, Zoccarato L, Aerts JW, Contarini PE, Gros O, Volland JM, Popa R, Ody J, Vellone D, Flot JF, Tighe S, Sarbu SM. Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species. THE ISME JOURNAL 2023; 17:340-353. [PMID: 36528730 PMCID: PMC9938260 DOI: 10.1038/s41396-022-01350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
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Affiliation(s)
- Mina Bizic
- Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany. .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
| | - Traian Brad
- "Emil Racoviţă" Institute of Speleology, Clinicilor 5-7, 400006, Cluj-Napoca Romania, Romania.
| | - Danny Ionescu
- Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany. .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
| | - Lucian Barbu-Tudoran
- grid.7399.40000 0004 1937 1397Center for Electron Microscopy, “Babeș-Bolyai” University, Clinicilor 5, 400006 Cluj-Napoca, Romania
| | - Luca Zoccarato
- Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775 Stechlin, Germany ,grid.5173.00000 0001 2298 5320Institute of Computational Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 3, 31180 Vienna, Austria
| | - Joost W. Aerts
- grid.12380.380000 0004 1754 9227Department of Molecular Cell Physiology, Faculty of Earth and Life sciences, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Paul-Emile Contarini
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 97110 Pointe-à-Pitre, France ,Laboratory for Research in Complex Systems, Menlo Park, CA USA
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 97110 Pointe-à-Pitre, France
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA USA ,grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 94720 Berkeley, CA USA
| | - Radu Popa
- River Road Research, 62 Leslie St, Buffalo, NY 1421 USA
| | - Jessica Ody
- grid.4989.c0000 0001 2348 0746Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
| | - Daniel Vellone
- grid.59062.380000 0004 1936 7689Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, VT 05405 USA
| | - Jean-François Flot
- grid.4989.c0000 0001 2348 0746Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels—(IB)², Brussels, Belgium
| | - Scott Tighe
- grid.59062.380000 0004 1936 7689Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, VT 05405 USA
| | - Serban M. Sarbu
- grid.501624.40000 0001 2260 1489“Emil Racoviţă” Institute of Speleology, Frumoasă 31-B, 010986 Bucureşti, Romania ,grid.253555.10000 0001 2297 1981Department of Biological Sciences, California State University, Chico, CA 95929 USA
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19
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Nielsen TK, Forero-Junco LM, Kot W, Moineau S, Hansen LH, Riber L. Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software. Mol Ecol 2023; 32:1236-1247. [PMID: 36052951 DOI: 10.1111/mec.16679] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.
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Affiliation(s)
- Tue Kjaergaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Quebec, Canada
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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20
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"French Phage Network" Annual Conference-Seventh Meeting Report. Viruses 2023; 15:v15020495. [PMID: 36851708 PMCID: PMC9966839 DOI: 10.3390/v15020495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The French Phage Network (Phages.fr) has continuously grown since its foundation, eight years ago. The annual conference, held at the Institut Pasteur in Paris, attracted 164 participants from the 11th to the 13th of October 2022. Researchers from academic laboratories, hospitals and private companies shared their ongoing projects and breakthroughs in the very institute where Felix d'Hérelle developed phage therapy over a century ago. The conference was divided into four thematic sessions, each opened by a keynote lecture: "Interaction between phages, mobile genetic elements and bacterial immune system," "Ecology and evolution of phage-bacteria interactions," "Molecular interplay between phages and their hosts" and "Therapeutic and biotechnological applications of phages." A total of 32 talks and 33 posters were presented during the conference.
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21
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Fokina AS, Karyagina AS, Rusinov IS, Moshensky DM, Spirin SA, Alexeevski AV. Evolution of Restriction–Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases. BIOCHEMISTRY (MOSCOW) 2023; 88:253-261. [PMID: 37072330 DOI: 10.1134/s0006297923020086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.
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Affiliation(s)
- Anastasiya S Fokina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna S Karyagina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Ivan S Rusinov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Denis M Moshensky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Sergey A Spirin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
- National Research University Higher School of Economics, Moscow, 109028, Russia
- Federal State Institution "Scientific Research Institute for System Analysis of the Russian Academy of Sciences", Moscow, 117218, Russia
| | - Andrey V Alexeevski
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Federal State Institution "Scientific Research Institute for System Analysis of the Russian Academy of Sciences", Moscow, 117218, Russia
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22
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Schneider TD. Generalizing the isothermal efficiency by using Gaussian distributions. PLoS One 2023; 18:e0279758. [PMID: 36626367 PMCID: PMC9831307 DOI: 10.1371/journal.pone.0279758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023] Open
Abstract
Unlike the Carnot heat engine efficiency published in 1824, an isothermal efficiency derived from thermodynamics and information theory can be applied to biological systems. The original approach by Pierce and Cutler in 1959 to derive the isothermal efficiency equation came from Shannon's channel capacity of 1949 and from Felker's 1952 determination of the minimum energy dissipation needed to gain a bit. In 1991 and 2010 Schneider showed how the isothermal efficiency equation can be applied to molecular machines and that this can be used to explain why several molecular machines are 70% efficient. Surprisingly, some macroscopic biological systems, such as whole ecosystems, are also 70% efficient but it is hard to see how this could be explained by a thermodynamic and molecular theory. The thesis of this paper is that the isothermal efficiency can be derived without using thermodynamics by starting from a set of independent Gaussian distributions. This novel derivation generalizes the isothermal efficiency equation for use at all levels of biology, from molecules to ecosystems.
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Affiliation(s)
- Thomas D. Schneider
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, RNA Biology Laboratory, Frederick, MD, United States of America
- * E-mail:
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23
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Kirillov A, Morozova N, Kozlova S, Polinovskaya V, Smirnov S, Khodorkovskii M, Zeng L, Ispolatov Y, Severinov K. Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population. Nucleic Acids Res 2022; 50:12355-12368. [PMID: 36477901 PMCID: PMC9757035 DOI: 10.1093/nar/gkac1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites. We here show that protection from phage infection increases as the copy number of plasmids carrying the Type II RM Esp1396I system is increased. However, since increased plasmid copy number leads to both increased absolute intracellular RM enzyme levels and to a decreased MTase/REase ratio, it is impossible to determine which factor determines resistance/susceptibility to infection. By controlled expression of individual Esp1396I MTase or REase genes in cells carrying the Esp1396I system, we show that a shift in the MTase to REase ratio caused by overproduction of MTase or REase leads, respectively, to decreased or increased protection from infection. Consistently, due to stochastic variation of MTase and REase amount in individual cells, bacterial cells that are productively infected by bacteriophage have significantly higher MTase to REase ratios than cells that ward off the infection. Our results suggest that cells with transiently increased MTase to REase ratio at the time of infection serve as entry points for unmodified phage DNA into protected bacterial populations.
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Affiliation(s)
- Alexander Kirillov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Natalia Morozova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Svetlana Kozlova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Vasilisa Polinovskaya
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Sergey Smirnov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Lanying Zeng
- Texas A&M University, Department of Biochemistry and Biophysics, Center for Phage Technology, College Station, TX 77843, USA
| | - Yaroslav Ispolatov
- University of Santiago of Chile (USACH), Physics Department, Av. Víctor Jara 3493, Santiago, Chile
| | - Konstantin Severinov
- To whom correspondence should be addressed. Tel: +7 9854570284; Fax: +1 848 445 5735;
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25
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Mahler M, Costa AR, van Beljouw SPB, Fineran PC, Brouns SJJ. Approaches for bacteriophage genome engineering. Trends Biotechnol 2022; 41:669-685. [PMID: 36117025 DOI: 10.1016/j.tibtech.2022.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 12/26/2022]
Abstract
In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. In addition, there is a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. However, the ability to manipulate phage genomes to understand and control gene functions, or alter phage properties such as host range, has remained challenging due to a lack of universal selectable markers. Here, we discuss the state-of-the-art techniques to engineer and select desired phage genomes using advances in cell-free methodologies and clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR-Cas) counter-selection approaches.
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Affiliation(s)
- Marina Mahler
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Sam P B van Beljouw
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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26
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Mikhailov N, Hämäläinen RH. Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases. Ann Biomed Eng 2022:10.1007/s10439-022-03051-7. [PMID: 36001180 DOI: 10.1007/s10439-022-03051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/01/2022]
Abstract
Mitochondria, mainly known as energy factories of eukaryotic cells, also exert several additional signaling and metabolic functions and are today recognized as major cellular biosynthetic and signaling hubs. Mitochondria possess their own genome (mitochondrial DNA-mtDNA), that encodes proteins essential for oxidative phosphorylation, and mutations in it are an important contributor to human disease. The mtDNA mutations often exist in heteroplasmic conditions, with both healthy and mutant versions of the mtDNA residing in patients' cells and the level of mutant mtDNA may vary between different tissues and organs and affect the clinical outcome of the disease. Thus, shifting the ratio between healthy and mutant mtDNA in patients' cells provides an intriguing therapeutic option for mtDNA diseases. In this review we describe current strategies for modulating mitochondrial heteroplasmy levels with engineered endonucleases including mitochondrially targeted TALENs and Zinc finger nucleases (ZFNs) and discuss their therapeutic potential. These gene therapy tools could in the future provide therapeutic help both for patients with mitochondrial disease as well as in preventing the transfer of pathogenic mtDNA mutations from a mother to her offspring.
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Affiliation(s)
- Nikita Mikhailov
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Riikka H Hämäläinen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
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Topological digestion drives time-varying rheology of entangled DNA fluids. Nat Commun 2022; 13:4389. [PMID: 35902575 PMCID: PMC9334285 DOI: 10.1038/s41467-022-31828-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalise using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents. Understanding and controlling the rheology of polymeric complex fluids is of fundamental importance in both industry and biology. Here, Michieletto et al. show how to achieve time-dependent rheology of DNA solutions via enzymatically-driven architectural alterations by restriction endonucleases.
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28
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Lin Q, Han G, Fang X, Chen H, Weng W, Kong J. Programmable Analysis of MicroRNAs by Thermus thermophilus Argonaute-Assisted Exponential Isothermal Amplification for Multiplex Detection (TEAM). Anal Chem 2022; 94:11290-11297. [PMID: 35894425 DOI: 10.1021/acs.analchem.2c01945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The simultaneous analysis of the levels of multiple microRNAs (miRNAs) is critical to the early diagnosis of cancer. However, this analysis is challenging because of the low concentrations of miRNAs and their high sequence homology. Here, we report a general and programmable diagnostic strategy for miRNA analysis: Thermus thermophilus Argonaute (TtAgo)-assisted exponential isothermal amplification for multiplex detection (TEAM). This system combines exponential isothermal amplification (EXPAR), for target amplification, with programmable TtAgo cleavage, for the generation of the reporting signal. The TEAM assay achieved attomolar sensitivity with a rapid turnaround time (30-35 min). Because of the single-nucleotide precision of TtAgo, the system demonstrated robust multiplex capability in the simultaneous detection of four miRNA targets and the classification of let-7 family members. The TEAM assay was superior in differentiating colorectal cancer patients from healthy individuals relative to the conventional EXPAR and reverse transcription polymerase chain reaction (RT-PCR) methods. This tunable and scalable approach is a powerful nucleic acid analysis tool that holds promise in scientific and clinical applications.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, 2005 Songhu Road, 200438 Shanghai, China
| | - Guobin Han
- Department of Chemistry, Fudan University, 2005 Songhu Road, 200438 Shanghai, China
| | - Xueen Fang
- Department of Chemistry, Fudan University, 2005 Songhu Road, 200438 Shanghai, China
| | - Hui Chen
- Department of Chemistry, Fudan University, 2005 Songhu Road, 200438 Shanghai, China
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, 450 Tengyue Road, 200090 Shanghai, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, 2005 Songhu Road, 200438 Shanghai, China
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Krause AL, Stinear TP, Monk IR. Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions. FEMS Microbiol Rev 2022; 46:6650352. [PMID: 35883217 PMCID: PMC9779914 DOI: 10.1093/femsre/fuac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.
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Affiliation(s)
- Alexandra L Krause
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Ian R Monk
- Corresponding author: Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia. E-mail:
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30
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Evolution of plasmid-construction. Int J Biol Macromol 2022; 209:1319-1326. [PMID: 35452702 DOI: 10.1016/j.ijbiomac.2022.04.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022]
Abstract
Developing for almost half a century, plasmid-construction has explored more than 37 methods. Some methods have evolved into new versions. From a global and evolutionary viewpoint, a review will make a clear understand and an easy practice for plasmid-construction. The 37 methods employ three principles as creating single-strand overhang, recombining homology arms, or serving amplified insert as mega-primer, and are classified into three groups as single strand overhang cloning, homologous recombination cloning, and mega-primer cloning. The methods evolve along a route for easy, efficient, or/and seamless cloning. Mechanism of plasmid-construction is primer annealing or/and primer invasion. Scar junction is a must-be faced scientific problem in plasmid-construction.
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31
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Gidwani S, Heiter D, Xu SY. Expression and Purification of BsaXI Restriction Endonuclease and Engineering New Specificity From BsaXI Specificity Subunit. Front Microbiol 2022; 13:888435. [PMID: 35663886 PMCID: PMC9159934 DOI: 10.3389/fmicb.2022.888435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
It is stated that BsaXI is a Type IIB restriction endonuclease (REase) that cleaves both sides of its recognition sequence 5′↓N9 AC N5 CTCC N10↓ 3′ (complement strand 5′ ↓N7 GGAG N5 GT N12↓ 3′), creating 3-base 3′ overhangs. Here we report the cloning and expression of bsaXIS and bsaXIRM genes in Escherichia coli. The BsaXI activity was successfully reconstituted by mixing the BsaXI RM fusion subunit with the BsaXI S subunit and the enzyme complex further purified by chromatography over 6 columns. As expected, the S subunit consisted of two subdomains encoding TRD1-CR1 [target recognition domain (TRD), conserved region (CR)] for 5′ AC 3′, and TRD2-CR2 presumably specifying 5′ CTCC 3′. TRD1-CR1 (TRD2-CR2 deletion) or duplication of TRD1 (TRD1-CR1-TRD1-CR2) both generated a new specificity 5′ AC N5 GT 3′ when the S variants were complexed with the RM subunits. The circular permutation of TRD1 and TRD2, i.e., the relocation of TRD2-CR2 to the N-terminus and TRD1-CR1 to the C-terminus generated the same specificity with the RM subunits, although some wobble cleavage was detected. The TRD2 domain in the BsaXI S subunit can be substituted by a close homolog (∼59% sequence identity) and generated the same specificity. However, TRD2-CR2 domain alone failed to express in E. coli, but CR1-TRD2-CR2 protein could be expressed and purified which showed partial nicking activity with the RM subunits. This work demonstrated that like Type I restriction systems, the S subunit of a Type IIB system could also be manipulated to create new specificities. The genome mining of BsaXI TRD2 homologs in GenBank found more than 36 orphan TRD2 homologs, implying that quite a few orphan TRD2s are present in microbial genomes that may be potentially paired with other TRDs to create new restriction specificities.
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32
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Picton DM, Harling-Lee JD, Duffner SJ, Went SC, Morgan RD, Hinton JCD, Blower TR. A widespread family of WYL-domain transcriptional regulators co-localizes with diverse phage defence systems and islands. Nucleic Acids Res 2022; 50:5191-5207. [PMID: 35544231 PMCID: PMC9122601 DOI: 10.1093/nar/gkac334] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteria are under constant assault by bacteriophages and other mobile genetic elements. As a result, bacteria have evolved a multitude of systems that protect from attack. Genes encoding bacterial defence mechanisms can be clustered into 'defence islands', providing a potentially synergistic level of protection against a wider range of assailants. However, there is a comparative paucity of information on how expression of these defence systems is controlled. Here, we functionally characterize a transcriptional regulator, BrxR, encoded within a recently described phage defence island from a multidrug resistant plasmid of the emerging pathogen Escherichia fergusonii. Using a combination of reporters and electrophoretic mobility shift assays, we discovered that BrxR acts as a repressor. We present the structure of BrxR to 2.15 Å, the first structure of this family of transcription factors, and pinpoint a likely binding site for ligands within the WYL-domain. Bioinformatic analyses demonstrated that BrxR-family homologues are widespread amongst bacteria. About half (48%) of identified BrxR homologues were co-localized with a diverse array of known phage defence systems, either alone or clustered into defence islands. BrxR is a novel regulator that reveals a common mechanism for controlling the expression of the bacterial phage defence arsenal.
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Affiliation(s)
- David M Picton
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Joshua D Harling-Lee
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK.,The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Samuel J Duffner
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | | | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
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Dong J, Ouyang Y, Wang J, O’Hagan MP, Willner I. Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks. ACS NANO 2022; 16:6153-6164. [PMID: 35294174 PMCID: PMC9047661 DOI: 10.1021/acsnano.1c11631] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.
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Involvement of the DNA Phosphorothioation System in TorR Binding and Anaerobic TMAO Respiration in Salmonella enterica. mBio 2022; 13:e0069922. [PMID: 35420479 PMCID: PMC9239176 DOI: 10.1128/mbio.00699-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the phosphorothioate (PT) modification, in which the nonbridging oxygen in the DNA sugar-phosphate backbone is replaced by sulfur, has been reported to play versatile roles in multiple cellular processes, very little data have been obtained to define the role of PT in epigenetic regulation. In this study, we report that the PT system in Salmonella enterica serovar Cerro 87 is involved in the transcriptional regulation of the torCAD operon encoding the trimethylamine N-oxide (TMAO) respiration machinery that enables the use of TMAO as a terminal electron acceptor for respiration when oxygen is not available. In vitro, PT enhanced the binding of the transcriptional activator of the torCAD operon, namely, TorR, to its DNA substrate (tor boxes). However, in vivo, the PT modification protein complex DndCDE downregulated torCAD transcription through competing with the binding of TorR to the tor boxes. The altered expression of torCAD caused by PT modification proteins affected cell growth that relied on TMAO respiration. To our knowledge, this is the first report supporting that PT proteins participate in transcriptional regulation, showing a new function of PT systems.
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Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635. mBio 2022; 13:e0071622. [PMID: 35420474 PMCID: PMC9239217 DOI: 10.1128/mbio.00716-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 Å. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification.
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Pathirana S, Elvitigala D, Nanayakkara C, Suravajhala P, Rajapakse S, Hettiarachchi G, Chandrasekharan N. Identification and in-silico analysis of a novel restriction enzyme coding gene from Pseudomonas anguilliseptica. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilionis A, Kwiatkowska-Semrau K, Friðjónsson ÓH, Kaczorowska AK, Dabrowski S, Ævarsson A, Hreggviðsson GÓ, Al-Karadaghi S, Kaczorowski T, Nordberg Karlsson E. Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. Acta Crystallogr D Struct Biol 2022; 78:212-227. [PMID: 35102887 PMCID: PMC8805305 DOI: 10.1107/s2059798321012298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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Oliveira H, Domingues R, Evans B, Sutton JM, Adriaenssens EM, Turner D. Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter. Viruses 2022; 14:v14020181. [PMID: 35215775 PMCID: PMC8878043 DOI: 10.3390/v14020181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023] Open
Abstract
The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.
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Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Benjamin Evans
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - J. Mark Sutton
- United Kingdom Health Security Agency, Research and Evaluation, Porton Down, Salisbury SP4 OJG, UK;
| | | | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
- Correspondence:
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Vyas P, Harish. Anti-CRISPR proteins as a therapeutic agent against drug-resistant bacteria. Microbiol Res 2022; 257:126963. [PMID: 35033831 DOI: 10.1016/j.micres.2022.126963] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 02/08/2023]
Abstract
The continuous deployment of various antibiotics to treat multiple serious bacterial infections leads to multidrug resistance among the bacterial population. It has failed the standard treatment strategies through different antibacterial agents and serves as a significant threat to public health worldwide at devastating levels. The discovery of anti-CRISPR proteins catches the interest of researchers around the world as a promising therapeutic agent against drug-resistant bacteria. Anti-CRISPR proteins are known to inhibit bacterial CRISPR-Cas defense systems in multiple possible ways. The CRISPR-Cas nucleoprotein assembly provides adaptive immunity in bacteria against diverse categories of phage infections. Parallelly, phages also try to break the CRISPR-Cas barrier by producing anti-CRISPR proteins, leading to growth inhibition and bacterial lysis. This review begins with a brief description of the bacterial CRISPR-Cas system, followed by a detailed portrayal of anti-CRISPR proteins, including their discovery and evolution, mechanism of action, regulation of expression, and potential applications in the healthcare sector as an alternative therapeutic strategy to combat severe bacterial infections.
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Affiliation(s)
- Pallavi Vyas
- Plant Biotechnology Laboratory, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313 001, Rajasthan, India
| | - Harish
- Plant Biotechnology Laboratory, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313 001, Rajasthan, India.
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Birkholz N, Jackson SA, Fagerlund RD, Fineran P. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3348-3361. [PMID: 35286398 PMCID: PMC8989522 DOI: 10.1093/nar/gkac147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic DNA methylation plays an important role in bacteria by influencing gene expression and allowing discrimination between self-DNA and intruders such as phages and plasmids. Restriction–modification (RM) systems use a methyltransferase (MTase) to modify a specific sequence motif, thus protecting host DNA from cleavage by a cognate restriction endonuclease (REase) while leaving invading DNA vulnerable. Other REases occur solitarily and cleave methylated DNA. REases and RM systems are frequently mobile, influencing horizontal gene transfer by altering the compatibility of the host for foreign DNA uptake. However, whether mobile defence systems affect pre-existing host defences remains obscure. Here, we reveal an epigenetic conflict between an RM system (PcaRCI) and a methylation-dependent REase (PcaRCII) in the plant pathogen Pectobacterium carotovorum RC5297. The PcaRCI RM system provides potent protection against unmethylated plasmids and phages, but its methylation motif is targeted by the methylation-dependent PcaRCII. This potentially lethal co-existence is enabled through epigenetic silencing of the PcaRCII-encoding gene via promoter methylation by the PcaRCI MTase. Comparative genome analyses suggest that the PcaRCII-encoding gene was already present and was silenced upon establishment of the PcaRCI system. These findings provide a striking example for selfishness of RM systems and intracellular competition between different defences.
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- To whom correspondence should be addressed: Tel: +64 3 479 7735;
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Benamozig O, Baudrier L, Billon P. A detection method for the capture of genomic signatures: From disease diagnosis to genome editing. Methods Enzymol 2021; 661:251-282. [PMID: 34776215 DOI: 10.1016/bs.mie.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Variations in the genetic information originate from errors during DNA replication, error-prone repair of DNA damages, or genome editing. The most common approach to detect changes in DNA sequences employs sequencing technologies. However, they remain expensive and time-consuming, limiting their utility for routine laboratory experiments. We recently developed DinucleoTidE Signature CapTure (DTECT). DTECT is a marker-free and versatile detection method that captures targeted dinucleotide signatures resulting from the digestion of genomic amplicons by the type IIS restriction enzyme AcuI. Here, we describe the DTECT protocol to identify mutations introduced by CRISPR-based precision genome editing technologies or resulting from genetic variation. DTECT enables accurate detection of mutations using basic laboratory equipment and off-the-shelf reagents with qualitative or quantitative capture of signatures.
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Affiliation(s)
- Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
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Abrosimova LA, Kuznetsov NA, Astafurova NA, Samsonova AR, Karpov AS, Perevyazova TA, Oretskaya TS, Fedorova OS, Kubareva EA. Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 2021; 11:1420. [PMID: 34680052 PMCID: PMC8533099 DOI: 10.3390/biom11101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia A. Astafurova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | | | - Andrey S. Karpov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia;
| | - Tatiana S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
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Chen Z, Shen M, Mao C, Wang C, Yuan P, Wang T, Sun D. A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa. Front Microbiol 2021; 12:709571. [PMID: 34413842 PMCID: PMC8370563 DOI: 10.3389/fmicb.2021.709571] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Considered a “Generally Recognized As Safe” (GRAS) bacterium, the plant growth–promoting rhizobacterium Paenibacillus polymyxa has been widely applied in agriculture and animal husbandry. It also produces valuable compounds that are used in medicine and industry. Our previous work showed the presence of restriction modification (RM) system in P. polymyxa ATCC 842. Here, we further analyzed its genome and methylome by using SMRT sequencing, which revealed the presence of a larger number of genes, as well as a plasmid documented as a genomic region in a previous report. A number of mobile genetic elements (MGEs), including 78 insertion sequences, six genomic islands, and six prophages, were identified in the genome. A putative lysozyme-encoding gene from prophage P6 was shown to express lysin which caused cell lysis. Analysis of the methylome and genome uncovered a pair of reverse-complementary DNA methylation motifs which were widespread in the genome, as well as genes potentially encoding their cognate type I restriction-modification system PpoAI. Further genetic analysis confirmed the function of PpoAI as a RM system in modifying and restricting DNA. The average frequency of the DNA methylation motifs in MGEs was lower than that in the genome, implicating a role of PpoAI in restricting MGEs during genomic evolution of P. polymyxa. Finally, comparative analysis of R, M, and S subunits of PpoAI showed that homologs of the PpoAI system were widely distributed in species belonging to other classes of Firmicute, implicating a role of the ancestor of PpoAI in the genomic evolution of species beyond Paenibacillus.
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Affiliation(s)
- Ziyan Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Minjia Shen
- UMR 9198 Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Chengyao Mao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Chenyu Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics, Hangzhou, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Dimitriu T, Szczelkun MD, Westra ER. Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. Curr Biol 2021; 30:R1189-R1202. [PMID: 33022264 DOI: 10.1016/j.cub.2020.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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Affiliation(s)
- Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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Cameranesi MM, Kurth D, Repizo GD. Acinetobacter defence mechanisms against biological aggressors and their use as alternative therapeutic applications. Crit Rev Microbiol 2021; 48:21-41. [PMID: 34289313 DOI: 10.1080/1040841x.2021.1939266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Several Acinetobacter strains are important nosocomial pathogens, with Acinetobacter baumannii being the species of greatest worldwide concern due to its multi-drug resistance and the recent appearance of hyper-virulent strains in the clinical setting. Colonisation of this environment is associated with a multitude of bacterial factors, and the molecular features that promote environmental persistence in abiotic surfaces, including intrinsic desiccation resistance, biofilm formation and motility, have been previously addressed. On the contrary, mechanisms enabling Acinetobacter spp. survival when faced against other biological competitors are starting to be characterised. Among them, secretion systems (SS) of different types, such as the T5bSS (Contact-dependent inhibition systems) and the T6SS, confer adaptive advantages against bacterial aggressors. Regarding mechanisms of defence against bacteriophages, such as toxin-antitoxin, restriction-modification, Crispr-Cas and CBASS, among others, have been identified but remain poorly characterised. In view of this, we aimed to summarise the present knowledge on defence mechanisms that enable niche establishment in members of the Acinetobacter genus. Different proposals are also described for the use of some components of these systems as molecular tools to treat Acinetobacter infections.
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Affiliation(s)
- María Marcela Cameranesi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniel Kurth
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), San Miguel de Tucumán, Argentina
| | - Guillermo Daniel Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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50
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Improving mobilization of foreign DNA into Zymomonas mobilis ZM4 by removal of multiple restriction systems. Appl Environ Microbiol 2021; 87:e0080821. [PMID: 34288704 PMCID: PMC8432527 DOI: 10.1128/aem.00808-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis has emerged as a promising candidate for production of high-value bioproducts from plant biomass. However, a major limitation in equipping Z. mobilis with novel pathways to achieve this goal is restriction of heterologous DNA. Here, we characterized the contribution of several defense systems of Z. mobilis strain ZM4 to impeding heterologous gene transfer from an Escherichia coli donor. Bioinformatic analysis revealed that Z. mobilis ZM4 encodes a previously described mrr-like type IV restriction modification (RM) system, a type I-F CRISPR system, a chromosomal type I RM system (hsdMSc), and a previously uncharacterized type I RM system, located on an endogenous plasmid (hsdRMSp). The DNA recognition motif of HsdRMSp was identified by comparing the methylated DNA sequence pattern of mutants lacking one or both of the hsdMSc and hsdRMSp systems to that of the parent strain. The conjugation efficiency of synthetic plasmids containing single or combinations of the HsdMSc and HsdRMSp recognition sites indicated that both systems are active and decrease uptake of foreign DNA. In contrast, deletions of mrr and cas3 led to no detectable improvement in conjugation efficiency for the exogenous DNA tested. Thus, the suite of markerless restriction-negative strains that we constructed and the knowledge of this new restriction system and its DNA recognition motif provide the necessary platform to flexibly engineer the next generation of Z. mobilis strains for synthesis of valuable products. IMPORTANCEZymomonas mobilis is equipped with a number of traits that make it a desirable platform organism for metabolic engineering to produce valuable bioproducts. Engineering strains equipped with synthetic pathways for biosynthesis of new molecules requires integration of foreign genes. In this study, we developed an all-purpose strain, devoid of known host restriction systems and free of any antibiotic resistance markers, which dramatically improves the uptake efficiency of heterologous DNA into Z. mobilis ZM4. We also confirmed the role of a previously known restriction system as well as identifying a previously unknown type I RM system on an endogenous plasmid. Elimination of the barriers to DNA uptake as shown here will allow facile genetic engineering of Z. mobilis.
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