1
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Freeman KG, Lauer MJ, Jiang D, Roscher J, Sandler S, Mercado N, Fryberger R, Kovalski J, Lutz AR, Hughes LE, VanDemark AP, Hatfull GF. Characterization of mycobacteriophage Adephagia cytotoxic proteins. G3 (BETHESDA, MD.) 2024; 14:jkae166. [PMID: 39031590 PMCID: PMC11373665 DOI: 10.1093/g3journal/jkae166] [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: 04/29/2024] [Revised: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.
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Affiliation(s)
- Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael J Lauer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Danny Jiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jennifer Roscher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sterling Sandler
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicholas Mercado
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Robert Fryberger
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Julia Kovalski
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Abigail R Lutz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lee E Hughes
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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2
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Gauthier CH, Hatfull GF. A Bioinformatic Ecosystem for Bacteriophage Genomics: PhaMMSeqs, Phamerator, pdm_utils, PhagesDB, DEPhT, and PhamClust. Viruses 2024; 16:1278. [PMID: 39205252 PMCID: PMC11359507 DOI: 10.3390/v16081278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
The last thirty years have seen a meteoric rise in the number of sequenced bacteriophage genomes, spurred on by both the rise and success of groups working to isolate and characterize phages, and the rapid and significant technological improvements and reduced costs associated with sequencing their genomes. Over the course of these decades, the tools used to glean evolutionary insights from these sequences have grown more complex and sophisticated, and we describe here the suite of computational and bioinformatic tools used extensively by the integrated research-education communities such as SEA-PHAGES and PHIRE, which are jointly responsible for 25% of all complete phage genomes in the RefSeq database. These tools are used to integrate and analyze phage genome data from different sources, for identification and precise extraction of prophages from bacterial genomes, computing "phamilies" of related genes, and displaying the complex nucleotide and amino acid level mosaicism of these genomes. While over 50,000 SEA-PHAGES students have primarily benefitted from these tools, they are freely available for the phage community at large.
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Affiliation(s)
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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3
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Jansz N, Faulkner GJ. Viral genome sequencing methods: benefits and pitfalls of current approaches. Biochem Soc Trans 2024; 52:1431-1447. [PMID: 38747720 PMCID: PMC11346438 DOI: 10.1042/bst20231322] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/27/2024]
Abstract
Whole genome sequencing of viruses provides high-resolution molecular insights, enhancing our understanding of viral genome function and phylogeny. Beyond fundamental research, viral sequencing is increasingly vital for pathogen surveillance, epidemiology, and clinical applications. As sequencing methods rapidly evolve, the diversity of viral genomics applications and catalogued genomes continues to expand. Advances in long-read, single molecule, real-time sequencing methodologies present opportunities to sequence contiguous, haplotype resolved viral genomes in a range of research and applied settings. Here we present an overview of nucleic acid sequencing methods and their applications in studying viral genomes. We emphasise the advantages of different viral sequencing approaches, with a particular focus on the benefits of third-generation sequencing technologies in elucidating viral evolution, transmission networks, and pathogenesis.
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Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J. Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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4
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Nomura K, Onda K, Murase H, Hashiya F, Ono Y, Terai G, Oka N, Asai K, Suzuki D, Takahashi N, Hiraoka H, Inagaki M, Kimura Y, Shimizu Y, Abe N, Abe H. Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments. RSC Chem Biol 2024; 5:360-371. [PMID: 38576723 PMCID: PMC10989509 DOI: 10.1039/d3cb00212h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024] Open
Abstract
We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups with a tert-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.
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Affiliation(s)
- Kohei Nomura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
| | - Yukiteru Ono
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Natsuhisa Oka
- Department of Chemistry and Biomolecular Science Faculty of Engineering, Gifu University Gifu 501-1193 Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Daisuke Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naho Takahashi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research Suita Osaka 565-0874 Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
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5
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Jia B, Ojima-Kato T, Kojima T, Nakano H. Rapid and cost-effective epitope mapping using PURE ribosome display coupled with next-generation sequencing and bioinformatics. J Biosci Bioeng 2024; 137:321-328. [PMID: 38342664 DOI: 10.1016/j.jbiosc.2024.01.008] [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: 10/16/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/13/2024]
Abstract
A novel, efficient and cost-effective approach for epitope identification of an antibody has been developed using a ribosome display platform. This platform, known as PURE ribosome display, utilizes an Escherichia coli-based reconstituted cell-free protein synthesis system (PURE system). It stabilizes the mRNA-ribosome-peptide complex via a ribosome-arrest peptide sequence. This system was complemented by next-generation sequencing (NGS) and an algorithm for analyzing binding epitopes. To showcase the effectiveness of this method, selection conditions were refined using the anti-PA tag monoclonal antibody with the PA tag peptide as a model. Subsequently, a random peptide library was constructed using 10 NNK triplet oligonucleotides via the PURE ribosome display. The resulting random peptide library-ribosome-mRNA complex was selected using a commercially available anti-HA (YPYDVPDYA) tag monoclonal antibody, followed by NGS and bioinformatic analysis. Our approach successfully identified the DVPDY sequence as an epitope within the hemagglutinin amino acid sequence, which was then experimentally validated. This platform provided a valuable tool for investigating continuous epitopes in antibodies.
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Affiliation(s)
- Beixi Jia
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Teruyo Ojima-Kato
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takaaki Kojima
- Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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6
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Li T, Cheng N. Sensitive and Portable Signal Readout Strategies Boost Point-of-Care CRISPR/Cas12a Biosensors. ACS Sens 2023; 8:3988-4007. [PMID: 37870387 DOI: 10.1021/acssensors.3c01338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Point-of-care (POC) detection is getting more and more attention in many fields due to its accuracy and on-site test property. The CRISPR/Cas12a system is endowed with excellent sensitivity, target identification specificity, and signal amplification ability in biosensing because of its unique trans-cleavage ability. As a result, a lot of research has been made to develop CRISPR/Cas12a-based biosensors. In this review, we focused on signal readout strategies and summarized recent sensitivity-improving strategies in fluorescence, colorimetric, and electrochemical signaling. Then we introduced novel portability-improving strategies based on lateral flow assays (LFAs), microfluidic chips, simplified instruments, and one-pot design. In the end, we also provide our outlook for the future development of CRISPR/Cas12a biosensors.
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Affiliation(s)
- Tong Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Nan Cheng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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7
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Zhao Y, Huang F, Wang W, Gao R, Fan L, Wang A, Gao SH. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165867. [PMID: 37516185 DOI: 10.1016/j.scitotenv.2023.165867] [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: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.
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Affiliation(s)
- Yanmei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Fang Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Rui Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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8
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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9
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Shchaslyvyi AY, Antonenko SV, Tesliuk MG, Telegeev GD. Current State of Human Gene Therapy: Approved Products and Vectors. Pharmaceuticals (Basel) 2023; 16:1416. [PMID: 37895887 PMCID: PMC10609992 DOI: 10.3390/ph16101416] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
In the realm of gene therapy, a pivotal moment arrived with Paul Berg's groundbreaking identification of the first recombinant DNA in 1972. This achievement set the stage for future breakthroughs. Conditions once considered undefeatable, like melanoma, pancreatic cancer, and a host of other ailments, are now being addressed at their root cause-the genetic level. Presently, the gene therapy landscape stands adorned with 22 approved in vivo and ex vivo products, including IMLYGIC, LUXTURNA, Zolgensma, Spinraza, Patisiran, and many more. In this comprehensive exploration, we delve into a rich assortment of 16 drugs, from siRNA, miRNA, and CRISPR/Cas9 to DNA aptamers and TRAIL/APO2L, as well as 46 carriers, from AAV, AdV, LNPs, and exosomes to naked mRNA, sonoporation, and magnetofection. The article also discusses the advantages and disadvantages of each product and vector type, as well as the current challenges faced in the practical use of gene therapy and its future potential.
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Affiliation(s)
- Aladdin Y. Shchaslyvyi
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Zabolotnogo Str., 03143 Kyiv, Ukraine; (S.V.A.); (M.G.T.); (G.D.T.)
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10
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Bong S, Park CB, Cho SG, Bae J, Hapsari N, Jin X, Heo S, Lee JE, Hashiya K, Bando T, Sugiyama H, Jung KH, Sung B, Jo K. AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection. Nucleic Acids Res 2023; 51:5634-5646. [PMID: 37158237 PMCID: PMC10287942 DOI: 10.1093/nar/gkad340] [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: 10/18/2022] [Revised: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.
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Affiliation(s)
- Serang Bong
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Chung Bin Park
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Xuelin Jin
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- College of Agriculture, Yanbian University, Yanji133000, China
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Ji-eun Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
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11
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Browning DF, Hobman JL, Busby SJW. Laboratory strains of Escherichia coli K-12: things are seldom what they seem. Microb Genom 2023; 9:mgen000922. [PMID: 36745549 PMCID: PMC9997739 DOI: 10.1099/mgen.0.000922] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been repeatedly cultured, passaged and mutagenized, resulting in an organism that carries many genetic changes. To understand more about this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive laboratory-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains leads us to examine whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.
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Affiliation(s)
- Douglas F Browning
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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12
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Vasquez I, Retamales J, Parra B, Machimbirike V, Robeson J, Santander J. Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor. Viruses 2023; 15:v15020379. [PMID: 36851593 PMCID: PMC9961651 DOI: 10.3390/v15020379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
The polyvalent bacteriophage fp01, isolated from wastewater in Valparaiso, Chile, was described to have lytic activity across bacterial species, including Escherichia coli and Salmonella enterica serovars. Due to its polyvalent nature, the bacteriophage fp01 has potential applications in the biomedical, food and agricultural industries. Also, fundamental aspects of polyvalent bacteriophage biology are unknown. In this study, we sequenced and described the complete genome of the polyvalent phage fp01 (MH745368.2) using long- (MinION, Nanopore) and short-reads (MiSeq, Illumina) sequencing. The bacteriophage fp01 genome has 109,515 bp, double-stranded DNA with an average G+C content of 39%, and 158 coding sequences (CDSs). Phage fp01 has genes with high similarity to Escherichia coli, Salmonella enterica, and Shigella sp. phages. Phylogenetic analyses indicated that the phage fp01 is a new Tequintavirus fp01 specie. Receptor binding protein gp108 was identified as potentially responsible for fp01 polyvalent characteristics, which binds to conserved amino acid regions of the FhuA receptor of Enterobacteriaceae.
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Affiliation(s)
- Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Science, Memorial University, St. John’s, NL A1C 5S7, Canada
| | - Julio Retamales
- Instituto de Ciencias Naturales, Universidad de las Américas, Viña del Mar 2520000, Chile
| | - Barbara Parra
- Subdepartment of Molecular Genetics, Public Health Institute of Chile, Santiago 9140000, Chile
| | - Vimbai Machimbirike
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Science, Memorial University, St. John’s, NL A1C 5S7, Canada
| | - James Robeson
- Laboratory of Microbiology, Institute of Biology, Pontifical Catholic University of Valparaíso, Valparaiso 2370000, Chile
- Correspondence: (J.R.); (J.S.)
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Science, Memorial University, St. John’s, NL A1C 5S7, Canada
- Correspondence: (J.R.); (J.S.)
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13
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Biere N, Kreft D, Walhorn V, Schwarzbich S, Glaser T, Anselmetti D. Dinuclear complex-induced DNA melting. J Nanobiotechnology 2023; 21:26. [PMID: 36691056 PMCID: PMC9869567 DOI: 10.1186/s12951-023-01784-8] [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: 09/16/2022] [Accepted: 01/15/2023] [Indexed: 01/24/2023] Open
Abstract
Dinuclear copper complexes have been designed for molecular recognition in order to selectively bind to two neighboring phosphate moieties in the backbone of double strand DNA. Associated biophysical, biochemical and cytotoxic effects on DNA were investigated in previous works, where atomic force microscopy (AFM) in ambient conditions turned out to be a particular valuable asset, since the complexes influence the macromechanical properties and configurations of the strands. To investigate and scrutinize these effects in more depth from a structural point of view, cutting-edge preparation methods and scanning force microscopy under ultra-high vacuum (UHV) conditions were employed to yield submolecular resolution images. DNA strand mechanics and interactions could be resolved on the single base pair level, including the amplified formation of melting bubbles. Even the interaction of singular complex molecules could be observed. To better assess the results, the appearance of treated DNA is also compared to the behavior of untreated DNA in UHV on different substrates. Finally, we present data from a statistical simulation reasoning about the nanomechanics of strand dissociation. This sort of quantitative experimental insights paralleled by statistical simulations impressively shade light on the rationale for strand dissociations of this novel DNA interaction process, that is an important nanomechanistic key and novel approach for the development of new chemotherapeutic agents.
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Affiliation(s)
- Niklas Biere
- grid.7491.b0000 0001 0944 9128Experimental Biophysics & Applied Nanoscience, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Dennis Kreft
- grid.7491.b0000 0001 0944 9128Experimental Biophysics & Applied Nanoscience, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Volker Walhorn
- grid.7491.b0000 0001 0944 9128Experimental Biophysics & Applied Nanoscience, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Sabrina Schwarzbich
- grid.7491.b0000 0001 0944 9128Lehrstuhl für Anorganische Chemie I, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Thorsten Glaser
- grid.7491.b0000 0001 0944 9128Lehrstuhl für Anorganische Chemie I, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Dario Anselmetti
- grid.7491.b0000 0001 0944 9128Experimental Biophysics & Applied Nanoscience, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
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14
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Feiss M, Young R, Ramsey J, Adhya S, Georgopoulos C, Hendrix RW, Hatfull GF, Gilcrease EB, Casjens SR. Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology. Microbiol Mol Biol Rev 2022; 86:e0012421. [PMID: 36165780 PMCID: PMC9799177 DOI: 10.1128/mmbr.00124-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ryland Young
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, The National Cancer Institute, Bethesda, Maryland, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eddie B. Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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15
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Mohammad N, Katkam SS, Wei Q. A Sensitive and Nonoptical CRISPR Detection Mechanism by Sizing Double‐Stranded λ DNA Reporter. Angew Chem Int Ed Engl 2022; 61:e202213920. [PMID: 36239984 PMCID: PMC10100359 DOI: 10.1002/anie.202213920] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 11/12/2022]
Abstract
CRISPR-based biosensors often rely on colorimetric, fluorescent, or electrochemical signaling mechanism, which involves expensive reporters and/or sophisticated equipment. Here, we demonstrated a simple, inexpensive, nonoptical, and sensitive CRISPR-Cas12a-based sensing platform to detect ssDNA targets by sizing double-stranded λ DNA as novel report molecules. In this platform, the size reduction of λ DNA was quantified by gel electrophoresis analysis. We hypothesize that the massive trans-nuclease activity of Cas12a toward λ DNA is due to the presence of single-stranded looped structures along the λ DNA sequence. In addition, we observed a strong binding affinity between Cas12a and λ DNA, which further promotes the trans-cleavage activity and helps achieve sub-picomolar detection sensitivity, ≈100 times more sensitive than the fluorescent counterpart. The concept of utilizing the physical size change of λ DNA unlocks the possibility of using a variety of dsDNA as CRISPR reporters.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
- Department of Chemical Engineering Bangladesh University of Engineering and Technology 1000 Dhaka Bangladesh
| | - Shrinivas S. Katkam
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
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16
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Magaziner SJ, Salmond GPC. A novel T4- and λ-based receptor binding protein family for bacteriophage therapy host range engineering. Front Microbiol 2022; 13:1010330. [PMID: 36386655 PMCID: PMC9659904 DOI: 10.3389/fmicb.2022.1010330] [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: 08/03/2022] [Accepted: 10/10/2022] [Indexed: 11/21/2022] Open
Abstract
Widespread multidrug antimicrobial resistance in emerging pathogens has led to a renewed interest in phage therapy as an alternative or supplement to traditional small molecule drugs. The primary limiting factors of phage therapy deployment rest in the narrow host range specificity of phage as well as a poor understanding of many phages’ unintended downstream effects on host physiology and microbiota as well as on adverse pathogen evolution. Consequently, this has made assembling well-defined and safe “phage-cocktails” of solely naturally occurring phages labor- and time-intensive. To increase the speed, efficacy, and safety of therapeutic deployment, there is exceptional interest in modulating the host ranges of well-characterized lytic phages (e.g., T4 and T7) by using synthetic strategies to the swap phage tail components, the receptor binding proteins (RBPs) key for host specificity. Here we identify the RBP of the Citrobacter rodentium temperate phage ΦNP as ORF6. Through bioinformatic and phylogenetic assays, we demonstrate this RBP to be closely related to the known RBPs of T4 and λ. Further investigation reveals a novel, greater than 200 members RBP family with phages targeting several notable human pathogens, including Klebsiella pneumoniae, Escherichia coli O157:H7, Salmonella spp., and Shigella spp. With well characterized lytic members, this RBP family represents an ideal candidate for use in synthetic strategies for expanding therapeutic phage host ranges.
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17
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Morimitsu Y, Matsuno H, Oda Y, Yamamoto S, Tanaka K. Direct visualization of cooperative adsorption of a string-like molecule onto a solid. SCIENCE ADVANCES 2022; 8:eabn6349. [PMID: 36223469 PMCID: PMC9555780 DOI: 10.1126/sciadv.abn6349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Natural systems, composite materials, and thin-film devices adsorb macromolecules in different phases onto their surfaces. In general, polymer chains form interfacial layers where their aggregation states and thermal molecular motions differ from the bulk. Here, we visualize well-defined double-stranded DNAs (dsDNAs) using atomic force microscopy and molecular dynamics simulations to clarify the adsorption mechanism of polymer chains onto solid surfaces. Initially, short and long dsDNAs are individually and cooperatively adsorbed, respectively. Cooperative adsorption involves intertwining of multiple chains. The dependence of adsorption on the chain affects the formation of the interfacial layer, realizing different mechanical properties of DNA/filler bulk composites. These findings will contribute to the development of light and durable polymer composites and films for various industrial, biomedical, and environmental applications.
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Affiliation(s)
- Yuma Morimitsu
- Department of Applied Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hisao Matsuno
- Department of Applied Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Center for Polymer Interface and Molecular Adhesion Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yukari Oda
- Division of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Satoru Yamamoto
- Center for Polymer Interface and Molecular Adhesion Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Keiji Tanaka
- Department of Applied Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Center for Polymer Interface and Molecular Adhesion Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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18
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Nye DB, Tanner NA. Chimeric DNA byproducts in strand displacement amplification using the T7 replisome. PLoS One 2022; 17:e0273979. [PMID: 36121810 PMCID: PMC9484634 DOI: 10.1371/journal.pone.0273979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Recent advances in next generation sequencing technologies enable reading DNA molecules hundreds of kilobases in length and motivate development of DNA amplification methods capable of producing long amplicons. In vivo, DNA replication is performed not by a single polymerase enzyme, but multiprotein complexes called replisomes. Here, we investigate strand-displacement amplification reactions using the T7 replisome, a macromolecular complex of a helicase, a single-stranded DNA binding protein, and a DNA polymerase. The T7 replisome may initiate processive DNA synthesis from DNA nicks, and the reaction of a 48 kilobase linear double stranded DNA substrate with the T7 replisome and nicking endonucleases is shown to produce discrete DNA amplicons. To gain a mechanistic understanding of this reaction, we utilized Oxford Nanopore long-read sequencing technology. Sequence analysis of the amplicons revealed chimeric DNA reads and uncovered a connection between template switching and polymerase exonuclease activity. Nanopore sequencing provides insight to guide the further development of isothermal amplification methods for long DNA, and our results highlight the need for high-specificity, high-turnover nicking endonucleases to initiate DNA amplification without thermal denaturation.
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Affiliation(s)
- Dillon B. Nye
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Nathan A. Tanner
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail:
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19
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Complete Genome Sequences of Lambdoid Phages 21, 434, and 434B and Several Lambda Hybrids. Microbiol Resour Announc 2022; 11:e0012022. [PMID: 35412353 PMCID: PMC9119081 DOI: 10.1128/mra.00120-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recombinational hybrids between phage λ and its relatives were instrumental in the beginnings of molecular biology. Here, we report the complete genome sequences of lambdoid phages 21 and 434 and three of their λ hybrids. In addition, we describe 434B, where the entire lysis gene region was replaced by cryptic prophage sequences.
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20
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Ali SB, Oshido AB, Houlton A, Horrocks BR. Models for sensing by nanowire networks: application to organic vapour detection by multiwall carbon nanotube-DNA films. NANOTECHNOLOGY 2021; 33:045502. [PMID: 34624883 DOI: 10.1088/1361-6528/ac2e20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Electronic sensors for volatile organic compounds have been prepared by drop-casting dispersions of multi-wall carbon nanotubes (MWCNTs) in aqueous solutions ofλ-DNA onto Pt microband electrodes. The MWCNTs themselves show a metal-like temperature dependence of the conductance, but the conductance of DNA/MWCNT composites has an activated component that corresponds to inter-tube tunneling. The resistance of the composite was modelled by a series combination of a term linear in temperature for the nanotubes and a stretched exponential form for the inter-tube junctions. The resistance may increase or decrease with temperature according to the composition and may be tuned to be almost temperature-independent at 67% by mass of DNA. Upon exposure to organic vapours, the resistance of the composites increases and the time-dependence of this signal is consistent with diffusion of the vapour into the composite. The fractional change in resistance at steady-state provides an analytical signal with a linear calibration and the presence of DNA enhances the signal and adjusts the selectivity in favour of polar analytes. The temperature dependence of the signal is determined by the enthalpy of adsorption of the analyte in the inter-tube junctions and may be satisfactorily modelled using the Langmuir isotherm. Temperature and pressure-dependent studies indicate that neither charge injection by oxidation/reduction of the analyte nor condensation of analyte on the device is responsible for the signal. We suggest that the origin of the sensing response is an adsorption of the analyte in the inter-tube regions that modulates the tunneling barriers. This suggests a general route to tuning the selectivity of MWCNT gas sensors using non-conductive polymers of varying chemical functionality.
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Affiliation(s)
- Shams B Ali
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Laser and Optoelectronics Engineering, University of Technology, Baghdad, 10066, Iraq
| | - Atsinafe B Oshido
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Chemistry, Benue State University, Makurdi, 970222, Nigeria
| | - Andrew Houlton
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Benjamin R Horrocks
- Chemical Nanoscience Laboratories, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
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21
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Backer AS, King GA, Biebricher AS, Shepherd JW, Noy A, Leake MC, Heller I, Wuite GJL, Peterman EJG. Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy. J Phys Chem B 2021; 125:8351-8361. [PMID: 34309392 PMCID: PMC8350907 DOI: 10.1021/acs.jpcb.1c02708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The combination of DNA force spectroscopy and polarization microscopy of fluorescent DNA intercalator dyes can provide valuable insights into the structure of DNA under tension. These techniques have previously been used to characterize S-DNA-an elongated DNA conformation that forms when DNA overstretches at forces ≥ 65 pN. In this way, it was deduced that the base pairs of S-DNA are highly inclined, relative to those in relaxed (B-form) DNA. However, it is unclear whether and how topological constraints on the DNA may influence the base-pair inclinations under tension. Here, we apply polarization microscopy to investigate the impact of DNA pulling geometry, torsional constraint, and negative supercoiling on the orientations of intercalated dyes during overstretching. In contrast to earlier predictions, the pulling geometry (namely, whether the DNA molecule is stretched via opposite strands or the same strand) is found to have little influence. However, torsional constraint leads to a substantial reduction in intercalator tilting in overstretched DNA, particularly in AT-rich sequences. Surprisingly, the extent of intercalator tilting is similarly reduced when the DNA molecule is negatively supercoiled up to a critical supercoiling density (corresponding to ∼70% reduction in the linking number). We attribute these observations to the presence of P-DNA (an overwound DNA conformation). Our results suggest that intercalated DNA preferentially flanks regions of P-DNA rather than those of S-DNA and also substantiate previous suggestions that P-DNA forms predominantly in AT-rich sequences.
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Affiliation(s)
- Adam S. Backer
- Apple Inc, 1 Apple Park Way, Cupertino, California 95014, United States
| | - Graeme A. King
- Institute
of Structural and Molecular Biology, University
College London, Gower Street, London WC1E
6BT, U.K.
| | - Andreas S. Biebricher
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Jack W. Shepherd
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Agnes Noy
- Department
of Physics, University of York, York YO10 5DD, U.K.
| | - Mark C. Leake
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Iddo Heller
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Erwin J. G. Peterman
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
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22
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Grazioli S, Petris G. Synthetic genomics for curing genetic diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:477-520. [PMID: 34175051 DOI: 10.1016/bs.pmbts.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From the beginning of the genome sequencing era, it has become increasingly evident that genetics plays a role in all diseases, of which only a minority are single-gene disorders, the most common target of current gene therapies. However, the majority of people have some kind of health problems resulting from congenital genetic mutations (over 6000 diseases have been associated to genes, https://www.omim.org/statistics/geneMap) and most genetic disorders are rare and only incompletely understood. The vision and techniques applied to the synthesis of genomes may help to address unmet medical needs from a chromosome and genome-scale perspective. In this chapter, we address the potential therapy of genetic diseases from a different outlook, in which we no longer focus on small gene corrections but on higher-order tools for genome manipulation. These will play a crucial role in the next years, as they prelude to a much deeper understanding of the architecture of the human genome and a more accurate modeling of human diseases, offering new therapeutic opportunities.
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Affiliation(s)
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge, United Kingdom.
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23
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Abstract
Bacteriophages are the most abundant form of life on earth and are present everywhere. The total number of bacteriophages has been estimated to be 1032 virions. The main division of bacteriophages is based on the type of nucleic acid (DNA or RNA) and on the structure of the capsid. Due to the significant increase in the number of multi-drug-resistant bacteria, bacteriophages could be a useful tool as an alternative to antibiotics in experimental therapies to prevent and to control bacterial infections in people and animals. The aim of this review was to discuss the history of phage therapy as a replacement for antibiotics, in response to EU regulations prohibiting the use of antibiotics in livestock, and to present current examples and results of experimental phage treatments in comparison to antibiotics. The use of bacteriophages to control human infections has had a high success rate, especially in mixed infections caused mainly by Staphylococcus, Pseudomonas, Enterobacter, and Enterococcus. Bacteriophages have also proven to be an effective tool in experimental treatments for combating diseases in livestock.
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24
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Moore RL, Geraghty AA, Feehily C, Saldova R, Murphy EF, Van Sinderen D, Cotter PD, McAuliffe FM. Can a probiotic supplement in pregnancy result in transfer to the neonatal gut: A systematic review. Acta Obstet Gynecol Scand 2020; 99:1269-1277. [PMID: 32400910 DOI: 10.1111/aogs.13899] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The establishment of the neonatal gut microbiome is a crucial step that may have lifelong health implications. We aimed to systematically review evidence on maternal probiotic supplementation during pregnancy and vertical transfer of the corresponding strain to the infant gut. MATERIAL AND METHODS Medline, CINAHL, Embase, Web of Science, and OVID were searched from inception to September 2018. Studies of maternal probiotic supplementation for a minimum duration of 2 weeks and analyses of neonatal stool samples were included. The primary outcome was presence of the specific probiotic strain in the infant stool. Electronic databases were searched for relevant studies and references were cross-checked. Risk of bias among included studies was assessed and data were extracted independently by two authors. RESULTS Three studies were included in the review. Only one study was identified involving prenatal maternal probiotic supplementation alone. Neonatal colonization with the maternally administered probiotic was not demonstrated but supplementation with the probiotic influenced levels of a bacterial strain other than that found in the probiotic product. The other two studies identified included both prenatal and postnatal supplementation of either mother or infant. All three studies reported employing strain-specific isolation methodology to isolate the supplemented bacterial strain in infant stool but none used whole metagenome shotgun sequencing. CONCLUSIONS Few studies investigating transfer of a specific probiotic bacterial strain from mother to infant were identified, showing inconclusive evidence of vertical transfer.
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Affiliation(s)
- Rebecca L Moore
- UCD Perinatal Research Center, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Aisling A Geraghty
- UCD Perinatal Research Center, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Conor Feehily
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland.,Teagasc Food Research Center, Moorepark, Fermoy, Cork, Ireland
| | - Radka Saldova
- The National Institute for Bioprocessing, Research, and Training (NIBRT), Dublin, Ireland
| | - Eileen F Murphy
- Precision Biotics Ltd, Cork Airport Business Park, Cork, Ireland
| | - Douwe Van Sinderen
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland.,School of Microbiology, National University of Ireland, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland.,Teagasc Food Research Center, Moorepark, Fermoy, Cork, Ireland
| | - Fionnuala M McAuliffe
- UCD Perinatal Research Center, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
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25
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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26
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Ben Ali A, Luque G, Alba E. An efficient discrete PSO coupled with a fast local search heuristic for the DNA fragment assembly problem. Inf Sci (N Y) 2020. [DOI: 10.1016/j.ins.2019.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Giani AM, Gallo GR, Gianfranceschi L, Formenti G. Long walk to genomics: History and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 2019; 18:9-19. [PMID: 31890139 PMCID: PMC6926122 DOI: 10.1016/j.csbj.2019.11.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.
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Key Words
- BAC, Bacterial Artificial Chromosome
- Bioinformatics
- Genome assembly
- HGP, Human Genome Project
- HMW, high molecular weight
- HapMap, haplotype map
- NGS, Next Generation Sequencing
- Next-generation
- OLC, Overlap-Layout-Consensus
- QV, Quality Value (QV)
- Reference
- SBS, Sequencing by Synthesis
- SMRT, Single Molecule Real-Time
- SNPs, Single Nucleotide Polymorphisms
- SRA, Short Read Archive
- SV, Structural Variant
- Sequencing
- TGS, Third Generation Sequencing
- Third-generation
- WGS, Whole Genome Sequencing
- ZMW, Zero-Mode Waveguide
- bp, base pair
- dNTPs, deoxynucleoside triphosphates
- ddNTP, 2,3-dideoxynucleoside triphosphate
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Affiliation(s)
- Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
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28
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McCombie WR, McPherson JD, Mardis ER. Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a036798. [PMID: 30478097 DOI: 10.1101/cshperspect.a036798] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although DNA and RNA sequencing has a history spanning five decades, large-scale massively parallel sequencing, or next-generation sequencing (NGS), has only been commercially available for about 10 years. Nonetheless, the meteoric increase in sequencing throughput with NGS has dramatically changed our understanding of our genome and ourselves. Sequencing the first human genome as a haploid reference took nearly 10 years but now a full diploid human genome sequence can be accomplished in just a few days. NGS has also reduced the cost of generating sequence data and a plethora of sequence-based methods for probing a genome have emerged using NGS as the readout and have been applied to many species. NGS methods have also entered the medical realm and will see an increasing use in diagnosis and treatment. NGS has largely been driven by short-read generation (150 bp) but new platforms have emerged and are now capable of generating long multikilobase reads. These latter platforms enable reference-independent genome assemblies and long-range haplotype generation. Rapid DNA and RNA sequencing is now mainstream and will continue to have an increasing impact on biology and medicine.
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Affiliation(s)
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California 95817
| | - Elaine R Mardis
- Institute for Genomic Medicine at Nationwide Children's Hospital, The Ohio State University College of Medicine, The Institute for Genomic Medicine, Columbus, Ohio 43205
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29
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Schneider TD, Jejjala V. Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences. PLoS One 2019; 14:e0222419. [PMID: 31671158 PMCID: PMC6822723 DOI: 10.1371/journal.pone.0222419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/29/2019] [Indexed: 11/19/2022] Open
Abstract
Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.
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Affiliation(s)
- Thomas D. Schneider
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, RNA Biology Laboratory, Frederick, Maryland, United States of America
| | - Vishnu Jejjala
- Mandelstam Institute for Theoretical Physics, School of Physics, NITheP, and CoE-MaSS, University of the Witwatersrand, Johannesburg, South Africa
- David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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30
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Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T. The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre. Mol Microbiol 2019; 112:1831-1846. [PMID: 31556164 DOI: 10.1111/mmi.14396] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
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Affiliation(s)
- Rhys A Dunstan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sam Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Claire Cormie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joshua Hardy
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Fuyi Li
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Rhys Grinter
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, 3800, Australia
| | | | - Lu Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jiangning Song
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | | | - Jyoti Choudhary
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fasseli Coulibaly
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, 3052, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
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31
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Peyvan K, Karouia F, Cooper JJ, Chamberlain J, Suciu D, Slota M, Pohorille A. Gene Expression Measurement Module (GEMM) for space application: Design and validation. LIFE SCIENCES IN SPACE RESEARCH 2019; 22:55-67. [PMID: 31421849 DOI: 10.1016/j.lssr.2019.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/05/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.
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Affiliation(s)
| | - Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Space Biosciences Research Branch, Moffett Field, CA 94035, USA; NASA Ames Research Center, Exobiology Branch, MS 239-4, Moffett Field, CA 94035, USA.
| | | | | | | | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS 239-4, Moffett Field, CA 94035, USA.
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32
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Mitkin NA, Korneev K, Gorbacheva AM, Kuprash DV. Relative Efficiency of Transcription Factor Binding to Allelic Variants of Regulatory Regions of Human Genes in Immunoprecipitation and Real-Time PCR. Mol Biol 2019. [DOI: 10.1134/s0026893319030117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels. Q Rev Biophys 2019; 52:e2. [DOI: 10.1017/s0033583518000124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA–protein complexes in nanochannels. The chaperone activity is visualized as concatemerization and circularization of long DNA via annealing of short single-stranded DNA overhangs. The first ten amino acids of NC are important for the chaperone activity that is almost completely absent for Gag. Gag condenses DNA more efficiently than mature NC, suggesting that additional residues of Gag are involved. Importantly, this is the first single DNA molecule study of full-length Gag and we reveal important differences to the truncated Δ-p6 Gag that has been used before. In addition, the study also highlights how nanochannels can be used to study reactions on ends of long single DNA molecules, which is not trivial with competing single DNA molecule techniques.
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34
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Dlusskaya EA, Atrazhev AM, Ashbolt NJ. Colloid chemistry pitfall for flow cytometric enumeration of viruses in water. WATER RESEARCH X 2019; 2:100025. [PMID: 31194069 PMCID: PMC6549941 DOI: 10.1016/j.wroa.2019.100025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
Flow cytomtery (FCM) has become a standard approach to enumerate viruses in water research. However, the nature of the fluorescent signal in flow cytometric analysis of water samples and the mechanism of its formation, have not been addressed for bacteriophages expected in wastewaters. Here we assess the behaviour of fluorescent DNA-staining dyes in aqueous solutions, as well as sensitivity and accuracy of FCM for enumeration of DNA-stained model bacteriophages λ, P1, and T4. We demonstrate that in aqueous systems fluorescent dyes form a self-stabilized (pseudolyophilic) emulsion of auto-fluorescing colloid particles. Sample shaking and addition of surfactants enhance auto-fluorescence due to increased dispersion and, in the presence of surfactants, stabilization of the dye emulsion. Bacteriophages with genome sizes <100 kbp (i.e. λ & P1) did not generate a distinct population signal to be detected by one of the most sensitive FCM instruments available (BD LSR Fortessa™ X-20), whereas the larger T4 bacteriophage was resolved as a distinct population of events. These results indicate that the use of fluorescent dyes for bacteriophage enumeration by flow cytometry can produce false positive signals and lead to wrong estimation of total virus counts by misreporting colloid particles as virions, depending on instrument sensitivity.
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Affiliation(s)
- Elena A. Dlusskaya
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | | | - Nicholas J. Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
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35
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Guan J, Ibarra D, Zeng L. The role of side tail fibers during the infection cycle of phage lambda. Virology 2018; 527:57-63. [PMID: 30463036 DOI: 10.1016/j.virol.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
Bacteriophage λ has served as an important model for molecular biology and different cellular processes over the past few decades. In 1992, the phage strain used in most laboratories around the world, thought of as λ wild type, was discovered to carry a mutation in the stf gene which encodes four side tail fibers. Up to now, the role of the side tail fibers during the infection cycle, especially at the single-cell level, remains largely unknown. Here we utilized fluorescent reporter systems to characterize the effect of the side tail fibers on phage infection. We found that the side tail fibers interfere with phage DNA ejection process, most likely through the binding with their receptors, OmpC, leading to a more frequent failed infection. However, the side tail fibers do not seem to affect the lysis-lysogeny decision-making or lysis time.
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Affiliation(s)
- Jingwen Guan
- Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - David Ibarra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA.
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36
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Progress of analytical tools and techniques for human gut microbiome research. J Microbiol 2018; 56:693-705. [DOI: 10.1007/s12275-018-8238-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022]
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37
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Abstract
Roger W. Hendrix was at the forefront of bacteriophage biology for nearly 50 years and was central to our understanding of both viral capsid assembly and phage genomic diversity and evolution. Roger's warm and gentle demeanor belied a razor-sharp mind and warmed him to numerous highly productive collaborations that amplified his scientific impact. Roger was always completely open with scientific ideas while at the same time quietly agitating with a stream of new ways of thinking about problems and nudging our communities to search for innovative solutions: a gentle but highly effective provocateur.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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38
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Abstract
The sequencing of phage genomes has become a routine procedure for phage characterization. The protocol presented here allows rapid isolation of DNA from a single phage plaque followed by building ready-to-sequence Illumina-compatible library.
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Affiliation(s)
- Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark.
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39
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Turner D, Sutton JM, Reynolds DM, Sim EM, Petty NK. Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams. Methods Mol Biol 2018; 1681:239-260. [PMID: 29134600 DOI: 10.1007/978-1-4939-7343-9_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The presentation of bacteriophage genomes as diagrams allows the location and organization of features to be communicated in a clear and effective manner. A wide range of software applications are available for the clear and accurate visualization of genomic data. Several of these applications incorporate comparative analysis tools, allowing for insertions, deletions, rearrangements and variations in syntenic regions to be visualized. In this chapter, freely available software and resources for the generation of high-quality graphical maps of bacteriophage genomes are listed and discussed.
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Affiliation(s)
- Dann Turner
- Centre for Research in Biosciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
| | - J Mark Sutton
- Public Health England, Porton Down, Salisbury, SP4 0JG, Wiltshire, UK
| | - Darren M Reynolds
- Centre for Research in Biosciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Eby M Sim
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, Sydney, New South Wales, Australia
| | - Nicola K Petty
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, Sydney, New South Wales, Australia
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40
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Lin JY, Le BH, Chen M, Henry KF, Hur J, Hsieh TF, Chen PY, Pelletier JM, Pellegrini M, Fischer RL, Harada JJ, Goldberg RB. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci U S A 2017; 114:E9730-E9739. [PMID: 29078418 PMCID: PMC5692608 DOI: 10.1073/pnas.1716758114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis-regulatory elements and their cognate transcription factors are organized in genetic regulatory networks.
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Affiliation(s)
- Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Jungim Hur
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pao-Yang Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Julie M Pelletier
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, CA 95616
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - John J Harada
- Section of Plant Biology, Division of Biological Sciences, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
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41
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Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature 2017; 550:345-353. [DOI: 10.1038/nature24286] [Citation(s) in RCA: 552] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 12/31/2022]
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42
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Vahanian N, Oh CS, Sippy J, Feiss M. Natural history of a viral cohesive end site: cosN of the λ-like phages. Virology 2017. [PMID: 28646648 DOI: 10.1016/j.virol.2017.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The base pairs of cosN, the site where the 12 base-long cohesive ends are generated in λ-like phages, show partial-two fold rotational symmetry. In a bioinformatic survey, we found that the cosN changes in 12 natural cosN variants are restricted to bp 6-to-12 of the cohesive end sequence. In contrast, bp 1-5 of the cohesive end sequence are strictly conserved (13/13), as are the two bp flanking the left nicking site (bp -2 and -1). The bp flanking the right nick site (bp 13 and 14) are conserved in 12 of 13 variants. Five cosN variants differing by as many as five bp were used to replace lambda's cosN. No significant effects of the cosN changes on λ's virus yield were found. In sum, bp -2 to 5 are critical cosN function, and bp 6-12 of the cohesive end sequence are not critical for terminase recognition or virus fitness.
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Affiliation(s)
- Nicole Vahanian
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Choon Seok Oh
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Jean Sippy
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA.
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Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics. J Bacteriol 2016; 199:JB.00560-16. [PMID: 27672193 DOI: 10.1128/jb.00560-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Few discoveries have been more transformative to the biological sciences than the development of DNA sequencing technologies. The rapid advancement of sequencing and bioinformatics tools has revolutionized bacterial genetics, deepening our understanding of model and clinically relevant organisms. Although application of newer sequencing technologies to studies in bacterial genetics is increasing, the implementation of DNA sequencing technologies and development of the bioinformatics tools required for analyzing the large data sets generated remain a challenge for many. In this minireview, we have chosen to summarize three sequencing approaches that are particularly useful for bacterial genetics. We provide resources for scientists new to and interested in their application. Here, we discuss the analysis of data from transposon mutagenesis followed by deep sequencing (Tn-seq) to determine gene disruptions differentially represented in a mutant population and Illumina sequencing for identification of suppressor or other mutations, and we summarize single-molecule real-time (SMRT) sequencing for de novo genome assembly and the use of the output data for detection of DNA base modifications.
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Sand M, Bechara FG, Skrygan M, Sand D, Gambichler T, Bromba M, Stockfleth E, Hessam S. Mutation Scanning of D1705 and D1709 in the RNAse IIIb Domain of MicroRNA Processing Enzyme Dicer in Cutaneous Melanoma. Pathol Oncol Res 2016; 22:639-41. [PMID: 26683837 DOI: 10.1007/s12253-015-0034-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/15/2015] [Indexed: 11/30/2022]
Abstract
Since the discovery of microRNAs (miRNAs) there have been performed several studies showing perturbations in the expression of miRNAs and the miRNA expression machinery in cutaneous melanoma. Dicer, a pivotal cytosolic enzyme of miRNA maturation has shown to be affected by both somatic and germline mutations in a variety of cancers. Recent studies have shown that recurrent somatic mutations of Dicer frequently affect the metal-ion-binding sites D1709 and D1705 of its RNase IIIb domain, therefore called hot spot mutations. The present study investigates metal-ion-binding sites D1709 and D1705 of the Dicer RNase IIIb domain in cutaneous melanomas and melanoma metastasis by Sanger sequencing. All investigated samples showed wildtype sequence and no single mutation was detected. The miRNA processing enzyme Dicer of melanoma and melanoma metastasis does not appear to be affected by mutation in the metal-ion-binding sites D1709 and D1705 of its RNase IIIb domain.
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Affiliation(s)
- Michael Sand
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany.
- Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, Heidbergweg 22-24, 45257, Essen, Germany.
| | - Falk G Bechara
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany
| | - Marina Skrygan
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany
| | - Daniel Sand
- University of Michigan Kellogg Eye Center, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Thilo Gambichler
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany
| | - Michael Bromba
- Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, Heidbergweg 22-24, 45257, Essen, Germany
| | - Eggert Stockfleth
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany
| | - Schapoor Hessam
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum, St. Josef Hospital, Gudrunstr. 56, 44791, Bochum, Germany
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Perez Sepulveda B, Redgwell T, Rihtman B, Pitt F, Scanlan DJ, Millard A. Marine phage genomics: the tip of the iceberg. FEMS Microbiol Lett 2016; 363:fnw158. [PMID: 27338950 PMCID: PMC4928673 DOI: 10.1093/femsle/fnw158] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes. Only a tiny fraction of marine phages have been discovered, yet are known to have important roles in the ocean.
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Affiliation(s)
| | - Tamsin Redgwell
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Frances Pitt
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Andrew Millard
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Rihtman B, Meaden S, Clokie MRJ, Koskella B, Millard AD. Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ 2016; 4:e2055. [PMID: 27280068 PMCID: PMC4893331 DOI: 10.7717/peerj.2055] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ~98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick , Coventry , United Kingdom
| | - Sean Meaden
- College of Life and Environmental Sciences, University of Exeter , United Kingdom
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester
| | - Britt Koskella
- College of Life and Environmental Sciences, University of Exeter, United Kingdom; Department of Integrative Biology, University of California, Berkeley, California, United States
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Kwon KM, Kang SG, Sokolova TG, Cho SS, Kim YJ, Kim CH, Kwon ST. Characterization of a family B DNA polymerase from Thermococcus barophilus Ch5 and its application for long and accurate PCR. Enzyme Microb Technol 2016; 86:117-26. [DOI: 10.1016/j.enzmictec.2016.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/14/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
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48
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Huang KW, Chen JL, Yang CS, Tsai CW. A memetic gravitation search algorithm for solving DNA fragment assembly problems. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2016. [DOI: 10.3233/ifs-151994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Ko-Wei Huang
- Institute of Computer and Communication Engineering, Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C
- Department of Psychology, National Cheng Kung University, Tainan, Taiwan, R.O.C
| | - Jui-Le Chen
- Institute of Computer and Communication Engineering, Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C
- Department of Computer Science and Entertainment Technology, Tajen university, Pingtung, Taiwan, R.O.C
| | - Chu-Sing Yang
- Institute of Computer and Communication Engineering, Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C
| | - Chun-Wei Tsai
- Department of Computer Science and Information Engineering, National Ilan University, Yilan, Taiwan, R.O.C
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49
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Mahony J, Stockdale SR, Collins B, Spinelli S, Douillard FP, Cambillau C, van Sinderen D. Lactococcus lactis phage TP901-1 as a model for Siphoviridae virion assembly. BACTERIOPHAGE 2016; 6:e1123795. [PMID: 27144086 DOI: 10.1080/21597081.2015.1123795] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/28/2022]
Abstract
Phages infecting Lactococcus lactis pose a serious threat to the dairy fermentation sector. Consequently, they are among the most thoroughly characterized Gram positive-infecting phages. The majority of lactococcal phages belong to the tailed family of phages named the Siphoviridae. The coliphage lambda and the Bacillus subtilis phage SPP1 have been the predominant comparators for emerging siphophages both genomically and structurally and both phages recognize a membrane protein receptor. In contrast, the lactococcal P335 group phage TP901-1 attaches to cell wall surface polysaccharides. It is a typical "lambdoid" siphophage possessing a long non-contractile tail and a genomic architecture reminiscent of lambda and SPP1 despite low or undetectable sequence homology in many of its encoded products, especially those involved in host recognition. A functional analysis of the structural components of TP901-1 was undertaken based on the characterization of a series of mutants in the region encoding the capsid and tail morphogenetic elements. Through this analysis, it was possible to deduce that, despite the lack of sequence homology, the overall genomic architecture of Siphoviridae phages typified by functional synteny is conserved. Furthermore, a model of the TP901-1 assembly pathway was developed with potential implications for many tailed phages.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork , Cork, Ireland
| | - Stephen R Stockdale
- School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Barry Collins
- School of Microbiology, University College Cork , Cork, Ireland
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy , Marseille Cedex, France
| | | | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille Cedex, France; Centre National de la Recherche Scientifique, AFMB, Campus de Luminy, Marseille Cedex, France
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
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Abstract
Viruses that infect bacteria (bacteriophages; also known as phages) were discovered 100 years ago. Since then, phage research has transformed fundamental and translational biosciences. For example, phages were crucial in establishing the central dogma of molecular biology - information is sequentially passed from DNA to RNA to proteins - and they have been shown to have major roles in ecosystems, and help drive bacterial evolution and virulence. Furthermore, phage research has provided many techniques and reagents that underpin modern biology - from sequencing and genome engineering to the recent discovery and exploitation of CRISPR-Cas phage resistance systems. In this Timeline, we discuss a century of phage research and its impact on basic and applied biology.
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