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Jochheim A, Jochheim FA, Kolodyazhnaya A, Morice É, Steinegger M, Söding J. Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs. MICROBIOME 2024; 12:187. [PMID: 39354646 PMCID: PMC11443906 DOI: 10.1186/s40168-024-01904-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/07/2024] [Indexed: 10/03/2024]
Abstract
BACKGROUND Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read. RESULTS Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes. CONCLUSION PenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities. Video Abstract.
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Affiliation(s)
- Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max-Planck Research School for Genome Sciences, University of Göttingen, Göttingen, Germany
| | - Florian A Jochheim
- International Max-Planck Research School for Genome Sciences, University of Göttingen, Göttingen, Germany
- Dep. of Molecular Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandra Kolodyazhnaya
- Quantitative and Computational Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Étienne Morice
- Quantitative and Computational Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max-Planck Research School for Genome Sciences, University of Göttingen, Göttingen, Germany
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea.
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
| | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- International Max-Planck Research School for Genome Sciences, University of Göttingen, Göttingen, Germany.
- Campus Institute Data Science (CIDAS), University of Göttingen, Göttingen, Germany.
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Vasyagin EA, Zykova AA, Mardanova ES, Nikitin NA, Shuklina MA, Ozhereleva OO, Stepanova LA, Tsybalova LM, Blokhina EA, Ravin NV. Influenza A Vaccine Candidates Based on Virus-like Particles Formed by Coat Proteins of Single-Stranded RNA Phages Beihai32 and PQ465. Vaccines (Basel) 2024; 12:1033. [PMID: 39340063 PMCID: PMC11435553 DOI: 10.3390/vaccines12091033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Efficient control of influenza A infection can potentially be achieved through the development of broad-spectrum recombinant vaccines based on conserved antigens. The extracellular domain of the transmembrane protein M2 of influenza A virus (M2e) is highly conserved but poorly immunogenic and needs to be fused to an adjuvant protein or carrier virus-like particles (VLPs) to increase immunogenicity and provide protection against infection. In this study, we obtained VLPs based on capsid proteins (CPs) of single-stranded RNA phages Beihai32 and PQ465 bearing the M2e peptides. Four copies of the M2e peptide were linked to the C-terminus of the CP of phage Beihai32 and to the N and C termini of the CP of phage PQ465. The hybrid proteins, being expressed in Escherichia coli, formed spherical VLPs of about 30 nm in size. Immunogold transmission electron microscopy showed that VLPs formed by the phage PQ465 CP with a C-terminal M2e fusion present the M2e peptide on the surface. Subcutaneous immunization of mice with VLPs formed by both CPs containing four copies of the M2e peptide at the C termini induced high levels of M2e-specific IgG antibodies in serum and provided mice with protection against lethal influenza A virus challenge. In the case of an N-terminal fusion of M2e with the phage PQ465 CP, the immune response against M2e was significantly lower. CPs of phages Beihai32 and PQ465, containing four copies of the M2e peptide at their C termini, can be used to develop recombinant influenza A vaccine.
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Affiliation(s)
- Egor A Vasyagin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Zykova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Eugenia S Mardanova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai A Nikitin
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina A Shuklina
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376 St. Petersburg, Russia
| | - Olga O Ozhereleva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376 St. Petersburg, Russia
| | - Liudmila A Stepanova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376 St. Petersburg, Russia
| | - Liudmila M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376 St. Petersburg, Russia
| | - Elena A Blokhina
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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Filipić B, Pantelić I, Nikolić I, Majhen D, Stojić-Vukanić Z, Savić S, Krajišnik D. Nanoparticle-Based Adjuvants and Delivery Systems for Modern Vaccines. Vaccines (Basel) 2023; 11:1172. [PMID: 37514991 PMCID: PMC10385383 DOI: 10.3390/vaccines11071172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Ever since the development of the first vaccine, vaccination has had the great impact on global health, leading to the decrease in the burden of numerous infectious diseases. However, there is a constant need to improve existing vaccines and develop new vaccination strategies and vaccine platforms that induce a broader immune response compared to traditional vaccines. Modern vaccines tend to rely on certain nanotechnology platforms but are still expected to be readily available and easy for large-scale manufacturing and to induce a durable immune response. In this review, we present an overview of the most promising nanoadjuvants and nanoparticulate delivery systems and discuss their benefits from tehchnological and immunological standpoints as well as their objective drawbacks and possible side effects. The presented nano alums, silica and clay nanoparticles, nanoemulsions, adenoviral-vectored systems, adeno-associated viral vectors, vesicular stomatitis viral vectors, lentiviral vectors, virus-like particles (including bacteriophage-based ones) and virosomes indicate that vaccine developers can now choose different adjuvants and/or delivery systems as per the requirement, specific to combatting different infectious diseases.
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Affiliation(s)
- Brankica Filipić
- Department of Microbiology and Immunology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
| | - Ivana Pantelić
- Department of Pharmaceutical Technology and Cosmetology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
| | - Ines Nikolić
- Department of Pharmaceutical Technology and Cosmetology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
- Section of Pharmaceutical Sciences, University of Geneva, 1206 Geneva, Switzerland
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Zorica Stojić-Vukanić
- Department of Microbiology and Immunology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
| | - Snežana Savić
- Department of Pharmaceutical Technology and Cosmetology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
| | - Danina Krajišnik
- Department of Pharmaceutical Technology and Cosmetology, University of Belgrade-Faculty of Pharmacy, 11000 Belgrade, Serbia
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In vitro characterisation of the MS2 RNA polymerase complex reveals host factors that modulate emesviral replicase activity. Commun Biol 2022; 5:264. [PMID: 35338258 PMCID: PMC8956599 DOI: 10.1038/s42003-022-03178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
The RNA phage MS2 is one of the most important model organisms in molecular biology and virology. Despite its comprehensive characterisation, the composition of the RNA replication machinery remained obscure. Here, we characterised host proteins required to reconstitute the functional replicase in vitro. By combining a purified replicase sub-complex with elements of an in vitro translation system, we confirmed that the three host factors, EF-Ts, EF-Tu, and ribosomal protein S1, are part of the active replicase holocomplex. Furthermore, we found that the translation initiation factors IF1 and IF3 modulate replicase activity. While IF3 directly competes with the replicase for template binding, IF1 appears to act as an RNA chaperone that facilitates polymerase readthrough. Finally, we demonstrate in vitro formation of RNAs containing minimal motifs required for amplification. Our work sheds light on the MS2 replication machinery and provides a new promising platform for cell-free evolution.
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