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Tulloch RL, Kim K, Sikazwe C, Michie A, Burrell R, Holmes EC, Dwyer DE, Britton PN, Kok J, Eden JS. RAPID prep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 2023; 15:v15041006. [PMID: 37112986 PMCID: PMC10146689 DOI: 10.3390/v15041006] [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: 12/21/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
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Affiliation(s)
- Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karan Kim
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Alice Michie
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Philip N Britton
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jen Kok
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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2
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Mahler M, Costa AR, van Beljouw SPB, Fineran PC, Brouns SJJ. Approaches for bacteriophage genome engineering. Trends Biotechnol 2022; 41:669-685. [PMID: 36117025 DOI: 10.1016/j.tibtech.2022.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 12/26/2022]
Abstract
In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. In addition, there is a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. However, the ability to manipulate phage genomes to understand and control gene functions, or alter phage properties such as host range, has remained challenging due to a lack of universal selectable markers. Here, we discuss the state-of-the-art techniques to engineer and select desired phage genomes using advances in cell-free methodologies and clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR-Cas) counter-selection approaches.
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Affiliation(s)
- Marina Mahler
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Sam P B van Beljouw
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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3
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Shrestha N, Duvall MR, Bujarski JJ. Variability among the Isolates of Broad Bean Mottle Virus and Encapsidation of Host RNAs. Pathogens 2022; 11:pathogens11070817. [PMID: 35890061 PMCID: PMC9321246 DOI: 10.3390/pathogens11070817] [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] [Received: 05/25/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 02/05/2023] Open
Abstract
Broad bean mottle bromovirus infects legume plants and is transmissible by insects. Several broad bean mottle virus (BBMV) isolates have been identified, including one in England (isolate Ba) and five in the Mediterranean countries: Libya (LyV), Morocco (MV), Syria (SV), Sudan (TU) and Tunisia (TV). Previously, we analyzed the nucleotide sequence of the Ba RNA and here we report on and compare it with another five Mediterranean variants. The RNA segments in the latter ones were extensively homologous, with some SNPs, single nucleotide deletions and insertions, while the number of mutations was higher in isolate Ba. Both the 5′ and 3′ untranslated terminal regions (UTRs) among the corresponding RNAs are highly conserved, reflecting their functionality in virus replication. The AUG initiation codons are within suboptimal contexts, possibly to adjust/regulate translation. The proteins 1a, 2a, 3a and coat protein (CP) are almost identical among the five isolates, but in Ba they have more amino acid (aa) substitutions. Phylogenetic analysis revealed the isolates from Morocco and Syria clustering with the isolate from England, while the variants from Libya, Tunisia and Sudan created a different clade. The BBMV isolates encapsidate a high content of host (ribosomal and messenger) RNAs. Our studies present BBMV as a useful model for bromoviruses infecting legumes.
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Affiliation(s)
- Nipin Shrestha
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
| | | | - Jozef J. Bujarski
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
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Keown RA, Dums JT, Brumm PJ, MacDonald J, Mead DA, Ferrell BD, Moore RM, Harrison AO, Polson SW, Wommack KE. Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Front Microbiol 2022; 13:858366. [PMID: 35531281 PMCID: PMC9069017 DOI: 10.3389/fmicb.2022.858366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant and diverse biological entities on the planet and constitute a significant proportion of Earth's genetic diversity. Most of this diversity is not represented by isolated viral-host systems and has only been observed through sequencing of viral metagenomes (viromes) from environmental samples. Viromes provide snapshots of viral genetic potential, and a wealth of information on viral community ecology. These data also provide opportunities for exploring the biochemistry of novel viral enzymes. The in vitro biochemical characteristics of novel viral DNA polymerases were explored, testing hypothesized differences in polymerase biochemistry according to protein sequence phylogeny. Forty-eight viral DNA Polymerase I (PolA) proteins from estuarine viromes, hot spring metagenomes, and reference viruses, encompassing a broad representation of currently known diversity, were synthesized, expressed, and purified. Novel functionality was shown in multiple PolAs. Intriguingly, some of the estuarine viral polymerases demonstrated moderate to strong innate DNA strand displacement activity at high enzyme concentration. Strand-displacing polymerases have important technological applications where isothermal reactions are desirable. Bioinformatic investigation of genes neighboring these strand displacing polymerases found associations with SNF2 helicase-associated proteins. The specific function of SNF2 family enzymes is unknown for prokaryotes and viruses. In eukaryotes, SNF2 enzymes have chromatin remodeling functions but do not separate nucleic acid strands. This suggests the strand separation function may be fulfilled by the DNA polymerase for viruses carrying SNF2 helicase-associated proteins. Biochemical data elucidated from this study expands understanding of the biology and ecological behavior of unknown viruses. Moreover, given the numerous biotechnological applications of viral DNA polymerases, novel viral polymerases discovered within viromes may be a rich source of biological material for further in vitro DNA amplification advancements.
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Affiliation(s)
- Rachel A. Keown
- Department of Biological Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - Jacob T. Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | | | | | - David A. Mead
- Varigen Biosciences Corporation, Middleton, WI, United States
| | - Barbra D. Ferrell
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
| | - Ryan M. Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Amelia O. Harrison
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
- Department of Computer and Information Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - K. Eric Wommack
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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6
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Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site. Biochem J 2021; 478:2665-2679. [PMID: 34160020 DOI: 10.1042/bcj20200922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/25/2023]
Abstract
The crystal structure of full-length T7 DNA polymerase in complex with its processivity factor thioredoxin and double-stranded DNA in the polymerization active site exhibits two novel structural motifs in family-A DNA polymerases: an extended β-hairpin at the fingers subdomain, that interacts with the DNA template strand downstream the primer-terminus, and a helix-loop-helix motif (insertion1) located between residues 102 to 122 in the exonuclease domain. The extended β-hairpin is involved in nucleotide incorporation on substrates with 5'-overhangs longer than 2 nt, suggesting a role in stabilizing the template strand into the polymerization domain. Our biochemical data reveal that insertion1 of the exonuclease domain makes stabilizing interactions that facilitate proofreading by shuttling the primer strand into the exonuclease active site. Overall, our studies evidence conservation of the 3'-5' exonuclease domain fold between family-A DNA polymerases and highlight the modular architecture of T7 DNA polymerase. Our data suggest that the intercalating β-hairpin guides the template-strand into the polymerization active site after the T7 primase-helicase unwinds the DNA double helix ameliorating the formation of secondary structures and decreasing the appearance of indels.
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Song Y, Hyeon C. Thermodynamic Cost, Speed, Fluctuations, and Error Reduction of Biological Copy Machines. J Phys Chem Lett 2020; 11:3136-3143. [PMID: 32227999 DOI: 10.1021/acs.jpclett.0c00545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been a subject of active research; however, how error reduction of a process is balanced with its thermodynamic cost and dynamical properties remain largely unexplored. Here, we study the error reducing strategies in light of the recently discovered thermodynamic uncertainty relation (TUR) that sets a physical bound to the cost-precision trade-off for dissipative processes. We found that the two representative copying processes, DNA replication by the exonuclease-deficient T7 DNA polymerase and mRNA translation by the E. coli ribosome, reduce the error rates to biologically acceptable levels while also optimizing the processes close to the physical limit dictated by TUR.
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Affiliation(s)
- Yonghyun Song
- Korea Institute for Advanced Study, Seoul 02455, Korea
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Hay ID, Lithgow T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep 2019; 20:embr.201847427. [PMID: 30952693 DOI: 10.15252/embr.201847427] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.
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Affiliation(s)
- Iain D Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Vic., Australia
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Henno L, Tombak E, Geimanen J, Orav M, Ustav E, Ustav M. Analysis of Human Papillomavirus Genome Replication Using Two‐ and Three‐Dimensional Agarose Gel Electrophoresis. ACTA ACUST UNITED AC 2017; 45:14B.10.1-14B.10.37. [DOI: 10.1002/cpmc.28] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Liisi Henno
- University of Tartu, Institute of Technology Tartu Estonia
| | | | | | - Marit Orav
- University of Tartu, Institute of Technology Tartu Estonia
| | - Ene Ustav
- University of Tartu, Institute of Technology Tartu Estonia
| | - Mart Ustav
- University of Tartu, Institute of Technology Tartu Estonia
- Academy of Sciences Tallinn Estonia
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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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Gardner AF, Kelman Z. DNA polymerases in biotechnology. Front Microbiol 2014; 5:659. [PMID: 25520711 PMCID: PMC4249456 DOI: 10.3389/fmicb.2014.00659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/13/2014] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Zvi Kelman
- National Institute of Standards and Technology Gaithersburg, MD, USA ; Institute for Bioscience and Biotechnology Research Rockville, MD, USA
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Reha-Krantz LJ, Woodgate S, Goodman MF. Engineering processive DNA polymerases with maximum benefit at minimum cost. Front Microbiol 2014; 5:380. [PMID: 25136334 PMCID: PMC4120765 DOI: 10.3389/fmicb.2014.00380] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/07/2014] [Indexed: 11/25/2022] Open
Abstract
DNA polymerases need to be engineered to achieve optimal performance for biotechnological applications, which often require high fidelity replication when using modified nucleotides and when replicating difficult DNA sequences. These tasks are achieved for the bacteriophage T4 DNA polymerase by replacing leucine with methionine in the highly conserved Motif A sequence (L412M). The costs are minimal. Although base substitution errors increase moderately, accuracy is maintained for templates with mono- and dinucleotide repeats while replication efficiency is enhanced. The L412M substitution increases intrinsic processivity and addition of phage T4 clamp and single-stranded DNA binding proteins further enhance the ability of the phage T4 L412M-DNA polymerase to replicate all types of difficult DNA sequences. Increased pyrophosphorolysis is a drawback of increased processivity, but pyrophosphorolysis is curbed by adding an inorganic pyrophosphatase or divalent metal cations, Mn2+ or Ca2+. In the absence of pyrophosphorolysis inhibitors, the T4 L412M-DNA polymerase catalyzed sequence-dependent pyrophosphorolysis under DNA sequencing conditions. The sequence specificity of the pyrophosphorolysis reaction provides insights into how the T4 DNA polymerase switches between nucleotide incorporation, pyrophosphorolysis and proofreading pathways. The L-to-M substitution was also tested in the yeast DNA polymerases delta and alpha. Because the mutant DNA polymerases displayed similar characteristics, we propose that amino acid substitutions in Motif A have the potential to increase processivity and to enhance performance in biotechnological applications. An underlying theme in this chapter is the use of genetic methods to identify mutant DNA polymerases with potential for use in current and future biotechnological applications.
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Affiliation(s)
- Linda J Reha-Krantz
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
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