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Wang J, Zhu H, Gan J, Liang G, Li L, Zhao Y. Engineered mRNA Delivery Systems for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308029. [PMID: 37805865 DOI: 10.1002/adma.202308029] [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: 08/09/2023] [Revised: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and delivery system of engineered mRNA has greatly improved its stability, immunogenicity, and protein expression levels, which has led to a wider range of uses for mRNA therapeutics. Herein, a thorough analysis of the optimization strategies used in the structure of mRNA is first provided and delivery systems are described in great detail. Furthermore, the latest advancements in biomedical engineering for mRNA technology, including its applications in combatting infectious diseases, treating cancer, providing protein replacement therapy, conducting gene editing, and more, are summarized. Lastly, a perspective on forthcoming challenges and prospects concerning the advancement of mRNA therapeutics is offered. Despite these challenges, mRNA-based therapeutics remain promising, with the potential to revolutionize disease treatment and contribute to significant advancements in the biomedical field.
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Affiliation(s)
- Ji Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Haofang Zhu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jingjing Gan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gaofeng Liang
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| | - Ling Li
- Department of Endocrinology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
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Mishra A, Varshney A, Mishra S. Regulation of Atg8 membrane deconjugation by cysteine proteases in the malaria parasite Plasmodium berghei. Cell Mol Life Sci 2023; 80:344. [PMID: 37910326 PMCID: PMC11073460 DOI: 10.1007/s00018-023-05004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
During macroautophagy, the Atg8 protein is conjugated to phosphatidylethanolamine (PE) in autophagic membranes. In Apicomplexan parasites, two cysteine proteases, Atg4 and ovarian tumor unit (Otu), have been identified to delipidate Atg8 to release this protein from membranes. Here, we investigated the role of cysteine proteases in Atg8 conjugation and deconjugation and found that the Plasmodium parasite consists of both activities. We successfully disrupted the genes individually; however, simultaneously, they were refractory to deletion and essential for parasite survival. Mutants lacking Atg4 and Otu showed normal blood and mosquito stage development. All mice infected with Otu KO sporozoites became patent; however, Atg4 KO sporozoites either failed to establish blood infection or showed delayed patency. Through in vitro and in vivo analysis, we found that Atg4 KO sporozoites invade and normally develop into early liver stages. However, nuclear and organelle differentiation was severely hampered during late stages and failed to mature into hepatic merozoites. We found a higher level of Atg8 in Atg4 KO parasites, and the deconjugation of Atg8 was hampered. We confirmed Otu localization on the apicoplast; however, parasites lacking Otu showed no visible developmental defects. Our data suggest that Atg4 is the primary deconjugating enzyme and that Otu cannot replace its function completely because it cleaves the peptide bond at the N-terminal side of glycine, thereby irreversibly inactivating Atg8 during its recycling. These findings highlight a role for the Atg8 deconjugation pathway in organelle biogenesis and maintenance of the homeostatic cellular balance.
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Affiliation(s)
- Akancha Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aastha Varshney
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Li Y, Wang M, Peng X, Yang Y, Chen Q, Liu J, She Q, Tan J, Lou C, Liao Z, Li X. mRNA vaccine in cancer therapy: Current advance and future outlook. Clin Transl Med 2023; 13:e1384. [PMID: 37612832 PMCID: PMC10447885 DOI: 10.1002/ctm2.1384] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
Messenger ribonucleic acid (mRNA) vaccines are a relatively new class of vaccines that have shown great promise in the immunotherapy of a wide variety of infectious diseases and cancer. In the past 2 years, SARS-CoV-2 mRNA vaccines have contributed tremendously against SARS-CoV2, which has prompted the arrival of the mRNA vaccine research boom, especially in the research of cancer vaccines. Compared with conventional cancer vaccines, mRNA vaccines have significant advantages, including efficient production of protective immune responses, relatively low side effects and lower cost of acquisition. In this review, we elaborated on the development of cancer vaccines and mRNA cancer vaccines, as well as the potential biological mechanisms of mRNA cancer vaccines and the latest progress in various tumour treatments, and discussed the challenges and future directions for the field.
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Affiliation(s)
- Youhuai Li
- Department of Breast SurgeryBaoji Municipal Central HospitalWeibin DistrictBaojiShaanxiChina
| | - Mina Wang
- Graduate SchoolBeijing University of Chinese MedicineBeijingChina
- Department of Acupuncture and MoxibustionBeijing Hospital of Traditional Chinese MedicineCapital Medical UniversityBeijing Key Laboratory of Acupuncture NeuromodulationBeijingChina
| | - Xueqiang Peng
- Department of General SurgeryThe Fourth Affiliated HospitalChina Medical UniversityShenyangChina
| | - Yingying Yang
- Clinical Research CenterShanghai Key Laboratory of Maternal Fetal MedicineShanghai Institute of Maternal‐Fetal Medicine and Gynecologic OncologyShanghai First Maternity and Infant HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Qishuang Chen
- Graduate SchoolBeijing University of Chinese MedicineBeijingChina
| | - Jiaxing Liu
- Department of General SurgeryThe Fourth Affiliated HospitalChina Medical UniversityShenyangChina
| | - Qing She
- Department of Breast SurgeryBaoji Municipal Central HospitalWeibin DistrictBaojiShaanxiChina
| | - Jichao Tan
- Department of Breast SurgeryBaoji Municipal Central HospitalWeibin DistrictBaojiShaanxiChina
| | - Chuyuan Lou
- Department of OphthalmologyXi'an People's Hospital (Xi'an Fourth Hospital)Xi'anShaanxiChina
| | - Zehuan Liao
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Department of Microbiology, Tumor and Cell Biology (MTC)Karolinska InstitutetSweden
| | - Xuexin Li
- Department of Medical Biochemistry and Biophysics (MBB)Karolinska InstitutetBiomedicumStockholmSweden
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Asad N, Smith E, Shakya S, Stegman S, Timmons L. Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids. Methods Protoc 2023; 6:mps6020025. [PMID: 36961045 PMCID: PMC10037626 DOI: 10.3390/mps6020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive screening of difficult-to-obtain plasmids. Sustainability is increased when agarose is used ten times over by virtue of a thorough recycling regimen. The workflow optimizes workspaces and standardizes lab practices for handling potentially hazardous waste, minimizing environmental harm. Safety, efficiency, and sustainability improve laboratory productivity, help minimize environmental contamination, and increase cost-effectiveness.
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Affiliation(s)
- Nadeem Asad
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Biochemistry and Molecular Medicine, 64 Medical Center Drive, University of West Virginia Health Science Center, Morgantown, WV 26506, USA
| | - Emily Smith
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, CA 95618, USA
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618, USA
- Center for Neuroscience, University of California, Davis, CA 95618, USA
| | - Sudeep Shakya
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sutton Stegman
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Lisa Timmons
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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Blanch-Asensio M, Dey S, Sankaran S. In vitro assembly of plasmid DNA for direct cloning in Lactiplantibacillus plantarum WCSF1. PLoS One 2023; 18:e0281625. [PMID: 36795741 PMCID: PMC9934402 DOI: 10.1371/journal.pone.0281625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/27/2023] [Indexed: 02/17/2023] Open
Abstract
Lactobacilli are gram-positive bacteria that are growing in importance for the healthcare industry and genetically engineering them as living therapeutics is highly sought after. However, progress in this field is hindered since most strains are difficult to genetically manipulate, partly due to their complex and thick cell walls limiting our capability to transform them with exogenous DNA. To overcome this, large amounts of DNA (>1 μg) are normally required to successfully transform these bacteria. An intermediate host, like E. coli, is often used to amplify recombinant DNA to such amounts although this approach poses unwanted drawbacks such as an increase in plasmid size, different methylation patterns and the limitation of introducing only genes compatible with the intermediate host. In this work, we have developed a direct cloning method based on in-vitro assembly and PCR amplification to yield recombinant DNA in significant quantities for successful transformation in L. plantarum WCFS1. The advantage of this method is demonstrated in terms of shorter experimental duration and the possibility to introduce a gene incompatible with E. coli into L. plantarum WCFS1.
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Affiliation(s)
- Marc Blanch-Asensio
- Bioprogrammable Materials, INM—Leibniz Institute for New Materials Campus D2 2, Saarbrücken, Germany
| | - Sourik Dey
- Bioprogrammable Materials, INM—Leibniz Institute for New Materials Campus D2 2, Saarbrücken, Germany
| | - Shrikrishnan Sankaran
- Bioprogrammable Materials, INM—Leibniz Institute for New Materials Campus D2 2, Saarbrücken, Germany
- * E-mail:
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A Comprehensive Review of mRNA Vaccines. Int J Mol Sci 2023; 24:ijms24032700. [PMID: 36769023 PMCID: PMC9917162 DOI: 10.3390/ijms24032700] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
mRNA vaccines have been demonstrated as a powerful alternative to traditional conventional vaccines because of their high potency, safety and efficacy, capacity for rapid clinical development, and potential for rapid, low-cost manufacturing. These vaccines have progressed from being a mere curiosity to emerging as COVID-19 pandemic vaccine front-runners. The advancements in the field of nanotechnology for developing delivery vehicles for mRNA vaccines are highly significant. In this review we have summarized each and every aspect of the mRNA vaccine. The article describes the mRNA structure, its pharmacological function of immunity induction, lipid nanoparticles (LNPs), and the upstream, downstream, and formulation process of mRNA vaccine manufacturing. Additionally, mRNA vaccines in clinical trials are also described. A deep dive into the future perspectives of mRNA vaccines, such as its freeze-drying, delivery systems, and LNPs targeting antigen-presenting cells and dendritic cells, are also summarized.
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MAEBL Contributes to Plasmodium Sporozoite Adhesiveness. Int J Mol Sci 2022; 23:ijms23105711. [PMID: 35628522 PMCID: PMC9146008 DOI: 10.3390/ijms23105711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
The sole currently approved malaria vaccine targets the circumsporozoite protein-the protein that densely coats the surface of sporozoites, the parasite stage deposited in the skin of the mammalian host by infected mosquitoes. However, this vaccine only confers moderate protection against clinical diseases in children, impelling a continuous search for novel candidates. In this work, we studied the importance of the membrane-associated erythrocyte binding-like protein (MAEBL) for infection by Plasmodium sporozoites. Using transgenic parasites and live imaging in mice, we show that the absence of MAEBL reduces Plasmodium berghei hemolymph sporozoite infectivity to mice. Moreover, we found that maebl knockout (maebl-) sporozoites display reduced adhesion, including to cultured hepatocytes, which could contribute to the defects in multiple biological processes, such as in gliding motility, hepatocyte wounding, and invasion. The maebl- defective phenotypes in mosquito salivary gland and liver infection were reverted by genetic complementation. Using a parasite line expressing a C-terminal myc-tagged MAEBL, we found that MAEBL levels peak in midgut and hemolymph parasites but drop after sporozoite entry into the salivary glands, where the labeling was found to be heterogeneous among sporozoites. MAEBL was found associated, not only with micronemes, but also with the surface of mature sporozoites. Overall, our data provide further insight into the role of MAEBL in sporozoite infectivity and may contribute to the design of future immune interventions.
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McGrath SL, Huang SH, Kobryn K. The N-terminal domain of the Agrobacterium tumefaciens telomere resolvase, TelA, regulates its DNA cleavage and rejoining activities. J Biol Chem 2022; 298:101951. [PMID: 35447111 PMCID: PMC9111995 DOI: 10.1016/j.jbc.2022.101951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/04/2022] Open
Abstract
Linear replicons can be found in a minority of prokaryotic organisms, including Borrelia species and Agrobacterium tumefaciens. The problem with replicating the lagging strand end of linear DNAs is circumvented in these organisms by the presence of covalently closed DNA hairpin telomeres at the DNA termini. Telomere resolvases are enzymes responsible for generating these hairpin telomeres from a dimeric replication intermediate through a two-step DNA cleavage and rejoining reaction referred to as telomere resolution. It was previously shown that the agrobacterial telomere resolvase, TelA, possesses ssDNA annealing activity in addition to telomere resolution activity. The annealing activity derives, chiefly, from the N-terminal domain. This domain is dispensable for telomere resolution. In this study, we used activity analyses of an N-terminal domain deletion mutant, domain add back experiments, and protein–protein interaction studies and we report that the N-terminal domain of TelA is involved in inhibitory interactions with the remainder of TelA that are relieved by the binding of divalent metal ions. We also found that the regulation of telomere resolution by the N-terminal domain of TelA extends to suppression of inappropriate enzymatic activity, including hairpin telomere fusion (reaction reversal) and recombination between replicated telomeres to form a Holliday junction.
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Affiliation(s)
- Siobhan L McGrath
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, Academic Health Sciences Building, Saskatoon, Saskatchewan, Canada
| | - Shu Hui Huang
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, Academic Health Sciences Building, Saskatoon, Saskatchewan, Canada
| | - Kerri Kobryn
- Department of Biochemistry, Microbiology & Immunology, College of Medicine, University of Saskatchewan, Academic Health Sciences Building, Saskatoon, Saskatchewan, Canada.
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The TelN/tos-assisted Precise Targeting of Chromosome Segments (TAPE). J Adv Res 2022; 41:169-177. [PMID: 36328746 PMCID: PMC9637730 DOI: 10.1016/j.jare.2022.01.017] [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: 10/07/2021] [Revised: 01/12/2022] [Accepted: 01/29/2022] [Indexed: 01/04/2023] Open
Abstract
We first apply the TelN/tos system to target genomic segments in E. coli host. We successfully cloned the targeted bacterial DNA fragment up to 156 kb. The TAPE method takes no more than five days to directly obtain the large DNA sequence. The TAPE method has no preferences on genome sequence. The results showed a considerable improvement of cloning efficiency. The TAPE method provides a powerful tool to support the study on synthetic biology.
Introduction Performing genomic large segmentation experiments will promote the annotation of complex genomic functions and contribute to the synthesis of designed genomes. It is challenging to obtain and manipulate large or complex DNA sequences with high efficiency. Objectives This study aims to develop an effective method for direct cloning of target genome sequences from different species. Methods The TelN/tos system and a linear plasmid vector were first used to directly clone the large genomic segments in E. coli. For the in vitro cloning reaction, two telomeric sites were developed using TelN protelomerase at the end of the linear plasmid vector. The target DNA sequence can be easily hooked with the homology arms and maintained as a linear artificial chromosome with arbitrary restriction sites in a specific E. coli strain. Results Using the linear cloning strategy, we successfully cloned the bacterial DNA fragment of 156 kb, a yeast genomic fragment of 124 kb and mammalian mitochondrial fragment of 16 kb. The results showed a considerable improvement in cloning efficiency and demonstrated the important role of vector ratio in the cloning process. Conclusion Due to the high efficiency and stability, TAPE is an effective technique for DNA cloning and fundamental molecular biotechnology method in synthetic biology.
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Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF). Appl Environ Microbiol 2021; 87:e0054321. [PMID: 34232745 DOI: 10.1128/aem.00543-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.
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McGuffie MJ, Barrick JE. pLannotate: engineered plasmid annotation. Nucleic Acids Res 2021; 49:W516-W522. [PMID: 34019636 PMCID: PMC8262757 DOI: 10.1093/nar/gkab374] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Engineered plasmids are widely used in the biological sciences. Since many plasmids contain DNA sequences that have been reused and remixed by researchers for decades, annotation of their functional elements is often incomplete. Missing information about the presence, location, or precise identity of a plasmid feature can lead to unintended consequences or failed experiments. Many engineered plasmids contain sequences—such as recombinant DNA from all domains of life, wholly synthetic DNA sequences, and engineered gene expression elements—that are not predicted by microbial genome annotation pipelines. Existing plasmid annotation tools have limited feature libraries and do not detect incomplete fragments of features that are present in many plasmids for historical reasons and may impact their newly designed functions. We created the open source pLannotate web server so users can quickly and comprehensively annotate plasmid features. pLannotate is powered by large databases of genetic parts and proteins. It employs a filtering algorithm to display only the most relevant feature matches and also reports feature fragments. Finally, pLannotate displays a graphical map of the annotated plasmid, explains the provenance of each feature prediction, and allows results to be downloaded in a variety of formats. The webserver for pLannotate is accessible at: http://plannotate.barricklab.org/
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Affiliation(s)
- Matthew J McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, 2500 Speedway A5000, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, 2500 Speedway A5000, Austin, TX 78712, USA
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12
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Kim J, Eygeris Y, Gupta M, Sahay G. Self-assembled mRNA vaccines. Adv Drug Deliv Rev 2021; 170:83-112. [PMID: 33400957 PMCID: PMC7837307 DOI: 10.1016/j.addr.2020.12.014] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 01/08/2023]
Abstract
mRNA vaccines have evolved from being a mere curiosity to emerging as COVID-19 vaccine front-runners. Recent advancements in the field of RNA technology, vaccinology, and nanotechnology have generated interest in delivering safe and effective mRNA therapeutics. In this review, we discuss design and self-assembly of mRNA vaccines. Self-assembly, a spontaneous organization of individual molecules, allows for design of nanoparticles with customizable properties. We highlight the materials commonly utilized to deliver mRNA, their physicochemical characteristics, and other relevant considerations, such as mRNA optimization, routes of administration, cellular fate, and immune activation, that are important for successful mRNA vaccination. We also examine the COVID-19 mRNA vaccines currently in clinical trials. mRNA vaccines are ready for the clinic, showing tremendous promise in the COVID-19 vaccine race, and have pushed the boundaries of gene therapy.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Biomedical Engineering, Oregon Health & Science University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon 97239, USA.
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Nasamu AS, Falla A, Pasaje CFA, Wall BA, Wagner JC, Ganesan SM, Goldfless SJ, Niles JC. An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum. Sci Rep 2021; 11:342. [PMID: 33431920 PMCID: PMC7801740 DOI: 10.1038/s41598-020-77644-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
Establishing robust genome engineering methods in the malarial parasite, Plasmodium falciparum, has the potential to substantially improve the efficiency with which we gain understanding of this pathogen's biology to propel treatment and elimination efforts. Methods for manipulating gene expression and engineering the P. falciparum genome have been validated. However, a significant barrier to fully leveraging these advances is the difficulty associated with assembling the extremely high AT content DNA constructs required for modifying the P. falciparum genome. These are frequently unstable in commonly-used circular plasmids. We address this bottleneck by devising a DNA assembly framework leveraging the improved reliability with which large AT-rich regions can be efficiently manipulated in linear plasmids. This framework integrates several key functional genetics outcomes via CRISPR/Cas9 and other methods from a common, validated framework. Overall, this molecular toolkit enables P. falciparum genetics broadly and facilitates deeper interrogation of parasite genes involved in diverse biological processes.
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Affiliation(s)
- Armiyaw S Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Bridget A Wall
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Jeffrey C Wagner
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Suresh M Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Stephen J Goldfless
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA.
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14
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Nair RR, Tibbit C, Thompson D, McLeod R, Nakhuda A, Simon MM, Baloh RH, Fisher EMC, Isaacs AM, Cunningham TJ. Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs. Methods 2020; 191:15-22. [PMID: 32721467 PMCID: PMC8215685 DOI: 10.1016/j.ymeth.2020.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/15/2020] [Accepted: 07/16/2020] [Indexed: 11/29/2022] Open
Abstract
Large GGGGCC repeat expansions within BAC vectors are highly unstable. CRISPR-Cas9 screening of BAC vector clones to determine repeat length. CRISPR-Cas9 cloning of GGGGCC repeat expansion regions into the linear pJazz vector. pJazz dramatically stabilizes GGGGCC repeat expansions over 4 kb in length.
Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such repeats in bacterial vectors, especially with large repeat expansions. Designing constructs for more precise genome engineering projects, such as engineering knock-in mice, proves a greater challenge still, since these unstable repeats require numerous cloning steps in order to introduce homology arms or selection cassettes. Here, we report our efforts to clone a large hexanucleotide repeat in the C9orf72 gene, originating from within a BAC construct, derived from a C9orf72-ALS patient. We provide detailed methods for efficient repeat sizing and growth conditions in bacteria to facilitate repeat retention during growth and sub-culturing. We report that sub-cloning into a linear vector dramatically improves stability, but is dependent on the relative orientation of DNA replication through the repeat, consistent with previous studies. We envisage the findings presented here provide a relatively straightforward route to maintaining large-range microsatellite repeat-expansions, for efficient cloning into vectors.
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Affiliation(s)
- Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Charlotte Tibbit
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Ross McLeod
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Asif Nakhuda
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Robert H Baloh
- Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK; UK Dementia Research Institute at UCL, UCL Institute of Neurology, London WC1N 3BG, UK
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15
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Üstüntanır Dede AF, Arslanyolu M. Construction and dynamic characterization of a Tetrahymena thermophila macronuclear artificial chromosome. Gene 2020; 748:144697. [PMID: 32325092 DOI: 10.1016/j.gene.2020.144697] [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: 12/16/2019] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 11/18/2022]
Abstract
Artificial chromosomes were previously generated for use in bacteria, protists, yeast and human cells. A Tetrahymena thermophila artificial chromosome could serve as a versatile platform to study diverse aspects of Tetrahymena biology and beyond. Here, we placed a C3-type rDNA replication origin and telomere sequences from T. thermophila into a pNeo4 vector, producing the first T. thermophila macronuclear artificial chromosome (TtAC1). Circular or linear forms of TtAC1 can be stably transformed into both vegetative and conjugative T. thermophila cells. Linear TtAC1 was stably double in copy number under antibiotic selection, but its copy number was dropping without antibiotic selection pressure. Southern blot, Real-Time PCR and E. coli retransformation analyses together showed that TtAC1 vector did not integrate into the macronuclear genome, and was maintained as a linear or a circular chromosome in T. thermophila macronucleus under antibiotic selection. The use of TtAC1 for recombinant protein production was demonstrated by western blot analysis of a secreted 27 kDa TtsfGFP-12XHis protein. We present the first macronuclear artificial chromosome with species-specific chromosomal elements for use in T. thermophila studies and to aid broad recombinant biotechnology applications.
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Affiliation(s)
- Ayça Fulya Üstüntanır Dede
- Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir 26470, Turkey
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskisehir 26470, Turkey.
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16
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Marr EJ, Milne RM, Anar B, Girling G, Schwach F, Mooney JP, Nahrendorf W, Spence PJ, Cunningham D, Baker DA, Langhorne J, Rayner JC, Billker O, Bushell ES, Thompson J. An enhanced toolkit for the generation of knockout and marker-free fluorescent Plasmodium chabaudi. Wellcome Open Res 2020; 5:71. [PMID: 32500098 PMCID: PMC7236590 DOI: 10.12688/wellcomeopenres.15587.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 11/20/2022] Open
Abstract
The rodent parasite
Plasmodium chabaudi is an important
in vivo model of malaria. The ability to produce chronic infections makes it particularly useful for investigating the development of anti-
Plasmodium immunity, as well as features associated with parasite virulence during both the acute and chronic phases of infection.
P. chabaudi also undergoes asexual maturation (schizogony) and erythrocyte invasion in culture, so offers an experimentally-amenable
in vivo to
in vitro model for studying gene function and drug activity during parasite replication. To extend the usefulness of this model, we have further optimised transfection protocols and plasmids for
P. chabaudi and generated stable, fluorescent lines that are free from drug-selectable marker genes. These mother-lines show the same infection dynamics as wild-type parasites throughout the lifecycle in mice and mosquitoes; furthermore, their virulence can be increased by serial blood passage and reset by mosquito transmission. We have also adapted the large-insert, linear
PlasmoGEM vectors that have revolutionised the scale of experimental genetics in another rodent malaria parasite and used these to generate barcoded
P. chabaudi gene-deletion and –tagging vectors for transfection in our fluorescent
P. chabaudi mother-lines. This produces a tool-kit of
P. chabaudi lines, vectors and transfection approaches that will be of broad utility to the research community.
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Affiliation(s)
- Edward J Marr
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Rachel M Milne
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Burcu Anar
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Gareth Girling
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Frank Schwach
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jason P Mooney
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, EH25 9RG, UK
| | - Wiebke Nahrendorf
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Philip J Spence
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | | | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Julian C Rayner
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Oliver Billker
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Ellen S Bushell
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Joanne Thompson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
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17
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Marr EJ, Milne RM, Anar B, Girling G, Schwach F, Mooney JP, Nahrendorf W, Spence PJ, Cunningham D, Baker DA, Langhorne J, Rayner JC, Billker O, Bushell ES, Thompson J. An enhanced toolkit for the generation of knockout and marker-free fluorescent Plasmodium chabaudi. Wellcome Open Res 2020; 5:71. [PMID: 32500098 PMCID: PMC7236590 DOI: 10.12688/wellcomeopenres.15587.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 08/17/2023] Open
Abstract
The rodent parasite Plasmodium chabaudi is an important in vivo model of malaria. The ability to produce chronic infections makes it particularly useful for investigating the development of anti- Plasmodium immunity, as well as features associated with parasite virulence during both the acute and chronic phases of infection. P. chabaudi also undergoes asexual maturation (schizogony) and erythrocyte invasion in culture, so offers an experimentally-amenable in vivo to in vitro model for studying gene function and drug activity during parasite replication. To extend the usefulness of this model, we have further optimised transfection protocols and plasmids for P. chabaudi and generated stable, fluorescent lines that are free from drug-selectable marker genes. These mother-lines show the same infection dynamics as wild-type parasites throughout the lifecycle in mice and mosquitoes; furthermore, their virulence can be increased by serial blood passage and reset by mosquito transmission. We have also adapted the large-insert, linear PlasmoGEM vectors that have revolutionised the scale of experimental genetics in another rodent malaria parasite and used these to generate barcoded P. chabaudi gene-deletion and -tagging vectors for transfection in our fluorescent P. chabaudi mother-lines. This produces a tool-kit of P. chabaudi lines, vectors and transfection approaches that will be of broad utility to the research community.
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Affiliation(s)
- Edward J Marr
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Rachel M Milne
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Burcu Anar
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Gareth Girling
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Frank Schwach
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jason P Mooney
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, EH25 9RG, UK
| | - Wiebke Nahrendorf
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | - Philip J Spence
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
| | | | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Julian C Rayner
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Oliver Billker
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Ellen S Bushell
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Joanne Thompson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh, EH9 3FL, UK
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18
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Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy. Cell 2020; 178:521-535.e23. [PMID: 31348885 DOI: 10.1016/j.cell.2019.07.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 04/19/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Intracellular accumulation of misfolded proteins causes toxic proteinopathies, diseases without targeted therapies. Mucin 1 kidney disease (MKD) results from a frameshift mutation in the MUC1 gene (MUC1-fs). Here, we show that MKD is a toxic proteinopathy. Intracellular MUC1-fs accumulation activated the ATF6 unfolded protein response (UPR) branch. We identified BRD4780, a small molecule that clears MUC1-fs from patient cells, from kidneys of knockin mice and from patient kidney organoids. MUC1-fs is trapped in TMED9 cargo receptor-containing vesicles of the early secretory pathway. BRD4780 binds TMED9, releases MUC1-fs, and re-routes it for lysosomal degradation, an effect phenocopied by TMED9 deletion. Our findings reveal BRD4780 as a promising lead for the treatment of MKD and other toxic proteinopathies. Generally, we elucidate a novel mechanism for the entrapment of misfolded proteins by cargo receptors and a strategy for their release and anterograde trafficking to the lysosome.
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19
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Abstract
TelN and tos are a unique DNA linearization unit isolated from bacteriophage N15. While being transferable, the TelN cleaving-rejoining activities remained stable to function on tos in both bacterial and mammalian environments. However, TelN contribution in linear plasmid replication in mammalian cells remains unknown. Herein, we investigated the association of TelN in linear tos-containing DNA (tos-DNA) replication in mammalian cells. Additionally, the mammalian origin of replication (ori) that is well-known to initiate the replication event of plasmid vectors was also studied. In doing so, we identified that both TelN and mammalian initiation sites were essential for the replication of linear tos-DNA, determined by using methylation sensitive DpnI/MboI digestion and polymerase chain reaction (PCR) amplification approaches. Furthermore, we engineered the linear tos-DNA to be able to retain in mammalian cells using S/MAR technology. The resulting S/MAR containing tos-DNA was robust for at least 15 days, with (1) continuous tos-DNA replication, (2) correct splicing of gene transcripts, and (3) stable exogenous gene expression that was statistically comparable to the endogenous gene expression level. Understanding the activities of TelN and tos in mammalian cells can potentially provide insights for adapting this simple DNA linearization unit in developing novel genetic engineering tools, especially to the eukaryotic telomere/telomerase study.
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Affiliation(s)
- Pei Sheng Liew
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Tze Hao Tan
- Faculty of Science, Kyushu University, Ito campus, Fukuoka 819-0395, Japan
| | - Yin Cheng Wong
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Edmund Ui Hang Sim
- Faculty of Resource Sciences and Technology, University Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | - Choon Weng Lee
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kumaran Narayanan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
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20
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Systematic microsatellite repeat expansion cloning and validation. Hum Genet 2020; 139:1233-1246. [PMID: 32277284 DOI: 10.1007/s00439-020-02165-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/04/2020] [Indexed: 10/24/2022]
Abstract
Approximately 3% of the human genome is composed of short tandem repeat (STR) DNA sequence known as microsatellites, which can be found in both coding and non-coding regions. When associated with genic regions, expansion of microsatellite repeats beyond a critical threshold causes dozens of neurological repeat expansion disorders. To better understand the molecular pathology of repeat expansion disorders, precise cloning of microsatellite repeat sequence and expansion size is highly valuable. Unfortunately, cloning repeat expansions is often challenging and presents a significant bottleneck to practical investigation. Here, we describe a clear method for seamless and systematic cloning of practically any microsatellite repeat expansion. We use cloning and expansion of GGGGCC repeats, which are the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as an example. We employ a recursive directional ligation (RDL) technique to build multiple GGGGCC repeat-containing vectors. We describe methods to validate repeat expansion cloning, including diagnostic restriction digestion, PCR across the repeat, and next-generation long-read MinION nanopore sequencing. Validated cloning of microsatellite repeats beyond the critical expansion threshold can facilitate step-by-step characterization of disease mechanisms at the cellular and molecular level.
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21
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Polino AJ, Nasamu AS, Niles JC, Goldberg DE. Assessment of Biological Role and Insight into Druggability of the Plasmodium falciparum Protease Plasmepsin V. ACS Infect Dis 2020; 6:738-746. [PMID: 32069391 PMCID: PMC7155168 DOI: 10.1021/acsinfecdis.9b00460] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Indexed: 01/05/2023]
Abstract
Upon infecting a red blood cell (RBC), the malaria parasite Plasmodium falciparum drastically remodels its host by exporting hundreds of proteins into the RBC cytosol. This protein export program is essential for parasite survival. Hence export-related proteins could be potential drug targets. One essential enzyme in this pathway is plasmepsin V (PMV), an aspartic protease that processes export-destined proteins in the parasite endoplasmic reticulum (ER) at the Plasmodium export element (PEXEL) motif. Despite long-standing interest in this enzyme, functional studies have been hindered by the inability of previous technologies to produce a regulatable lethal depletion of PMV. To overcome this technical barrier, we designed a system for stringent post-transcriptional regulation allowing a tightly controlled, tunable knockdown of PMV. Using this system, we found that PMV must be dramatically depleted to affect parasite growth, suggesting the parasite maintains this enzyme in substantial excess. Surprisingly, depletion of PMV arrested parasite growth immediately after RBC invasion, significantly before the death from exported protein deficit that has previously been described. The data suggest that PMV inhibitors can halt parasite growth at two distinct points in the parasite life cycle. However, overcoming the functional excess of PMV in the parasite may require inhibitor concentrations far beyond the enzyme's IC50.
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Affiliation(s)
- Alexander J Polino
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Armiyaw S Nasamu
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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22
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Liew PS, Chen Q, Ng AWR, Chew YC, Ravin NV, Sim EUH, Lee CW, Narayanan K. Phage N15 protelomerase resolves its tos recognition site into hairpin telomeres within mammalian cells. Anal Biochem 2019; 583:113361. [DOI: 10.1016/j.ab.2019.113361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
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23
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Nagappa LK, Singh D, Dey S, Kumar KA, Balaram H. Biochemical and physiological investigations on adenosine 5' monophosphate deaminase from Plasmodium spp. Mol Microbiol 2019; 112:699-717. [PMID: 31132185 DOI: 10.1111/mmi.14313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 11/29/2022]
Abstract
The interplay between ATP generating and utilizing pathways in a cell is responsible for maintaining cellular ATP/energy homeostasis that is reflected by Adenylate Energy Charge (AEC) ratio. Adenylate kinase (AK), that catalyzes inter-conversion of ADP, ATP and AMP, plays a major role in maintaining AEC and is regulated by cellular AMP levels. Hence, the enzymes AMP deaminase (AMPD) and nucleotidases, which catabolize AMP, indirectly regulate AK activity and in-turn affect AEC. Here, we present the first report on AMPD from Plasmodium, the causative agent of malaria. The recombinant enzyme expressed in Saccharomyces cerevisiae was studied using functional complementation assay and residues vital for enzyme activity have been identified. Similarities and differences between Plasmodium falciparum AMPD (PfAMPD) and its homologs from yeast, Arabidopsis and humans are also discussed. The AMPD gene was deleted in the murine malaria parasite P. berghei and was found to be dispensable during all stages of the parasite life cycle. However, when episomal expression was attempted, viable parasites were not obtained, suggesting that perturbing AMP homeostasis by over-expressing AMPD might be lethal. As AMPD is known to be allosterically modulated by ATP, GTP and phosphate, allosteric activators of PfAMPD could be developed as anti-parasitic agents.
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Affiliation(s)
- Lakshmeesha Kempaiah Nagappa
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Dipti Singh
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sandeep Dey
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Kota Arun Kumar
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
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24
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Pasin F, Menzel W, Daròs J. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1010-1026. [PMID: 30677208 PMCID: PMC6523588 DOI: 10.1111/pbi.13084] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/09/2018] [Accepted: 01/15/2019] [Indexed: 05/12/2023]
Abstract
Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T-DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus-based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next-generation virus-based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.
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Affiliation(s)
- Fabio Pasin
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Wulf Menzel
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)ValenciaSpain
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25
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Yoshimura J, Ichikawa K, Shoura MJ, Artiles KL, Gabdank I, Wahba L, Smith CL, Edgley ML, Rougvie AE, Fire AZ, Morishita S, Schwarz EM. Recompleting the Caenorhabditis elegans genome. Genome Res 2019; 29:1009-1022. [PMID: 31123080 PMCID: PMC6581061 DOI: 10.1101/gr.244830.118] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
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Affiliation(s)
- Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Massa J Shoura
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Lamia Wahba
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Cheryl L Smith
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Mark L Edgley
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Ann E Rougvie
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55454, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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26
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Trepotec Z, Geiger J, Plank C, Aneja MK, Rudolph C. Segmented poly(A) tails significantly reduce recombination of plasmid DNA without affecting mRNA translation efficiency or half-life. RNA (NEW YORK, N.Y.) 2019; 25:507-518. [PMID: 30647100 PMCID: PMC6426288 DOI: 10.1261/rna.069286.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/22/2018] [Indexed: 05/27/2023]
Abstract
Extensive research in the past decade has brought mRNA closer to the clinical realization of its therapeutic potential. One common structural feature for all cellular messenger RNAs is a poly(A) tail, which can either be brought in cotranscriptionally via the DNA template (plasmid- or PCR-based) or added to the mRNA in a post-transcriptional enzymatic process. Plasmids containing poly(A) regions recombine in E. coli, resulting in extensive shortening of the poly(A) tail. Using a segmented poly(A) approach, we could significantly reduce recombination of plasmids in E. coli without any negative effect on mRNA half-life and protein expression. This effect was independent of the coding sequence. A segmented poly(A) tail is characterized in that it consists of at least two A-containing elements, each defined as a nucleotide sequence consisting of 40-60 adenosines, separated by a spacer element of different length. Furthermore, reducing the spacer length between the poly(A) segments resulted in higher translation efficiencies compared to homogeneous poly(A) tail and reduced recombination (depending upon the choice of spacer nucleotide). Our results demonstrate the superior potential of segmented poly(A) tails compared to the conventionally used homogeneous poly(A) tails with respect to recombination of the plasmids and the resulting mRNA performance (half-life and translational efficiency).
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Affiliation(s)
- Zeljka Trepotec
- Department of Pediatrics, Ludwig-Maximilian-University of Munich, 80337 Munich, Germany
| | | | - Christian Plank
- Ethris GmbH, Planegg, 82152 Planegg, Germany
- Institute of Molecular Immunology and Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | | | - Carsten Rudolph
- Department of Pediatrics, Ludwig-Maximilian-University of Munich, 80337 Munich, Germany
- Ethris GmbH, Planegg, 82152 Planegg, Germany
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Kempaiah Nagappa L, Satha P, Govindaraju T, Balaram H. Phosphoglycolate phosphatase is a metabolic proofreading enzyme essential for cellular function in Plasmodium berghei. J Biol Chem 2019; 294:4997-5007. [PMID: 30700551 PMCID: PMC6442027 DOI: 10.1074/jbc.ac118.007143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum (Pf) 4-nitrophenylphosphatase has been shown previously to be involved in vitamin B1 metabolism. Here, conducting a BLASTp search, we found that 4-nitrophenylphosphatase from Pf has significant homology with phosphoglycolate phosphatase (PGP) from mouse, human, and yeast, prompting us to reinvestigate the biochemical properties of the Plasmodium enzyme. Because the recombinant PfPGP enzyme is insoluble, we performed an extended substrate screen and extensive biochemical characterization of the recombinantly expressed and purified homolog from Plasmodium berghei (Pb), leading to the identification of 2-phosphoglycolate and 2-phospho-L-lactate as the relevant physiological substrates of PbPGP. 2-Phosphoglycolate is generated during repair of damaged DNA ends, 2-phospho-L-lactate is a product of pyruvate kinase side reaction, and both potently inhibit two key glycolytic enzymes, triosephosphate isomerase and phosphofructokinase. Hence, PGP-mediated clearance of these toxic metabolites is vital for cell survival and functioning. Our results differ significantly from those in a previous study, wherein the PfPGP enzyme has been inferred to act on 2-phospho-D-lactate and not on the L isomer. Apart from resolving the substrate specificity conflict through direct in vitro enzyme assays, we conducted PGP gene knockout studies in P. berghei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summary, our findings establish PbPGP as an essential enzyme for normal physiological function in P. berghei and suggest that drugs that specifically inhibit Plasmodium PGP may hold promise for use in anti-malarial therapies.
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Affiliation(s)
| | - Pardhasaradhi Satha
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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A novel method for cloning of coding sequences of highly toxic proteins. Biochim Biophys Acta Gen Subj 2018; 1863:521-527. [PMID: 30578833 DOI: 10.1016/j.bbagen.2018.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022]
Abstract
BACKGROUND During standard gene cloning, the recombinant protein appearing in bacteria as the result of expression leakage very often inhibits cell proliferation leading to blocking of the cloning procedure. Although different approaches can reduce transgene basal expression, the recombinant proteins, which even in trace amounts inhibit bacterial growth, can completely prevent the cloning process. METHODS Working to solve the problem of DNase II-like cDNA cloning, we developed a novel cloning approach. The method is based on separate cloning of the 5' and 3' fragments of target cDNA into a vector in such a way that the short Multiple Cloning Site insertion remaining between both fragments changes the reading frame and prevents translation of mRNA arising as a result of promoter leakage. Subsequently, to get the vector with full, uninterrupted Open Reading Frame, the Multiple Cloning Site insertion is removed by in vitro restriction/ligation reactions, utilizing the unique restriction site present in native cDNA. RESULTS Using this designed method, we cloned a coding sequence of AcDNase II that is extremely toxic for bacteria cells. Then, we demonstrated the usefulness of the construct prepared in this way for overexpression of AcDNase II in eukaryotic cells. CONCLUSIONS The designed method allows cloning of toxic protein coding sequences that cannot be cloned by standard methods. GENERAL SIGNIFICANCE Cloning of cDNAs encoding toxic proteins is still a troublesome problem that hinders the progress of numerous studies. The method described here is a convenient solution to cloning problems that are common in research on toxic proteins.
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Ávila-Pérez G, Nogales A, Martín V, Almazán F, Martínez-Sobrido L. Reverse Genetic Approaches for the Generation of Recombinant Zika Virus. Viruses 2018; 10:E597. [PMID: 30384426 PMCID: PMC6266887 DOI: 10.3390/v10110597] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/26/2018] [Accepted: 10/28/2018] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV) is an emergent mosquito-borne member of the Flaviviridae family that was responsible for a recent epidemic in the Americas. ZIKV has been associated with severe clinical complications, including neurological disorder such as Guillain-Barré syndrome in adults and severe fetal abnormalities and microcephaly in newborn infants. Given the significance of these clinical manifestations, the development of tools and reagents to study the pathogenesis of ZIKV and to develop new therapeutic options are urgently needed. In this respect, the implementation of reverse genetic techniques has allowed the direct manipulation of the viral genome to generate recombinant (r)ZIKVs, which have provided investigators with powerful systems to answer important questions about the biology of ZIKV, including virus-host interactions, the mechanism of transmission and pathogenesis or the function of viral proteins. In this review, we will summarize the different reverse genetic strategies that have been implemented, to date, for the generation of rZIKVs and the applications of these platforms for the development of replicon systems or reporter-expressing viruses.
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Affiliation(s)
- Ginés Ávila-Pérez
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Verónica Martín
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 3 Darwin street, 28049 Madrid, Spain.
| | - Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 3 Darwin street, 28049 Madrid, Spain.
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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Purcell O, Cao J, Müller IE, Chen YC, Lu TK. Artificial Repeat-Structured siRNA Precursors as Tunable Regulators for Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:2403-2412. [PMID: 30176724 DOI: 10.1021/acssynbio.8b00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA interference (RNAi) is widely used as a research tool for studying biological systems and implementing artificial genetic circuits that function by modulating RNA concentrations. Here we engineered Saccharomyces cerevisiae containing a heterologous Saccharomyces castelli RNAi system as a test-bed for RNAi-based circuits. Unlike prior approaches, we describe a strategy that leverages repeat-structured siRNA precursors with incrementally sized stems formed from 23 bp-repeats to achieve modular RNAi-based gene regulation. These enable repression strength to be tuned in a systematic manner by changing the size of the siRNA precursor hairpin stem, without modifying the number or sequence of target sites in the target RNA. We demonstrate that this hairpin-based regulation is able to target both cytoplasmic and nuclear localized RNAs and is stable over extended growth periods. This platform enables the targeting of cellular RNAs as a tunable regulatory layer for sophisticated gene circuits in Saccharomyces cerevisiae.
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Affiliation(s)
- Oliver Purcell
- Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jicong Cao
- Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Isaak E. Müller
- Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Microbiology Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ying-Chou Chen
- Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Ratnayake D, Newman M, Lardelli M. Degenerate codon mixing for PCR-based manipulation of highly repetitive sequences. BMC Res Notes 2018; 11:202. [PMID: 29587822 PMCID: PMC5870680 DOI: 10.1186/s13104-018-3298-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/20/2018] [Indexed: 11/24/2022] Open
Abstract
Objective Repeat expansion of polyglutamine tracks leads to a group of inherited human neurodegenerative disorders. Studying such repetitive sequences is required to gain insight into the pathophysiology of these diseases. PCR-based manipulation of repetitive sequences, however, is challenging due to the absence of unique primer binding sites or the generation of non-specific products. Results We have utilised the degeneracy of the genetic code to generate a polyglutamine sequence with low repeat similarity. This strategy allowed us to use conventional PCR to generate multiple constructs with approximately defined numbers of glutamine repeats. We then used these constructs to measure the in vivo variation in autophagic degradation activity related to the different numbers of glutamine repeats, providing an example of their applicability to study repeat expansion diseases. Our simple and easily generalised method of generating low repetition DNA sequences coding for uniform stretches of amino acid residues provides a strategy for generating particular lengths of polyglutamine tracts using standard PCR and cloning protocols. Electronic supplementary material The online version of this article (10.1186/s13104-018-3298-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dhanushika Ratnayake
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.,Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, 3800, Australia
| | - Morgan Newman
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Michael Lardelli
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
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Zika Virus Encoding Nonglycosylated Envelope Protein Is Attenuated and Defective in Neuroinvasion. J Virol 2017; 91:JVI.01348-17. [PMID: 28931684 DOI: 10.1128/jvi.01348-17] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/13/2017] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV), a mosquito-transmitted flavivirus responsible for sporadic outbreaks of mild and febrile illness in Africa and Asia, reemerged in the last decade causing serious human diseases, including microcephaly, congenital malformations, and Guillain-Barré syndrome. Although genomic and phylogenetic analyses suggest that genetic evolution may have led to the enhanced virulence of ZIKV, experimental evidence supporting the role of specific genetic changes in virulence is currently lacking. One sequence motif, VNDT, containing an N-linked glycosylation site in the envelope (E) protein, is polymorphic; it is absent in many of the African isolates but present in all isolates from the recent outbreaks. In the present study, we investigated the roles of this sequence motif and glycosylation of the E protein in the pathogenicity of ZIKV. We first constructed a stable full-length cDNA clone of ZIKV in a novel linear vector from which infectious virus was recovered. The recombinant ZIKV generated from the infectious clone, which contains the VNDT motif, is highly pathogenic and causes lethality in a mouse model. In contrast, recombinant viruses from which the VNDT motif is deleted or in which the N-linked glycosylation site is mutated by single-amino-acid substitution are highly attenuated and nonlethal. The mutant viruses replicate poorly in the brains of infected mice when inoculated subcutaneously but replicate well following intracranial inoculation. Our findings provide the first evidence that N-linked glycosylation of the E protein is an important determinant of ZIKV virulence and neuroinvasion.IMPORTANCE The recent emergence of Zika virus (ZIKV) in the Americas has caused major worldwide public health concern. The virus appears to have gained significant pathogenicity, causing serious human diseases, including microcephaly and Guillain-Barré syndrome. The factors responsible for the emergence of pathogenic ZIKV are not understood at this time, although genetic changes have been shown to facilitate virus transmission. All isolates from the recent outbreaks contain an N-linked glycosylation site within the viral envelope (E) protein, whereas many isolates of the African lineage virus lack this site. To elucidate the functional significance of glycosylation in ZIKV pathogenicity, recombinant ZIKVs from infectious clones with or without the glycan on the E protein were generated. ZIKVs lacking the glycan were highly attenuated for the ability to cause mortality in a mouse model and were severely compromised for neuroinvasion. Our studies suggest glycosylation of the E protein is an important factor contributing to ZIKV pathogenicity.
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HOSSEINI FARASH BR, MOHEBALI M, KAZEMI B, HAJJARAN H, AKHOUNDI B, RAOOFIAN R, FATA A, MOJARRAD M, SHARIFI-YAZDI MK. Cloning of K26 Hydrophilic Antigen from Iranian Strain of Leishmania infantum. IRANIAN JOURNAL OF PUBLIC HEALTH 2017; 46:1359-1365. [PMID: 29308379 PMCID: PMC5750347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Visceral leishmaniasis (VL) caused by Leishmania infantum is the most severe form of leishmaniasis in Iran, which causes a high mortality rate in the case of inaccurate diagnosis and treatment. This study aimed to clone of K26 gene from Iranian strain of L. infantum and register the sequencing results in Genbank to facilitate the preparation a new K26 antigen for the detection of L. infantum infection. METHODS L. infantum was obtained from an infected domestic dog in Meshkin-Shahr area from northwestern Iran in 2015. Canine visceral leishmaniasis was confirmed by direct agglutination test (DAT), rK39 dipstick and parasitological methods. L. infantum was confirmed by N-acetyl glucosamine -1-phosphate transferase (nagt)-PCR and its sequencing. The band of interest for k26 form Iranian strain of L. infantum was purified by gel extraction kit after PCR amplification and then ligated into pBluescript II SK (+) and pET-32a (+), respectively. The sequences of recombinant plasmids were analyzed and submitted to Genbank. RESULTS The submission of rk26 nucleotide sequence was performed to the GeneBank/NCBI Data Base under accession number KY212883. The related gene was showed a homology about 99% to L. chagasi and L. infantum k26 gene, while the level of homology in comparison with different strains of L. donovani ranged from 84-94%. CONCLUSION The successful rk26 cloning into an expression vector performed in this study could help to produce a new recombinant antigen for serodiagnosis of VL especially in areas where L. infantum is the main causative agent.
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Affiliation(s)
- Bibi Razieh HOSSEINI FARASH
- Dept. of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi MOHEBALI
- Dept. of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran,Center for Research of Endemic Parasites of Iran, Tehran University of Medical Sciences, Tehran, Iran,Corresponding Author:
| | - Bahram KAZEMI
- Dept. of Biotechnology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Homa HAJJARAN
- Dept. of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnaz AKHOUNDI
- Dept. of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza RAOOFIAN
- Legal Medicine Research Center, Iranian Legal Medicine Organization, Tehran, Iran
| | - Abdolmajid FATA
- Dept. of Medical Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid MOJARRAD
- Dept. of Medical Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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A Plasmodium plasma membrane reporter reveals membrane dynamics by live-cell microscopy. Sci Rep 2017; 7:9740. [PMID: 28851956 PMCID: PMC5575152 DOI: 10.1038/s41598-017-09569-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/26/2017] [Indexed: 11/08/2022] Open
Abstract
During asexual replication within the Anopheles mosquito and their vertebrate host, Plasmodium parasites depend on the generation of a massive amount of new plasma membrane to produce thousands of daughter parasites. How the parasite plasma membrane (PPM) is formed has mostly been studied by electron microscopy, which does not allow an insight into the dynamics of this process. We generated a Plasmodium berghei reporter parasite line by GFP-tagging of a non-essential PPM-localized protein, and followed plasma membrane development in living parasites through the entire Plasmodium life cycle. By generating double-fluorescent parasites in which the PPM is visualized in combination with the parasite endoplasmic reticulum, we show that membrane contact sites are formed between both membrane systems during oocyst and liver stage development that might be used to deliver lipids to the dramatically expanding PPM. In conclusion, we have established a powerful tool to follow PPM development in living parasites, which promises to greatly expand our knowledge of membrane biology in the Plasmodium parasite.
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Zhang S, Zou Z, Kreth J, Merritt J. Recombineering in Streptococcus mutans Using Direct Repeat-Mediated Cloning-Independent Markerless Mutagenesis (DR-CIMM). Front Cell Infect Microbiol 2017; 7:202. [PMID: 28589101 PMCID: PMC5440470 DOI: 10.3389/fcimb.2017.00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/08/2017] [Indexed: 01/13/2023] Open
Abstract
Studies of the dental caries pathogen Streptococcus mutans have benefitted tremendously from its sophisticated genetic system. As part of our own efforts to further improve upon the S. mutans genetic toolbox, we previously reported the development of the first cloning-independent markerless mutagenesis (CIMM) system for S. mutans and illustrated how this approach could be adapted for use in many other organisms. The CIMM approach only requires overlap extension PCR (OE-PCR) protocols to assemble counterselectable allelic replacement mutagenesis constructs, and thus greatly increased the speed and efficiency with which markerless mutations could be introduced into S. mutans. Despite its utility, the system is still subject to a couple limitations. Firstly, CIMM requires negative selection with the conditionally toxic phenylalanine analog p-chlorophenylalanine (4-CP), which is efficient, but never perfect. Typically, 4-CP negative selection results in a small percentage of naturally resistant background colonies. Secondly, CIMM requires two transformation steps to create markerless mutants. This can be inherently problematic if the transformability of the strain is negatively impacted after the first transformation step, which is used to insert the counterselection cassette at the mutation site on the chromosome. In the current study, we develop a next-generation counterselection cassette that eliminates 4-CP background resistance and combine this with a new direct repeat-mediated cloning-independent markerless mutagenesis (DR-CIMM) system to specifically address the limitations of the prior approach. DR-CIMM is even faster and more efficient than CIMM for the creation of all types of deletions, insertions, and point mutations and is similarly adaptable for use in a wide range of genetically tractable bacteria.
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Affiliation(s)
- Shan Zhang
- Department of Restorative Dentistry, Oregon Health and Science UniversityPortland, OR, United States.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Zhengzhong Zou
- Department of Restorative Dentistry, Oregon Health and Science UniversityPortland, OR, United States
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health and Science UniversityPortland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science UniversityPortland, OR, United States.,Department of Molecular Microbiology and Immunology, Oregon Health and Science UniversityPortland, OR, United States
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Koussis K, Goulielmaki E, Chalari A, Withers-Martinez C, Siden-Kiamos I, Matuschewski K, Loukeris TG. Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host. PLoS One 2017; 12:e0170260. [PMID: 28107409 PMCID: PMC5249076 DOI: 10.1371/journal.pone.0170260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/01/2017] [Indexed: 12/26/2022] Open
Abstract
Site-2 proteases (S2P) belong to the M50 family of metalloproteases, which typically perform essential roles by mediating activation of membrane–bound transcription factors through regulated intramembrane proteolysis (RIP). Protease-dependent liberation of dormant transcription factors triggers diverse cellular responses, such as sterol regulation, Notch signalling and the unfolded protein response. Plasmodium parasites rely on regulated proteolysis for controlling essential pathways throughout the life cycle. In this study we examine the Plasmodium-encoded S2P in a murine malaria model and show that it is expressed in all stages of Plasmodium development. Localisation studies by endogenous gene tagging revealed that in all invasive stages the protein is in close proximity to the nucleus. Ablation of PbS2P by reverse genetics leads to reduced growth rates during liver and blood infection and, hence, virulence attenuation. Strikingly, absence of PbS2P was compatible with parasite life cycle progression in the mosquito and mammalian hosts under physiological conditions, suggesting redundant or dispensable roles in vivo.
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Affiliation(s)
- Konstantinos Koussis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Parasitology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Anna Chalari
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | | | - Inga Siden-Kiamos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Kai Matuschewski
- Parasitology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Thanasis G. Loukeris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
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De Bustos A, Cuadrado A, Jouve N. Sequencing of long stretches of repetitive DNA. Sci Rep 2016; 6:36665. [PMID: 27819354 PMCID: PMC5098217 DOI: 10.1038/srep36665] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/18/2016] [Indexed: 01/13/2023] Open
Abstract
Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.
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Affiliation(s)
- Alfredo De Bustos
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Angeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
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Conradie AM, Stassen L, Huismans H, Potgieter CA, Theron J. Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus. Virology 2016; 499:144-155. [PMID: 27657835 PMCID: PMC7172382 DOI: 10.1016/j.virol.2016.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 12/24/2022]
Abstract
In an effort to simplify and expand the utility of African horse sickness virus (AHSV) reverse genetics, different plasmid-based reverse genetics systems were developed. Plasmids containing cDNAs corresponding to each of the full-length double-stranded RNA genome segments of AHSV-4 under control of a T7 RNA polymerase promoter were co-transfected in cells expressing T7 RNA polymerase, and infectious AHSV-4 was recovered. This reverse genetics system was improved by reducing the required plasmids from 10 to five and resulted in enhanced virus recovery. Subsequently, a T7 RNA polymerase expression cassette was incorporated into one of the AHSV-4 rescue plasmids. This modified 5-plasmid set enabled virus recovery in BSR or L929 cells, thus offering the possibility to generate AHSV-4 in any cell line. Moreover, mutant and cross-serotype reassortant viruses were recovered. These plasmid DNA-based reverse genetics systems thus offer new possibilities for investigating AHSV biology and development of designer AHSV vaccine strains. An entirely plasmid-based reverse genetics system was developed for AHSV. Novel improvements were made that increases flexibility of AHSV plasmid-based reverse genetics. Virus recovery efficiency was increased by reducing plasmids required for rescue from 10 to 5. T7 RNA polymerase encoded by rescue plasmid backbone allows virus recovery in different cell lines. Recombinant wild-type AHSV, mutant and reassortant viruses were rescued from plasmid cDNA only.
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Affiliation(s)
- Andelé M Conradie
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
| | - Liesel Stassen
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
| | - Henk Huismans
- Department of Genetics, University of Pretoria, Pretoria 0002, South Africa
| | - Christiaan A Potgieter
- Deltamune (Pty) Ltd., Lyttelton, Centurion, South Africa; Department of Biochemistry, Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa
| | - Jacques Theron
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa.
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Grier AE, Burleigh S, Sahni J, Clough CA, Cardot V, Choe DC, Krutein MC, Rawlings DJ, Jensen MC, Scharenberg AM, Jacoby K. pEVL: A Linear Plasmid for Generating mRNA IVT Templates With Extended Encoded Poly(A) Sequences. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e306. [PMID: 27093168 PMCID: PMC5014522 DOI: 10.1038/mtna.2016.21] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/01/2016] [Indexed: 11/23/2022]
Abstract
Increasing demand for large-scale synthesis of in vitro transcribed (IVT) mRNA is being driven by the increasing use of mRNA for transient gene expression in cell engineering and therapeutic applications. An important determinant of IVT mRNA potency is the 3′ polyadenosine (poly(A)) tail, the length of which correlates with translational efficiency. However, present methods for generation of IVT mRNA rely on templates derived from circular plasmids or PCR products, in which homopolymeric tracts are unstable, thus limiting encoded poly(A) tail lengths to ~120 base pairs (bp). Here, we have developed a novel method for generation of extended poly(A) tracts using a previously described linear plasmid system, pJazz. We find that linear plasmids can successfully propagate poly(A) tracts up to ~500 bp in length for IVT mRNA production. We then modified pJazz by removing extraneous restriction sites, adding a T7 promoter sequence upstream from an extended multiple cloning site, and adding a unique type-IIS restriction site downstream from the encoded poly(A) tract to facilitate generation of IVT mRNA with precisely defined encoded poly(A) tracts and 3′ termini. The resulting plasmid, designated pEVL, can be used to generate IVT mRNA with consistent defined lengths and terminal residue(s).
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Affiliation(s)
- Alexandra E Grier
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA.,Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Immunology Department, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen Burleigh
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jaya Sahni
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Courtnee A Clough
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Victoire Cardot
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Dongwook C Choe
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Michelle C Krutein
- Pathology Department, University of Washington School of Medicine, Seattle, Washington, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA.,Immunology Department, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael C Jensen
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Bioengineering Department, University of Washington School of Medicine, Seattle, Washington, USA.,Immunology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew M Scharenberg
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA.,Immunology Department, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kyle Jacoby
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
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Mukai A, Ichiraku A, Horikawa K. Reliable handling of highly A/T-rich genomic DNA for efficient generation of knockin strains of Dictyostelium discoideum. BMC Biotechnol 2016; 16:37. [PMID: 27075750 PMCID: PMC4831088 DOI: 10.1186/s12896-016-0267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022] Open
Abstract
Background Social amoeba, Dictyostelium discoideum, is a well-established model organism for studying cellular physiology and developmental pattern formation. Its haploid genome facilitates functional analysis of genes by a single round of mutagenesis including targeted disruption. Although the efficient generation of knockout strains based on an intrinsically high homologous recombination rate has been demonstrated, successful reports for knockin strains have been limited. As social amoeba has an exceptionally high adenine and thymine (A/T)-content, conventional plasmid-based vector construction has been constrained due to deleterious deletion in E. coli. Results We describe here a simple and efficient strategy to construct GFP-knockin cassettes by using a linear DNA cloning vector derived from N15 bacteriophage. This allows reliable handling of DNA fragments whose A/T-content may be as high as 85 %, and which cannot be cloned into a circular plasmid. By optimizing the length of recombination arms, we successfully generate GFP-knockin strains for five genes involved in cAMP signalling, including a triple-colour knockin strain. Conclusions This robust strategy would be useful in handling DNA fragments with biased A/T-contents such as the genome of lower organisms and the promoter/terminator regions of higher organisms. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0267-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asuka Mukai
- Division of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima City, Tokushima, 770-8503, Japan
| | - Aya Ichiraku
- Division of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima City, Tokushima, 770-8503, Japan
| | - Kazuki Horikawa
- Division of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima City, Tokushima, 770-8503, Japan.
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41
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Abstract
The lambdoid phage N15 of Escherichia coli is very unusual among temperate phages in that its prophage is not integrated into the chromosome but is a linear plasmid molecule with covalently closed ends (telomeres). Upon infection, the phage DNA circularizes via cohesive ends, and then a special phage enzyme of the tyrosine recombinase family, protelomerase, cuts at another site and joins the ends, forming hairpin telomeres of the linear plasmid prophage. Replication of the N15 prophage is initiated at an internally located ori site and proceeds bidirectionally, resulting in the formation of duplicated telomeres. The N15 protelomerase cuts them, generating two linear plasmid molecules with hairpin telomeres. Stable inheritance of the plasmid prophage is ensured by a partitioning operon similar to the F factor sop operon. Unlike the F centromere, the N15 centromere consists of four inverted repeats dispersed in the genome. The multiplicity and dispersion of centromeres are required for efficient partitioning of a linear plasmid. The centromeres are located in the N15 genome regions involved in phage replication and control of lytic development, and binding of partition proteins at these sites regulates these processes. The family of N15-like linear phage-plasmids includes lambdoid phages ɸKO2 and pY54, as well as Myoviridae phages ΦHAP-1, VHML, VP882, Vp58.5, and vB_VpaM_MAR of marine gamma-proteobacteria. The genomes of these phages contain similar protelomerase genes, lysogeny control modules, and replication genes, suggesting that these phages may belong to a group diverged from a common ancestor.
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42
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Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. FRONTIERS IN PLANT SCIENCE 2016; 7:308. [PMID: 27047500 PMCID: PMC4806543 DOI: 10.3389/fpls.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/27/2016] [Indexed: 05/02/2023]
Abstract
The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
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Affiliation(s)
- Thomas K. Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Megan M. Nakashima
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Kevin L. Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Anupma Sharma
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Patrice S. Albert
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Ronghui Xu
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Paul Bilinski
- Department of Plant Sciences, University of California DavisDavis, CA, USA
| | - R. Kelly Dawe
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
| | | | - James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Gernot G. Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
- *Correspondence: Gernot G. Presting
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43
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Schwach F, Bushell E, Gomes AR, Anar B, Girling G, Herd C, Rayner JC, Billker O. PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites. Nucleic Acids Res 2015; 43:D1176-82. [PMID: 25593348 PMCID: PMC4383951 DOI: 10.1093/nar/gku1143] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Schwach
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Ellen Bushell
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Ana Rita Gomes
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Gareth Girling
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Colin Herd
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
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44
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Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC. Current and future resources for functional metagenomics. Front Microbiol 2015; 6:1196. [PMID: 26579102 PMCID: PMC4625089 DOI: 10.3389/fmicb.2015.01196] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/14/2015] [Indexed: 11/18/2022] Open
Abstract
Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries—physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.
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Affiliation(s)
- Kathy N Lam
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Jiujun Cheng
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo Waterloo, ON, Canada
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45
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McFarland KN, Liu J, Landrian I, Godiska R, Shanker S, Yu F, Farmerie WG, Ashizawa T. SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure. PLoS One 2015; 10:e0135906. [PMID: 26295943 PMCID: PMC4546671 DOI: 10.1371/journal.pone.0135906] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/28/2015] [Indexed: 12/02/2022] Open
Abstract
A large, non-coding ATTCT repeat expansion causes the neurodegenerative disorder, spinocerebellar ataxia type 10 (SCA10). In a subset of SCA10 patients, interruption motifs are present at the 5’ end of the expansion and strongly correlate with epileptic seizures. Thus, interruption motifs are a predictor of the epileptic phenotype and are hypothesized to act as a phenotypic modifier in SCA10. Yet, the exact internal sequence structure of SCA10 expansions remains unknown due to limitations in current technologies for sequencing across long extended tracts of tandem nucleotide repeats. We used the third generation sequencing technology, Single Molecule Real Time (SMRT) sequencing, to obtain full-length contiguous expansion sequences, ranging from 2.5 to 4.4 kb in length, from three SCA10 patients with different clinical presentations. We obtained sequence spanning the entire length of the expansion and identified the structure of known and novel interruption motifs within the SCA10 expansion. The exact interruption patterns in expanded SCA10 alleles will allow us to further investigate the potential contributions of these interrupting sequences to the pathogenic modification leading to the epilepsy phenotype in SCA10. Our results also demonstrate that SMRT sequencing is useful for deciphering long tandem repeats that pose as “gaps” in the human genome sequence.
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Affiliation(s)
- Karen N. McFarland
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Jilin Liu
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Ivette Landrian
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Ronald Godiska
- Lucigen Corporation, Middleton, Wisconsin, 53562, United States of America
| | - Savita Shanker
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
- * E-mail:
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46
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Rosengarten RD, Beltran PR, Shaulsky G. A deep coverage Dictyostelium discoideum genomic DNA library replicates stably in Escherichia coli. Genomics 2015; 106:249-55. [PMID: 26028264 DOI: 10.1016/j.ygeno.2015.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/11/2015] [Accepted: 05/18/2015] [Indexed: 01/18/2023]
Abstract
The natural history of the amoeba Dictyostelium discoideum has inspired scientific inquiry for seventy-five years. A genetically tractable haploid eukaryote, D. discoideum appeals as a laboratory model as well. However, certain rote molecular genetic tasks, such as PCR and cloning, are difficult due to the AT-richness and low complexity of its genome. Here we report on the construction of a ~20 fold coverage D. discoideum genomic library in Escherichia coli, cloning 4-10 kilobase partial restriction fragments into a linear vector. End-sequencing indicates that most clones map to the six chromosomes in an unbiased distribution. Over 70% of these clones contain at least one complete open reading frame. We demonstrate that individual clones and library composition are stable over multiple replication cycles. Our library will enable numerous molecular biological applications and the completion of additional species' genome sequences, and suggests a path towards the long-elusive goal of genetic complementation.
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Affiliation(s)
- Rafael D Rosengarten
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Pamela R Beltran
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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47
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Lam KN, Charles TC. Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. MICROBIOME 2015; 3:22. [PMID: 26056565 PMCID: PMC4459075 DOI: 10.1186/s40168-015-0086-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/01/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Clone libraries provide researchers with a powerful resource to study nucleic acid from diverse sources. Metagenomic clone libraries in particular have aided in studies of microbial biodiversity and function, and allowed the mining of novel enzymes. Libraries are often constructed by cloning large inserts into cosmid or fosmid vectors. Recently, there have been reports of GC bias in fosmid metagenomic libraries, and it was speculated to be a result of fragmentation and loss of AT-rich sequences during cloning. However, evidence in the literature suggests that transcriptional activity or gene product toxicity may play a role. RESULTS To explore possible mechanisms responsible for sequence bias in clone libraries, we constructed a cosmid library from a human microbiome sample and sequenced DNA from different steps during library construction: crude extract DNA, size-selected DNA, and cosmid library DNA. We confirmed a GC bias in the final cosmid library, and we provide evidence that the bias is not due to fragmentation and loss of AT-rich sequences but is likely occurring after DNA is introduced into Escherichia coli. To investigate the influence of strong constitutive transcription, we searched the sequence data for promoters and found that rpoD/σ(70) promoter sequences were underrepresented in the cosmid library. Furthermore, when we examined the genomes of taxa that were differentially abundant in the cosmid library relative to the original sample, we found the bias to be more correlated with the number of rpoD/σ(70) consensus sequences in the genome than with simple GC content. CONCLUSIONS The GC bias of metagenomic libraries does not appear to be due to DNA fragmentation. Rather, analysis of promoter sequences provides support for the hypothesis that strong constitutive transcription from sequences recognized as rpoD/σ(70) consensus-like in E. coli may lead to instability, causing loss of the plasmid or loss of the insert DNA that gives rise to the transcription. Despite widespread use of E. coli to propagate foreign DNA in metagenomic libraries, the effects of in vivo transcriptional activity on clone stability are not well understood. Further work is required to tease apart the effects of transcription from those of gene product toxicity.
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Affiliation(s)
- Kathy N. Lam
- Department of Biology, University of Waterloo, Waterloo, ON Canada
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48
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Burda PC, Roelli MA, Schaffner M, Khan SM, Janse CJ, Heussler VT. A Plasmodium phospholipase is involved in disruption of the liver stage parasitophorous vacuole membrane. PLoS Pathog 2015; 11:e1004760. [PMID: 25786000 PMCID: PMC4364735 DOI: 10.1371/journal.ppat.1004760] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/22/2015] [Indexed: 11/18/2022] Open
Abstract
The coordinated exit of intracellular pathogens from host cells is a process critical to the success and spread of an infection. While phospholipases have been shown to play important roles in bacteria host cell egress and virulence, their role in the release of intracellular eukaryotic parasites is largely unknown. We examined a malaria parasite protein with phospholipase activity and found it to be involved in hepatocyte egress. In hepatocytes, Plasmodium parasites are surrounded by a parasitophorous vacuole membrane (PVM), which must be disrupted before parasites are released into the blood. However, on a molecular basis, little is known about how the PVM is ruptured. We show that Plasmodium berghei phospholipase, PbPL, localizes to the PVM in infected hepatocytes. We provide evidence that parasites lacking PbPL undergo completely normal liver stage development until merozoites are produced but have a defect in egress from host hepatocytes. To investigate this further, we established a live-cell imaging-based assay, which enabled us to study the temporal dynamics of PVM rupture on a quantitative basis. Using this assay we could show that PbPL-deficient parasites exhibit impaired PVM rupture, resulting in delayed parasite egress. A wild-type phenotype could be re-established by gene complementation, demonstrating the specificity of the PbPL deletion phenotype. In conclusion, we have identified for the first time a Plasmodium phospholipase that is important for PVM rupture and in turn for parasite exit from the infected hepatocyte and therefore established a key role of a parasite phospholipase in egress. Leaving their host cell is a crucial process for intracellular pathogens, allowing successful infection of other cells and thereby spreading of infection. Plasmodium parasites infect hepatocytes and red blood cells, and inside these cells they are contained within a vacuole like many other intracellular pathogens. Before parasites can infect other cells, the surrounding parasitophorous vacuole membrane (PVM) needs to be ruptured. However, little is known about this process on a molecular level and Plasmodium proteins mediating lysis of the PVM during parasite egress have not so far been identified. In this study, we characterize a Plasmodium phospholipase and show that it localizes to the PVM of parasites within hepatocytes. We demonstrate that parasites lacking this protein have a defect in rupture of the PVM and thereby in host cell egress. In conclusion, our study shows for the first time that a phospholipase plays a role in PVM disruption of an intracellular eukaryotic parasite.
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Affiliation(s)
- Paul-Christian Burda
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School of Cellular Biology, University of Bern, Bern, Switzerland
- * E-mail:
| | | | - Marco Schaffner
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Shahid M. Khan
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris J. Janse
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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49
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Gomes AR, Bushell E, Schwach F, Girling G, Anar B, Quail MA, Herd C, Pfander C, Modrzynska K, Rayner JC, Billker O. A genome-scale vector resource enables high-throughput reverse genetic screening in a malaria parasite. Cell Host Microbe 2015; 17:404-413. [PMID: 25732065 PMCID: PMC4362957 DOI: 10.1016/j.chom.2015.01.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/01/2014] [Accepted: 01/07/2015] [Indexed: 10/30/2022]
Abstract
The genome-wide identification of gene functions in malaria parasites is hampered by a lack of reverse genetic screening methods. We present a large-scale resource of barcoded vectors with long homology arms for effective modification of the Plasmodium berghei genome. Cotransfecting dozens of vectors into the haploid blood stages creates complex pools of barcoded mutants, whose competitive fitness can be measured during infection of a single mouse using barcode sequencing (barseq). To validate the utility of this resource, we rescreen the P. berghei kinome, using published kinome screens for comparison. We find that several protein kinases function redundantly in asexual blood stages and confirm the targetability of kinases cdpk1, gsk3, tkl3, and PBANKA_082960 by genotyping cloned mutants. Thus, parallel phenotyping of barcoded mutants unlocks the power of reverse genetic screening for a malaria parasite and will enable the systematic identification of genes essential for in vivo parasite growth and transmission.
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Affiliation(s)
- Ana Rita Gomes
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Ellen Bushell
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Frank Schwach
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Gareth Girling
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Colin Herd
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Claudia Pfander
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | | | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK.
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK.
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50
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Guo YY, Shi ZY, Fu XZ, Chen JC, Wu Q, Chen GQ. A strategy for enhanced circular DNA construction efficiency based on DNA cyclization after microbial transformation. Microb Cell Fact 2015; 14:18. [PMID: 25896825 PMCID: PMC4455692 DOI: 10.1186/s12934-015-0204-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background With the rapid development of synthetic biology, the demand for assembling multiple DNA (genes) fragments into a large circular DNA structure in one step has dramatically increased. However, for constructions of most circular DNA, there are two contradictions in the ligation/assembly and transformation steps. The ligation/assembly consists of two different reactions: 1) the ligation/assembly between any two pieces of a linear form DNA; 2) the cyclization (or self-ligation) of a single linear form DNA. The first contradiction is that the bimolecular ligation/assembly requires a higher DNA concentration while the cyclization favors a lower one; the second contradiction is that a successful transformation of a ligation/assembly product requires a relatively high DNA concentration again. This study is the first attempt to use linear plasmid and Cyclization After Transformation (CAT) strategy to neutralize those contradictions systematically. Results The linear assembly combined with CAT method was demonstrated to increase the overall construction efficiency by 3–4 times for both the traditional ligation and for the new in vitro recombination-based assembly methods including recombinant DNA, Golden Gate, SLIC (Sequence and Ligation Independent Cloning) and Gibson Isothermal Assembly. Finally, the linear assembly combined with CAT method was successfully applied to assemble a pathway of 7 gene fragments responsible for synthesizing precorrin 3A which is an important intermediate in VB12 production. Conclusion The linear assembly combined with CAT strategy method can be regarded as a general strategy to enhance the efficiency of most existing circular DNA construction technologies and could be used in construction of a metabolic pathway consisting of multiple genes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0204-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying-Ying Guo
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Zhen-Yu Shi
- Synthenome.com, Dingley Village, VIC3172, Australia.
| | - Xiao-Zhi Fu
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Nano and Micro Mechanics, Tsinghua University, Beijing, 100084, China.
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