1
|
Veríssimo NVP, Mussagy CU, Bento HBS, Pereira JFB, Santos-Ebinuma VDC. Ionic liquids and deep eutectic solvents for the stabilization of biopharmaceuticals: A review. Biotechnol Adv 2024; 71:108316. [PMID: 38199490 DOI: 10.1016/j.biotechadv.2024.108316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Biopharmaceuticals have allowed the control of previously untreatable diseases. However, their low solubility and stability still hinder their application, transport, and storage. Hence, researchers have applied different compounds to preserve and enhance the delivery of biopharmaceuticals, such as ionic liquids (ILs) and deep eutectic solvents (DESs). Although the biopharmaceutical industry can employ various substances for enhancing formulations, their effect will change depending on the properties of the target biomolecule and environmental conditions. Hence, this review organized the current state-of-the-art on the application of ILs and DESs to stabilize biopharmaceuticals, considering the properties of the biomolecules, ILs, and DESs classes, concentration range, types of stability, and effect. We also provided a critical discussion regarding the potential utilization of ILs and DESs in pharmaceutical formulations, considering the restrictions in this field, as well as the advantages and drawbacks of these substances for medical applications. Overall, the most applied IL and DES classes for stabilizing biopharmaceuticals were cholinium-, imidazolium-, and ammonium-based, with cholinium ILs also employed to improve their delivery. Interestingly, dilute and concentrated ILs and DESs solutions presented similar results regarding the stabilization of biopharmaceuticals. With additional investigation, ILs and DESs have the potential to overcome current challenges in biopharmaceutical formulation.
Collapse
Affiliation(s)
- Nathalia Vieira Porphirio Veríssimo
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil; Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, São Paulo University, CEP: 14040-020 Ribeirão Preto, SP, Brazil.
| | - Cassamo Usemane Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile.
| | - Heitor Buzetti Simões Bento
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
| | | | - Valéria de Carvalho Santos-Ebinuma
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
| |
Collapse
|
2
|
Thulasi Devendrakumar K, Goldstein M, Kronstad J, Li X. Deletions within intronic T-DNA lead to reversion of T-DNA mutant phenotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:161-176. [PMID: 37773774 DOI: 10.1111/tpj.16482] [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: 01/24/2023] [Accepted: 09/15/2023] [Indexed: 10/01/2023]
Abstract
Agrobacterium-mediated transformation enables random transfer-DNA (T-DNA) insertion into plant genomes. T-DNA insertion into a gene's exons, introns or untranscribed regions close to the start or stop codon can disrupt gene function. Such T-DNA mutants have been useful for reverse genetics analysis, especially in Arabidopsis thaliana. As T-DNAs are inserted into genomic DNA, they are generally believed to be stably inherited. Here, we report a phenomenon of reversion of intronic T-DNA mutant phenotypes. From a suppressor screen using intronic T-DNA pi4kβ1,2 double mutant, we recovered intragenic mutants of pi4kβ1, which suppressed the autoimmunity of the double mutant. These mutants carried deletions in the intronic T-DNAs, resulting in elevated transcription of normal PI4Kβ1. Such reversion of T-DNA insertional mutant phenotype stresses the need for caution when using intronic T-DNA mutants and reiterates the importance of using irreversible null mutant alleles in genetic analyses.
Collapse
Affiliation(s)
- Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Madeleine Goldstein
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
3
|
Limaye A, Cho K, Hall B, Khillan JS, Kulkarni AB. Genotyping Protocols for Genetically Engineered Mice. Curr Protoc 2023; 3:e929. [PMID: 37984376 PMCID: PMC10754054 DOI: 10.1002/cpz1.929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Historically, the laboratory mouse has been the mammalian species of choice for studying gene function and for modeling diseases in humans. This was mainly due to their availability from mouse fanciers. In addition, their short generation time, small size, and minimal food consumption compared to that of larger mammals were definite advantages. This led to the establishment of large hubs for the development of genetically modified mouse models, such as the Jackson Laboratory. Initial research into inbred mouse strains in the early 1900s revolved around coat color genetics and cancer studies, but gene targeting in embryonic stem cells and the introduction of transgenes through pronuclear injection of a mouse zygote, along with current clustered regularly interspaced short palindromic repeat (CRISPR) RNA gene editing, have allowed easy manipulation of the mouse genome. Originally, to distribute a mouse model to other facilities, standard methods had to be developed to ensure that each modified mouse trait could be consistently identified no matter which laboratory requested it. The task of establishing uniform protocols became easier with the development of the polymerase chain reaction (PCR). This chapter will provide guidelines for identifying genetically modified mouse models, mainly using endpoint PCR. In addition, we will discuss strategies to identify genetically modified mouse models that have been established using newer gene-editing technology such as CRISPR. Published 2023. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Digestion with proteinase K followed by purification of genomic DNA using phenol/chloroform Alternate Protocol: Digestion with proteinase K followed by crude isopropanol extraction of genomic DNA for tail biopsy and ear punch samples Basic Protocol 2: Purification of genomic DNA using a semi-automated system Basic Protocol 3: Purification of genomic DNA from semen, blood, or buccal swabs Basic Protocol 4: Purification of genomic DNA from mouse blastocysts to assess CRISPR gene editing Basic Protocol 5: Routine endpoint-PCR-based genotyping using DNA polymerase and thermal cycler Basic Protocol 6: T7E1/Surveyor assays to detect insertion or deletions following CRISPR editing Basic Protocol 7: Detecting off-target mutations following CRISPR editing Basic Protocol 8: Detecting genomic sequence deletion after CRISPR editing using a pair of guide RNAs Basic Protocol 9: Detecting gene knock-in events following CRISPR editing Basic Protocol 10: Screening of conditional knockout floxed mice.
Collapse
Affiliation(s)
- Advait Limaye
- National Institute of Dental and Craniofacial Research
| | - Kyoungin Cho
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bradford Hall
- National Institute of Dental and Craniofacial Research
| | - Jaspal S. Khillan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | |
Collapse
|
4
|
Cai T, Chen H, Yan L, Zhang C, Deng Y, Wu S, Yang Q, Pan R, Raza A, Chen S, Zhuang W. The root-specific NtR12 promoter-based expression of RIP increased the resistance against bacterial wilt disease in tobacco. Mol Biol Rep 2022; 49:11503-11514. [PMID: 36097128 DOI: 10.1007/s11033-022-07817-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/21/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Tobacco is an important economic crop, but the quality and yield have been severely impaired by bacterial wilt disease (BWD) caused by Ralstonia solanacearum. METHODS AND RESULTS Here, we describe a transgenic approach to prevent BWD in tobacco plants. A new root-specific promoter of an NtR12 gene was successfully cloned. The NtR12 promoter drove GUS reporter gene expression to a high level in roots but to less extent in stems, and no significant expression was detected in leaves. The Ribosome-inactivating proteins (RIP) gene from Momordica charantia was also cloned, and its ability to inhibit Ralstonia solanacearum was evaluated using RIP protein produced by the prokaryotic expression system. The RIP gene was constructed downstream of the NtR12 promoter and transformed into the tobacco cultivar "Cuibi No. 1" (CB-1), resulting in many descendants. The resistance against BWD was significantly improved in transgenic tobacco lines expressing NtR12::RIP. CONCLUSION This study confirms that the RIP gene confers resistance to BWD and the NtR12 as a new promoter for its specific expression in root and stem. Our findings pave a novel avenue for transgenic engineering to prevent the harmful impact of diseases and pests in roots and stems.
Collapse
Affiliation(s)
- Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liming Yan
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ye Deng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shengxin Wu
- Fujian Province Bureau of Tobacco, Tobacco Agriculture and Scientific Research Institute, Fuzhou, 350001, Fujian, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ronglong Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Shunhui Chen
- Fujian Province Bureau of Tobacco, Tobacco Agriculture and Scientific Research Institute, Fuzhou, 350001, Fujian, China.
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China. .,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
5
|
Wan TW, Liu YJ, Wang YT, Lin YT, Hsu JC, Tsai JC, Chiu HC, Hsueh PR, Hung WC, Teng LJ. Potentially conjugative plasmids harboring Tn6636, a multidrug-resistant and composite mobile element, in Staphylococcus aureus. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:225-233. [PMID: 33840606 DOI: 10.1016/j.jmii.2021.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES This study aimed to provide detailed genetic characterization of Tn6636, a multidrug-resistant and composite mobile element, in clinical isolates of Staphylococcus aureus. METHODS A total of 112 ermB-positive methicillin-susceptible S. aureus (MSSA) and 224 ermB-positive methicillin-resistant S. aureus (MRSA) isolates collected from 2000 to 2015 were tested for the presence of Tn6636. Detection of the plasmids harboring Tn6636 was performed by S1 nuclease digestion pulsed-field gel electrophoresis (PFGE) analysis, conjugation test, and whole genome sequencing (WGS). RESULTS Prevalence of Tn6636 in MSSA is higher than that in MRSA. Ten MSSA isolates and 10 MRSA isolates carried Tn6636. The 10 MSSA isolates belonged to three sequence types (ST), including ST7 (n = 6), ST5 (n = 3), and ST59 (n = 1). The 10 MRSA isolates belonged to ST188 (n = 8) and ST965 (n = 2). Analysis of plasmid sequences revealed that Tn6636 was harbored by six different mosaic plasmids. In addition to resistance genes, some plasmids also harbored toxin genes. CONCLUSION The presence of multi-resistant Tn6636 in plasmids of both MSSA and MRSA with various STs suggests its broad dissemination. Results indicate that Tn6636 has existed for at least 16 years in Taiwan. The mosaic plasmids harboring Tn6636 can be transferred by conjugation. Ongoing surveillance of Tn6636 is essential to avoid continued spreading of resistant plasmids.
Collapse
Affiliation(s)
- Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Yu-Jung Liu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jia-Chuan Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Jui-Chang Tsai
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| |
Collapse
|
6
|
Rodríguez-Rubio L, Serna C, Ares-Arroyo M, Matamoros BR, Delgado-Blas JF, Montero N, Bernabe-Balas C, Wedel EF, Mendez IS, Muniesa M, Gonzalez-Zorn B. Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages. J Antimicrob Chemother 2020; 75:3173-3180. [PMID: 32719862 PMCID: PMC7566468 DOI: 10.1093/jac/dkaa311] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particles. METHODS Several databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT-PCR and Southern blotting. RESULTS Multicopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number. CONCLUSIONS Multicopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.
Collapse
Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Serna
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Bosco R Matamoros
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Jose F Delgado-Blas
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Emilia F Wedel
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Irene S Mendez
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit ARU, Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
7
|
Meco V, Egea I, Ortíz-Atienza A, Drevensek S, Esch E, Yuste-Lisbona FJ, Barneche F, Vriezen W, Bolarin MC, Lozano R, Flores FB. The Salt Sensitivity Induced by Disruption of Cell Wall-Associated Kinase 1 ( SlWAK1) Tomato Gene Is Linked to Altered Osmotic and Metabolic Homeostasis. Int J Mol Sci 2020; 21:E6308. [PMID: 32878190 PMCID: PMC7503591 DOI: 10.3390/ijms21176308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
Tomato cell wall-associated kinase 1 (SlWAK1) has only been studied in biotic stress response and hence its function in abiotic stress remains unknown. In a screening under salinity of an insertional mutant collection of tomato (Solanum lycopersicum L.), a mutant exhibiting lower degree of leaf chlorosis than wild type (WT) together with reduced leaf Na+ accumulation was selected. Genetic analysis of the mutation revealed that a single T-DNA insertion in the SlWAK1 gene was responsible of the mutant phenotype. Slwak1 null mutant reduced its shoot growth compared with WT, despite its improved Na+ homeostasis. SlWAK1 disruption affected osmotic homeostasis, as leaf water content was lower in mutant than in WT under salt stress. In addition, Slwak1 altered the source-sink balance under salinity, by increasing sucrose content in roots. Finally, a significant fruit yield reduction was found in Slwak1 vs. WT under long-term salt stress, mainly due to lower fruit weight. Our results show that disruption of SlWAK1 induces a higher sucrose transport from source leaf to sink root, negatively affecting fruit, the main sink at adult stage.
Collapse
Affiliation(s)
- Victoriano Meco
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (I.E.); (M.C.B.); (F.B.F.)
| | - Isabel Egea
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (I.E.); (M.C.B.); (F.B.F.)
| | - Ana Ortíz-Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL). Universidad de Almería, 04120 Almería, Spain; (A.O.-A.); (F.J.Y.-L.); (R.L.)
| | - Stéphanie Drevensek
- Institut de Biologie de l’École Normale Supérieure (IBENS), Paris Sciences et Lettres Research University, F-75005 Paris, France; (S.D.); (F.B.)
| | - Elisabeth Esch
- BASF Vegetable Seeds, Napoleonsweg 152, 6083AB Nunhem, The Netherlands; (E.E.); (W.V.)
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL). Universidad de Almería, 04120 Almería, Spain; (A.O.-A.); (F.J.Y.-L.); (R.L.)
| | - Fredy Barneche
- Institut de Biologie de l’École Normale Supérieure (IBENS), Paris Sciences et Lettres Research University, F-75005 Paris, France; (S.D.); (F.B.)
| | - Wim Vriezen
- BASF Vegetable Seeds, Napoleonsweg 152, 6083AB Nunhem, The Netherlands; (E.E.); (W.V.)
| | - María C. Bolarin
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (I.E.); (M.C.B.); (F.B.F.)
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL). Universidad de Almería, 04120 Almería, Spain; (A.O.-A.); (F.J.Y.-L.); (R.L.)
| | - Francisco B. Flores
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (I.E.); (M.C.B.); (F.B.F.)
| |
Collapse
|
8
|
Wilson SK, Heckendorn J, Martorelli Di Genova B, Koch LL, Rooney PJ, Morrissette N, Lebrun M, Knoll LJ. A Toxoplasma gondii patatin-like phospholipase contributes to host cell invasion. PLoS Pathog 2020; 16:e1008650. [PMID: 32628723 PMCID: PMC7365478 DOI: 10.1371/journal.ppat.1008650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 07/16/2020] [Accepted: 05/22/2020] [Indexed: 11/23/2022] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite that can invade any nucleated cell of any warm-blooded animal. In a previous screen to identify virulence determinants, disruption of gene TgME49_305140 generated a T. gondii mutant that could not establish a chronic infection in mice. The protein product of TgME49_305140, here named TgPL3, is a 277 kDa protein with a patatin-like phospholipase (PLP) domain and a microtubule binding domain. Antibodies generated against TgPL3 show that it is localized to the apical cap. Using a rapid selection FACS-based CRISPR/Cas-9 method, a TgPL3 deletion strain (ΔTgPL3) was generated. ΔTgPL3 parasites have defects in host cell invasion, which may be caused by reduced rhoptry secretion. We generated complementation clones with either wild type TgPL3 or an active site mutation in the PLP domain by converting the catalytic serine to an alanine, ΔTgPL3::TgPL3S1409A (S1409A). Complementation of ΔTgPL3 with wild type TgPL3 restored all phenotypes, while S1409A did not, suggesting that phospholipase activity is necessary for these phenotypes. ΔTgPL3 and S1409A parasites are also virtually avirulent in vivo but induce a robust antibody response. Vaccination with ΔTgPL3 and S1409A parasites protected mice against subsequent challenge with a lethal dose of Type I T. gondii parasites, making ΔTgPL3 a compelling vaccine candidate. These results demonstrate that TgPL3 has a role in rhoptry secretion, host cell invasion and survival of T. gondii during acute mouse infection.
Collapse
Affiliation(s)
- Sarah K. Wilson
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Linden Drive, Madison, Wisconsin, United States of America
| | | | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Linden Drive, Madison, Wisconsin, United States of America
| | - Lindsey L. Koch
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Linden Drive, Madison, Wisconsin, United States of America
| | - Peggy J. Rooney
- Stratatech Corporation, Charmany Drive, Madison, Wisconsin, United States of America
| | - Naomi Morrissette
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | | | - Laura J. Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Linden Drive, Madison, Wisconsin, United States of America
| |
Collapse
|
9
|
Bryant EE, Šunjevarić I, Berchowitz L, Rothstein R, Reid RJD. Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. Nucleic Acids Res 2019; 47:9144-9159. [PMID: 31350889 PMCID: PMC6753471 DOI: 10.1093/nar/gkz631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 06/14/2019] [Accepted: 07/25/2019] [Indexed: 01/19/2023] Open
Abstract
The postreplication repair gene, HLTF, is often amplified and overexpressed in cancer. Here we model HLTF dysregulation through the functionally conserved Saccharomyces cerevisiae ortholog, RAD5. Genetic interaction profiling and landscape enrichment analysis of RAD5 overexpression (RAD5OE) reveals requirements for genes involved in recombination, crossover resolution, and DNA replication. While RAD5OE and rad5Δ both cause cisplatin sensitivity and share many genetic interactions, RAD5OE specifically requires crossover resolving genes and drives recombination in a region of repetitive DNA. Remarkably, RAD5OE induced recombination does not require other post-replication repair pathway members, or the PCNA modification sites involved in regulation of this pathway. Instead, the RAD5OE phenotype depends on a conserved domain necessary for binding 3' DNA ends. Analysis of DNA replication intermediates supports a model in which dysregulated Rad5 causes aberrant template switching at replication forks. The direct effect of Rad5 on replication forks in vivo, increased recombination, and cisplatin sensitivity predicts similar consequences for dysregulated HLTF in cancer.
Collapse
Affiliation(s)
- Eric E Bryant
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ivana Šunjevarić
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Luke Berchowitz
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rodney Rothstein
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Robert J D Reid
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| |
Collapse
|
10
|
Wheeler JH, Young CKJ, Young MJ. Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization. CURRENT PROTOCOLS IN TOXICOLOGY 2019; 80:e75. [PMID: 30982231 PMCID: PMC6581606 DOI: 10.1002/cptx.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Joel H. Wheeler
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K. J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Matthew J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| |
Collapse
|
11
|
Rajendran A, Shigi N, Sumaoka J, Komiyama M. Artificial Restriction DNA Cutter Using Nuclease S1 for Site-Selective Scission of Genomic DNA. ACTA ACUST UNITED AC 2019; 76:e72. [PMID: 30720929 DOI: 10.1002/cpnc.72] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
By combining a pair of pseudo-complementary peptide nucleic acids (pcPNAs) with S1 nuclease, a novel tool to cut DNA at a predetermined site can be obtained. Complementary pcPNAs invade the DNA duplex and base pair to each strand of a target site, creating single-stranded regions that are cleaved by S1 nuclease. The scission site can be freely modulated by the design of pcPNAs. This method can be used to cleave a single site in the human genome. This protocol presents experimental details for site-selective scission using this versatile new tool. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Arivazhagan Rajendran
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan.,Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,Department of Applied Chemistry, School of Engineering, Tokyo University of Technology, Tokyo, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,College of Food Science and Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
12
|
Che P, Zhao ZY, Hinds M, Rinehart K, Glassman K, Albertsen M. Evaluation of Agronomic Performance of β-Carotene Elevated Sorghum in Confined Field Conditions. Methods Mol Biol 2019; 1931:209-220. [PMID: 30652293 DOI: 10.1007/978-1-4939-9039-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To help alleviate vitamin A deficiency in Africa, we have developed nutritionally enhanced sorghum with stabilized high all-trans-β-carotene accumulation. Toward the finalization of this nutritionally enhanced sorghum for food production, confined field trials were conducted to determine the agronomic performance of thirteen independent transgenic events in Iowa and Hawaii. Through these trials, three leading events with no negative impact on agronomic performance were identified. The studies described in this chapter have laid the groundwork for development of the next generation of β-carotene elevated sorghum as a food product.
Collapse
Affiliation(s)
- Ping Che
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Zuo-Yu Zhao
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA.
| | - Mark Hinds
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Kristen Rinehart
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Kimberly Glassman
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| | - Marc Albertsen
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
| |
Collapse
|
13
|
Smith LJ, Wright J, Clark G, Ul-Hasan T, Jin X, Fong A, Chandra M, St Martin T, Rubin H, Knowlton D, Ellsworth JL, Fong Y, Wong KK, Chatterjee S. Stem cell-derived clade F AAVs mediate high-efficiency homologous recombination-based genome editing. Proc Natl Acad Sci U S A 2018; 115:E7379-E7388. [PMID: 30018062 PMCID: PMC6077703 DOI: 10.1073/pnas.1802343115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise correction of genetic mutations at the nucleotide level is an attractive permanent therapeutic strategy for human disease. However, despite significant progress, challenges to efficient and accurate genome editing persist. Here, we report a genome editing platform based upon a class of hematopoietic stem cell (HSC)-derived clade F adeno-associated virus (AAV), which does not require prior nuclease-mediated DNA breaks and functions exclusively through BRCA2-dependent homologous recombination. Genome editing is guided by complementary homology arms and is highly accurate and seamless, with no evidence of on-target mutations, including insertion/deletions or inclusion of AAV inverted terminal repeats. Efficient genome editing was demonstrated at different loci within the human genome, including a safe harbor locus, AAVS1, and the therapeutically relevant IL2RG gene, and at the murine Rosa26 locus. HSC-derived AAV vector (AAVHSC)-mediated genome editing was robust in primary human cells, including CD34+ cells, adult liver, hepatic endothelial cells, and myocytes. Importantly, high-efficiency gene editing was achieved in vivo upon a single i.v. injection of AAVHSC editing vectors in mice. Thus, clade F AAV-mediated genome editing represents a promising, highly efficient, precise, single-component approach that enables the development of therapeutic in vivo genome editing for the treatment of a multitude of human gene-based diseases.
Collapse
Affiliation(s)
- Laura J Smith
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | | | - Gabriella Clark
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Taihra Ul-Hasan
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Xiangyang Jin
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Abigail Fong
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Manasa Chandra
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | | | | | | | | | - Yuman Fong
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Kamehameha K Wong
- Department of Hematology and Stem Cell Transplantation, City of Hope Medical Center, Duarte, CA 91010
| | - Saswati Chatterjee
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010;
| |
Collapse
|
14
|
Rivas-Marín E, Canosa I, Santero E, Devos DP. Development of Genetic Tools for the Manipulation of the Planctomycetes. Front Microbiol 2016; 7:914. [PMID: 27379046 PMCID: PMC4910669 DOI: 10.3389/fmicb.2016.00914] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/27/2016] [Indexed: 01/03/2023] Open
Abstract
Bacteria belonging to the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) superphylum are of interest for biotechnology, evolutionary cell biology, ecology, and human health. Some PVC species lack a number of typical bacterial features while others possess characteristics that are usually more associated to eukaryotes or archaea. For example, the Planctomycetes phylum is atypical for the absence of the FtsZ protein and for the presence of a developed endomembrane system. Studies of the cellular and molecular biology of these infrequent characteristics are currently limited due to the lack of genetic tools for most of the species. So far, genetic manipulation in Planctomycetes has been described in Planctopirus limnophila only. Here, we show a simple approach that allows mutagenesis by homologous recombination in three different planctomycetes species (i.e., Gemmata obscuriglobus, Gimesia maris, and Blastopirellula marina), in addition to P. limnophila, thus extending the repertoire of genetically modifiable organisms in this superphylum. Although the Planctomycetes show high resistance to most antibiotics, we have used kanamycin resistance genes in G. obscuriglobus, P. limnophila, and G. maris, and tetracycline resistance genes in B. marina, as markers for mutant selection. In all cases, plasmids were introduced in the strains by mating or electroporation, and the genetic modification was verified by Southern Blotting analysis. In addition, we show that the green fluorescent protein (gfp) is expressed in all four backgrounds from an Escherichia coli promoter. The genetic manipulation achievement in four phylogenetically diverse planctomycetes will enable molecular studies in these strains, and opens the door to developing genetic approaches not only in other planctomycetes but also other species of the superphylum, such as the Lentisphaerae.
Collapse
Affiliation(s)
- Elena Rivas-Marín
- Laboratory of Evolutionary Innovations, Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de OlavideSeville, Spain
| | - Inés Canosa
- Microbiology Area, Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de OlavideSeville, Spain
| | - Eduardo Santero
- Microbiology Area, Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de OlavideSeville, Spain
| | - Damien P. Devos
- Laboratory of Evolutionary Innovations, Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de OlavideSeville, Spain
| |
Collapse
|
15
|
Ishizuka T, Xu Y, Komiyama M. Clipping of Telomere from Human Chromosomes Using a Chemistry-Based Artificial Restriction DNA Cutter. ACTA ACUST UNITED AC 2015; 61:6.13.1-6.13.13. [PMID: 26344230 DOI: 10.1002/0471142700.nc0613s61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The detection of individual telomere lengths of human chromosomes can provide crucial information on genome stability, cancer, and telomere-related diseases. However, current methods to measure telomere length entail shortcomings that have limited their use. Recently, we have developed a method for detection of individual telomere lengths (DITL) that uses a chemistry-based DNA-cutting approach. The most beneficial feature of the DITL approach is to cleave the sequence adjacent to the telomere followed by resolution of the telomere length at the nucleotide level of a single chromosome. In this unit, a protocol for successful detection of individual telomere lengths from individual chromosomes is described in detail.
Collapse
Affiliation(s)
- Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
16
|
Odell AV, Tran F, Foderaro JE, Poupart S, Pathak R, Westwood NJ, Ward GE. Yeast three-hybrid screen identifies TgBRADIN/GRA24 as a negative regulator of Toxoplasma gondii bradyzoite differentiation. PLoS One 2015; 10:e0120331. [PMID: 25789621 PMCID: PMC4366382 DOI: 10.1371/journal.pone.0120331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/06/2015] [Indexed: 12/17/2022] Open
Abstract
Differentiation of the protozoan parasite Toxoplasma gondii into its latent bradyzoite stage is a key event in the parasite's life cycle. Compound 2 is an imidazopyridine that was previously shown to inhibit the parasite lytic cycle, in part through inhibition of parasite cGMP-dependent protein kinase. We show here that Compound 2 can also enhance parasite differentiation, and we use yeast three-hybrid analysis to identify TgBRADIN/GRA24 as a parasite protein that interacts directly or indirectly with the compound. Disruption of the TgBRADIN/GRA24 gene leads to enhanced differentiation of the parasite, and the TgBRADIN/GRA24 knockout parasites show decreased susceptibility to the differentiation-enhancing effects of Compound 2. This study represents the first use of yeast three-hybrid analysis to study small-molecule mechanism of action in any pathogenic microorganism, and it identifies a previously unrecognized inhibitor of differentiation in T. gondii. A better understanding of the proteins and mechanisms regulating T. gondii differentiation will enable new approaches to preventing the establishment of chronic infection in this important human pathogen.
Collapse
Affiliation(s)
- Anahi V Odell
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Fanny Tran
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Jenna E Foderaro
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Séverine Poupart
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Ravi Pathak
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St Andrews, Fife, Scotland, United Kingdom
| | - Gary E Ward
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| |
Collapse
|
17
|
Pbx proteins in Cryptococcus neoformans cell wall remodeling and capsule assembly. EUKARYOTIC CELL 2014; 13:560-71. [PMID: 24585882 DOI: 10.1128/ec.00290-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cryptococcal capsule is a critical virulence factor of an important pathogen, but little is known about how it is associated with the cell or released into the environment. Two mutants lacking PBX1 and PBX2 were found to shed reduced amounts of the capsule polysaccharide glucuronoxylomannan (GXM). Nuclear magnetic resonance, composition, and physical analyses showed that the shed material was of normal mass but was slightly enriched in xylose. In contrast to previous reports, this material contained no glucose. Notably, the capsule fibers of pbxΔ mutant cells grown under capsule-inducing conditions were present at a lower than usual density and were loosely attached to the cell wall. Mutant cell walls were also defective, as indicated by phenotypes including abnormal cell morphology, reduced mating filamentation, and altered cell integrity. All observed phenotypes were shared between the two mutants and exacerbated in a double mutant. Consistent with a role in surface glycan synthesis, the Pbx proteins localized to detergent-resistant membrane domains. These results, together with the sequence motifs in the Pbx proteins, suggest that Pbx1 and Pbx2 are redundant proteins that act in remodeling the cell wall to maintain normal cell morphology and precursor availability for other glycan synthetic processes. Their absence results in aberrant cell wall growth and metabolic imbalance, which together impact cell wall and capsule synthesis, cell morphology, and capsule association. The surface changes also lead to increased engulfment by host phagocytes, consistent with the lack of virulence of pbx mutants in animal models.
Collapse
|
18
|
Gillen AE, Lucas CA, Haussecker PL, Kosak ST, Harris A. Characterization of a large human transgene following invasin-mediated delivery in a bacterial artificial chromosome. Chromosoma 2013; 122:351-61. [PMID: 23749207 DOI: 10.1007/s00412-013-0418-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 12/31/2022]
Abstract
Bacterial artificial chromosomes (BACs) are widely used in transgenesis, particularly for the humanization of animal models. Moreover, due to their extensive capacity, BACs provide attractive tools to study distal regulatory elements associated with large gene loci. However, despite their widespread use, little is known about the integration dynamics of these large transgenes in mammalian cells. Here, we investigate the post-integration structure of a ~260 kb BAC carrying the cystic fibrosis transmembrane conductance regulator (CFTR) locus following delivery by bacterial invasion and compare this to the outcome of a more routine lipid-based delivery method. We find substantial variability in integrated copy number and expression levels of the BAC CFTR transgene after bacterial invasion-mediated delivery. Furthermore, we frequently observed variation in the representation of different regions of the CFTR transgene within individual cell clones, indicative of BAC fragmentation. Finally, using fluorescence in situ hybridization, we observed that the integrated BAC forms extended megabase-scale structures in some clones that are apparently stably maintained at cell division. These data demonstrate that the utility of large BACs to investigate cis-regulatory elements in the genomic context may be limited by recombination events that complicate their use.
Collapse
Affiliation(s)
- Austin E Gillen
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA
| | | | | | | | | |
Collapse
|
19
|
Demayo JL, Wang J, Liang D, Zhang R, Demayo FJ. Genetically Engineered Mice by Pronuclear DNA microinjection. ACTA ACUST UNITED AC 2012; 2:245-262. [PMID: 23024927 DOI: 10.1002/9780470942390.mo110168] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The generation of transgenic mice by DNA microinjection is a powerful tool to investigate the molecular regulation of gene expression, development, and disease. The power of this technology is that foreign DNA can be introduced into every cell of a developing organism and the phenotypic impact of this genetic modification can be investigated in a system under the constraints of normal development and physiology. The generation of transgenic mice requires the preparation of the transgene DNA construction, collection of one-cell fertilized mouse embryos, injection of the transgene into mouse embryos, and transfer of the surviving embryos. Mice born from such manipulations are then screened for the presence of the transgene. The execution of these procedures requires a highly efficient system otherwise the cost of the generation of these mice can be cost prohibitive. However, the production of these animals can serve as an invaluable research resource.
Collapse
Affiliation(s)
- Janet L Demayo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | | | | | | | | |
Collapse
|
20
|
Gray SJ, Choi VW, Asokan A, Haberman RA, McCown TJ, Samulski RJ. Production of recombinant adeno-associated viral vectors and use in in vitro and in vivo administration. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.17. [PMID: 21971848 DOI: 10.1002/0471142301.ns0417s57] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Adeno-associated virus is a nonpathogenic human virus that has been developed into a gene-delivery vector due to its high efficiency of infection for many different cell types and its ability to persist and lead to long-term gene expression. This unit describes efficient methods to generate high-titer, research-grade, adenovirus-free recombinant single-stranded and self-complementary adeno-associated virus in various serotypes, along with methods to quantify the viral vectors. Two detailed methods are provided for viral vector delivery into the rodent brain and spinal cord, and for histological detection of transgene expression of GFP.
Collapse
Affiliation(s)
- Steven J Gray
- University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | | | | | | | | | | |
Collapse
|
21
|
Abstract
This unit covers genetic manipulation protocols for M. abscessus, including nucleic acid extraction (plasmid DNA, genomic DNA, and RNA), transformation, and a recombineering mutagenesis method. M. abscessus is a Biosafety Level 2 (BSL-2) bacterium, and working considerations are also discussed.
Collapse
Affiliation(s)
- Halima Medjahed
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | | |
Collapse
|
22
|
Limaye A, Hall B, Kulkarni AB. Manipulation of mouse embryonic stem cells for knockout mouse production. ACTA ACUST UNITED AC 2009; Chapter 19:Unit 19.13 19.13.1-24. [PMID: 19731225 DOI: 10.1002/0471143030.cb1913s44] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The establishment of mouse embryonic stem (ES) cell lines has allowed for the gene?ration of the knockout mouse. ES cells that are genetically altered in culture can then be manipulated to derive a whole mouse containing the desired mutation. To successfully generate a knockout mouse, however, the ES cells must be carefully cultivated in a pluripotent state throughout the gene-targeting experiment. This unit describes detailed step-by-step protocols, reagents, equipment, and strategies needed for the successful generation of gene knockout embryonic stem cells using homologous recombination technologies.
Collapse
Affiliation(s)
- Advait Limaye
- Department of Health and Human Services, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | | | | |
Collapse
|
23
|
Abstract
This unit describes detailed step-by-step protocols, reagents, and equipment required for successful generation of transgenic mice using pronuclear injection. The experimental methods and practical tips given here will help guide beginners in understanding what is required and what to avoid in these standard protocols for efficiently generating transgenic mice.
Collapse
Affiliation(s)
- Andrew Cho
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | | | | |
Collapse
|
24
|
Abstract
The unintegrated viral DNA synthesized during human immunodeficiency virus type 1 infection includes linear and circular forms. Circular forms of viral DNA are surrogate markers for nuclear import of viral DNA during virus replication as well as events surrounding the completion of reverse transcription. Analysis of 2-LTR circles is convenient and the quantity of 2-LTR circle formed is directly proportional to the amount of viral DNA imported into the cell nucleus. In addition, correct synthesis of 2-LTR circles is an outcome of HIV-1 Gag-Pol function. Thus, quantitation and sequence analysis of 2-LTR circles have been very important in studying the structure and function relationship of key viral proteins. In this chapter, we describe the methods of quantitation and analysis of 2-LTR circle junctions isolated from HIV-1 infected cells.
Collapse
Affiliation(s)
- Dibyakanti Mandal
- Department of Microbiology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | |
Collapse
|
25
|
|