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Chen KN, Peng QL, Cao DF, Wang ZJ, Zhang K, Zhou XY, Min DY, Zhou BT, Mao XY. Inhibition of lysyl oxidase by pharmacological intervention and genetic manipulation alleviates epilepsy-associated cognitive disorder. Brain Res Bull 2024; 210:110928. [PMID: 38493836 DOI: 10.1016/j.brainresbull.2024.110928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Epilepsy-associated cognitive disorder (ECD), a prevalent comorbidity in epilepsy patients, has so far uncharacterized etiological origins. Our prior work revealed that lysyl oxidase (Lox) acted as a novel contributor of ferroptosis, a recently discovered cell death mode in the regulation of brain function. However, the role of Lox-mediated ferroptosis in ECD remains unknown. ECD mouse model was established 2 months later following a single injection of kainic acid (KA) for. After chronic treatment with KA, mice were treated with different doses (30 mg/kg, 100 mg/kg and 300 mg/kg) of Lox inhibitor BAPN. Additionally, hippocampal-specific Lox knockout mice was also constructed and employed to validate the role of Lox in ECD. Cognitive functions were assessed using novel object recognition test (NOR) and Morris water maze test (MWM). Protein expression of phosphorylated cAMP-response element binding (CREB), a well-known molecular marker for evaluation of cognitive performance, was also detected by Western blot. The protein distribution of Lox was analyzed by immunofluorescence. In KA-induced ECD mouse model, ferroptosis process was activated according to upregulation of 4-HNE protein and a previously discovered ferroptosis in our group, namely, Lox was remarkably increased. Pharmacological inhibition of Lox by BAPN at the dose of 100 mg/kg significantly increased the discrimination index following NOR test and decreased escape latency as well as augmented passing times within 60 s following MWM test in ECD mouse model. Additionally, deficiency of Lox in hippocampus also led to pronounced improvement of deficits in ECD model. These findings indicate that the ferroptosis regulatory factor, Lox, is activated in ECD. Ablation of Lox by either pharmacological intervention or genetic manipulation ameliorates the impairment in ECD mouse model, which suggest that Lox serves as a promising therapeutic target for treating ECD in clinic.
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Affiliation(s)
- Kang-Ni Chen
- Key Laboratory of Ministry of Education for TCM Viscera-State Theory and Applications, Liaoning University of Traditional Chinese Medicine, Shenyang 116600, China; Department of Clinical Pharmacology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha 410008, China; Institute of Clinical Pharmacology and Engineering Research Center of Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, China
| | - Qi-Lin Peng
- Department of Pharmacy, Xiangya Hospital Central South University, Changsha 410008, China
| | - Dan-Feng Cao
- Academician Workstation and Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha 410219, China
| | - Zhao-Jun Wang
- Department of Clinical Pharmacology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha 410008, China; Institute of Clinical Pharmacology and Engineering Research Center of Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, China
| | - Kai Zhang
- Department of Clinical Pharmacology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha 410008, China; Institute of Clinical Pharmacology and Engineering Research Center of Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, China
| | - Xin-Yu Zhou
- Department of Neurology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang 222000, China; Department of Neurology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang 222000, China.
| | - Dong-Yu Min
- Key Laboratory of Ministry of Education for TCM Viscera-State Theory and Applications, Liaoning University of Traditional Chinese Medicine, Shenyang 116600, China; Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang 110032, China.
| | - Bo-Ting Zhou
- Department of Pharmacy, Xiangya Hospital Central South University, Changsha 410008, China.
| | - Xiao-Yuan Mao
- Department of Clinical Pharmacology and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha 410008, China; Institute of Clinical Pharmacology and Engineering Research Center of Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, China.
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Guo Q, Yu Y, Suo J, Tang X, Zhang S, Crouch C, Bruton B, Tarpey I, Liu X, Zhao G, Suo X. Oral delivery of Eimeria acervulina transfected sequentially with two copies of the VP2 gene induces immunity against infectious bursal disease virus in chickens. Front Vet Sci 2024; 11:1367912. [PMID: 38659453 PMCID: PMC11041627 DOI: 10.3389/fvets.2024.1367912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024] Open
Abstract
Chicken coccidiosis caused by Eimeria spp. can occur on almost all poultry farms, causing huge economic losses to the industry. Genetically manipulated Eimeria parasites as a vaccine vector to deliver viral antigens have been reported. In our preliminary study, transgenic E. acervulina expressing a VP2 gene (Ea-VP2) of the infectious bursal disease virus (IBDV) demonstrated partial protection against IBDV infection. To enhance immune responses, we aimed to increase the VP2 gene copy number in transgenic E. acervulina. In this study, we used a novel plasmid vector carrying a VP2 gene fused with three flag tags and a red fluorescent reporter gene (mCherry). The vector was introduced into Ea-VP2 sporozoites through nucleofection, leading to the generation of Ea-2VP2. Subsequent analysis revealed a notable escalation in the fluorescent rate, increasing from 0.11 to 95.1% following four consecutive passages facilitated by fluorescent-activated cell sorting. Verification via PCR, Western blot, and immunofluorescence confirmed the successful construction of the Ea-2VP2 population. Despite lower fecundity compared to wild-type E. acervulina, Ea-2VP2 maintained immunogenicity. Our research effectively created a transgenic E. acervulina strain transfected sequentially with two copies of the VP2 gene from IBDV. This modification resulted in an increased humoral immune response after primary immunization in chickens. Additionally, it demonstrated a degree of protection within the bursa against IBDV infection. Future studies will focus on further enhancing immune response levels.
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Affiliation(s)
- Qingbin Guo
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ying Yu
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingxia Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xinming Tang
- Key Laboratory of Animal Biosafety Risk Prevention and Control (North) of MARA, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sixin Zhang
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Colin Crouch
- MSD Animal Health, Milton Keynes, United Kingdom
| | - Beth Bruton
- MSD Animal Health, Milton Keynes, United Kingdom
| | - Ian Tarpey
- MSD Animal Health, Milton Keynes, United Kingdom
| | - Xianyong Liu
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guanghui Zhao
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xun Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
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Morin S, Atkinson PW, Walling LL. Whitefly-Plant Interactions: An Integrated Molecular Perspective. Annu Rev Entomol 2024; 69:503-525. [PMID: 37816261 DOI: 10.1146/annurev-ento-120120-093940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
The rapid advances in available transcriptomic and genomic data and our understanding of the physiology and biochemistry of whitefly-plant interactions have allowed us to gain new and significant insights into the biology of whiteflies and their successful adaptation to host plants. In this review, we provide a comprehensive overview of the mechanisms that whiteflies have evolved to overcome the challenges of feeding on phloem sap. We also highlight the evolution and functions of gene families involved in host perception, evaluation, and manipulation; primary metabolism; and metabolite detoxification. We discuss the emerging themes in plant immunity to whiteflies, focusing on whitefly effectors and their sites of action in plant defense-signaling pathways. We conclude with a discussion of advances in the genetic manipulation of whiteflies and the potential that they hold for exploring the interactions between whiteflies and their host plants, as well as the development of novel strategies for the genetic control of whiteflies.
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Affiliation(s)
- Shai Morin
- Department of Entomology, Hebrew University of Jerusalem, Rehovot, Israel;
| | - Peter W Atkinson
- Department of Entomology, University of California, Riverside, California, USA;
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA;
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Ye Y, Liu M, Yu L, Sun H, Liu J. Nannochloropsis as an Emerging Algal Chassis for Light-Driven Synthesis of Lipids and High-Value Products. Mar Drugs 2024; 22:54. [PMID: 38393025 PMCID: PMC10890015 DOI: 10.3390/md22020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
In light of the escalating global energy crisis, microalgae have emerged as highly promising producers of biofuel and high-value products. Among these microalgae, Nannochloropsis has received significant attention due to its capacity to generate not only triacylglycerol (TAG) but also eicosapentaenoic acid (EPA) and valuable carotenoids. Recent advancements in genetic tools and the field of synthetic biology have revolutionized Nannochloropsis into a powerful biofactory. This comprehensive review provides an initial overview of the current state of cultivation and utilization of the Nannochloropsis genus. Subsequently, our review examines the metabolic pathways governing lipids and carotenoids, emphasizing strategies to enhance oil production and optimize carbon flux redirection toward target products. Additionally, we summarize the utilization of advanced genetic manipulation techniques in Nannochloropsis. Together, the insights presented in this review highlight the immense potential of Nannochloropsis as a valuable model for biofuels and synthetic biology. By effectively integrating genetic tools and metabolic engineering, the realization of this potential becomes increasingly feasible.
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Affiliation(s)
- Ying Ye
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China; (Y.Y.); (M.L.); (L.Y.)
| | - Meijing Liu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China; (Y.Y.); (M.L.); (L.Y.)
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Center for Algae Innovation & Engineering Research, School of Resources and Environment, Nanchang University, Nanchang 330031, China
| | - Lihua Yu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China; (Y.Y.); (M.L.); (L.Y.)
| | - Han Sun
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jin Liu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China; (Y.Y.); (M.L.); (L.Y.)
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Center for Algae Innovation & Engineering Research, School of Resources and Environment, Nanchang University, Nanchang 330031, China
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Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. J Agric Food Chem 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
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Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Liu Y, Han J, Fang J, Li R. The Beneficial Effects of Mesenchymal Stem Cells in Acute Kidney Injury: A Narrative Review. Curr Stem Cell Res Ther 2024; 19:200-209. [PMID: 36748221 PMCID: PMC10680085 DOI: 10.2174/1574888x18666230206115046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/29/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023]
Abstract
BACKGROUND Acute kidney injury (AKI) is a multifaced disease characterized by a rapid decline in renal function. However, with growing insight into the pathophysiologic mechanisms of AKI, currently available interventions for AKI are merely supportive. Thus, novel therapies are urgently needed to improve the outcomes of patients with AKI. This narrative review aims to explore enhancing the beneficial effects of Mesenchymal Stem Cells(MSCs) in AKI. METHODS The authors examined all studies regarding the role of MSCs in AKI. And the authors undertook a structured search of bibliographic databases for peer-reviewed research literature using a focused review question. The most relevant and up-to-date research was included. RESULTS AND DISCUSSION Based on encouraging preclinical results, stem cell therapy has been widely explored over the last decade. Among the various stem cell types investigated, mesenchymal stem cells are being intensely investigated by virtue of their numerous strengths, such as easy derivation, undemanding cell culture conditions, anti-apoptosis, immunomodulation, and anti-inflammation effects. Mounting evidence suggests that MSCs hold great potential in accelerating kidney repair following AKI in various preclinical models. Unfortunately, low engrafting efficiency and poor survival rate of injected MSCs in the injured renal tissue are major obstacles MSCs clinical application faces. CONCLUSION Various strategies, including genetic manipulation, mimicking the cellular microenvironment with different culture conditions, optimizing MSCs preparation and administration schedule, and screening patients who may more like benefit from MSCs therapy, have been developed to enhance the therapeutic potential of MSCs in AKI.
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Affiliation(s)
- Yuxiang Liu
- Department of Nephrology, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, 030012, Shanxi, China
- Department of the Fifth Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Department of Nephrology, First Hospital of Shanxi Medical University, Taiyuan, Taiyuan, 030012, Shanxi, China
| | - Jibin Han
- Department of Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
| | - Jingai Fang
- Department of Nephrology, First Hospital of Shanxi Medical University, Taiyuan, Taiyuan, 030012, Shanxi, China
| | - Rongshan Li
- Department of Nephrology, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, 030012, Shanxi, China
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Singh AK, Malviya R, Prakash A, Verma S. Neuropsychiatric Manifestations in Alzheimer's Disease Patients: Genetics and Treatment Options. CNS Neurol Disord Drug Targets 2024; 23:39-54. [PMID: 36856177 DOI: 10.2174/1871527322666230301111216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/03/2022] [Accepted: 12/27/2022] [Indexed: 03/02/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by neuropsychiatric symptoms (NPS), which cause great misery to those with dementia and those who care for them and may lead to early institutionalization. OBJECTIVE The present systematic review aims to discuss the various aspects of Alzheimer's, including treatment options. METHODS The databases Embase, PubMed, and Web of Science were searched to collect data. RESULTS Incipient cognitive deterioration is commonly accompanied by these early warning signals of neurocognitive diseases. The neurobiology of NPSs in Alzheimer's disease, as well as particular symptoms, including psychosis, agitation, apathy, sadness, and sleep disorders, will be examined in this review. For NPSs in Alzheimer's disease, clinical trial designs, as well as regulatory issues, were also addressed. A fresh wave of research, however, is helping to push the discipline ahead. For medication development and repurposing, we highlight the most recent results in genetics, neuroimaging, and neurobiology. Even though identifying and treating psychosis in adults with dementia is still a challenging endeavor, new options are coming up that give the field fresh focus and hope. Conclsuion: It can be concluded from the complete literature survey that Alzheimer's-related psychosis as well as other symptoms that are not psychotic, have made significant progress in the last decade. These milestones in the development of safer, more effective treatments have been achieved as a consequence of great focus on non-pharmacological interventions like DICE or WHELD; the investigation into ways to improve existing drugs like aripiprazole, risperidone, amisulpride, and Escitalopram for safer precision-based treatment; and the development of a clinical trial program for pimavanserin.
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Affiliation(s)
- Arun Kumar Singh
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University Greater Noida, Uttar Pradesh, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University Greater Noida, Uttar Pradesh, India
| | - Anuj Prakash
- Reference Standard Division, Indian Pharmacopoeia Commission, Sec-23, Raj Nagar, Ghaziabad, Uttar Pradesh, India
| | - Swati Verma
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University Greater Noida, Uttar Pradesh, India
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Li Y, Zhou Y, Wang B, Mu N, Miao Y, Tang D, Shen Y, Cheng Z. FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis. Plant J 2023; 116:717-727. [PMID: 37632767 DOI: 10.1111/tpj.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/11/2023] [Indexed: 08/28/2023]
Abstract
Crossovers (COs) are necessary for generating genetic diversity that breeders can select, but there are conserved mechanisms that regulate their frequency and distribution. Increasing CO frequency may raise the efficiency of selection by increasing the chance of integrating more desirable traits. In this study, we characterize rice FANCM and explore its functions in meiotic CO control. FANCM mutations do not affect fertility in rice, but they cause a great boost in the overall frequency of COs in both inbred and hybrid rice, according to genetic analysis of the complete set of fancm zmm (hei10, ptd, shoc1, mer3, zip4, msh4, msh5, and heip1) mutants. Although the early homologous recombination events proceed normally in fancm, the meiotic extra COs are not marked with HEI10 and require MUS81 resolvase for resolution. FANCM depends on PAIR1, COM1, DMC1, and HUS1 to perform its functions. Simultaneous disruption of FANCM and MEICA1 synergistically increases CO frequency, but it is accompanied by nonhomologous chromosome associations and fragmentations. FANCM interacts with the MHF complex, and ablation of rice MHF1 or MHF2 could restore the formation of 12 bivalents in the absence of the ZMM gene ZIP4. Our data indicate that unleashing meiotic COs by mutating any member of the FANCM-MHF complex could be an effective procedure to accelerate the efficiency of rice breeding.
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Affiliation(s)
- Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yue Zhou
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxin Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Mu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongjie Miao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
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Abstract
Klebsiella pneumoniae is a Gram-negative, rod-shaped bacterium commonly found in the human intestine. Although it typically exists as part of the normal flora, it can also cause healthcare-associated infections with severe consequences. Understanding the specific genes responsible for its virulence through genetic manipulation is crucial for potential therapeutic interventions. However, manipulating K. pneumoniae presents challenges due to its exopolysaccharide capsule. This article presents a comprehensive collection of protocols designed to facilitate the genetic manipulation of K. pneumoniae. By following these protocols, researchers will acquire the necessary skills to prepare electrocompetent cells, utilize electroporation for efficient plasmid DNA introduction, construct isogenic mutants using the λ Red recombinase system, and generate a complementation vector for restoring the phenotypic traits of knockout strains. These protocols provide valuable tools and techniques to navigate the intricacies associated with studying and modifying K. pneumoniae. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparing electrocompetent K. pneumoniae cells Alternate Protocol 1: Preparing electrocompetent K. pneumoniae cells for recombineering Basic Protocol 2: Transforming K. pneumoniae using electroporation Basic Protocol 3: Constructing isogenic mutants in K. pneumoniae using the λ Red recombinase system Support Protocol 1: Confirming a knockout via colony PCR Support Protocol 2: Verifying absence of secondary mutations Basic Protocol 4: Generating unmarked knockout mutants in K. pneumoniae using the pFLP plasmid Basic Protocol 5: Constructing a complementation vector for K. pneumoniae.
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Affiliation(s)
- Brooke Ring
- Department of Medical Microbiology and Immunology, The University of Toledo College of Medicine and Life Sciences
| | - Saroj Khadka
- Department of Medical Microbiology and Immunology, The University of Toledo College of Medicine and Life Sciences
| | - Drew Pariseau
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences
| | - Laura Mike
- Department of Medical Microbiology and Immunology, The University of Toledo College of Medicine and Life Sciences
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Kumphune S, Piot C, Barrere-Lemaire S. Editorial: New strategies to inhibit cell death in myocardial ischemia-reperfusion injury: how to succeed? Volume II. Front Cardiovasc Med 2023; 10:1260800. [PMID: 37614941 PMCID: PMC10443641 DOI: 10.3389/fcvm.2023.1260800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Affiliation(s)
- Sarawut Kumphune
- Biomedical Engineering and Innovation Research Centre, Chiang Mai University, Chiang Mai, Thailand
- Biomedical Engineering Institute, Chiang Mai University, Chiang Mai, Thailand
| | - Christophe Piot
- IGF, Université de Montpellier, CNRS, INSERM, Montpellier, France
- Département de Cardiologie Interventionnelle, Clinique du Millénaire, Montpellier, France
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Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. J Phycol 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
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Palmiotti A, Lichak MR, Shih PY, Kwon YM, Bendesky A. Genetic manipulation of betta fish. Front Genome Ed 2023; 5:1167093. [PMID: 37545763 PMCID: PMC10401044 DOI: 10.3389/fgeed.2023.1167093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023] Open
Abstract
Betta splendens, also known as Siamese fighting fish or "betta," is a freshwater fish species renowned for its astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l, and mitfa, and analyzed their effects on viability and pigmentation. Furthermore, we knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
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Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Madison R. Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Young Mi Kwon
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
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Abstract
Chlamydia trachomatis, one species of Chlamydia spp., has the greatest impact on human health and is the main cause of bacterial sexually transmitted diseases and preventable blindness among all Chamydia spp. species. The obligate intracellular parasitism and unique biphasic developmental cycle of C. trachomatis are the main barriers for the development of tools of genetic manipulation. The past decade has witnessed significant gains in genetic manipulation of C. trachomatis, including chemical mutagenesis, group II intron-based targeted gene knockout, fluorescence-reported allelic exchange mutagenesis (FRAEM), CRISPR interference (CRISPRi) and the recently developed transposon mutagenesis. In this review, we discuss the current status of genetic manipulations of C. trachomatis and highlights new challenges in the nascent field of Chlamydia genetics.
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Affiliation(s)
- Weiqiang Wan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Danni Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dan Li
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Li J, Tong H, Wu Y. [Tools for large-scale genetic manipulation of yeast genome]. Sheng Wu Gong Cheng Xue Bao 2023; 39:2465-2484. [PMID: 37401604 DOI: 10.13345/j.cjb.230278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Large-scale genetic manipulation of the genome refers to the genetic modification of large fragments of DNA using knockout, integration and translocation. Compared to small-scale gene editing, large-scale genetic manipulation of the genome allows for the simultaneous modification of more genetic information, which is important for understanding the complex mechanisms such as multigene interactions. At the same time, large-scale genetic manipulation of the genome allows for larger-scale design and reconstruction of the genome, and even the creation of entirely new genomes, with great potential in reconstructing complex functions. Yeast is an important eukaryotic model organism that is widely used because of its safety and easiness of manipulation. This paper systematically summarizes the toolkit for large-scale genetic manipulation of the yeast genome, including recombinase-mediated large-scale manipulation, nuclease-mediated large-scale manipulation, de novo synthesis of large DNA fragments and other large-scale manipulation tools, and introduces their basic working principles and typical application cases. Finally, the challenges and developments in large-scale genetic manipulation are presented.
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Affiliation(s)
- Jieyi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
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15
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Hänggeli KPA, Hemphill A, Müller N, Heller M, Uldry AC, Braga-Lagache S, Müller J, Boubaker G. Comparative Proteomic Analysis of Toxoplasma gondii RH Wild-Type and Four SRS29B (SAG1) Knock-Out Clones Reveals Significant Differences between Individual Strains. Int J Mol Sci 2023; 24:10454. [PMID: 37445632 DOI: 10.3390/ijms241310454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
In T. gondii, as well as in other model organisms, gene knock-out using CRISPR-Cas9 is a suitable tool to identify the role of specific genes. The general consensus implies that only the gene of interest is affected by the knock-out. Is this really the case? In a previous study, we generated knock-out (KO) clones of TgRH88_077450 (SRS29B; SAG1) which differed in the numbers of the integrated dihydrofolate-reductase-thymidylate-synthase (MDHFR-TS) drug-selectable marker. Clones 18 and 33 had a single insertion of MDHFR-TS within SRS29B. Clone 6 was disrupted by the insertion of a short unrelated DNA-sequence, but the marker was integrated elsewhere. In clone 30, the marker was inserted into SRS29B, and several other MDHFR-TS copies were found in the genome. KO and wild-type (WT) tachyzoites had similar shapes, dimensions, and vitality. This prompted us to investigate the impact of genetic engineering on the overall proteome patterns of the four clones as compared to the respective WT. Comparative shotgun proteomics of the five strains was performed. Overall, 3236 proteins were identified. Principal component analysis of the proteomes revealed five distinct clusters corresponding to the five strains by both iTop3 and iLFQ algorithms. Detailed analysis of the differentially expressed proteins revealed that the target of the KO, srs29B, was lacking in all KO clones. In addition to this protein, 20 other proteins were differentially expressed between KO clones and WT or between different KO clones. The protein exhibiting the highest variation between the five strains was srs36D encoded by TgRH_016110. The deregulated expression of SRS36D was further validated by quantitative PCR. Moreover, the transcript levels of three other selected SRS genes, namely SRS36B, SRS46, and SRS57, exhibited significant differences between individual strains. These results indicate that knocking out a given gene may affect the expression of other genes. Therefore, care must be taken when specific phenotypes are regarded as a direct consequence of the KO of a given gene.
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Affiliation(s)
- Kai Pascal Alexander Hänggeli
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, 3012 Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, 3012 Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility (PMSCF), Department for BioMedical Research (DBMR), University of Bern, 3012 Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility (PMSCF), Department for BioMedical Research (DBMR), University of Bern, 3012 Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility (PMSCF), Department for BioMedical Research (DBMR), University of Bern, 3012 Bern, Switzerland
| | - Joachim Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, 3012 Bern, Switzerland
| | - Ghalia Boubaker
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, 3012 Bern, Switzerland
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16
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Handelman M, Osherov N. Efficient Generation of Multiple Seamless Point Mutations Conferring Triazole Resistance in Aspergillus fumigatus. J Fungi (Basel) 2023; 9:644. [PMID: 37367580 DOI: 10.3390/jof9060644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
Aspergillus fumigatus is a common human fungal pathogen that can cause a range of diseases. Triazoles are used to treat A. fumigatus infections, but resistance is increasing due to mutations in genes such as cyp51A, hmg1 and overexpression of efflux pumps. Verifying the importance of these mutations is time-consuming, and although the use of CRISPR-Cas9 methods has shortened this process, it still relies on the construction of repair templates containing a selectable marker. Here, employing in vitro-assembled CRISPR-Cas9 along with a recyclable selectable marker, we devised a quick and easy way to effectively and seamlessly introduce mutations conferring triazole resistance in A. fumigatus. We used it to introduce, alone and in combination, triazole resistance-conferring mutations in cyp51A, cyp51B and hmg1. With the potential to seamlessly introduce genes imparting resistance to additional existing and novel antifungals, toxic metals, and environmental stressors, this technique can considerably improve the ability to introduce dominant mutations in A. fumigatus.
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Affiliation(s)
- Mariana Handelman
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
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17
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Moreira POL, Nogueira PM, Monte-Neto RL. Next-Generation Leishmanization: Revisiting Molecular Targets for Selecting Genetically Engineered Live-Attenuated Leishmania. Microorganisms 2023; 11:microorganisms11041043. [PMID: 37110466 PMCID: PMC10145799 DOI: 10.3390/microorganisms11041043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Despite decades of research devoted to finding a vaccine against leishmaniasis, we are still lacking a safe and effective vaccine for humans. Given this scenario, the search for a new prophylaxis alternative for controlling leishmaniasis should be a global priority. Inspired by leishmanization-a first generation vaccine strategy where live L. major parasites are inoculated in the skin to protect against reinfection-live-attenuated Leishmania vaccine candidates are promising alternatives due to their robust elicited protective immune response. In addition, they do not cause disease and could provide long-term protection upon challenge with a virulent strain. The discovery of a precise and easy way to perform CRISPR/Cas-based gene editing allowed the selection of safer null mutant live-attenuated Leishmania parasites obtained by gene disruption. Here, we revisited molecular targets associated with the selection of live-attenuated vaccinal strains, discussing their function, their limiting factors and the ideal candidate for the next generation of genetically engineered live-attenuated Leishmania vaccines to control leishmaniasis.
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Affiliation(s)
- Paulo O L Moreira
- Biotechnology Applied to Pathogens (BAP), Instituto René Rachou, Fundação Oswaldo Cruz, Fiocruz Minas, Belo Horizonte 30190-009, Brazil
| | - Paula M Nogueira
- Biotechnology Applied to Pathogens (BAP), Instituto René Rachou, Fundação Oswaldo Cruz, Fiocruz Minas, Belo Horizonte 30190-009, Brazil
| | - Rubens L Monte-Neto
- Biotechnology Applied to Pathogens (BAP), Instituto René Rachou, Fundação Oswaldo Cruz, Fiocruz Minas, Belo Horizonte 30190-009, Brazil
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18
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Xu M, He L, Sun P, Wu M, Cui X, Liu D, Adomako-Bonsu AG, Geng M, Xiong G, Guo L, Maser E. Critical Role of Monooxygenase in Biodegradation of 2,4,6-Trinitrotoluene by Buttiauxella sp. S19-1. Molecules 2023; 28. [PMID: 36838956 DOI: 10.3390/molecules28041969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
2,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for bioremediation of TNT has received much attention from scholars. In this paper, transcriptome analysis of the efficient degrading bacterium Buttiauxella sp. S19-1 revealed that the monooxygenase gene (BuMO) was significantly up-regulated during TNT degradation. S-ΔMO (absence of BuMO gene in S19-1 mutant) degraded TNT 1.66-fold less efficiently than strain S19-1 (from 71.2% to 42.9%), and E-MO mutant (Escherichia coli BuMO-expressing strain) increased the efficiency of TNT degradation 1.33-fold (from 52.1% to 69.5%) for 9 h at 180 rpm at 27 °C in LB medium with 1.4 µg·mL-1 TNT. We predicted the structure of BuMO and purified recombinant BuMO (rBuMO). Its specific activity was 1.81 µmol·min-1·mg-1 protein at pH 7.5 and 35 °C. The results of gas chromatography mass spectrometry (GC-MS) analysis indicated that 4-amino-2,6-dinitrotoluene (ADNT) is a metabolite of TNT biodegradation. We speculate that MO is involved in catalysis in the bacterial degradation pathway of TNT in TNT-polluted environment.
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Palmiotti A, Lichak MR, Shih PY, Bendesky A. Genetic manipulation of betta fish. bioRxiv 2023:2023.02.16.528733. [PMID: 36824853 PMCID: PMC9948955 DOI: 10.1101/2023.02.16.528733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Betta splendens , also known as Siamese fighting fish or 'betta', are renowned for their astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l , and mitfa , and analyzed their effects on viability and pigmentation. Furthermore, we successfully knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
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Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Madison R Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Present address: Department of Ecology and Evolutionary Biology, Princeton University, NJ, USA
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
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20
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Venken KJ, Matinyan N, Gonzalez Y, Dierick HA. Multiplexed Transgenic Selection and Counterselection Strategies to Expedite Genetic Manipulation Workflows Using Drosophila melanogaster. Curr Protoc 2023; 3:e652. [PMID: 36757287 PMCID: PMC9923875 DOI: 10.1002/cpz1.652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We recently described a set of four selectable and two counterselectable markers that provide resistance and sensitivity, respectively, against their corresponding drugs using the model organism Drosophila melanogaster. The four selectable markers provide animals with resistance against G418 sulfate, puromycin HCl, blasticidin S, or hygromycin B, whereas the two counterselection markers make animals sensitive to ganciclovir/acyclovir or 5-fluorocytosine. Unlike classical phenotypic markers, whether visual or fluorescent, which require extensive screening of progeny of a genetic cross for desired genotypes, resistance and sensitivity markers eliminate this laborious procedure by directly selecting for, or counterselecting against, the desired genotypes. We demonstrated the usefulness of these markers with three applications: 1) generating dual transgenic animals for binary overexpression (e.g., GAL4/UAS) analysis in a single step through the process of co-injection, followed by co-selection resulting in co-transgenesis; 2) obtaining balancer chromosomes that are both selectable and counterselectable to manipulate crossing schemes for, or against, the presence of the modified balancer chromosome; and 3) making both selectable and fluorescently tagged P[acman] BAC transgenic animals for gene expression and proteomic analysis. Here, we describe detailed procedures for how to use these drug-based selection and counterselection markers in the fruit fly D. melanogaster when making dual transgenic animals for binary overexpression as an example. Dual transgenesis integrates site-specifically into two sites in the genome in a single step, namely both components of the binary GAL4/UAS overexpression system, via a G418 sulfate-selectable GAL4 transactivator plasmid and a blasticidin S-selectable UAS responder plasmid. The process involves co-injecting the two plasmids, followed by co-selection using G418 sulfate and blasticidin S, resulting in co-transgenesis of the two plasmids in the fly genome. We demonstrate the functionality of the procedure based on the expression pattern obtained after dual transgenesis of the two plasmids. We provide protocols on how to prepare drugged fly food vials, determine the effective drug concentration for markers used during transgenic selection and counterselection strategies, and prepare and confirm plasmid DNA for microinjection, followed by the microinjection procedure itself and setting up crossing schemes to isolate desired progeny through selection and/or counterselection. These protocols can be easily adapted to any combination of the six selectable and counterselectable markers we described or any new marker that is resistant or sensitive to a novel drug. Protocols on how to build plasmids by synthetic-assembly DNA cloning or modify plasmids by serial recombineering to perform a plethora of selection, counterselection, or any other genetic strategies are presented in two accompanying Current Protocols articles. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparing drugged fly food vials for transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 2: Determining the effective drug concentration for resistance and sensitivity markers used during transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 3: Preparing and confirming plasmid DNA for microinjection to perform transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 4: Microinjecting plasmid DNA into fly embryos to perform transgenic selection and counterselection strategies using D. melanogaster Basic Protocol 5: Crossing schemes to isolate desired progeny through transgenic selection and counterselection strategies using D. melanogaster.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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Sheridan PO, Odat MA, Scott KP. Establishing genetic manipulation for novel strains of human gut bacteria. Microbiome Res Rep 2023; 2:1. [PMID: 38059211 PMCID: PMC10696588 DOI: 10.20517/mrr.2022.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 12/12/2022] [Indexed: 12/08/2023]
Abstract
Recent years have seen the development of high-accuracy and high-throughput genetic manipulation techniques, which have greatly improved our understanding of genetically tractable microbes. However, challenges remain in establishing genetic manipulation techniques in novel organisms, owing largely to exogenous DNA defence mechanisms, lack of selectable markers, lack of efficient methods to introduce exogenous DNA and an inability of genetic vectors to replicate in their new host. In this review, we describe some of the techniques that are available for genetic manipulation of novel microorganisms. While many reviews exist that focus on the final step in genetic manipulation, the editing of recipient DNA, we particularly focus on the first step in this process, the transfer of exogenous DNA into a strain of interest. Examples illustrating the use of these techniques are provided for a selection of human gut bacteria in which genetic tractability has been established, such as Bifidobacterium, Bacteroides and Roseburia. Ultimately, this review aims to provide an information source for researchers interested in developing genetic manipulation techniques for novel bacterial strains, particularly those of the human gut microbiota.
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Affiliation(s)
- Paul O. Sheridan
- School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Ma’en Al Odat
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
| | - Karen P. Scott
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK
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22
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Zegeye ED, Aspholm M. Efficient Electrotransformation of Bacillus thuringiensis for Gene Manipulation and Expression. Curr Protoc 2022; 2:e588. [PMID: 36350250 DOI: 10.1002/cpz1.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genetic manipulation of Bacillus spp., such as B. thuringiensis and B. cereus, is laborious and time consuming due to challenges in transformation of the plasmid DNA construct. Larger shuttle plasmids, such as pMAD, that are commonly used in markerless gene replacement are particularly difficult to transform into Bacillus spp. Here, we present robust protocols that work efficiently for the transformation of both small and large plasmid constructs into B. thuringiensis. Our protocols involve preparation of efficient electrocompetent Bacillus cells by cultivating the cells in the presence of a cell wall-weakening agent, followed by washing the cells with optimized solutions. The protocols further highlight the importance of using unmethylated plasmid DNA for the efficient transformation of B. thuringiensis. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of electrocompetent B. thuringiensis Basic Protocol 2: Transformation of B. thuringiensis.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Marina Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
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23
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Sundram S, Malviya R, Awasthi R. Genetic Causes of Alzheimer's Disease and the Neuroprotective Role of Melatonin in its Management. CNS Neurol Disord Drug Targets 2022; 22:CNSNDDT-EPUB-126085. [PMID: 36056839 DOI: 10.2174/1871527321666220901125730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Dementia is a global health concern owing to its complexity, which also poses a great challenge to pharmaceutical scientists and neuroscientists. The global dementia prevalence is approximately 47 million, which may increase by three times by 2050. Alzheimer's disease (AD) is the most common cause of dementia. AD is a severe age-related neurodegenerative disorder characterized by short-term memory loss, aphasia, mood imbalance, and executive function. The etiology of AD is still unknown, and the exact origin of the disease is still under investigation. Aggregation of Amyloid β (Aβ) plaques or neurotoxic Aβo oligomers outside the neuron is the most common cause of AD development. Amyloid precursor protein (APP) processing by β secretase and γ secretase produces abnormal Aβ monomers. This aggregation of Aβ and NFT is promoted by various genes like BACE1, ADAM10, PIN1, GSK-3, APOE, PPARα, etc. Identification of these genes can discover several therapeutic targets that can be useful in studying pathogenesis and underlying treatments. Melatonin modulates the activities of these genes, thereby reducing Aβ production and increasing its clearance. Melatonin also reduces the expression of APP by attenuating cAMP, thereby enhancing the non-amyloidogenic process. Present communication explored and discussed the neuroprotective role of melatonin against Aβ-dependent AD pathogenesis. The manuscript also discussed potential molecular and genetic mechanisms of melatonin in the production and clearance of Aβ that could ameliorate neurotoxicity.
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Affiliation(s)
- Sonali Sundram
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, U.P., India
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector-125, Noida 201313, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, U.P., India
| | - Rajendra Awasthi
- Department of Pharmaceutical Sciences, School of Health Science and Technology, University of Petroleum and Energy Studies (UPES), Energy Acres, Bidholi, Via-Prem Nagar, Dehradun - 248 007, Uttarakhand, India
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Fuchs LK, Holland AH, Ludlow RA, Coates RJ, Armstrong H, Pickett JA, Harwood JL, Scofield S. Genetic Manipulation of Biosynthetic Pathways in Mint. Front Plant Sci 2022; 13:928178. [PMID: 35774811 PMCID: PMC9237610 DOI: 10.3389/fpls.2022.928178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In recent years, the study of aromatic plants has seen an increase, with great interest from industrial, academic, and pharmaceutical industries. Among plants attracting increased attention are the Mentha spp. (mint), members of the Lamiaceae family. Mint essential oils comprise a diverse class of molecules known as terpenoids/isoprenoids, organic chemicals that are among the most diverse class of naturally plant derived compounds. The terpenoid profile of several Mentha spp. is dominated by menthol, a cyclic monoterpene with some remarkable biological properties that make it useful in the pharmaceutical, medical, cosmetic, and cleaning product industries. As the global market for Mentha essential oils increases, the desire to improve oil composition and yield follows. The monoterpenoid biosynthesis pathway is well characterised so metabolic engineering attempts have been made to facilitate this improvement. This review focuses on the Mentha spp. and attempts at altering the carbon flux through the biosynthetic pathways to increase the yield and enhance the composition of the essential oil. This includes manipulation of endogenous and heterologous biosynthetic enzymes through overexpression and RNAi suppression. Genes involved in the MEP pathway, the menthol and carvone biosynthetic pathways and transcription factors known to affect secondary metabolism will be discussed along with non-metabolic engineering approaches including environmental factors and the use of plant growth regulators.
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Affiliation(s)
- Lorenz K. Fuchs
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | | | - Ryan J. Coates
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Harvey Armstrong
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - John A. Pickett
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - John L. Harwood
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Simon Scofield
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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25
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Drețcanu G, Știrbu I, Leoplold N, Cruceriu D, Danciu C, Stănilă A, Fărcaș A, Borda IM, Iuhas C, Diaconeasa Z. Chemical Structure, Sources and Role of Bioactive Flavonoids in Cancer Prevention: A Review. Plants (Basel) 2022; 11:plants11091117. [PMID: 35567117 PMCID: PMC9101215 DOI: 10.3390/plants11091117] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/18/2022] [Indexed: 05/12/2023]
Abstract
There has been a major shift in the collective mindset around the world in recent decades, both in terms of food and in terms of the treatment of chronic diseases. Increasing numbers of people are choosing to prevent rather than treat, which is why many consumers are choosing plant-based diets, mainly due to their bioactive compounds. A significant case of bioactive compound is flavonoids-a wide subclass of an even wider class of phytochemicals: polyphenols. Flavonoids are a broad topic of study for researchers due to their potential in the prevention and treatment of a broad range of cancers. The aim of this review is to inform/update the reader on the diversity, accessibility and importance of flavonoids as biomolecules that are essential for optimal health, focusing on the potential of these compounds in the prevention of various types of cancer. Along with conventional sources, this review presents some of the possible methods for obtaining significant amounts of flavonoids based on a slightly different approach, genetic manipulation.
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Affiliation(s)
- Georgiana Drețcanu
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Mănăştur, 400372 Cluj-Napoca, Romania; (G.D.); (A.S.); (A.F.); (Z.D.)
| | - Ioana Știrbu
- Faculty of Physics, Babes-Bolyai University, Kogalniceanu 1, 400084 Cluj-Napoca, Romania; (I.Ș.); (N.L.)
| | - Nicolae Leoplold
- Faculty of Physics, Babes-Bolyai University, Kogalniceanu 1, 400084 Cluj-Napoca, Romania; (I.Ș.); (N.L.)
| | - Daniel Cruceriu
- Department of Molecular Biology and Biotechnology, Babes-Bolyai University, 5-7 Clinicilor Street, 400006 Cluj-Napoca, Romania;
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Corina Danciu
- Department of Pharmacognosy, Victor Babes University of Medicine and Pharmacy, 2 Eftimie Murgu Sq., 300041 Timisoara, Romania;
| | - Andreea Stănilă
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Mănăştur, 400372 Cluj-Napoca, Romania; (G.D.); (A.S.); (A.F.); (Z.D.)
| | - Anca Fărcaș
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Mănăştur, 400372 Cluj-Napoca, Romania; (G.D.); (A.S.); (A.F.); (Z.D.)
| | - Ileana Monica Borda
- Sixth Department of Medical Specialties, Medical Rehabilitation, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Cristian Iuhas
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400372 Cluj-Napoca, Romania
- Correspondence: ; Tel.: +40-264-596893
| | - Zorița Diaconeasa
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Mănăştur, 400372 Cluj-Napoca, Romania; (G.D.); (A.S.); (A.F.); (Z.D.)
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26
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Lou L, Kong S, Sun Y, Zhang Z, Wang H. Human Endometrial Organoids: Recent Research Progress and Potential Applications. Front Cell Dev Biol 2022; 10:844623. [PMID: 35242764 PMCID: PMC8885623 DOI: 10.3389/fcell.2022.844623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022] Open
Abstract
Since traditional two-dimensional (2D) cell culture cannot meet the demand of simulating physiological conditions in vivo, three-dimensional (3D) culture systems have been developed. To date, most of these systems have been applied for the culture of gastrointestinal and neural tissue. As for the female reproductive system, the culture of endometrial and oviductal tissues in Matrigel has also been performed, but there are still some problems that remain unsolved. This review highlights recent progress regarding endometrial organoids, focusing on the signal for organoid derivation and maintenance, the coculture of the epithelium and stroma, the drug screening using organoids from cancer patients, and provides a potential guideline for genome editing in endometrial organoids.
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Affiliation(s)
- Liqun Lou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China.,Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yunyan Sun
- Department of Obstetrics and Gynecology, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenbo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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27
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Lorenz A, Papon N. New tools for the new bug Candida auris. Trends Microbiol 2022; 30:203-205. [PMID: 35115186 DOI: 10.1016/j.tim.2022.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Candida auris is a recently emerged yeast pathogen of humans causing severe hospital-acquired systemic infections. It is of the utmost importance to understand the genetic and cellular basis of its virulence and pathogenicity. In a recent study, Santana and O'Meara generated forward and reverse genetic tools to manipulate C. auris.
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Affiliation(s)
- Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
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28
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Kowalczyk T, Merecz-Sadowska A, Picot L, Brčić Karačonji I, Wieczfinska J, Śliwiński T, Sitarek P. Genetic Manipulation and Bioreactor Culture of Plants as a Tool for Industry and Its Applications. Molecules 2022; 27:795. [PMID: 35164060 DOI: 10.3390/molecules27030795] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/31/2022]
Abstract
In recent years, there has been a considerable increase in interest in the use of transgenic plants as sources of valuable secondary metabolites or recombinant proteins. This has been facilitated by the advent of genetic engineering technology with the possibility for direct modification of the expression of genes related to the biosynthesis of biologically active compounds. A wide range of research projects have yielded a number of efficient plant systems that produce specific secondary metabolites or recombinant proteins. Furthermore, the use of bioreactors allows production to be increased to industrial scales, which can quickly and cheaply deliver large amounts of material in a short time. The resulting plant production systems can function as small factories, and many of them that are targeted at a specific operation have been patented. This review paper summarizes the key research in the last ten years regarding the use of transgenic plants as small, green biofactories for the bioreactor-based production of secondary metabolites and recombinant proteins; it simultaneously examines the production of metabolites and recombinant proteins on an industrial scale and presents the current state of available patents in the field.
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29
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Huang PW, Xu YS, Sun XM, Shi TQ, Gu Y, Ye C, Huang H. Development of an Efficient Gene Editing Tool in Schizochytrium sp. and Improving Its Lipid and Terpenoid Biosynthesis. Front Nutr 2022; 8:795651. [PMID: 34970583 PMCID: PMC8712325 DOI: 10.3389/fnut.2021.795651] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Schizochytrium sp. HX-308 is a marine microalga with fast growth and high lipid content, which has potential as microbial cell factories for lipid compound biosynthesis. It is significant to develop efficient genetic editing tool and discover molecular target in Schizochytrium sp. HX-308 for lipid compound biosynthesis. In this study, we developed an efficient gene editing tool in HX-308 which was mediated by Agrobacterium tumefaciens AGL-1. Results showed that the random integration efficiency reached 100%, and the homologous recombination efficiency reached about 30%. Furthermore, the metabolic pathway of lipid and terpenoid biosynthesis were engineered. Firstly, the acetyl-CoA c-acetyltransferase was overexpressed in HX-308 with a strong constitutive promoter. With the overexpression of acetyl-CoA c-acetyltransferase, more acetyl-CoA was used to synthesize terpenoids, and the production of squalene, β-carotene and astaxanthin was increased 5.4, 1.8, and 2.4 times, respectively. Interestingly, the production of saturated fatty acids and polyunsaturated fatty acids also changed. Moreover, three Acyl-CoA oxidase genes which catalyze the first step of β-oxidation were knocked out using homologous recombination. Results showed that the production of lipids increased in the three knock-out strains. Our results demonstrated that the A. tumefaciens-mediated transformation method will be of great use for the study of function genes, as well as developing Schizochytrium sp. as a strong cell factory for producing high value products.
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Affiliation(s)
- Peng-Wei Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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30
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Xie Y, Yao J, Jin W, Ren L, Li X. Induction and Maturation of Hepatocyte-Like Cells In Vitro: Focus on Technological Advances and Challenges. Front Cell Dev Biol 2021; 9:765980. [PMID: 34901010 PMCID: PMC8662991 DOI: 10.3389/fcell.2021.765980] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Limited by the poor proliferation and restricted sources of adult hepatocytes, there is an urgent need to find substitutes for proliferation and cultivation of mature hepatocytes in vitro for use in disease treatment, drug approval, and toxicity testing. Hepatocyte-like cells (HLCs), which originate from undifferentiated stem cells or modified adult cells, are considered good candidates because of their advantages in terms of cell source and in vitro expansion ability. However, the majority of induced HLCs are in an immature state, and their degree of differentiation is heterogeneous, diminishing their usability in basic research and limiting their clinical application. Therefore, various methods have been developed to promote the maturation of HLCs, including chemical approaches, alteration of cell culture systems, and genetic manipulation, to meet the needs of in vivo transplantation and in vitro model establishment. This review proposes different cell types for the induction of HLCs, and provide a comprehensive overview of various techniques to promote the generation and maturation of HLCs in vitro.
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Affiliation(s)
- Ye Xie
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Jia Yao
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou, China
| | - Weilin Jin
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Institute of Cancer Neuroscience, The First Hospital of Lanzhou University, Lanzhou, China.,The Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Longfei Ren
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,The Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xun Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou, China.,The Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China.,The Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China.,Hepatopancreatobiliary Surgery Institute of Gansu Province, Lanzhou, China
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31
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Abe F. Molecular Responses to High Hydrostatic Pressure in Eukaryotes: Genetic Insights from Studies on Saccharomyces cerevisiae. Biology (Basel) 2021; 10:1305. [PMID: 34943220 DOI: 10.3390/biology10121305] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 01/19/2023]
Abstract
Simple Summary High hydrostatic pressure generally has an adverse effect on the biological systems of organisms inhabiting lands or shallow sea regions. Deep-sea piezophiles that prefer high hydrostatic pressure for growth have garnered considerable scientific attention. However, the underlying molecular mechanisms of their adaptation to high pressure remains unclear owing to the challenges of culturing and manipulating the genome of piezophiles. Humans also experience high hydrostatic pressure during exercise. A long-term stay in space can cause muscle weakness in astronauts. Thus, the human body indubitably senses mechanical stresses such as hydrostatic pressure and gravity. Nonetheless, the mechanisms underlying biological responses to high pressures are not clearly understood. This review summarizes the occurrence and significance of high-pressure effects in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Abstract High hydrostatic pressure is common mechanical stress in nature and is also experienced by the human body. Organisms in the Challenger Deep of the Mariana Trench are habitually exposed to pressures up to 110 MPa. Human joints are intermittently exposed to hydrostatic pressures of 3–10 MPa. Pressures less than 50 MPa do not deform or kill the cells. However, high pressure can have various effects on the cell’s biological processes. Although Saccharomyces cerevisiae is not a deep-sea piezophile, it can be used to elucidate the molecular mechanism underlying the cell’s responses to high pressures by applying basic knowledge of the effects of pressure on industrial processes involving microorganisms. We have explored the genes associated with the growth of S. cerevisiae under high pressure by employing functional genomic strategies and transcriptomics analysis and indicated a strong association between high-pressure signaling and the cell’s response to nutrient availability. This review summarizes the occurrence and significance of high-pressure effects on complex metabolic and genetic networks in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Mechanosensation in humans has also been discussed.
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32
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Li J, Gálvez EJC, Amend L, Almási É, Iljazovic A, Lesker TR, Bielecka AA, Schorr EM, Strowig T. A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems. EMBO J 2021; 40:e108287. [PMID: 34676563 PMCID: PMC8634118 DOI: 10.15252/embj.2021108287] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant‐rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs) and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan, and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan‐processing PULs (PULAra) and that the type‐II PULAra is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in future.
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Affiliation(s)
- Jing Li
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Éva Almási
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Aida Iljazovic
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eva-Magdalena Schorr
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany.,Centre for Individualized Infection Medicine, Hannover, Germany
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Abstract
A large number of fuselloviruses have been found in acidic hot springs around the globe. They share a set of highly conserved genes (core genes) and possess a varying number of less-conserved genes (non-core genes). However, the functions of most of these genes are unknown. Recent studies show that as many as half of these genes tolerate mutation. In this study, we conducted a genetic analysis on Saccharolobus spindle-shaped virus 22 (SSV22), an alphafusellovirus with fewer open reading frames (ORFs) than most of the isolated fuselloviruses. Both deletion and frame-shift mutations were introduced into nearly all of the 26 ORFs of the viral genome. A total of 17 ORFs were indispensable, and two additional ORFs were required for the optimal infectivity of the virus. Deletion of either VP2 or VP3, the two structural proteins, did not affect the morphology or infectivity of the virus. An infectious SSV22 derivative carrying a minimal genome of 20 ORFs was obtained. The SSV22 capsid was capable of accommodating a genome as large as ∼18 kb, or ∼7 kb larger than that of the wild-type virus. The viral capsid varied in both the length and width, but not in shape, with the size of the genome. Our results will facilitate the analysis of crucial protein-protein interactions between SSV22 and the host during viral infection and help explore the use of SSV22 as a vector for DNA delivery in potential applications.
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Affiliation(s)
- Junxia Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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34
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Xu X, Huang R, Yin WB. An Optimized and Efficient CRISPR/Cas9 System for the Endophytic Fungus Pestalotiopsis fici. J Fungi (Basel) 2021; 7:809. [PMID: 34682231 PMCID: PMC8539907 DOI: 10.3390/jof7100809] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Endophytic fungi are emerging as attractive producers of natural products with diverse bioactivities and novel structures. However, difficulties in the genetic manipulation of endophytic fungi limit the search of novel secondary metabolites. In this study, we improved the polyethylene glycol (PEG)-mediated protoplast transformation method by introducing the CRISPR/Cas9 system into endophytic fungus Pestalotiopsis fici. Using this approach, we performed genome editing such as site-specific gene insertion, dual-locus mutations, and long DNA fragment deletions in P. fici efficiently. The average efficiency for site-specific gene insertion and two-site gene editing was up to 48.0% and 44.4%, respectively. In addition, the genetic manipulation time with long DNA fragment (5-10 kb) deletion was greatly shortened to one week in comparison with traditional methods such as Agrobacterium tumefaciens-mediated transformation (ATMT). Taken together, the development of the CRISPR/Cas9 system in the endophytic fungus will accelerate the discovery of novel natural products and further biological study.
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Affiliation(s)
- Xinran Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runye Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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35
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Xu M, Liu D, Sun P, Li Y, Wu M, Liu W, Maser E, Xiong G, Guo L. Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1. Toxics 2021; 9:231. [PMID: 34678927 DOI: 10.3390/toxics9100231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/22/2022]
Abstract
Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.
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Matinyan N, Karkhanis MS, Gonzalez Y, Jain A, Saltzman A, Malovannaya A, Sarrion-Perdigones A, Dierick HA, Venken KJT. Multiplexed drug-based selection and counterselection genetic manipulations in Drosophila. Cell Rep 2021; 36:109700. [PMID: 34525356 PMCID: PMC8480232 DOI: 10.1016/j.celrep.2021.109700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/10/2021] [Accepted: 08/20/2021] [Indexed: 01/27/2023] Open
Abstract
The power of Drosophila melanogaster as a model system relies on tractable germline genetic manipulations. Despite Drosophila's expansive genetics toolbox, such manipulations are still accomplished one change at a time and depend predominantly on phenotypic screening. We describe a drug-based genetic platform consisting of four selection and two counterselection markers, eliminating the need to screen for modified progeny. These markers work reliably individually or in combination to produce specific genetic outcomes. We demonstrate three example applications of multiplexed drug-based genetics by generating (1) transgenic animals, expressing both components of binary overexpression systems in a single transgenesis step; (2) dual selectable and counterselectable balancer chromosomes; and (3) selectable, fluorescently tagged P[acman] bacterial artificial chromosome (BAC) strains. We perform immunoprecipitation followed by proteomic analysis on one tagged BAC line, demonstrating our platform's applicability to biological discovery. Lastly, we provide a plasmid library resource to facilitate custom transgene design and technology transfer to other model systems.
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Affiliation(s)
- Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mansi S Karkhanis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Saltzman
- Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Advanced Technology Cores, Mass Spectrometry Proteomics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Herman A Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX 77030, USA.
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Hachisuka SI, Nishii T, Yoshida S. Development of a Targeted Gene Disruption System in the Poly(Ethylene Terephthalate)-Degrading Bacterium Ideonella sakaiensis and Its Applications to PETase and MHETase Genes. Appl Environ Microbiol 2021; 87:e0002021. [PMID: 34260304 DOI: 10.1128/AEM.00020-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Poly(ethylene terephthalate) (PET) is a commonly used synthetic plastic; however, its nonbiodegradability results in a large amount of waste accumulation that has a negative impact on the environment. Recently, a PET-degrading bacterium, Ideonella sakaiensis 201-F6 strain, was isolated, and the enzymes involved in PET digestion, PET hydrolase (PETase), and mono(2-hydroxyethyl) terephthalic acid (MHET) hydrolase (MHETase) were identified. Despite the great potentials of I. sakaiensis in bioremediation and biorecycling, approaches to studying this bacterium remain limited. In this study, to enable the functional analysis of PETase and MHETase genes in vivo, we have developed a gene disruption system in I. sakaiensis. The pT18mobsacB-based disruption vector harboring directly connected 5'- and 3'-flanking regions of the target gene for homologous recombination was introduced into I. sakaiensis cells via conjugation. First, we deleted the orotidine 5'-phosphate decarboxylase gene (pyrF) from the genome of the wild-type strain, producing the ΔpyrF strain with 5-fluoroorotic acid (5-FOA) resistance. Next, using the ΔpyrF strain as a parent strain and pyrF as a counterselection marker, we disrupted the genes for PETase and MHETase. The growth of both Δpetase and Δmhetase strains on terephthalic acid (TPA; one of the PET hydrolytic products) was comparable to that of the parent strain. However, these mutant strains dramatically decreased the growth level on PET to that on a no-carbon source. Moreover, the Δpetase strain completely abolished PET degradation capacity. These results demonstrate that PETase and MHETase are essential for I. sakaiensis metabolism of PET. IMPORTANCE The poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis possesses two unique enzymes able to serve in PET hydrolysis. PET hydrolase (PETase) hydrolyzes PET into mono(2-hydroxyethyl) terephthalic acid (MHET), and MHET hydrolase (MHETase) hydrolyzes MHET into terephthalic acid (TPA) and ethylene glycol (EG). These enzymes have attracted global attention, as they have potential to be used for bioconversion of PET. Compared to many in vitro studies, including biochemical and crystal structure analyses, few in vivo studies have been reported. Here, we developed a targeted gene disruption system in I. sakaiensis, which was then applied for constructing Δpetase and Δmhetase strains. Growth of these disruptants revealed that PETase is the sole enzyme responsible for PET degradation in I. sakaiensis, while PETase and MHETase play essential roles in its PET assimilation.
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Mangold K, Mašek J, He J, Lendahl U, Fuchs E, Andersson ER. Highly efficient manipulation of nervous system gene expression with NEPTUNE. Cell Rep Methods 2021; 1:100043. [PMID: 34557863 PMCID: PMC8457050 DOI: 10.1016/j.crmeth.2021.100043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/07/2021] [Accepted: 06/11/2021] [Indexed: 11/03/2022]
Abstract
Genetic loss and gain of function in mice have typically been studied by using knockout or knockin mice that take months to years to generate. To address this problem for the nervous system, we developed NEPTUNE (NEural Plate Targeting by in Utero NanoinjEction) to rapidly and flexibly transduce the neural plate with virus prior to neurulation, and thus manipulate the future nervous system. Stable integration in >95% of cells in the brain enabled long-term overexpression, and conditional expression was achieved by using cell-type-specific MiniPromoters. Knockdown of Olig2 by using NEPTUNE recapitulated the phenotype of Olig2 -/- embryos. We used NEPTUNE to investigate Sptbn2, mutations in which cause spinocerebellar ataxia type 5. Sptbn2 knockdown induced dose-dependent defects in the neural tube, embryonic turning, and abdominal wall closure, previously unreported functions for Sptbn2. NEPTUNE thus offers a rapid and cost-effective technique to test gene function in the nervous system and can reveal phenotypes incompatible with life.
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Affiliation(s)
- Katrin Mangold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Jan Mašek
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden
| | - Jingyan He
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Emma R. Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 17177, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden
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Fallon AM. Growth and Maintenance of Wolbachia in Insect Cell Lines. Insects 2021; 12:706. [PMID: 34442272 DOI: 10.3390/insects12080706] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary Wolbachia is an intracellular bacterium that occurs in arthropods and in filarial worms. First described nearly a century ago in the reproductive tissues of Culex pipiens mosquitoes, Wolbachia is now known to occur in roughly 50% of insect species, and has been considered the most abundant intracellular bacterium on earth. In insect hosts, Wolbachia modifies reproduction in ways that facilitate spread of the microbe within the host population, but otherwise is relatively benign. In this “gene drive” capacity, Wolbachia provides a tool for manipulating mosquito populations. In mosquitoes, Wolbachia causes cytoplasmic incompatibility, in which the fusion of egg and sperm nuclei is disrupted, and eggs fail to hatch, depending on the presence/absence of Wolbachia in the parent insects. Recent findings demonstrate that Wolbachia from infected insects can be transferred into mosquito species that do not host a natural infection. When transinfected into Aedes aegypti, an important vector of dengue and Zika viruses, Wolbachia causes cytoplasmic incompatibility and, in addition, decreases the mosquito’s ability to transmit viruses to humans. This review addresses the maintenance of Wolbachia in insect cell lines, which provide a tool for high-level production of infectious bacteria. In vitro technologies will improve use of Wolbachia for pest control, and provide the microbiological framework for genetic engineering of this promising biocontrol agent. Abstract The obligate intracellular microbe, Wolbachia pipientis (Rickettsiales; Anaplasmataceae), is a Gram-negative member of the alpha proteobacteria that infects arthropods and filarial worms. Although closely related to the genera Anaplasma and Ehrlichia, which include pathogens of humans, Wolbachia is uniquely associated with invertebrate hosts in the clade Ecdysozoa. Originally described in Culex pipiens mosquitoes, Wolbachia is currently represented by 17 supergroups and is believed to occur in half of all insect species. In mosquitoes, Wolbachia acts as a gene drive agent, with the potential to modify vector populations; in filarial worms, Wolbachia functions as a symbiont, and is a target for drug therapy. A small number of Wolbachia strains from supergroups A, B, and F have been maintained in insect cell lines, which are thought to provide a more permissive environment than the natural host. When transferred back to an insect host, Wolbachia produced in cultured cells are infectious and retain reproductive phenotypes. Here, I review applications of insect cell lines in Wolbachia research and describe conditions that facilitate Wolbachia infection and replication in naive host cells. Progress in manipulation of Wolbachia in vitro will enable genetic and biochemical advances that will facilitate eventual genetic engineering of this important biological control agent.
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Afolabi LO, Afolabi MO, Sani MM, Okunowo WO, Yan D, Chen L, Zhang Y, Wan X. Exploiting the CRISPR-Cas9 gene-editing system for human cancers and immunotherapy. Clin Transl Immunology 2021; 10:e1286. [PMID: 34188916 PMCID: PMC8219901 DOI: 10.1002/cti2.1286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
The discovery of clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) technology has brought advances in the genetic manipulation of eukaryotic cells, which has revolutionised cancer research and treatment options. It is increasingly being used in cancer immunotherapy, including adoptive T and natural killer (NK) cell transfer, secretion of antibodies, cytokine stimulation and overcoming immune checkpoints. CRISPR-Cas9 technology is used in autologous T cells and NK cells to express various innovative antigen designs and combinations of chimeric antigen receptors (CARs) targeted at specific antigens for haematological and solid tumors. Additionally, advanced engineering in immune cells to enhance their sensing circuits with sophisticated functionality is now possible. Intensive research on the CRISPR-Cas9 system has provided scientists with the ability to overcome the hostile tumor microenvironment and generate more products for future clinical use, especially off-the-shelf, universal cellular products, bringing exciting milestones for immunotherapy. This review discussed the application and challenges of CRISPR technology in cancer research and immunotherapy, its advances and prospects for promoting new cell-based therapeutic beyond immune oncology.
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Affiliation(s)
- Lukman O Afolabi
- Guangdong Immune Cell therapy Engineering and Technology research CenterCenter for Protein and Cell‐based DrugsInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- Department of BiochemistryFaculty of ScienceFederal University DutseDutseNigeria
| | - Mariam O Afolabi
- Open FIESTA CenterTsinghua UniversityShenzhenChina
- State Key Laboratory of Chemical OncogenomicsGraduate School at ShenzhenTsinghua UniversityShenzhenChina
| | - Musbahu M Sani
- Department of BiochemistryFaculty of ScienceFederal University DutseDutseNigeria
| | - Wahab O Okunowo
- Department of BiochemistryCollege of MedicineUniversity of LagosLagosNigeria
| | - Dehong Yan
- Guangdong Immune Cell therapy Engineering and Technology research CenterCenter for Protein and Cell‐based DrugsInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Liang Chen
- Guangdong Immune Cell therapy Engineering and Technology research CenterCenter for Protein and Cell‐based DrugsInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaou Zhang
- Open FIESTA CenterTsinghua UniversityShenzhenChina
- State Key Laboratory of Chemical OncogenomicsGraduate School at ShenzhenTsinghua UniversityShenzhenChina
- School of Life SciencesTsinghua UniversityBeijingChina
| | - Xiaochun Wan
- Guangdong Immune Cell therapy Engineering and Technology research CenterCenter for Protein and Cell‐based DrugsInstitute of Biomedicine and BiotechnologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
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Seshu J, Moy BE, Ingle TM. Transformation of Borrelia burgdorferi. Curr Protoc 2021; 1:e61. [PMID: 33661557 DOI: 10.1002/cpz1.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Transformation techniques used to genetically manipulate Borrelia burgdorferi, the agent of Lyme disease, play a critical role in generating mutants that facilitate analyses of the role of genes in the pathophysiology of this bacterium. A number of borrelial mutants have been successfully isolated and characterized since the first electrotransformation procedure was established 25 years ago (Samuels, 1995). This article is directed at additional considerations for transforming infectious B. burgdorferi to generate strains retaining the plasmid profile of the parental strain, enabling analysis of transformants for in vitro and in vivo phenotypes. These methods are built on previously published protocols and are intended to add steps and tips to enhance transformation efficiency and recovery of strains amenable for studies involving colonization, survival, and transmission of B. burgdorferi during the vector and vertebrate phases of infection. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of stock cultures, propagation of spirochetes, and analysis of plasmid profiles Basic Protocol 2: Preparation of plasmid and linear DNA templates for transformation Basic Protocol 3: Transformation of B. burgdorferi Basic Protocol 4: Antibiotic selection of borrelial transformants Basic Protocol 5: Isolation of borrelial transformants in agar overlays Basic Protocol 6: Complementation of mutant borrelial strains in cis or in trans.
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Affiliation(s)
- J Seshu
- Department of Biology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas
| | - Brian E Moy
- Department of Biology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas
| | - Taylor MacMackin Ingle
- Department of Biology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas
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Nascimento PT, Fadini MAM, Rocha MS, Souza CSF, Barros BA, Melo JOF, Von Pinho RG, Valicente FH. Olfactory response of Trichogramma pretiosum (Hymenoptera: Trichogrammatidae) to volatiles induced by transgenic maize. Bull Entomol Res 2021; 111:1-14. [PMID: 34130764 DOI: 10.1017/s0007485321000341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plants not only respond to herbivorous damage but adjust their defense system after egg deposition by pest insects. Thereby, parasitoids use oviposition-induced plant volatiles to locate their hosts. We investigated the olfactory behavioral responses of Trichogramma pretiosum Riley, 1879 (Hymenoptera: Trichogrammatidae) to volatile blends emitted by maize (Zea mays L.) with singular and stacked events after oviposition by Spodoptera frugiperda Smith, 1797 (Hymenoptera: Trichogrammatidae) moths. Additionally, we examined possible variations in gene expression and on oviposition-induced volatiles. We used a Y-tube olfactometer to test for the wasp responses to volatiles released by maize plants oviposited by S. frugiperda and not-oviposited plants. Using the real-time PCR technique (qRT-PCR), we analyzed the expression of lipoxygenase and three terpene synthases genes, which are enzymes involved in the synthesis of volatile compounds that attract parasitoids of S. frugiperda. Olfactometer tests showed that T. pretiosum is strongly attracted by volatiles from transgenic maize emitted by S. frugiperda oviposition (VTPRO 3, more than 75% individuals were attracted). The relative expression of genes TPS10, LOX e STC was higher in transgenic hybrids than in the conventional (isogenic line) hybrids. The GC-MS analysis revealed that some volatile compounds are released exclusively by transgenic maize. This study provides evidence that transgenic hybrids enhanced chemical cues under oviposition-induction and helped to increase T. pretiosum efficiency in S. frugiperda control. This finding shows that among the evaluated hybrids, genetically modified hybrids can improve the biological control programs, since they potentialize the egg parasitoid foraging, integrating pest management.
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Affiliation(s)
| | - M A M Fadini
- Universidade Federal de São João del-Rei - UFSJ, São João del-Rei, Brasil
| | - M S Rocha
- Universidade Federal de São João del-Rei - UFSJ, São João del-Rei, Brasil
| | - C S F Souza
- Universidade Federal de Lavras - UFLA, Lavras, Brasil
| | - B A Barros
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Milho e Sorgo, Sete Lagoas, Brasil
| | - J O F Melo
- Universidade Federal de São João del-Rei - UFSJ, São João del-Rei, Brasil
| | - R G Von Pinho
- Universidade Federal de Lavras - UFLA, Lavras, Brasil
| | - F H Valicente
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Milho e Sorgo, Sete Lagoas, Brasil
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Wang X, Copmans D, de Witte PAM. Using Zebrafish as a Disease Model to Study Fibrotic Disease. Int J Mol Sci 2021; 22:ijms22126404. [PMID: 34203824 PMCID: PMC8232822 DOI: 10.3390/ijms22126404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
In drug discovery, often animal models are used that mimic human diseases as closely as possible. These animal models can be used to address various scientific questions, such as testing and evaluation of new drugs, as well as understanding the pathogenesis of diseases. Currently, the most commonly used animal models in the field of fibrosis are rodents. Unfortunately, rodent models of fibrotic disease are costly and time-consuming to generate. In addition, present models are not very suitable for screening large compounds libraries. To overcome these limitations, there is a need for new in vivo models. Zebrafish has become an attractive animal model for preclinical studies. An expanding number of zebrafish models of human disease have been documented, for both acute and chronic diseases. A deeper understanding of the occurrence of fibrosis in zebrafish will contribute to the development of new and potentially improved animal models for drug discovery. These zebrafish models of fibrotic disease include, among others, cardiovascular disease models, liver disease models (categorized into Alcoholic Liver Diseases (ALD) and Non-Alcoholic Liver Disease (NALD)), and chronic pancreatitis models. In this review, we give a comprehensive overview of the usage of zebrafish models in fibrotic disease studies, highlighting their potential for high-throughput drug discovery and current technical challenges.
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Affiliation(s)
- Xixin Wang
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KULeuven-University of Leuven, O&N II Herestraat 49-Box 824, 3000 Leuven, Belgium; (X.W.); (D.C.)
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), 28789 East Jingshi Road, Jinan 250103, China
| | - Daniëlle Copmans
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KULeuven-University of Leuven, O&N II Herestraat 49-Box 824, 3000 Leuven, Belgium; (X.W.); (D.C.)
| | - Peter A. M. de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KULeuven-University of Leuven, O&N II Herestraat 49-Box 824, 3000 Leuven, Belgium; (X.W.); (D.C.)
- Correspondence: ; Tel.: +32-16-323432
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Zoppo M, Poma N, Di Luca M, Bottai D, Tavanti A. Genetic Manipulation as a Tool to Unravel Candida parapsilosis Species Complex Virulence and Drug Resistance: State of the Art. J Fungi (Basel) 2021; 7:459. [PMID: 34200514 DOI: 10.3390/jof7060459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 01/12/2023] Open
Abstract
An increase in the rate of isolation of Candida parapsilosis in the past decade, as well as increased identification of azole-resistant strains are concerning, and require better understanding of virulence-like factors and drug-resistant traits of these species. In this regard, the present review “draws a line” on the information acquired, thus far, on virulence determinants and molecular mechanisms of antifungal resistance in these opportunistic pathogens, mainly derived from genetic manipulation studies. This will provide better focus on where we stand in our understanding of the C. parapsilosis species complex–host interaction, and how far we are from defining potential novel targets or therapeutic strategies—key factors to pave the way for a more tailored management of fungal infections caused by these fungal pathogens.
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Sakamoto H, Kita K, Matsuzaki M. A Novel 2A-peptide-containing Plasmid to Generate Stable Perkinsus marinus Cells Expressing Organelle-targeted Genes. J Eukaryot Microbiol 2021; 68:e12861. [PMID: 34051022 DOI: 10.1111/jeu.12861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic manipulation techniques for marine protists are not well-established, despite immense efforts. However, Perkinsus marinus is an exception and can be developed as a genetically tractable model organism for related protists. Here, we designed a new plasmid for P. marinus that allows two proteins from a single mRNA to be differently localized using a self-cleaving 2A peptide. This enabled us to establish a stable transfectant expressing a mitochondrially targeted fluorescent protein. The system can be applied to any protein in theory and would make a powerful tool for investigating unique organelles in P. marinus and related dinoflagellates.
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Affiliation(s)
- Hirokazu Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
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Abstract
This article describes several established approaches for genetic manipulation of Corynebacterium diphtheriae, the causative agent of diphtheria that is known to have provided key evidence for Koch's postulates on the germ theory. First, it includes a detailed gene deletion method that generates nonpolar, in-frame, markerless deletion mutants, utilizing the levansucrase SacB as a counter-selectable marker. Second, it provides a thorough protocol for rescuing deletion mutants using Escherichia coli-Corynebacterium shuttle vectors. Finally, a Tn5 transposon mutagenesis procedure is described. In principle, these protocols can be used for other Corynebacterium species, including Corynebacterium glutamicum and Corynebacterium matruchotii. © 2020 Wiley Periodicals LLC Basic Protocol 1: Gene deletion in Corynebacterium diphtheriae Basic Protocol 2: Complementation of a mutant strain Basic Protocol 3: Tn5 transposon mutagenesis of Corynebacterium diphtheriae.
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Affiliation(s)
- Chungyu Chang
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California
| | - Minh Tan Nguyen
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California.,NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hung Ton-That
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California.,Molecular Biology Institute, University of California, Los Angeles, California
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Lloyd CJ, Mejia-Santana A, Dalia TN, Dalia AB, Klose KE. Natural Transformation in a Classical-Biotype Vibrio cholerae Strain. Appl Environ Microbiol 2021; 87:e00060-21. [PMID: 33712424 DOI: 10.1128/AEM.00060-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae causes the gastrointestinal illness cholera, which spreads throughout the globe in large pandemics. The current pandemic is caused by O1 El Tor biotype strains, whereas previous pandemics were caused by O1 classical biotype strains. El Tor V. cholerae is noted for its ability to acquire exogenous DNA through chitin-induced natural transformation, which has been exploited for genetic manipulation of El Tor strains in the laboratory. In contrast, the prototypical classical strain O395 lacks this ability, which was suspected to be due to a mutation in the regulatory gene hapR HapR and the regulator TfoX control expression of a third competence regulator, QstR. We found that artificial induction of both TfoX and QstR in the presence of HapR in O395 was required for efficient DNA uptake. However, natural transformation in the classical strain is still orders of magnitude below that of an El Tor strain. O395 expressing HapR could also undergo natural transformation after growth on chitin, which could be increased by artificial induction of TfoX and/or QstR. A plasmid that expresses both TfoX and QstR was created that allowed for consistent DNA uptake in O395 carrying a hapR plasmid. This technique was also used to facilitate cotransformation into O395 of unmarked DNA (ΔlacZ, ΔflaA, ΔflgG) for multiplex genome editing by natural transformation (MuGENT). These results demonstrate that the classical biotype O395 strain is functionally capable of DNA uptake, which allows for the rapid genetic manipulation of its genome.IMPORTANCE Natural transformation (uptake of exogenous DNA) in Vibrio cholerae has contributed to the evolution of these human pathogens. Classical biotype V. cholerae strains were responsible for the first six cholera pandemics but were replaced by El Tor biotype V. cholerae in the current pandemic. This study demonstrates that classical V. cholerae is functionally capable of natural transformation, but inactivation of the transformation regulator HapR and inherent levels of transformation that are lower than those of El Tor V. cholerae suggest that the classical biotype may be less able to utilize natural transformation for horizontal gene transfer.
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Wege SM, Gejer K, Becker F, Bölker M, Freitag J, Sandrock B. Versatile CRISPR/Cas9 Systems for Genome Editing in Ustilago maydis. J Fungi (Basel) 2021; 7:149. [PMID: 33670568 DOI: 10.3390/jof7020149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/24/2022] Open
Abstract
The phytopathogenic smut fungus Ustilago maydis is a versatile model organism to study plant pathology, fungal genetics, and molecular cell biology. Here, we report several strategies to manipulate the genome of U. maydis by the CRISPR/Cas9 technology. These include targeted gene deletion via homologous recombination of short double-stranded oligonucleotides, introduction of point mutations, heterologous complementation at the genomic locus, and endogenous N-terminal tagging with the fluorescent protein mCherry. All applications are independent of a permanent selectable marker and only require transient expression of the endonuclease Cas9hf and sgRNA. The techniques presented here are likely to accelerate research in the U. maydis community but can also act as a template for genome editing in other important fungi.
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Meng J, Qiu Y, Shi S. CRISPR/Cas9 Systems for the Development of Saccharomyces cerevisiae Cell Factories. Front Bioeng Biotechnol 2020; 8:594347. [PMID: 33330425 PMCID: PMC7710542 DOI: 10.3389/fbioe.2020.594347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/19/2020] [Indexed: 01/09/2023] Open
Abstract
Synthetic yeast cell factories provide a remarkable solution for the sustainable supply of a range of products, ranging from large-scale industrial chemicals to high-value pharmaceutical compounds. Synthetic biology is a field in which metabolic pathways are intensively studied and engineered. The clustered, regularly interspaced, short, palindromic repeat-associated (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has emerged as the state-of-the-art gene editing technique for synthetic biology. Recently, the use of different CRISPR/Cas9 systems has been extended to the field of yeast engineering for single-nucleotide resolution editing, multiple-gene editing, transcriptional regulation, and genome-scale modifications. Such advancing systems have led to accelerated microbial engineering involving less labor and time and also enhanced the understanding of cellular genetics and physiology. This review provides a brief overview of the latest research progress and the use of CRISPR/Cas9 systems in genetic manipulation, with a focus on the applications of Saccharomyces cerevisiae cell factory engineering.
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Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Abstract
Achieving a harmonious gut microbial ecosystem has been hypothesized to be a successful method for alleviating metabolic disorders. The administration of probiotics, such as Lactobacillus and Bifidobacteria, is a known traditional and safe pathway to regulate human commensal microbes. With advancements in genetic sequencing and genetic editing tools, more bacteria are able to function as engineered probiotics with multiple therapeutic properties. As one of the next-generation probiotic candidates, Akkermansia muciniphila (A. muciniphila) has been discovered to enhance the gut barrier function and moderate inflammatory responses, exhibit improved effects with pasteurization and display beneficial probiotic effects in individuals with obesity, type 2 diabetes, atherosclerosis and autism-related gastrointestinal disturbances. In view of this knowledge, the present review aimed to summarize the effects of A. muciniphila in the treatment of metabolic disorders and to discuss several mature recombination systems for the genetic modification of A. muciniphila. From gaining an enhanced understanding of its genetic background, ingested A. muciniphila is expected to be used in various applications, including as a diagnostic tool, and in the site-specific delivery of therapeutic drugs.
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Affiliation(s)
- Yixuan Zou
- Institute of Translational Medicine, National Engineering Research Center for Bioengineering Drugs and Technologies, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Tingtao Chen
- Institute of Translational Medicine, National Engineering Research Center for Bioengineering Drugs and Technologies, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
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