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Wang S, Kong H, Zhuo C, Liu L, Lv S, Cheng D, Lao YH, Tao Y, Li M. Functionalized extracellular nanovesicles as advanced CRISPR delivery systems. Biomater Sci 2024. [PMID: 38808607 DOI: 10.1039/d4bm00054d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) system, an emerging tool for genome editing, has garnered significant public interest for its potential in treating genetic diseases. Despite the rapid advancements in CRISPR technology, the progress in developing effective delivery strategies lags, impeding its clinical application. Extracellular nanovesicles (EVs), either in their endogenous forms or with engineered modifications, have emerged as a promising solution for CRISPR delivery. These EVs offer several advantages, including high biocompatibility, biological permeability, negligible immunogenicity, and straightforward production. Herein, we first summarize various types of functional EVs for CRISPR delivery, such as unmodified, modified, engineered virus-like particles (VLPs), and exosome-liposome hybrid vesicles, and examine their distinct intracellular pathways. Then, we outline the cutting-edge techniques for functionalizing extracellular vesicles, involving producer cell engineering, vesicle engineering, and virus-like particle engineering, emphasizing the diverse CRISPR delivery capabilities of these nanovesicles. Lastly, we address the current challenges and propose rational design strategies for their clinical translation, offering future perspectives on the development of functionalized EVs.
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Affiliation(s)
- Siqing Wang
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Huimin Kong
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Chenya Zhuo
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Li Liu
- Department of Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518000, China
| | - Shixian Lv
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Du Cheng
- PCFM Lab of Ministry of Education, School of Material Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yeh-Hsing Lao
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA.
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou 510630, China
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2
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Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
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3
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Miller SA, Testen AL, Jacobs JM, Ivey MLL. Mitigating Emerging and Reemerging Diseases of Fruit and Vegetable Crops in a Changing Climate. PHYTOPATHOLOGY 2024:PHYTO10230393KC. [PMID: 38170665 DOI: 10.1094/phyto-10-23-0393-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Fruit and vegetable crops are important sources of nutrition and income globally. Producing these high-value crops requires significant investment of often scarce resources, and, therefore, the risks associated with climate change and accompanying disease pressures are especially important. Climate change influences the occurrence and pressure of plant diseases, enabling new pathogens to emerge and old enemies to reemerge. Specific environmental changes attributed to climate change, particularly temperature fluctuations and intense rainfall events, greatly alter fruit and vegetable disease incidence and severity. In turn, fruit and vegetable microbiomes, and subsequently overall plant health, are also affected by climate change. Changing disease pressures cause growers and researchers to reassess disease management and climate change adaptation strategies. Approaches such as climate smart integrated pest management, smart sprayer technology, protected culture cultivation, advanced diagnostics, and new soilborne disease management strategies are providing new tools for specialty crops growers. Researchers and educators need to work closely with growers to establish fruit and vegetable production systems that are resilient and responsive to changing climates. This review explores the effects of climate change on specialty food crops, pathogens, insect vectors, and pathosystems, as well as adaptations needed to ensure optimal plant health and environmental and economic sustainability.
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Affiliation(s)
- Sally A Miller
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691
| | - Anna L Testen
- U.S. Department of Agriculture-Agricultural Research Service Application Technology Research Unit, Wooster, OH 44691
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
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Feng S, Rcheulishvili N, Jiang X, Zhu P, Pan X, Wei M, Wang PG, Ji Y, Papukashvili D. A review on Gaucher disease: therapeutic potential of β-glucocerebrosidase-targeted mRNA/saRNA approach. Int J Biol Sci 2024; 20:2111-2129. [PMID: 38617529 PMCID: PMC11008270 DOI: 10.7150/ijbs.87741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/07/2024] [Indexed: 04/16/2024] Open
Abstract
Gaucher disease (GD), a rare hereditary lysosomal storage disorder, occurs due to a deficiency in the enzyme β-glucocerebrosidase (GCase). This deficiency leads to the buildup of substrate glucosylceramide (GlcCer) in macrophages, eventually resulting in various complications. Among its three types, GD2 is particularly severe with neurological involvements. Current treatments, such as enzyme replacement therapy (ERT), are not effective for GD2 and GD3 due to their inability to cross the blood-brain barrier (BBB). Other treatment approaches, such as gene or chaperone therapies are still in experimental stages. Additionally, GD treatments are costly and can have certain side effects. The successful use of messenger RNA (mRNA)-based vaccines for COVID-19 in 2020 has sparked interest in nucleic acid-based therapies. Remarkably, mRNA technology also offers a novel approach for protein replacement purposes. Additionally, self-amplifying RNA (saRNA) technology shows promise, potentially producing more protein at lower doses. This review aims to explore the potential of a cost-effective mRNA/saRNA-based approach for GD therapy. The use of GCase-mRNA/saRNA as a protein replacement therapy could offer a new and promising direction for improving the quality of life and extending the lifespan of individuals with GD.
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Affiliation(s)
- Shunping Feng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
| | - Nino Rcheulishvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Pan Zhu
- Cheerland Biomedicine, Shenzhen, China
| | - Xuehua Pan
- Shenzhen Pengbo Biotech Co. Ltd, Shenzhen, China
| | - Meilan Wei
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
| | - Peng George Wang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
| | - Yang Ji
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
| | - Dimitri Papukashvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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Han Y, Li F, Wu Y, Wang D, Luo G, Wang X, Wang X, Kuang H, Larkin RM. PSEUDO-ETIOLATION IN LIGHT proteins reduce greening by binding GLK transcription factors. PLANT PHYSIOLOGY 2024; 194:1722-1744. [PMID: 38051979 DOI: 10.1093/plphys/kiad641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Knocking out genes encoding proteins that downregulate the accumulation of pigments may lead to increases in crop quality and yield. PSEUDO-ETIOLATION IN LIGHT 1 (PEL1) downregulates the accumulation of carotenoids in carrot and chlorophyll in Arabidopsis and rice and may inhibit GOLDEN 2-LIKE (GLK) transcription factors. PEL1 belongs to a previously unstudied gene family found only in plants. We used CRISPR/Cas9 technology to knock out each member of the 4-member PEL gene family and both GLK genes in Arabidopsis. In pel mutants, chlorophyll levels were elevated in seedlings; after flowering, chloroplasts increased in size, and anthocyanin levels increased. Although the chlorophyll-deficient phenotype of glk1 glk2 was epistatic to pel1 pel2 pel3 pel4 in most of our experiments, glk1 glk2 was not epistatic to pel1 pel2 pel3 pel4 for the accumulation of anthocyanins in most of our experiments. The pel alleles attenuated growth, altered the accumulation of nutrients in seeds, disrupted an abscisic acid-inducible inhibition of seedling growth response that promotes drought tolerance, and affected the expression of genes associated with diverse biological functions, such as stress responses, cell wall metabolism hormone responses, signaling, growth, and the accumulation of phenylpropanoids and pigments. We found that PEL proteins specifically bind 6 transcription factors that influence the accumulation of anthocyanins, GLK2, and the carboxy termini of GLK1 and Arabidopsis thaliana myeloblastosis oncogene homolog 4 (AtMYB4). Our data indicate that the PEL proteins influence the accumulation of chlorophyll and many other processes, possibly by inhibiting GLK transcription factors and via other mechanisms, and that multiple mechanisms downregulate chlorophyll content.
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Affiliation(s)
- Yuting Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Fengfei Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ying Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Dong Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Guangbao Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xinning Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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Behrouzian Fard G, Ahmadi MH, Gholamin M, Amirfakhrian R, Saberi Teimourian E, Karimi MA, Hosseini Bafghi M. CRISPR-Cas9 technology: As an efficient genome modification tool in the cancer diagnosis and treatment. Biotechnol Bioeng 2024; 121:472-488. [PMID: 37986642 DOI: 10.1002/bit.28603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Cancer is the second most common cause of death globally and is a major public health concern. Managing this disease is difficult due to its multiple stages and numerous genetic and epigenetic changes. Traditional cancer diagnosis and treatment methods have limitations, making it crucial to develop new modalities to combat the increasing burden of cancer. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has transformed genetic engineering due to its simplicity, specificity, low cytotoxicity, and cost-effectiveness. It has been proposed as an effective technology to enhance cancer diagnosis and treatment strategies. This article presents the most recent discoveries regarding the structure, mechanism, and delivery methods of the highly powerful genome editing tool, CRISPR-Cas9. In terms of diagnosis, the article examines the role of CRISPR-Cas9 in detecting microRNAs and DNA methylation, and discusses two popular gene detection techniques that utilize the CRISPR-Cas system: DNA endonuclease-targeted CRISPR trans reporter and specific high sensitivity enzymatic reporter unlocking. Regarding treatment, the article explores several genes that have been identified and modified by CRISPR-Cas9 for effective tumorigenesis of common cancers such as breast, lung, and colorectal cancer. The present review also addresses the challenges and ethical issues associated with using CRISPR-Cas9 as a diagnostic and therapeutic tool. Despite some limitations, CRISPR-Cas9-based cancer diagnosis has the potential to become the next generation of cancer diagnostic tools, and the continuous progress of CRISPR-Cas9 can greatly aid in cancer treatment.
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Affiliation(s)
- Ghazaleh Behrouzian Fard
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hossein Ahmadi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehran Gholamin
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Razieh Amirfakhrian
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elahe Saberi Teimourian
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ali Karimi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdi Hosseini Bafghi
- Department of Laboratory Sciences, Faculty of Paramedical and Rehabilitation Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
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8
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Lou Y, Deng Z, Gao J. Genomics refined: AI-powered perspectives on structural analysis. TRENDS IN PLANT SCIENCE 2024; 29:123-125. [PMID: 37827897 DOI: 10.1016/j.tplants.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
Understanding protein function by deciphering 3D structure has distinct limitations. A recent study by Huang et al. used AlphaFold2, an artificial intelligence (AI) protein-folding prediction model, to predict and classify deaminase proteins based on structural similarities, highlighting the untapped potential of AI in functional genomics and protein engineering.
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Affiliation(s)
- Yi Lou
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jiangtao Gao
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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9
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Harisa GI, Faris TM, Sherif AY, Alzhrani RF, Alanazi SA, Kohaf NA, Alanazi FK. Gene-editing technology, from macromolecule therapeutics to organ transplantation: Applications, limitations, and prospective uses. Int J Biol Macromol 2023; 253:127055. [PMID: 37758106 DOI: 10.1016/j.ijbiomac.2023.127055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Gene editing technologies (GETs) could induce gene knockdown or gene knockout for biomedical applications. The clinical success of gene silence by RNAi therapies pays attention to other GETs as therapeutic approaches. This review aims to highlight GETs, categories, mechanisms, challenges, current use, and prospective applications. The different academic search engines, electronic databases, and bibliographies of selected articles were used in the preparation of this review with a focus on the fundamental considerations. The present results revealed that, among GETs, CRISPR/Cas9 has higher editing efficiency and targeting specificity compared to other GETs to insert, delete, modify, or replace the gene at a specific location in the host genome. Therefore, CRISPR/Cas9 is talented in the production of molecular, tissue, cell, and organ therapies. Consequently, GETs could be used in the discovery of innovative therapeutics for genetic diseases, pandemics, cancer, hopeless diseases, and organ failure. Specifically, GETs have been used to produce gene-modified animals to spare human organ failure. Genetically modified pigs are used in clinical trials as a source of heart, liver, kidneys, and lungs for xenotransplantation (XT) in humans. Viral, non-viral, and hybrid vectors have been utilized for the delivery of GETs with some limitations. Therefore, extracellular vesicles (EVs) are proposed as intelligent and future cargoes for GETs delivery in clinical applications. This study concluded that GETs are promising for the production of molecular, cellular, and organ therapies. The use of GETs as XT is still in the early stage as well and they have ethical and biosafety issues.
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Affiliation(s)
- Gamaleldin I Harisa
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Biochemistry and Molecular Biology, College of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Tarek M Faris
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Abdelrahman Y Sherif
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Riyad F Alzhrani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Nanobiotechnology Research Unit, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alanazi
- Pharmaceutical Care Services, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Science Collage of Pharmacy, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Neveen A Kohaf
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Fars K Alanazi
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Khanna K, Ohri P, Bhardwaj R. Nanotechnology and CRISPR/Cas9 system for sustainable agriculture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118049-118064. [PMID: 36973619 DOI: 10.1007/s11356-023-26482-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), a genome editing tool, has gained a tremendous position due to its therapeutic efficacy, ability to counteract abiotic/biotic stresses in plants, environmental remediation and sustainable agriculture with the aim of food security. This is mainly due to their potential of precised genome modification and numerous genetic engineering protocols with versatility as well as simplicity. This technique is quite useful for crop refinement and overcoming the agricultural losses and regaining the soil fertility hampered by hazardous chemicals. Since CRISPR/Cas9 has been widely accepted in genome editing in plants, however, their revolutionised nature and progress enable genetic engineers to face numerous challenges in plant biotechnology. Therefore, nanoparticles have addressed these challenges and improved cargo delivery and genomic editing processes. Henceforth, this barrier prevents CRISPR-based genetic engineering in plants in order to show efficacy in full potential and eliminate all the barriers. This advancement accelerates the genome editing process and its applications in plant biotechnology enable us to sustain and feed the massive population under varying environments. Genome editing tools using CRISPR/Cas9 and nanotechnology are advantageous that produce transgenic-free plants that overcome global food demands. Here, in this review, we have aimed towards the mechanisms/delivery systems linked with CRISPR/Cas9 system. We have elaborated on the applications of CRISPR/Cas9 and nanotechnology-based systems for sustainable agriculture. Moreover, the challenges and limitations associated with genome editing and delivery systems have also been discussed with a special emphasis on crop improvement.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
- Department of Microbiology, DAV University, Sarmastpur, Jalandhar, 144001, Punjab, India.
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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Ahmad A, Jamil A, Munawar N. GMOs or non-GMOs? The CRISPR Conundrum. FRONTIERS IN PLANT SCIENCE 2023; 14:1232938. [PMID: 37877083 PMCID: PMC10591184 DOI: 10.3389/fpls.2023.1232938] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023]
Abstract
CRISPR-Cas9, the "genetic scissors", is being presaged as a revolutionary technology, having tremendous potential to create designer crops by introducing precise and targeted modifications in the genome to achieve global food security in the face of climate change and increasing population. Traditional genetic engineering relies on random and unpredictable insertion of isolated genes or foreign DNA elements into the plant genome. However, CRISPR-Cas based gene editing does not necessarily involve inserting a foreign DNA element into the plant genome from different species but introducing new traits by precisely altering the existing genes. CRISPR edited crops are touching markets, however, the world community is divided over whether these crops should be considered genetically modified (GM) or non-GM. Classification of CRISPR edited crops, especially transgene free crops as traditional GM crops, will significantly affect their future and public acceptance in some regions. Therefore, the future of the CRISPR edited crops is depending upon their regulation as GM or non-GMs, and their public perception. Here we briefly discuss how CRISPR edited crops are different from traditional genetically modified crops. In addition, we discuss different CRISPR reagents and their delivery tools to produce transgene-free CRISPR edited crops. Moreover, we also summarize the regulatory classification of CRISPR modifications and how different countries are regulating CRISPR edited crops. We summarize that the controversy of CRISPR-edited plants as GM or non-GM will continue until a universal, transparent, and scalable regulatory framework for CRISPR-edited plants will be introduced worldwide, with increased public awareness by involving all stakeholders.
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Affiliation(s)
- Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
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12
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Allemailem KS, Alsahli MA, Almatroudi A, Alrumaihi F, Al Abdulmonem W, Moawad AA, Alwanian WM, Almansour NM, Rahmani AH, Khan AA. Innovative Strategies of Reprogramming Immune System Cells by Targeting CRISPR/Cas9-Based Genome-Editing Tools: A New Era of Cancer Management. Int J Nanomedicine 2023; 18:5531-5559. [PMID: 37795042 PMCID: PMC10547015 DOI: 10.2147/ijn.s424872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023] Open
Abstract
The recent developments in the study of clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system have revolutionized the art of genome-editing and its applications for cellular differentiation and immune response behavior. This technology has further helped in understanding the mysteries of cancer progression and possible designing of novel antitumor immunotherapies. CRISPR/Cas9-based genome-editing is now often used to engineer universal T-cells, equipped with recombinant T-cell receptor (TCR) or chimeric antigen receptor (CAR). In addition, this technology is used in cytokine stimulation, antibody designing, natural killer (NK) cell transfer, and to overcome immune checkpoints. The innovative potential of CRISPR/Cas9 in preparing the building blocks of adoptive cell transfer (ACT) immunotherapy has opened a new window of antitumor immunotherapy and some of them have gained FDA approval. The manipulation of immunogenetic regulators has opened a new interface for designing, implementation and interpretation of CRISPR/Cas9-based screening in immuno-oncology. Several cancers like lymphoma, melanoma, lung, and liver malignancies have been treated with this strategy, once thought to be impossible. The safe and efficient delivery of CRISPR/Cas9 system within the immune cells for the genome-editing strategy is a challenging task which needs to be sorted out for efficient immunotherapy. Several targeting approaches like virus-mediated, electroporation, microinjection and nanoformulation-based methods have been used, but each procedure offers some limitations. Here, we elaborate the recent updates of cancer management through immunotherapy in partnership with CRISPR/Cas9 technology. Further, some innovative methods of targeting this genome-editing system within the immune system cells for reprogramming them, as a novel strategy of anticancer immunotherapy is elaborated. In addition, future prospects and clinical trials are also discussed.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Amira A Moawad
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Wanian M Alwanian
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Sabra DM, Krin A, Romeral AB, Frieß JL, Jeremias G. Anthrax revisited: how assessing the unpredictable can improve biosecurity. Front Bioeng Biotechnol 2023; 11:1215773. [PMID: 37795173 PMCID: PMC10546327 DOI: 10.3389/fbioe.2023.1215773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 10/06/2023] Open
Abstract
B. anthracis is one of the most often weaponized pathogens. States had it in their bioweapons programs and criminals and terrorists have used or attempted to use it. This study is motivated by the narrative that emerging and developing technologies today contribute to the amplification of danger through greater easiness, accessibility and affordability of steps in the making of an anthrax weapon. As states would have way better preconditions if they would decide for an offensive bioweapons program, we focus on bioterrorism. This paper analyzes and assesses the possible bioterrorism threat arising from advances in synthetic biology, genome editing, information availability, and other emerging, and converging sciences and enabling technologies. Methodologically we apply foresight methods to encourage the analysis of contemporary technological advances. We have developed a conceptual six-step foresight science framework approach. It represents a synthesis of various foresight methodologies including literature review, elements of horizon scanning, trend impact analysis, red team exercise, and free flow open-ended discussions. Our results show a significant shift in the threat landscape. Increasing affordability, widespread distribution, efficiency, as well as ease of use of DNA synthesis, and rapid advances in genome-editing and synthetic genomic technologies lead to an ever-growing number and types of actors who could potentially weaponize B. anthracis. Understanding the current and future capabilities of these technologies and their potential for misuse critically shapes the current and future threat landscape and underlines the necessary adaptation of biosecurity measures in the spheres of multi-level political decision making and in the science community.
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Affiliation(s)
- Dunja Manal Sabra
- Carl Friedrich von Weizsäcker-Centre for Science and Peace Research (ZNF), University of Hamburg, Bogenallee, Hamburg, Germany
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15
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Trump BD, Cummings CL, Loschin N, Keisler JM, Wells EM, Linkov I. The worsening divergence of biotechnology: the importance of risk culture. Front Bioeng Biotechnol 2023; 11:1250298. [PMID: 37711457 PMCID: PMC10499176 DOI: 10.3389/fbioe.2023.1250298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Abstract
In the last 20 years, the field of biotechnology has made significant progress and attracted substantial investments, leading to different paths of technological modernization among nations. As a result, there is now an international divide in the commercial and intellectual capabilities of biotechnology, and the implications of this divergence are not well understood. This raises important questions about why global actors are motivated to participate in biotechnology modernization, the challenges they face in achieving their goals, and the possible future direction of global biotechnology development. Using the framework of prospect theory, this paper explores the role of risk culture as a fundamental factor contributing to this divergence. It aims to assess the risks and benefits associated with the early adoption of biotechnology and the regulatory frameworks that shape the development and acceptance of biotechnological innovations. By doing so, it provides valuable insights into the future of biotechnology development and its potential impact on the global landscape.
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Affiliation(s)
- Benjamin D. Trump
- United States Army Corps of Engineers, Washington, DC, United States
| | - Christopher L. Cummings
- United States Army Corps of Engineers, Washington, DC, United States
- Department of Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, United States
- Department of Sociology, Iowa State University, Ames, IA, United States
| | - Nicholas Loschin
- Department of Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, United States
| | - Jeffrey M. Keisler
- Department of Management Science & Info Sys, University of Massachusetts Boston, Boston, MA, United States
| | - Emily M. Wells
- United States Army Corps of Engineers, Washington, DC, United States
| | - Igor Linkov
- United States Army Corps of Engineers, Washington, DC, United States
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16
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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17
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Garg D, Samota MK, Kontis N, Patel N, Bala S, Rosado AS. Revolutionizing biofuel generation: Unleashing the power of CRISPR-Cas mediated gene editing of extremophiles. Microbiol Res 2023; 274:127443. [PMID: 37399654 DOI: 10.1016/j.micres.2023.127443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
Molecular biology techniques like gene editing have altered the specific genes in micro-organisms to increase their efficiency to produce biofuels. This review paper investigates the outcomes of Clustered regularly interspaced short palindromic repeats (CRISPR) for gene editing in extremophilic micro-organisms to produce biofuel. Commercial production of biofuel from lignocellulosic waste is limited due to various constraints. A potential strategy to enhance the capability of extremophiles to produce biofuel is gene-editing via CRISPR-Cas technology. The efficiency of intracellular enzymes like cellulase, hemicellulose in extremophilic bacteria, fungi and microalgae has been increased by alteration of genes associated with enzymatic activity and thermotolerance. extremophilic microbes like Thermococcus kodakarensis, Thermotoga maritima, Thermus thermophilus, Pyrococcus furiosus and Sulfolobus sp. are explored for biofuel production. The conversion of lignocellulosic biomass into biofuels involves pretreatment, hydrolysis and fermentation. The challenges like off-target effect associated with use of extremophiles for biofuel production is also addressed. The appropriate regulations are required to maximize effectiveness while minimizing off-target cleavage, as well as the total biosafety of this technique. The latest discovery of the CRISPR-Cas system should provide a new channel in the creation of microbial biorefineries through site- specific gene editing that might boost the generation of biofuels from extremophiles. Overall, this review study highlights the potential for genome editing methods to improve the potential of extremophiles to produce biofuel, opening the door to more effective and environmentally friendly biofuel production methods.
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Affiliation(s)
- Diksha Garg
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
| | | | - Nicholas Kontis
- Red Sea Research Center, Biological and Environmental Science and Engineering Division,King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia; Computational Bioscience Research Center, Biological and Environmental Science and, Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Niketan Patel
- Red Sea Research Center, Biological and Environmental Science and Engineering Division,King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia; Computational Bioscience Research Center, Biological and Environmental Science and, Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Saroj Bala
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
| | - Alexandre Soares Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division,King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia; Computational Bioscience Research Center, Biological and Environmental Science and, Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia.
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18
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Joshi A, Song HG, Yang SY, Lee JH. Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2454. [PMID: 37447014 DOI: 10.3390/plants12132454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Hyung-Geun Song
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
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19
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Wei T, Jiang L, You X, Ma P, Xi Z, Wang NN. Generation of Herbicide-Resistant Soybean by Base Editing. BIOLOGY 2023; 12:biology12050741. [PMID: 37237553 DOI: 10.3390/biology12050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Weeds cause the largest yield loss in soybean production. The development of herbicide-resistant soybean germplasm is of great significance for weed control and yield improvement. In this study, we used the cytosine base editor (BE3) to develop novel herbicide-resistant soybean. We have successfully introduced base substitutions in GmAHAS3 and GmAHAS4 and obtained a heritable transgene-free soybean with homozygous P180S mutation in GmAHAS4. The GmAHAS4 P180S mutants have apparent resistance to chlorsulfuron, flucarbazone-sodium, and flumetsulam. In particular, the resistance to chlorsulfuron was more than 100 times that of with wild type TL-1. The agronomic performance of the GmAHAS4 P180S mutants showed no significant differences to TL-1 under natural growth conditions. In addition, we developed allele-specific PCR markers for the GmAHAS4 P180S mutants, which can easily discriminate homozygous, heterozygous mutants, and wild-type plants. This study demonstrates a feasible and effective way to generate herbicide-resistant soybean by using CRISPR/Cas9-mediated base editing.
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Affiliation(s)
- Tao Wei
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Linjian Jiang
- Key Laboratory of Pest Monitoring and Green Management, MOA, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiang You
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Pengyu Ma
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Engineering Research Center of Pesticide, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ning Ning Wang
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
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20
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Stapleton P, Torres Yabar A. Playing God? Media coverage of CRISPR in the United States. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2023; 32:504-521. [PMID: 36527362 DOI: 10.1177/09636625221138953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Announcements in 2017 and 2018 that scientists used a gene editing technique called Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to permanently alter human embryos have highlighted the urgency in regulating the technology's ethical, political, and legal implications. To better understand how a regulatory regime might evolve in response to CRISPR, we must examine how the media covers it. This article reviews online and television news sources in the United States to determine the tone, content, and frequency in media coverage of CRISPR. We find that coverage remained ambiguous and infrequent, as scientific research into CRISPR's clinical potential for treating human disease surged. This infrequent coverage indicates that the media have not yet established the salience of CRISPR to a degree that engages the public or policymakers, though the issue will continue to gain importance as CRISPR transitions from experimental efforts into clinical practice.
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21
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Allemailem KS, Almatroodi SA, Almatroudi A, Alrumaihi F, Al Abdulmonem W, Al-Megrin WAI, Aljamaan AN, Rahmani AH, Khan AA. Recent Advances in Genome-Editing Technology with CRISPR/Cas9 Variants and Stimuli-Responsive Targeting Approaches within Tumor Cells: A Future Perspective of Cancer Management. Int J Mol Sci 2023; 24:7052. [PMID: 37108214 PMCID: PMC10139162 DOI: 10.3390/ijms24087052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
The innovative advances in transforming clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) into different variants have taken the art of genome-editing specificity to new heights. Allosteric modulation of Cas9-targeting specificity by sgRNA sequence alterations and protospacer adjacent motif (PAM) modifications have been a good lesson to learn about specificity and activity scores in different Cas9 variants. Some of the high-fidelity Cas9 variants have been ranked as Sniper-Cas9, eSpCas9 (1.1), SpCas9-HF1, HypaCas9, xCas9, and evoCas9. However, the selection of an ideal Cas9 variant for a given target sequence remains a challenging task. A safe and efficient delivery system for the CRISPR/Cas9 complex at tumor target sites faces considerable challenges, and nanotechnology-based stimuli-responsive delivery approaches have significantly contributed to cancer management. Recent innovations in nanoformulation design, such as pH, glutathione (GSH), photo, thermal, and magnetic responsive systems, have modernized the art of CRISPR/Cas9 delivery approaches. These nanoformulations possess enhanced cellular internalization, endosomal membrane disruption/bypass, and controlled release. In this review, we aim to elaborate on different CRISPR/Cas9 variants and advances in stimuli-responsive nanoformulations for the specific delivery of this endonuclease system. Furthermore, the critical constraints of this endonuclease system on clinical translations towards the management of cancer and prospects are described.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Saleh A. Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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22
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Khan AH, Min L, Ma Y, Zeeshan M, Jin S, Zhang X. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:680-697. [PMID: 36221230 PMCID: PMC10037161 DOI: 10.1111/pbi.13946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 05/16/2023]
Abstract
Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Muhammad Zeeshan
- Guangxi Key Laboratory for Agro‐Environment and Agro‐Product Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, College of AgricultureGuanxi UniversityNanningChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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23
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López-Casado G, Sánchez-Raya C, Ric-Varas PD, Paniagua C, Blanco-Portales R, Muñoz-Blanco J, Pose S, Matas AJ, Mercado JA. CRISPR/Cas9 editing of the polygalacturonase FaPG1 gene improves strawberry fruit firmness. HORTICULTURE RESEARCH 2023; 10:uhad011. [PMID: 36960432 PMCID: PMC10028403 DOI: 10.1093/hr/uhad011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Firmness is one of the most important fruit quality traits in strawberries. The postharvest shelf life of this soft fruit is highly limited by the loss of firmness, where cell wall disassembly plays an important role. Previous studies demonstrated that the polygalacturonase FaPG1 has a key role in remodelling pectins during strawberry softening. In this study, FaPG1 knockout strawberry plants have been generated using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens. Ten independent lines, cv. "Chandler", were obtained, and all of them were successfully edited as determined by PCR amplification and T7 endonuclease assay. The targeted mutagenesis insertion and deletion rates were analyzed using targeted deep sequencing. The percentage of edited sequences varied from 47% up to almost 100%, being higher than 95% for seven of the selected lines. Phenotypic analyses showed that 7 out of the eight lines analyzed produced fruits significantly firmer than the control, ranging from 33 to 70% increase in firmness. There was a positive relationship between the degree of FaPG1 editing and the rise in fruit firmness. Minor changes were observed in other fruit quality traits, such as colour, soluble solids, titratable acidity or anthocyanin content. Edited fruits showed a reduced softening rate during postharvest, displayed a reduced transpirational water loss, and were less damaged by Botrytis cinerea inoculation. The analysis of four potential off-target sites revealed no mutation events. In conclusion, editing the FaPG1 gene using the CRISPR/Cas9 system is an efficient method for improving strawberry fruit firmness and shelf life.
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Affiliation(s)
| | | | - Pablo D Ric-Varas
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ (IHSM-UMA-CSIC), Universidad de Málaga, 29071 Málaga, Spain
| | - Candelas Paniagua
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ (IHSM-UMA-CSIC), Universidad de Málaga, 29071 Málaga, Spain
| | - Rosario Blanco-Portales
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Juan Muñoz-Blanco
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Sara Pose
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ (IHSM-UMA-CSIC), Universidad de Málaga, 29071 Málaga, Spain
| | - Antonio J Matas
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ (IHSM-UMA-CSIC), Universidad de Málaga, 29071 Málaga, Spain
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24
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CRISPR Gene Therapy: A Promising One-Time Therapeutic Approach for Transfusion-Dependent β-Thalassemia—CRISPR-Cas9 Gene Editing for β-Thalassemia. THALASSEMIA REPORTS 2023. [DOI: 10.3390/thalassrep13010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
β-Thalassemia is an inherited hematological disorder that results from genetic changes in the β-globin gene, leading to the reduced or absent synthesis of β-globin. For several decades, the only curative treatment option for β-thalassemia has been allogeneic hematopoietic cell transplantation (allo-HCT). Nonetheless, rapid progress in genome modification technologies holds great potential for treating this disease and will soon change the current standard of care for β-thalassemia. For instance, the emergence of the CRISPR/Cas9 genome editing platform has opened the door for precision gene editing and can serve as an effective molecular treatment for a multitude of genetic diseases. Investigational studies were carried out to treat β-thalassemia patients utilizing CRISPR-based CTX001 therapy targeting the fetal hemoglobin silencer BCL11A to restore γ-globin expression in place of deficient β-globin. The results of recently carried out clinical trials provide hope of CTX001 being a promising one-time therapeutic option to treat β-hemoglobinopathies. This review provides an insight into the key scientific steps that led to the development and application of novel CRISPR/Cas9–based gene therapies as a promising therapeutic platform for transfusion-dependent β-thalassemia (TDT). Despite the resulting ethical, moral, and social challenges, CRISPR provides an excellent treatment option against hemoglobin-associated genetic diseases.
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25
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Anders C, Hoengenaert L, Boerjan W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102329. [PMID: 36586396 PMCID: PMC7614060 DOI: 10.1016/j.pbi.2022.102329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The high economic value of wood requires intensive breeding towards multipurpose biomass. However, long breeding cycles hamper the fast development of novel tree varieties that have improved biomass properties, are tolerant to biotic and abiotic stresses, and resilient to climate change. To speed up domestication, the integration of conventional breeding and new breeding techniques is needed. In this review, we discuss recent advances in genome editing and Cas-DNA-free genome engineering of forest trees, and briefly discuss how multiplex editing combined with multi-omics approaches can accelerate the genetic improvement of forest trees, with a focus on wood.
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Affiliation(s)
- Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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26
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Rahman SU, McCoy E, Raza G, Ali Z, Mansoor S, Amin I. Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies. Mol Biotechnol 2023; 65:162-180. [PMID: 35119645 DOI: 10.1007/s12033-022-00456-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/21/2022] [Indexed: 01/18/2023]
Abstract
Soybean is considered one of the important crops among legumes. Due to high nutritional contents in seed (proteins, sugars, oil, fatty acids, and amino acids), soybean is used globally for food, feed, and fuel. The primary consumption of soybean is vegetable oil and feed for chickens and livestock. Apart from this, soybean benefits soil fertility by fixing atmospheric nitrogen through root nodular bacteria. While conventional breeding is practiced for soybean improvement, with the advent of new biotechnological methods scientists have also engineered soybean to improve different traits (herbicide, insect, and disease resistance) to fulfill consumer requirements and to meet the global food deficiency. Genetic engineering (GE) techniques such as transgenesis and gene silencing help to minimize the risks and increase the adaptability of soybean. Recently, new plant breeding technologies (NPBTs) emerged such as zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), which paved the way for enhanced genetic modification of soybean. These NPBTs have the potential to improve soybean via gene functional characterization precision genome engineering for trait improvement. Importantly, these NPBTs address the ethical and public acceptance issues related to genetic modifications and transgenesis in soybean. In the present review, we summarized the improvement of soybean through GE and NPBTs. The valuable traits that have been improved through GE for different constraints have been discussed. Moreover, the traits that have been improved through NPBTs and potential targets for soybean improvements via NPBTs and solutions for ethical and public acceptance are also presented.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Evan McCoy
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, USA
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zahir Ali
- Laboratory for Genome Engineering, Center for Desert Agriculture and Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
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27
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Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) genome editing, coupled with advances in computing and imaging capabilities, has initiated a new era in which genetic diseases and individual disease susceptibilities are both predictable and actionable. Likewise, genes responsible for plant traits can be identified and altered quickly, transforming the pace of agricultural research and plant breeding. In this Review, we discuss the current state of CRISPR-mediated genetic manipulation in human cells, animals, and plants along with relevant successes and challenges and present a roadmap for the future of this technology.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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28
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Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms. Foods 2023; 12:foods12030455. [PMID: 36765984 PMCID: PMC9914749 DOI: 10.3390/foods12030455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.
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29
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Malla RR, Middela K. CRISPR-Based Approaches for Cancer Immunotherapy. Crit Rev Oncog 2023; 28:1-14. [PMID: 38050977 DOI: 10.1615/critrevoncog.2023048723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) technology is a powerful gene editing tool that has the potential to revolutionize cancer treatment. It allows for precise and efficient editing of specific genes that drive cancer growth and progression. CRISPR-based approaches gene knock-out, which deletes specific genes or sequences of DNA within a cancer cell, and gene knock-in, which inserts new sequences of DNA into a cancer cell to identify potential targets for cancer therapy. Further, genome-wide CRISPR-Cas9-based screens identify specific markers for diagnosis of cancers. Recently, immunotherapy has become a highly efficient strategy for the treatment of cancer. The use of CRISPR in cancer immunotherapy is focused on enhancing the function of T cells, making them more effective at attacking cancer cells and inactivating the immune evasion mechanisms of cancer cells. It has the potential to generate CAR-T cells, which are T cells that have been genetically engineered to target and attack cancer cells specifically. This review uncovers the latest developments in CRISPR-based gene editing strategies and delivery of their components in cancer cells. In addition, the applications of CRISPR in cancer immune therapy are discussed. Overall, this review helps to explore the potential of CRISPR-based strategies in cancer immune therapy in clinical settings.
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Affiliation(s)
- Rama Rao Malla
- Cancer Biology Laboratory, Department of Biochemistry and Bioinformatics, School of Science, Gandhi Institute of Technology and Management (GITAM) (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India; Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
| | - Keerthana Middela
- Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
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30
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González MN, Massa GA, Andersson M, Storani L, Olsson N, Décima Oneto CA, Hofvander P, Feingold SE. CRISPR/Cas9 Technology for Potato Functional Genomics and Breeding. Methods Mol Biol 2023; 2653:333-361. [PMID: 36995636 DOI: 10.1007/978-1-0716-3131-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cultivated potato (Solanum tuberosum L.) is one of the most important staple food crops worldwide. Its tetraploid and highly heterozygous nature poses a great challenge to its basic research and trait improvement through traditional mutagenesis and/or crossbreeding. The establishment of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) as a gene editing tool has allowed the alteration of specific gene sequences and their concomitant gene function, providing powerful technology for potato gene functional analysis and improvement of elite cultivars. This technology relies on a short RNA molecule called single guide RNA (sgRNA) that directs the Cas9 nuclease to induce a site-specific double-stranded break (DSB). Further, repair of the DSB by the error-prone non-homologous end joining (NHEJ) mechanism leads to the introduction of targeted mutations, which can be used to produce the loss of function of specific gene(s). In this chapter, we describe experimental procedures to apply the CRISPR/Cas9 technology for potato genome editing. First, we provide strategies for target selection and sgRNA design and describe a Golden Gate-based cloning system to obtain a sgRNA/Cas9-encoding binary vector. We also describe an optimized protocol for ribonucleoprotein (RNP) complex assembly. The binary vector can be used for both Agrobacterium-mediated transformation and transient expression in potato protoplasts, while the RNP complexes are intended to obtain edited potato lines through protoplast transfection and plant regeneration. Finally, we describe procedures to identify the gene-edited potato lines. The methods described here are suitable for potato gene functional analysis and breeding.
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Affiliation(s)
- Matías Nicolás González
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Gabriela Alejandra Massa
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Leonardo Storani
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica, Buenos Aires, Argentina
| | - Niklas Olsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Andrea Décima Oneto
- Laboratorio de Agrobiotecnología, IPADS (INTA - CONICET), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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31
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Wang Y, Tang Q, Pu L, Zhang H, Li X. CRISPR-Cas technology opens a new era for the creation of novel maize germplasms. FRONTIERS IN PLANT SCIENCE 2022; 13:1049803. [PMID: 36589095 PMCID: PMC9800880 DOI: 10.3389/fpls.2022.1049803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Maize (Zea mays) is one of the most important food crops in the world with the greatest global production, and contributes to satiating the demands for human food, animal feed, and biofuels. With population growth and deteriorating environment, efficient and innovative breeding strategies to develop maize varieties with high yield and stress resistance are urgently needed to augment global food security and sustainable agriculture. CRISPR-Cas-mediated genome-editing technology (clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated)) has emerged as an effective and powerful tool for plant science and crop improvement, and is likely to accelerate crop breeding in ways dissimilar to crossbreeding and transgenic technologies. In this review, we summarize the current applications and prospects of CRISPR-Cas technology in maize gene-function studies and the generation of new germplasm for increased yield, specialty corns, plant architecture, stress response, haploid induction, and male sterility. Optimization of gene editing and genetic transformation systems for maize is also briefly reviewed. Lastly, the challenges and new opportunities that arise with the use of the CRISPR-Cas technology for maize genetic improvement are discussed.
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Affiliation(s)
- Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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32
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CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:cells11233928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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33
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Nerva L, Sandrini M, Moffa L, Velasco R, Balestrini R, Chitarra W. Breeding toward improved ecological plant-microbiome interactions. TRENDS IN PLANT SCIENCE 2022; 27:1134-1143. [PMID: 35803843 DOI: 10.1016/j.tplants.2022.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
| | - Marco Sandrini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Loredana Moffa
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy
| | - Raffaella Balestrini
- National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy.
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
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Obermeier C, Mason AS, Meiners T, Petschenka G, Rostás M, Will T, Wittkop B, Austel N. Perspectives for integrated insect pest protection in oilseed rape breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3917-3946. [PMID: 35294574 PMCID: PMC9729155 DOI: 10.1007/s00122-022-04074-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/01/2022] [Indexed: 05/02/2023]
Abstract
In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.
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Affiliation(s)
- Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Torsten Meiners
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
| | - Georg Petschenka
- Department of Applied Entomology, University of Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
| | - Michael Rostás
- Division of Agricultural Entomology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany
| | - Torsten Will
- Insitute for Resistance Research and Stress Tolerance, Julius Kühn Insitute, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Nadine Austel
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
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Zandberg JD, Fernandez CT, Danilevicz MF, Thomas WJW, Edwards D, Batley J. The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. PLANTS (BASEL, SWITZERLAND) 2022; 11:2740. [PMID: 36297764 PMCID: PMC9610009 DOI: 10.3390/plants11202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.
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Affiliation(s)
- Jaco D. Zandberg
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | - Monica F. Danilevicz
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- Center for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
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Ding X, Yu L, Chen L, Li Y, Zhang J, Sheng H, Ren Z, Li Y, Yu X, Jin S, Cao J. Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants. Cells 2022; 11:3045. [PMID: 36231007 PMCID: PMC9564188 DOI: 10.3390/cells11193045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining the dCas9 protein and transcriptional activator to achieve specific regulation of gene expression has made important contributions to biotechnology in medical research as well as agriculture. CRISPR/dCas9 activation (CRISPRa) can increase the transcription of endogenous genes. Overexpression of foreign genes by traditional transgenic technology in plant cells is the routine method to verify gene function by elevating genes transcription. One of the main limitations of the overexpression is the vector capacity constraint that makes it difficult to express multiple genes using the typical Ti plasmid vectors from Agrobacterium. The CRISPRa system can overcome these limitations of the traditional gene overexpression method and achieve multiple gene activation by simply designating several guide RNAs in one vector. This review summarizes the latest progress based on the development of CRISPRa systems, including SunTag, dCas9-VPR, dCas9-TV, scRNA, SAM, and CRISPR-Act and their applications in plants. Furthermore, limitations, challenges of current CRISPRa systems and future prospective applications are also discussed.
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Affiliation(s)
- Xiao Ding
- Institute of Cotton, Shanxi Agricultural University, Yuncheng 044000, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Luo Chen
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujie Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinlun Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanyan Sheng
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengwei Ren
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunlong Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohan Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinglin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
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Li B, Fu C, Zhou J, Hui F, Wang Q, Wang F, Wang G, Xu Z, Che L, Yuan D, Wang Y, Zhang X, Jin S. Highly Efficient Genome Editing Using Geminivirus-Based CRISPR/Cas9 System in Cotton Plant. Cells 2022; 11:cells11182902. [PMID: 36139477 PMCID: PMC9496795 DOI: 10.3390/cells11182902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Upland cotton (Gossypium hirsutum), an allotetraploid, contains At- and Dt- subgenome and most genes have multiple homologous copies, which pose a huge challenge to investigate genes’ function due to the functional redundancy. Therefore, it is of great significance to establish effective techniques for the functional genomics in cotton. In this study, we tested two novel genome editing vectors and compared them with the CRISPR/Cas9 system (pRGEB32-GhU6.7) developed in our laboratory previously. In the first new vector, the sgRNA transcription unite was constructed into the replicon (LIR-Donor-SIR-Rep-LIR) of the bean yellow dwarf virus (BeYDV) and named as pBeYDV-Cas9-KO and in the second vector, the ubiquitin promoter that drives Cas9 protein was replaced with a constitutive CaMV 35S promoter and defined as pRGEB32-35S. The results from transgenic cotton calli/plants revealed that pBeYDV-Cas9-KO vector showed the highest editing efficiency of GhCLA1 in At and Dt subgenomes edited simultaneously up to 73.3% compared to the 44.6% of pRGEB32-GhU6.7 and 51.2% of pRGEB32-35S. The editing efficiency of GhCLA1 in At and Dt subgenome by pBeYDV-Cas9-KO was 85.7% and 97.2%, respectively, whereas the efficiency by pRGEB32-GhU6.7 and pRGEB32-35S vectors was 67.7%, 86.5%, 84%, and 87.2%, respectively. The editing profile of pBeYDV-Cas9-KO was mainly composed of fragment deletion, accounting for 84.0% and ranging 1–10 bp in length. The main editing sites are located at positions 11–17 upstream of PAM site. The off-target effects were not detected in all potential off-target sites. Taken together, the pBeYDV-Cas9-KO system has high editing efficiency and specificity with wide editing range than the traditional CRISPR/Cas9 system, which provides a powerful tool for cotton functional genomics research and molecular breeding.
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Affiliation(s)
- Bo Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Crop Biotechnology, Urumqi 830091, China
| | - Chunyang Fu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Zhou
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengjiao Hui
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiongqiong Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fuqiu Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guanying Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianlian Che
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojun Yuan
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanqin Wang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer 843300, China
- Correspondence: (Y.W.); (S.J.)
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Y.W.); (S.J.)
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Recent progress on mechanisms that allocate cellular space to plastids. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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The Spread of Antibiotic Resistance Genes In Vivo Model. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:3348695. [PMID: 35898691 PMCID: PMC9314185 DOI: 10.1155/2022/3348695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/20/2022]
Abstract
Infections caused by antibiotic-resistant bacteria are a major public health threat. The emergence and spread of antibiotic resistance genes (ARGs) in the environment or clinical setting pose a serious threat to human and animal health worldwide. Horizontal gene transfer (HGT) of ARGs is one of the main reasons for the dissemination of antibiotic resistance in vitro and in vivo environments. There is a consensus on the role of mobile genetic elements (MGEs) in the spread of bacterial resistance. Most drug resistance genes are located on plasmids, and the spread of drug resistance genes among microorganisms through plasmid-mediated conjugation transfer is the most common and effective way for the spread of multidrug resistance. Experimental studies of the processes driving the spread of antibiotic resistance have focused on simple in vitro model systems, but the current in vitro protocols might not correctly reflect the HGT of antibiotic resistance genes in realistic conditions. This calls for better models of how resistance genes transfer and disseminate in vivo. The in vivo model can better mimic the situation that occurs in patients, helping study the situation in more detail. This is crucial to develop innovative strategies to curtail the spread of antibiotic resistance genes in the future. This review aims to give an overview of the mechanisms of the spread of antibiotic resistance genes and then demonstrate the spread of antibiotic resistance genes in the in vivo model. Finally, we discuss the challenges in controlling the spread of antibiotic resistance genes and their potential solutions.
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Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
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Ren C, Kuang Y, Lin Y, Guo Y, Li H, Fan P, Li S, Liang Z. Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis. BMC PLANT BIOLOGY 2022; 22:271. [PMID: 35655129 PMCID: PMC9161562 DOI: 10.1186/s12870-022-03663-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/27/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Abscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grape PYL genes in response to different abiotic stresses, particularly cold stress, remain less studied. RESULTS In this study, we investigated the expression profiles of grape PYL genes upon cold treatment and isolated the VaPYL4 gene from Vitis amurensis, a cold-hardy grape species. Overexpression of VaPYL4 gene in grape calli and Arabidopsis resulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressing VaPYL4 in Arabidopsis. More importantly, we evaluated the contribution of VaPYL4 to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such as RD29A (Responsive to desiccation 29A), COR15A (Cold responsive 15A) and KIN2 (Kinase 2) were also significantly up-regulated in VaPYL4-overexpressing Arabidopsis plants. CONCLUSIONS Our results show that overexpression of VaPYL4 could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yanping Lin
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yuchen Guo
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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Wu M, Pei W, Wedegaertner T, Zhang J, Yu J. Genetics, Breeding and Genetic Engineering to Improve Cottonseed Oil and Protein: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:864850. [PMID: 35360295 PMCID: PMC8961181 DOI: 10.3389/fpls.2022.864850] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/15/2022] [Indexed: 05/17/2023]
Abstract
Upland cotton (Gossypium hirsutum) is the world's leading fiber crop and one of the most important oilseed crops. Genetic improvement of cotton has primarily focused on fiber yield and quality. However, there is an increased interest and demand for enhanced cottonseed traits, including protein, oil, fatty acids, and amino acids for broad food, feed and biofuel applications. As a byproduct of cotton production, cottonseed is an important source of edible oil in many countries and could also be a vital source of protein for human consumption. The focus of cotton breeding on high yield and better fiber quality has substantially reduced the natural genetic variation available for effective cottonseed quality improvement within Upland cotton. However, genetic variation in cottonseed oil and protein content exists within the genus of Gossypium and cultivated cotton. A plethora of genes and quantitative trait loci (QTLs) (associated with cottonseed oil, fatty acids, protein and amino acids) have been identified, providing important information for genetic improvement of cottonseed quality. Genetic engineering in cotton through RNA interference and insertions of additional genes of other genetic sources, in addition to the more recent development of genome editing technology has achieved considerable progress in altering the relative levels of protein, oil, fatty acid profile, and amino acids composition in cottonseed for enhanced nutritional value and expanded industrial applications. The objective of this review is to summarize and discuss the cottonseed oil biosynthetic pathway and major genes involved, genetic basis of cottonseed oil and protein content, genetic engineering, genome editing through CRISPR/Cas9, and QTLs associated with quantity and quality enhancement of cottonseed oil and protein.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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Guo M, Chen H, Dong S, Zhang Z, Luo H. CRISPR-Cas gene editing technology and its application prospect in medicinal plants. Chin Med 2022; 17:33. [PMID: 35246186 PMCID: PMC8894546 DOI: 10.1186/s13020-022-00584-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/11/2022] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency. An increasing number of plant species have been subjected to site-directed gene editing through this technology. However, the application of CRISPR-Cas technology to medicinal plants is still in the early stages. Here, we review the research history, structural characteristics, working mechanism and the latest derivatives of CRISPR-Cas technology, and discussed their application in medicinal plants for the first time. Furthermore, we creatively put forward the development direction of CRISPR technology applied to medicinal plant gene editing. The aim is to provide a reference for the application of this technology to genome functional studies, synthetic biology, genetic improvement, and germplasm innovation of medicinal plants. CRISPR-Cas is expected to revolutionize medicinal plant biotechnology in the near future.
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Affiliation(s)
- Miaoxian Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongyu Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuting Dong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Marco S, Loredana M, Riccardo V, Raffaella B, Walter C, Luca N. Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience. HORTICULTURE RESEARCH 2022; 9:uhac160. [PMID: 36204199 PMCID: PMC9531342 DOI: 10.1093/hr/uhac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/22/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.
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Affiliation(s)
| | | | - Velasco Riccardo
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
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Silva TN, Thomas JB, Dahlberg J, Rhee SY, Mortimer JC. Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:646-664. [PMID: 34644381 PMCID: PMC8793871 DOI: 10.1093/jxb/erab450] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/10/2021] [Indexed: 05/09/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.
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Affiliation(s)
- Tallyta N Silva
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jason B Thomas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Jeff Dahlberg
- Joint BioEnergy Institute, Emeryville, CA, USA
- UC-ANR-KARE, 9240 S. Riverbend Ave, Parlier, CA, USA
| | - Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
- Correspondence: or
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, SA, Australia
- Correspondence: or
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Mateos Fernández R, Petek M, Gerasymenko I, Juteršek M, Baebler Š, Kallam K, Moreno Giménez E, Gondolf J, Nordmann A, Gruden K, Orzaez D, Patron NJ. Insect pest management in the age of synthetic biology. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:25-36. [PMID: 34416790 PMCID: PMC8710903 DOI: 10.1111/pbi.13685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/04/2021] [Accepted: 08/08/2021] [Indexed: 05/10/2023]
Abstract
Arthropod crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingly sophisticated chemical formulations to control insect pests but, as the scale of agriculture expanded to meet the needs of the global population, concerns about the negative impacts of agricultural practices on biodiversity have grown. While biological solutions, such as biological control agents and pheromones, have previously had relatively minor roles in pest management, biotechnology has opened the door to numerous new approaches for controlling insect pests. In this review, we look at how advances in synthetic biology and biotechnology are providing new options for pest control. We discuss emerging technologies for engineering resistant crops and insect populations and examine advances in biomanufacturing that are enabling the production of new products for pest control.
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Affiliation(s)
| | - Marko Petek
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Iryna Gerasymenko
- Plant Biotechnology and Metabolic EngineeringTechnische Universität DarmstadtDarmstadtGermany
| | - Mojca Juteršek
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
- Jožef Stefan International Postgraduate SchoolLjubljanaSlovenia
| | - Špela Baebler
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | | | | | - Janine Gondolf
- Institut für PhilosophieTechnische Universität DarmstadtDarmstadtGermany
| | - Alfred Nordmann
- Institut für PhilosophieTechnische Universität DarmstadtDarmstadtGermany
| | - Kristina Gruden
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Diego Orzaez
- Institute for Plant Molecular and Cell Biology (IBMCP)UPV‐CSICValenciaSpain
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Garcia-Gimenez G, Jobling SA. Gene editing for barley grain quality improvement. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2021.103394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Venegas-Rioseco J, Ginocchio R, Ortiz-Calderón C. Increase in Phytoextraction Potential by Genome Editing and Transformation: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 11:86. [PMID: 35009088 PMCID: PMC8747683 DOI: 10.3390/plants11010086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Soil metal contamination associated with productive activities is a global issue. Metals are not biodegradable and tend to accumulate in soils, posing potential risks to surrounding ecosystems and human health. Plant-based techniques (phytotechnologies) for the in situ remediation of metal-polluted soils have been developed, but these have some limitations. Phytotechnologies are a group of technologies that take advantage of the ability of certain plants to remediate soil, water, and air resources to rehabilitate ecosystem services in managed landscapes. Regarding soil metal pollution, the main objectives are in situ stabilization (phytostabilization) and the removal of contaminants (phytoextraction). Genetic engineering strategies such as gene editing, stacking genes, and transformation, among others, may improve the phytoextraction potential of plants by enhancing their ability to accumulate and tolerate metals and metalloids. This review discusses proven strategies to enhance phytoextraction efficiency and future perspectives on phytotechnologies.
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Affiliation(s)
- Javiera Venegas-Rioseco
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center of Applied Ecology and Sustainability, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rosanna Ginocchio
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center of Applied Ecology and Sustainability, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Claudia Ortiz-Calderón
- Laboratorio de Bioquímica Vegetal y Fitorremediación, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9160000, Chile;
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