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Xie Y, Liu W, Guo L, Zhang X. Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements. Front Genet 2024; 15:1395805. [PMID: 38903753 PMCID: PMC11188483 DOI: 10.3389/fgene.2024.1395805] [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: 03/04/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and repetitive DNA sequences. Despite larger sizes, plant mitogenomes do not have significantly more genes. They exhibit diverse structures due to variations in size, repetitive DNA, recombination frequencies, low gene densities, and reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of Stemona sessilifolia using Nanopore and Illumina sequencing. De-novo assembly and annotation were conducted using Unicycler, Geseq, tRNAscan-SE and BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, and phylogenetic analyses. S. sessilifolia's mitogenome consisted of one linear contig and six circular contigs totaling 724,751 bp. It had 39 protein-coding genes, 27 tRNA genes, and 3 rRNA genes. Transfer of chloroplast sequences accounted for 13.14% of the mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, and phylogenetic placement. Further investigations can explore transferred genes' functions and RNA-editing's role in mitochondrial gene expression in S. sessilifolia.
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Affiliation(s)
- Yuning Xie
- School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Wenqiong Liu
- Public Health Department, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liwen Guo
- College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Xuemei Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, China
- College of Life Science, North China University of Science and Technology, Tangshan, China
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2
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Mirzaee M, Leung A, Parulekar M, Candia A, Matsuoka A, Lutz KA, Maliga P. Seed plastids: A novel platform for recombinant protein expression. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38803087 DOI: 10.1111/pbi.14369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Malihe Mirzaee
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
| | - Alyssa Leung
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
| | - Mugdha Parulekar
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
| | - Ana Candia
- Department of Biology, Farmingdale State College, Farmingdale, New York, USA
| | - Aki Matsuoka
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
| | - Kerry A Lutz
- Department of Biology, Farmingdale State College, Farmingdale, New York, USA
| | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
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3
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Arimura SI, Nakazato I. Genome Editing of Plant Mitochondrial and Chloroplast Genomes. PLANT & CELL PHYSIOLOGY 2024; 65:477-483. [PMID: 38113380 PMCID: PMC11094758 DOI: 10.1093/pcp/pcad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria, yet they maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures and undergoing frequent homologous recombination. To date, it has proven to be challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene-editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially transcription activator-like effector nucleases (TALENs) and artificial enzymes utilizing DNA-binding domains of TALENs (TALEs), have been successfully used to modify these genomes by harnessing organellar-targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors in organellar genomes, their effects and their potential applications in plant science and breeding.
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Affiliation(s)
- Shin-ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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4
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Wang X, Fang T, Lu J, Tripathi L, Qi Y. Broad range plastid genome editing with monomeric TALE-linked cytosine and dual base editors. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38709858 DOI: 10.1111/pbi.14358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024]
Affiliation(s)
- Xiaoyu Wang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Tyson Fang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Jason Lu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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5
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Xu F, Su T, Zhang X, Qiu L, Yang X, Koizuka N, Arimura S, Hu Z, Zhang M, Yang J. Editing of ORF138 restores fertility of Ogura cytoplasmic male sterile broccoli via mitoTALENs. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1325-1334. [PMID: 38213067 PMCID: PMC11022808 DOI: 10.1111/pbi.14268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/03/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Cytoplasmic male sterility (CMS), encoded by the mitochondrial open reading frames (ORFs), has long been used to economically produce crop hybrids. However, the utilization of CMS also hinders the exploitation of sterility and fertility variation in the absence of a restorer line, which in turn narrows the genetic background and reduces biodiversity. Here, we used a mitochondrial targeted transcription activator-like effector nuclease (mitoTALENs) to knock out ORF138 from the Ogura CMS broccoli hybrid. The knockout was confirmed by the amplification and re-sequencing read mapping to the mitochondrial genome. As a result, knockout of ORF138 restored the fertility of the CMS hybrid, and simultaneously manifested a cold-sensitive male sterility. ORF138 depletion is stably inherited to the next generation, allowing for direct use in the breeding process. In addition, we proposed a highly reliable and cost-effective toolkit to accelerate the life cycle of fertile lines from CMS-derived broccoli hybrids. By applying the k-mean clustering and interaction network analysis, we identified the central gene networks involved in the fertility restoration and cold-sensitive male sterility. Our study enables mitochondrial genome editing via mitoTALENs in Brassicaceae vegetable crops and provides evidence that the sex production machinery and its temperature-responsive ability are regulated by the mitochondria.
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Affiliation(s)
- Fengyuan Xu
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanyaChina
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Tongbing Su
- Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xiaochen Zhang
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanyaChina
| | - Lei Qiu
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Xiaodong Yang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | | | - Shin‐ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Zhongyuan Hu
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanyaChina
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
| | - Mingfang Zhang
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanyaChina
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
| | - Jinghua Yang
- Hainan Institute, Zhejiang UniversityYazhou Bay Science and Technology CitySanyaChina
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
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6
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Liu J, Feng Y, Chen C, Yan J, Bai X, Li H, Lin C, Xiang Y, Tian W, Qi Z, Yu J, Yan X. Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications. FRONTIERS IN PLANT SCIENCE 2024; 15:1347945. [PMID: 38516667 PMCID: PMC10954886 DOI: 10.3389/fpls.2024.1347945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024]
Abstract
Background The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations. Conclusion Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.
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Affiliation(s)
- Jing Liu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuqing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jing Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xinyu Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Huiru Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chen Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yinan Xiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wen Tian
- Animal Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Zhechen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jing Yu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Xiaoling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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7
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Lin JY, Liu YC, Tseng YH, Chan MT, Chang CC. TALE-based organellar genome editing and gene expression in plants. PLANT CELL REPORTS 2024; 43:61. [PMID: 38336900 DOI: 10.1007/s00299-024-03150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE TALE-based editors provide an alternative way to engineer the organellar genomes in plants. We update and discuss the most recent developments of TALE-based organellar genome editing in plants. Gene editing tools have been widely used to modify the nuclear genomes of plants for various basic research and biotechnological applications. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 editing platform is the most commonly used technique because of its ease of use, fast speed, and low cost; however, it encounters difficulty when being delivered to plant organelles for gene editing. In contrast, protein-based editing technologies, such as transcription activator-like effector (TALE)-based tools, could be easily delivered, expressed, and targeted to organelles in plants via Agrobacteria-mediated nuclear transformation. Therefore, TALE-based editors provide an alternative way to engineer the organellar genomes in plants since the conventional chloroplast transformation method encounters technical challenges and is limited to certain species, and the direct transformation of mitochondria in higher plants is not yet possible. In this review, we update and discuss the most recent developments of TALE-based organellar genome editing in plants.
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Affiliation(s)
- Jer-Young Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chang Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
| | - Yan-Hao Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan.
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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8
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Kim JS, Chen J. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol 2024; 25:34-45. [PMID: 37794167 DOI: 10.1038/s41580-023-00663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Mitochondria and chloroplasts are organelles that include their own genomes, which encode key genes for ATP production and carbon dioxide fixation, respectively. Mutations in mitochondrial DNA can cause diverse genetic disorders and are also linked to ageing and age-related diseases, including cancer. Targeted editing of organellar DNA should be useful for studying organellar genes and developing novel therapeutics, but it has been hindered by lack of efficient tools in living cells. Recently, CRISPR-free, protein-only base editors, such as double-stranded DNA deaminase toxin A-derived cytosine base editors (DdCBEs) and adenine base editors (ABEs), have been developed, which enable targeted organellar DNA editing in human cell lines, animals and plants. In this Review, we present programmable deaminases developed for base editing of organellar DNA in vitro and discuss mitochondrial DNA editing in animals, and plastid genome (plastome) editing in plants. We also discuss precision and efficiency limitations of these tools and propose improvements for therapeutic, agricultural and environmental applications.
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Affiliation(s)
- Jin-Soo Kim
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore.
- Edgene, Seoul, South Korea.
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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9
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Forner J, Kleinschmidt D, Meyer EH, Gremmels J, Morbitzer R, Lahaye T, Schöttler MA, Bock R. Targeted knockout of a conserved plant mitochondrial gene by genome editing. NATURE PLANTS 2023; 9:1818-1831. [PMID: 37814021 PMCID: PMC10654050 DOI: 10.1038/s41477-023-01538-2] [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: 02/20/2023] [Accepted: 09/07/2023] [Indexed: 10/11/2023]
Abstract
Fusion proteins derived from transcription activator-like effectors (TALEs) have emerged as genome editing tools for mitochondria. TALE nucleases (TALENs) have been applied to delete chimaeric reading frames and duplicated (redundant) genes but produced complex genomic rearrangements due to the absence of non-homologous end-joining. Here we report the targeted deletion of a conserved mitochondrial gene, nad9, encoding a subunit of respiratory complex I. By generating a large number of TALEN-mediated mitochondrial deletion lines, we isolated, in addition to mutants with rearranged genomes, homochondriomic mutants harbouring clean nad9 deletions. Characterization of the knockout plants revealed impaired complex I biogenesis, male sterility and defects in leaf and flower development. We show that these defects can be restored by expressing a functional Nad9 protein from the nuclear genome, thus creating a synthetic cytoplasmic male sterility system. Our data (1) demonstrate the feasibility of using genome editing to study mitochondrial gene functions by reverse genetics, (2) highlight the role of complex I in plant development and (3) provide proof-of-concept for the construction of synthetic cytoplasmic male sterility systems for hybrid breeding by genome editing.
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Affiliation(s)
- Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Dennis Kleinschmidt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jürgen Gremmels
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Robert Morbitzer
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Thomas Lahaye
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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10
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Bulle M, Sheri V, Aileni M, Zhang B. Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3448. [PMID: 37836188 PMCID: PMC10574609 DOI: 10.3390/plants12193448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad 500030, India
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Mahender Aileni
- Department of Biotechnology, Telangana University, Dichpally, Nizamabad 503322, India;
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
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11
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Munasinghe M, Ågren JA. When and why are mitochondria paternally inherited? Curr Opin Genet Dev 2023; 80:102053. [PMID: 37245242 DOI: 10.1016/j.gde.2023.102053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/30/2023]
Abstract
In contrast with nuclear genes that are passed on through both parents, mitochondrial genes are maternally inherited in most species, most of the time. The genetic conflict stemming from this transmission asymmetry is well-documented, and there is an abundance of population-genetic theory associated with it. While occasional or aberrant paternal inheritance occurs, there are only a few cases where exclusive paternal inheritance of mitochondrial genomes is the evolved state. Why this is remains poorly understood. By examining commonalities between species with exclusive paternal inheritance, we discuss what they may tell us about the evolutionary forces influencing mitochondrial inheritance patterns. We end by discussing recent technological advances that make exploring the causes and consequences of paternal inheritance feasible.
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Affiliation(s)
- Manisha Munasinghe
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA. https://twitter.com/@ManishaMuna
| | - J Arvid Ågren
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden; Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
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12
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Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
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Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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13
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Ghandour R, Gao Y, Laskowski J, Barahimipour R, Ruf S, Bock R, Zoschke R. Transgene insertion into the plastid genome alters expression of adjacent native chloroplast genes at the transcriptional and translational levels. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:711-725. [PMID: 36529916 PMCID: PMC10037153 DOI: 10.1111/pbi.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
In plant biotechnology and basic research, chloroplasts have been used as chassis for the expression of various transgenes. However, potential unintended side effects of transgene insertion and high-level transgene expression on the expression of native chloroplast genes are often ignored and have not been studied comprehensively. Here, we examined expression of the chloroplast genome at both the transcriptional and translational levels in five transplastomic tobacco (Nicotiana tabacum) lines carrying the identical aadA resistance marker cassette in diverse genomic positions. Although none of the lines exhibits a pronounced visible phenotype, the analysis of three lines that contain the aadA insertion in different locations within the petL-petG-psaJ-rpl33-rps18 transcription unit demonstrates that transcriptional read-through from the aadA resistance marker is unavoidable, and regularly causes overexpression of downstream sense-oriented chloroplast genes at the transcriptional and translational levels. Investigation of additional lines that harbour the aadA intergenically and outside of chloroplast transcription units revealed that expression of the resistance marker can also cause antisense effects by interference with transcription/transcript accumulation and/or translation of downstream antisense-oriented genes. In addition, we provide evidence for a previously suggested role of genomically encoded tRNAs in chloroplast transcription termination and/or transcript processing. Together, our data uncover principles of neighbouring effects of chloroplast transgenes and suggest general strategies for the choice of transgene insertion sites and expression elements to minimize unintended consequences of transgene expression on the transcription and translation of native chloroplast genes.
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Affiliation(s)
- Rabea Ghandour
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Yang Gao
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | | | | | - Stephanie Ruf
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
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Rozov SM, Zagorskaya AA, Konstantinov YM, Deineko EV. Three Parts of the Plant Genome: On the Way to Success in the Production of Recombinant Proteins. PLANTS (BASEL, SWITZERLAND) 2022; 12:38. [PMID: 36616166 PMCID: PMC9824153 DOI: 10.3390/plants12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are the most important product of current industrial biotechnology. They are indispensable in medicine (for diagnostics and treatment), food and chemical industries, and research. Plant cells combine advantages of the eukaryotic protein production system with simplicity and efficacy of the bacterial one. The use of plants for the production of recombinant proteins is an economically important and promising area that has emerged as an alternative to traditional approaches. This review discusses advantages of plant systems for the expression of recombinant proteins using nuclear, plastid, and mitochondrial genomes. Possibilities, problems, and prospects of modifications of the three parts of the genome in light of obtaining producer plants are examined. Examples of successful use of the nuclear expression platform for production of various biopharmaceuticals, veterinary drugs, and technologically important proteins are described, as are examples of a high yield of recombinant proteins upon modification of the chloroplast genome. Potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated. Although these opportunities have not yet been exploited, potential utility of plant mitochondria as an expression system for the production of recombinant proteins and its advantages over the nucleus and chloroplasts are substantiated.
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Affiliation(s)
- Sergey M. Rozov
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Alla A. Zagorskaya
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, Lermontova Str. 132, Irkutsk 664033, Russia
| | - Elena V. Deineko
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, pr. Akad. Lavrentieva 10, Novosibirsk 630090, Russia
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