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Xiao F, Zhao Y, Wang X, Jian X, Zhou H. Analysis of differential mRNA and miRNA expression induced by heterogeneous grafting in Gleditsia sinensis. Int J Biol Macromol 2024; 270:132235. [PMID: 38734341 DOI: 10.1016/j.ijbiomac.2024.132235] [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: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Gleditsia sinensis Lam. is a multifaceted plant with medicinal, edible, chemical, timber, and ornamental applications. However, the effect of rootstocks on scions after grafting is still unclear. This study examined the mRNA and miRNA transcriptome among homografts, heterografts, and seedlings. GO enrichment analysis between seedlings and homograft/heterograft combinations revealed that biosynthesis, degradation, and transport were enriched. The KEGG enrichment results showed that plant hormone signal transduction and the plant MAPK signaling pathway were enriched in both seedlings and heterograft combinations. Through weighted correlation network analysis (WGCNA), the hub genes related to the content of plant hormones were obtained. Taking G. sinensis as the scion, there were 4594, 2887, 3429, and 5959 mRNAs that were specifically expressed in the grafted plants of G. sinensis/G. fera, G. sinensis/G. delavayi, G. sinensis/G. microphylla, and G. sinensis/G. japonica, respectively. The specifically expressed mRNA genes may participate in such processes and pathways as the rhythmic process, circadian rhythm, gibberellic-acid-mediated signaling pathway, and peptide-based amino acid modification. Additionally, 3, 16, 2, and 15 specifically expressed miRNAs were identified. This study examines the impact of grafting on gene expression in Gleditsia plants and establishes a foundation for the development of new resources and rootstock breeding.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji 133002, Jilin, China
| | - Heying Zhou
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
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2
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Sun H, Liu Y. Exosomal DNA: an alternative vehicle for soma-to-germline communication? J Physiol 2024; 602:2665-2666. [PMID: 38224265 DOI: 10.1113/jp286170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024] Open
Affiliation(s)
- Haili Sun
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, China
| | - Yongsheng Liu
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, China
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3
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Feng M, Augstein F, Kareem A, Melnyk CW. Plant grafting: Molecular mechanisms and applications. MOLECULAR PLANT 2024; 17:75-91. [PMID: 38102831 DOI: 10.1016/j.molp.2023.12.006] [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: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.
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Affiliation(s)
- Ming Feng
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Frauke Augstein
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Abdul Kareem
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden.
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4
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Sanchez-Puerta MV, Ceriotti LF, Gatica-Soria LM, Roulet ME, Garcia LE, Sato HA. Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. ANNALS OF BOTANY 2023; 132:909-928. [PMID: 37503831 PMCID: PMC10808021 DOI: 10.1093/aob/mcad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. SCOPE This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. CONCLUSIONS Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Hector A Sato
- Facultad de Ciencias Agrarias, Cátedra de Botánica General–Herbario JUA, Alberdi 47, Universidad Nacional de Jujuy, 4600 Jujuy, Argentina
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Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
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Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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6
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Loupit G, Brocard L, Ollat N, Cookson SJ. Grafting in plants: recent discoveries and new applications. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2433-2447. [PMID: 36846896 DOI: 10.1093/jxb/erad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Grafting is a traditional horticultural technique that makes use of plant wound healing mechanisms to join two different genotypes together to form one plant. In many agricultural systems, grafting with rootstocks controls the vigour of the scion and/or provides tolerance to deleterious soil conditions such as the presence of soil pests or pathogens or limited or excessive water or mineral nutrient supply. Much of our knowledge about the limits to grafting different genotypes together comes from empirical knowledge of horticulturalists. Until recently, researchers believed that grafting monocotyledonous plants was impossible, because they lack a vascular cambium, and that graft compatibility between different scion/rootstock combinations was restricted to closely related genotypes. Recent studies have overturned these ideas and open up the possibility of new research directions and applications for grafting in agriculture. The objective of this review is to describe and assess these recent advances in the field of grafting and, in particular, the molecular mechanisms underlining graft union formation and graft compatibility between different genotypes. The challenges of characterizing the different stages of graft union formation and phenotyping graft compatibility are examined.
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Affiliation(s)
- Grégoire Loupit
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Lysiane Brocard
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US4, F-33000 Bordeaux, France
| | - Nathalie Ollat
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Sarah Jane Cookson
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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7
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Liu J, Xiang J, Jin C, Ye L, Wang L, Gao Y, Lv N, Zhang J, You F, Qiao H, Shi L. Medicinal plant-derived mtDNA via nanovesicles induces the cGAS-STING pathway to remold tumor-associated macrophages for tumor regression. J Nanobiotechnology 2023; 21:78. [PMID: 36879291 PMCID: PMC9990354 DOI: 10.1186/s12951-023-01835-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Plant-derived nanovesicles (PDNVs) have been proposed as a major mechanism for the inter-kingdom interaction and communication, but the effector components enclosed in the vesicles and the mechanisms involved are largely unknown. The plant Artemisia annua is known as an anti-malaria agent that also exhibits a wide range of biological activities including the immunoregulatory and anti-tumor properties with the mechanisms to be further addressed. Here, we isolated and purified the exosome-like particles from A. annua, which were characterized by nano-scaled and membrane-bound shape and hence termed artemisia-derived nanovesicles (ADNVs). Remarkably, the vesicles demonstrated to inhibit tumor growth and boost anti-tumor immunity in a mouse model of lung cancer, primarily through remolding the tumor microenvironment and reprogramming tumor-associated macrophages (TAMs). We identified plant-derived mitochondrial DNA (mtDNA), upon internalized into TAMs via the vesicles, as a major effector molecule to induce the cGAS-STING pathway driving the shift of pro-tumor macrophages to anti-tumor phenotype. Furthermore, our data showed that administration of ADNVs greatly improved the efficacy of PD-L1 inhibitor, a prototypic immune checkpoint inhibitor, in tumor-bearing mice. Together, the present study, for the first time, to our knowledge, unravels an inter-kingdom interaction wherein the medical plant-derived mtDNA, via the nanovesicles, induces the immunostimulatory signaling in mammalian immune cells for resetting anti-tumor immunity and promoting tumor eradication.
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Affiliation(s)
- Jinfeng Liu
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jiaxin Xiang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Cuiyuan Jin
- Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China
| | - Lusha Ye
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Lei Wang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Yanan Gao
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Nianyin Lv
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Junfeng Zhang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, 100191, China
| | - Hongzhi Qiao
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, Jiangsu Engineering Research Center for Efficient Delivery System of TCM, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Liyun Shi
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China. .,Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China.
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8
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Chung KP, Gonzalez-Duran E, Ruf S, Endries P, Bock R. Control of plastid inheritance by environmental and genetic factors. NATURE PLANTS 2023; 9:68-80. [PMID: 36646831 PMCID: PMC9873568 DOI: 10.1038/s41477-022-01323-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/26/2022] [Indexed: 06/01/2023]
Abstract
The genomes of cytoplasmic organelles (mitochondria and plastids) are maternally inherited in most eukaryotes, thus excluding organellar genomes from the benefits of sexual reproduction and recombination. The mechanisms underlying maternal inheritance are largely unknown. Here we demonstrate that two independently acting mechanisms ensure maternal inheritance of the plastid (chloroplast) genome. Conducting large-scale genetic screens for paternal plastid transmission, we discovered that mild chilling stress during male gametogenesis leads to increased entry of paternal plastids into sperm cells and strongly increased paternal plastid transmission. We further show that the inheritance of paternal plastid genomes is controlled by the activity of a genome-degrading exonuclease during pollen maturation. Our data reveal that (1) maternal inheritance breaks down under specific environmental conditions, (2) an organelle exclusion mechanism and a genome degradation mechanism act in concert to prevent paternal transmission of plastid genes and (3) plastid inheritance is determined by complex gene-environment interactions.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | | | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Pierre Endries
- Universität Hamburg, Institut für Pflanzenwissenschaften und Mikrobiologie, Hamburg, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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9
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Han Q, Song H, Yang C, Zhang S, Korpelainen H, Li C. Integrated DNA methylation, transcriptome and physiological analyses reveal new insights into superiority of poplars formed by interspecific grafting. TREE PHYSIOLOGY 2022; 42:1481-1500. [PMID: 35134240 DOI: 10.1093/treephys/tpac013] [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: 11/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Plant grafting has a long history and it is extensively employed to improve plant performance. In our previous research, reciprocal grafts of Populus cathayana Rehder (C) and Populus deltoides Bart. Ex Marsh (D) were generated. The results showed that interspecific grafting combinations (scion/rootstock: C/D and D/C) grew better than intraspecific grafting combinations (C/C and D/D). To further understand differences in molecular mechanisms between interspecific and intraspecific grafting, we performed an integrated analysis, including bisulfite sequencing, RNA sequencing and measurements of physiological indicators, to investigate leaves of different grafting combinations. We found that the difference at the genome-wide methylation level was greater in D/C vs D/D than in C/D vs C/C, but no difference was detected at the transcription level in D/C vs D/D. Furthermore, the grafting superiority of D/C vs D/D was not as strong as that of C/D vs C/C. These results may be associated with the different methylation forms, mCHH (71.76%) and mCG (57.16%), that accounted for the highest percentages in C/D vs C/C and D/C vs D/D, respectively. In addition, the interspecific grafting superiority was found mainly related to the process of photosynthesis, phytohormone signal transduction, biosynthesis of secondary metabolites, cell wall and transcriptional regulation based on both physiological and molecular results. Overall, the results indicated that the physiological and molecular phenotypes of grafted plants are affected by the interaction between scion and rootstock. Thus, our study provides a theoretical basis for developing suitable scion-rootstock combinations for grafted plants.
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Affiliation(s)
- Qingquan Han
- Institute of Physical Education, Ludong University, Yantai 264025, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Haifeng Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Congcong Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, Helsinki FI-00014, Finland
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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10
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Viswan A, Yamagishi A, Hoshi M, Furuhata Y, Kato Y, Makimoto N, Takeshita T, Kobayashi T, Iwata F, Kimura M, Yoshizumi T, Nakamura C. Microneedle Array-Assisted, Direct Delivery of Genome-Editing Proteins Into Plant Tissue. FRONTIERS IN PLANT SCIENCE 2022; 13:878059. [PMID: 35812975 PMCID: PMC9263851 DOI: 10.3389/fpls.2022.878059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Genome editing in plants employing recombinant DNA often results in the incorporation of foreign DNA into the host genome. The direct delivery of genome-editing proteins into plant tissues is desired to prevent undesirable genetic alterations. However, in most currently available methods, the point of entry of the genome-editing proteins cannot be controlled and time-consuming processes are required to select the successfully transferred samples. To overcome these limitations, we considered a novel microneedle array (MNA)-based delivery system, in which the needles are horizontally aligned from the substrate surface, giving it a comb-like configuration. We aimed to deliver genome-editing proteins directly into the inner layers of leaf tissues; palisade, the spongy and subepidermal L2 layers of the shoot apical meristem (SAM) which include cells that can differentiate into germlines. The array with needles 2 μm wide and 60 μm long was effective in inserting into Arabidopsis thaliana leaves and Glycine max (L.) Merr. (soybeans) SAM without the needles buckling or breaking. The setup was initially tested for the delivery of Cre recombinase into the leaves of the reporter plant A. thaliana by quantifying the GUS (β-glucuronidase) expression that occurred by the recombination of the loxP sites. We observed GUS expression at every insertion. Additionally, direct delivery of Cas9 ribonucleoprotein (RNP) targeting the PDS11/18 gene in soybean SAM showed an 11 bp deletion in the Cas9 RNP target site. Therefore, this method effectively delivered genome-editing proteins into plant tissues with precise control over the point of entry.
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Affiliation(s)
- Anchu Viswan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ayana Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masamichi Hoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yuichi Furuhata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Natsumi Makimoto
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Toshihiro Takeshita
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takeshi Kobayashi
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Futoshi Iwata
- Graduate School of Medical Photonics, Shizuoka University, Hamamatsu, Japan
| | - Mitsuhiro Kimura
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Takeshi Yoshizumi
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Chikashi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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11
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Chambaud C, Cookson SJ, Ollat N, Bayer E, Brocard L. A correlative light electron microscopy approach reveals plasmodesmata ultrastructure at the graft interface. PLANT PHYSIOLOGY 2022; 188:44-55. [PMID: 34687300 PMCID: PMC8774839 DOI: 10.1093/plphys/kiab485] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 06/01/2023]
Abstract
Despite recent progress in our understanding of graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy (CLEM) approach to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing yellow FP or monomeric red FP in the endoplasmic reticulum (ER) allowed efficient targeting of the grafting interface for examination under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that four classes of PD were formed at the interface and that PD introgression into the cell wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these incomplete PD gives us insights into the process of secondary PD biogenesis. We found that the establishment of successful symplastic connections between the scion and rootstock occurred predominantly in the presence of thin cell walls and ER-plasma membrane tethering. The resolution reached in this work shows that our CLEM method advances the study of biological processes requiring the combination of light and electron microscopy.
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Affiliation(s)
- Clément Chambaud
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Sarah Jane Cookson
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882 Villenave d’Ornon, France
| | - Emmanuelle Bayer
- Laboratoire de Biogénèse Membranaire (LBM), CNRS, Univ. Bordeaux, UMR 5200, F-33882 Villenave d’Ornon, France
| | - Lysiane Brocard
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000 Bordeaux, France
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12
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Surridge C. Swapping plastids. NATURE PLANTS 2021; 7:1528. [PMID: 34907300 DOI: 10.1038/s41477-021-01073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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13
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Kurotani KI, Notaguchi M. Cell-to-Cell Connection in Plant Grafting-Molecular Insights into Symplasmic Reconstruction. PLANT & CELL PHYSIOLOGY 2021; 62:1362-1371. [PMID: 34252186 DOI: 10.1093/pcp/pcab109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/17/2021] [Accepted: 07/12/2021] [Indexed: 05/06/2023]
Abstract
Grafting is a means to connect tissues from two individual plants and grow a single chimeric plant through the establishment of both apoplasmic and symplasmic connections. Recent molecular studies using RNA-sequencing data have provided genetic information on the processes involved in tissue reunion, including wound response, cell division, cell-cell adhesion, cell differentiation and vascular formation. Thus, studies on grafting increase our understanding of various aspects of plant biology. Grafting has also been used to study systemic signaling and transport of micromolecules and macromolecules in the plant body. Given that graft viability and molecular transport across graft junctions largely depend on vascular formation, a major focus in grafting biology has been the mechanism of vascular development. In addition, it has been thought that symplasmic connections via plasmodesmata are fundamentally important to share cellular information among newly proliferated cells at the graft interface and to accomplish tissue differentiation correctly. Therefore, this review focuses on plasmodesmata formation during grafting. We take advantage of interfamily grafts for unambiguous identification of the graft interface and summarize morphological aspects of de novo formation of plasmodesmata. Important molecular events are addressed by re-examining the time-course transcriptome of interfamily grafts, from which we recently identified the cell-cell adhesion mechanism. Plasmodesmata-associated genes upregulated during graft healing that may provide a link to symplasm establishment are described. We also discuss future research directions.
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Affiliation(s)
- Ken-Ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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14
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Hunter P. The molecular biology of grafting: Recent research may provide new applications for a millennia-old agricultural technology. EMBO Rep 2021; 22:e54098. [PMID: 34648669 DOI: 10.15252/embr.202154098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Plant biologists have begun to unravel the molecular mechanisms behind grafting, yielding insights into plant evolution and expanding the scope of this technique.
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15
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Andreeva OE, Sorokin DV, Mikhaevich EI, Bure IV, Shchegolev YY, Nemtsova MV, Gudkova MV, Scherbakov AM, Krasil’nikov MA. Towards Unravelling the Role of ERα-Targeting miRNAs in the Exosome-Mediated Transferring of the Hormone Resistance. Molecules 2021; 26:molecules26216661. [PMID: 34771077 PMCID: PMC8588049 DOI: 10.3390/molecules26216661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 01/09/2023] Open
Abstract
Hormone therapy is one of the most effective breast cancer treatments, however, its application is limited by the progression of hormonal resistance, both primary or acquired. The development of hormonal resistance is caused either by an irreversible block of hormonal signalling (suppression of the activity or synthesis of hormone receptors), or by activation of oestrogen-independent signalling pathways. Recently the effect of exosome-mediated intercellular transfer of hormonal resistance was revealed, however, the molecular mechanism of this effect is still unknown. Here, the role of exosomal miRNAs (microRNAs) in the transferring of hormonal resistance in breast cancer cells has been studied. The methods used in the work include extraction, purification and RNAseq of miRNAs, transfection of miRNA mimetics, immunoblotting, reporter analysis and the MTT test. Using MCF7 breast cancer cells and MCF7/T tamoxifen-resistant sub-line, we have found that some miRNAs, suppressors of oestrogen receptor signalling, are overexpressed in the exosomes of the resistant breast cancer cells. The multiple (but not single) transfection of one of the identified miRNA, miR-181a-2, into oestrogen-dependent MCF7 cells induced the irreversible tamoxifen resistance associated with the continuous block of the oestrogen receptor signalling and the activation of PI3K/Akt pathway. We suppose that the miRNAs-ERα suppressors may act as trigger agents inducing the block of oestrogen receptor signalling and breast cancer cell transition to an aggressive oestrogen-independent state.
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Affiliation(s)
- Olga E. Andreeva
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
| | - Danila V. Sorokin
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
| | - Ekaterina I. Mikhaevich
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
| | - Irina V. Bure
- Laboratory of Medical Genetics, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (I.V.B.); (M.V.N.)
| | - Yuri Y. Shchegolev
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
| | - Marina V. Nemtsova
- Laboratory of Medical Genetics, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (I.V.B.); (M.V.N.)
| | - Margarita V. Gudkova
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
| | - Alexander M. Scherbakov
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
- Correspondence: or
| | - Mikhail A. Krasil’nikov
- Department of Experimental Tumour Biology, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115522 Moscow, Russia; (O.E.A.); (D.V.S.); (E.I.M.); (Y.Y.S.); (M.V.G.); (M.A.K.)
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16
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Welchen E, Gonzalez DH. Breaking boundaries: exploring short- and long-distance mitochondrial signalling in plants. THE NEW PHYTOLOGIST 2021; 232:494-501. [PMID: 34255867 DOI: 10.1111/nph.17614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/29/2021] [Indexed: 05/20/2023]
Abstract
Communication of mitochondria with other cell compartments is essential for the coordination of cellular functions. Mitochondria send retrograde signals through metabolites, redox changes, direct organelle contacts and protein trafficking. Accumulating evidence indicates that, in animal systems, changes in mitochondrial function also trigger responses in other, either neighbouring or distantly located, cells. Although not clearly established, there are indications that this type of communication may also be operative in plants. Grafting experiments suggested that the translocation of entire mitochondria or submitochondrial vesicles between neighbouring cells is possible in plants, as already documented in animals. Changes in mitochondrial function also regulate cell-to-cell communication via plasmodesmata and may be transmitted over long distances through plant hormones acting as mitokines to relay mitochondrial signals to distant tissues. Long-distance movement of transcripts encoding mitochondrial proteins involved in crucial aspects of metabolism and retrograde signalling was also described. Finally, changes in mitochondrial reactive species (ROS) production may affect the 'ROS wave' that triggers systemic acquired acclimation throughout the plant. In this review, we summarise available evidence suggesting that mitochondria establish sophisticated communications not only within the cell but also with neighbouring cells and distant tissues to coordinate plant growth and stress responses in a cell nonautonomous manner.
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Affiliation(s)
- Elina Welchen
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
| | - Daniel H Gonzalez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
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17
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Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics 2021; 22:672. [PMID: 34536995 PMCID: PMC8449883 DOI: 10.1186/s12864-021-07967-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Weidong Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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Hibdige SGS, Raimondeau P, Christin PA, Dunning LT. Widespread lateral gene transfer among grasses. THE NEW PHYTOLOGIST 2021; 230:2474-2486. [PMID: 33887801 DOI: 10.1111/nph.17328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Lateral gene transfer (LGT) occurs in a broad range of prokaryotes and eukaryotes, occasionally promoting adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT. We scanned the genomes of a diverse set of 17 grass species that span more than 50 Ma of divergence and include major crops to identify grass-to-grass protein-coding LGT. We identified LGTs in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species indicates that transfers can occur across almost the entire family. Overall, we showed that LGT is a widespread phenomenon in grasses that has moved functional genes across the grass family into domesticated and wild species alike. Successful LGTs appear to increase with both opportunity and compatibility.
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Affiliation(s)
- Samuel G S Hibdige
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pauline Raimondeau
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | | | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist. PLoS Biol 2021; 19:e3001126. [PMID: 33891594 PMCID: PMC8099122 DOI: 10.1371/journal.pbio.3001126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/05/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.
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20
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Iswanto ABB, Shelake RM, Vu MH, Kim JY, Kim SH. Genome Editing for Plasmodesmal Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:679140. [PMID: 34149780 PMCID: PMC8207191 DOI: 10.3389/fpls.2021.679140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/08/2023]
Abstract
Plasmodesmata (PD) are cytoplasmic canals that facilitate intercellular communication and molecular exchange between adjacent plant cells. PD-associated proteins are considered as one of the foremost factors in regulating PD function that is critical for plant development and stress responses. Although its potential to be used for crop engineering is enormous, our understanding of PD biology was relatively limited to model plants, demanding further studies in crop systems. Recently developed genome editing techniques such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associate protein (CRISPR/Cas) might confer powerful approaches to dissect the molecular function of PD components and to engineer elite crops. Here, we assess several aspects of PD functioning to underline and highlight the potential applications of CRISPR/Cas that provide new insight into PD biology and crop improvement.
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Affiliation(s)
- Arya Bagus Boedi Iswanto
- Division of Applied Life Sciences (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Sciences (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Minh Huy Vu
- Division of Applied Life Sciences (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Jae-Yean Kim
- Division of Applied Life Sciences (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
- Jae-Yean Kim,
| | - Sang Hee Kim
- Division of Applied Life Sciences (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
- *Correspondence: Sang Hee Kim,
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