1
|
Luo S, Li A, Luo J, Liao G, Li X, Yao S, Wang A, Xiao D, He L, Zhan J. Mutator-like transposable element 9A interacts with metacaspase 1 and modulates the incidence of Al-induced programmed cell death in peanut. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2113-2126. [PMID: 38069635 DOI: 10.1093/jxb/erad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/05/2023] [Indexed: 03/28/2024]
Abstract
The toxicity of aluminum (Al) in acidic soil inhibits plant root development and reduces crop yields. In the plant response to Al toxicity, the initiation of programmed cell death (PCD) appears to be an important mechanism for the elimination of Al-damaged cells to ensure plant survival. In a previous study, the type I metacaspase AhMC1 was found to regulate the Al stress response and to be essential for Al-induced PCD. However, the mechanism by which AhMC1 is altered in the peanut response to Al stress remained unclear. Here, we show that a nuclear protein, mutator-like transposable element 9A (AhMULE9A), directly interacts with AhMC1 in vitro and in vivo. This interaction occurs in the nucleus in peanut and is weakened during Al stress. Furthermore, a conserved C2HC zinc finger domain of AhMULE9A (residues 735-751) was shown to be required for its interaction with AhMC1. Overexpression of AhMULE9A in Arabidopsis and peanut strongly inhibited root growth with a loss of root cell viability under Al treatment. Conversely, knock down of AhMULE9A in peanut significantly reduced Al uptake and Al inhibition of root growth, and alleviated the occurrence of typical hallmarks of Al-induced PCD. These findings provide novel insight into the regulation of Al-induced PCD.
Collapse
Affiliation(s)
- Shuzhen Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ailing Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jin Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Guoting Liao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Xia Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Shaochang Yao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Dong Xiao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jie Zhan
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| |
Collapse
|
2
|
Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids. Int J Mol Sci 2022; 23:ijms231911993. [PMID: 36233292 PMCID: PMC9569675 DOI: 10.3390/ijms231911993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs.
Collapse
|
3
|
de Oliveira DS, Rosa MT, Vieira C, Loreto ELS. Oxidative and radiation stress induces transposable element transcription in Drosophila melanogaster. J Evol Biol 2021; 34:628-638. [PMID: 33484011 DOI: 10.1111/jeb.13762] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/27/2020] [Accepted: 12/06/2020] [Indexed: 12/20/2022]
Abstract
It has been shown that stressors are capable of activating transposable elements (TEs). Currently, there is a hypothesis that stress activation of TEs may be involved in adaptive evolution, favouring the increase in genetic variability when the population is under adverse conditions. However, TE activation under stress is still poorly understood. In the present study, we estimated the fraction of differentially expressed TEs (DETEs) under ionizing radiation (144, 360 and 864 Gy) and oxidative stress (dioxin, formaldehyde and toluene) treatments. The stress intensity of each treatment was estimated by measuring the number of differentially expressed genes, and we show that several TEs families are activated by stress whereas others are repressed. The proportion of DETEs was positively related to stress intensity. However, even under the strongest stress, only a small fraction of TE families were activated (9.28%) and 17.72% were repressed. Considering all treatments together, the activated proportion was 19.83%. Nevertheless, as several TEs are incomplete or degenerated, only 10.55% of D. melanogaster mobilome is, at same time, activated by the stressors and able to transpose or at least code a protein. Thus, our study points out that although stress activates TEs, it is not a generalized activation process, and for some families, the stress induces repression.
Collapse
Affiliation(s)
- Daniel Siqueira de Oliveira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marcos Trindade Rosa
- PPG Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Elgion L S Loreto
- Dep de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| |
Collapse
|
4
|
Guio L, González J. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans. Methods Mol Biol 2019; 1910:505-530. [PMID: 31278675 DOI: 10.1007/978-1-4939-9074-0_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.
Collapse
Affiliation(s)
- Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| |
Collapse
|
5
|
Isobe S, Shirasawa K, Hirakawa H. Challenges to genome sequence dissection in sweetpotato. BREEDING SCIENCE 2017; 67:35-40. [PMID: 28465666 PMCID: PMC5407923 DOI: 10.1270/jsbbs.16186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/23/2017] [Indexed: 05/23/2023]
Abstract
The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato. Meanwhile, several research groups have begun the challenging task of directly sequencing the sweetpotato genome. In this manuscript, we review the recent results and activities of large-scale genome and transcriptome analysis related to genome sequence dissection in sweetpotato under the sections as follows: I. trifida genome and transcript sequencing, genome sequences of I. nil (Japanese morning glory), transcript sequences in sweetpotato, chloroplast sequences, transposable elements and transfer DNA. The recent international activities of de novo whole genome sequencing in sweetpotato are also described. The large-scale publically available genome and transcript sequence resources and the international genome sequencing streams are expected to promote the genome sequence dissection in sweetpotato.
Collapse
|