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Zhao Q, Li X, Jiao Y, Chen Y, Yan Y, Wang Y, Hamiaux C, Wang Y, Ma F, Atkinson RG, Li P. Identification of two key genes involved in flavonoid catabolism and their different roles in apple resistance to biotic stresses. THE NEW PHYTOLOGIST 2024; 242:1238-1256. [PMID: 38426393 DOI: 10.1111/nph.19644] [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: 11/09/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Biosynthesis of flavonoid aglycones and glycosides is well established. However, key genes involved in their catabolism are poorly understood, even though the products of hydrolysis and oxidation play important roles in plant resistance to biotic stress. Here, we report on catabolism of dihydrochalcones (DHCs), the most abundant flavonoids in domesticated apple and wild Malus. Two key genes, BGLU13.1 and PPO05, were identified by activity-directed protein purification. BGLU13.1-A hydrolyzed phlorizin, (the most abundant DHC in domesticated apple) to produce phloretin which was then oxidized by PPO05. The process differed in some wild Malus, where trilobatin (a positional isomer of phlorizin) was mainly oxidized by PPO05. The effects of DHC catabolism on apple resistance to biotic stresses was investigated using transgenic plants. Either directly or indirectly, phlorizin hydrolysis affected resistance to the phytophagous pest two-spotted spider mite, while oxidation of trilobatin was involved in resistance to the biotrophic fungus Podosphaera leucotricha. DHC catabolism did not affect apple resistance to necrotrophic pathogens Valsa mali and Erwinia amylovara. These results suggest that different DHC catabolism pathways play different roles in apple resistance to biotic stresses. The role of DHC catabolism on apple resistance appeared closely related to the mode of invasion/damage used by pathogen/pest.
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Affiliation(s)
- Qian Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoning Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yu Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ying Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanfang Yan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuzhu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cyril Hamiaux
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, 1142, New Zealand
| | - Yule Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, 1142, New Zealand
| | - Pengmin Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Kumar K, Mandal SN, Pradhan B, Kaur P, Kaur K, Neelam K. From Evolution to Revolution: Accelerating Crop Domestication through Genome Editing. PLANT & CELL PHYSIOLOGY 2022; 63:1607-1623. [PMID: 36018059 DOI: 10.1093/pcp/pcac124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Crop domestication has a tremendous impact on socioeconomic conditions and human civilization. Modern cultivars were domesticated from their wild progenitors thousands of years ago by the selection of natural variation by humans. New cultivars are being developed by crossing two or more compatible individuals. But the limited genetic diversity in the cultivars severely affects the yield and renders the crop susceptible to many biotic and abiotic stresses. Crop wild relatives (CWRs) are the rich reservoir for many valuable agronomic traits. The incorporation of useful genes from CWR is one of the sustainable approaches for enriching the gene pool of cultivated crops. However, CWRs are not suited for urban and intensive cultivation because of several undesirable traits. Researchers have begun to study the domestication traits in the CWRs and modify them using genome-editing tools to make them suitable for extensive cultivation. Growing evidence has shown that modification in these genes is not sufficient to bring the desired change in the neodomesticated crop. However, the other dynamic genetic factors such as microRNAs (miRNAs), transposable elements, cis-regulatory elements and epigenetic changes have reshaped the domesticated crops. The creation of allelic series for many valuable domestication traits through genome editing holds great potential for the accelerated development of neodomesticated crops. The present review describes the current understanding of the genetics of domestication traits that are responsible for the agricultural revolution. The targeted mutagenesis in these domestication genes via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 could be used for the rapid domestication of CWRs.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Swarupa Nanda Mandal
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79415, USA
| | - Bhubaneswar Pradhan
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata 700103, India
| | - Pavneet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Karminderbir Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004, India
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3
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Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. THE PLANT CELL 2022; 34:4143-4172. [PMID: 35961044 PMCID: PMC9614464 DOI: 10.1093/plcell/koac249] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/24/2022] [Indexed: 05/05/2023]
Abstract
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
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Affiliation(s)
| | | | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - David D Curdie
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel Wang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hyun Don Ham
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Juan K Q Solomon
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Annaliese S Mason
- Plant Breeding Department, INRES, The University of Bonn, Bonn 53115, Germany
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, , University of Missouri, Columbia, Missouri 65211, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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Deneweth J, Van de Peer Y, Vermeirssen V. Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum. BMC Genomics 2022; 23:18. [PMID: 34983397 PMCID: PMC8725346 DOI: 10.1186/s12864-021-08215-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. RESULTS We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato. CONCLUSIONS Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
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Affiliation(s)
- Jan Deneweth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Vanessa Vermeirssen
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .,Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant ( Solanum melongena). FRONTIERS IN PLANT SCIENCE 2021; 12:683681. [PMID: 34367211 PMCID: PMC8346255 DOI: 10.3389/fpls.2021.683681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/30/2021] [Indexed: 05/20/2023]
Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
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Affiliation(s)
- Saad Serfraz
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- *Correspondence: Pierre-Yves Teycheney,
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Gill KS, Kaur G, Kaur G, Kaur J, Kaur Sra S, Kaur K, Gurpreet K, Sharma M, Bansal M, Chhuneja P, Banga SS. Development and Validation of Kompetitive Allele-Specific PCR Assays for Erucic Acid Content in Indian Mustard [ Brassica juncea (L.) Czern and Coss.]. FRONTIERS IN PLANT SCIENCE 2021; 12:738805. [PMID: 34975937 PMCID: PMC8714676 DOI: 10.3389/fpls.2021.738805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/20/2021] [Indexed: 05/10/2023]
Abstract
Brassica juncea L. is the most widely cultivated oilseed crop in Indian subcontinent. Its seeds contain oil with very high concentration of erucic acid (≈50%). Of late, there is increasing emphasis on the development of low erucic acid varieties because of reported association of the consumption of high erucic acid oil with cardiac lipidosis. Erucic acid is synthesized from oleic acid by an elongation process involving two cycles of four sequential steps. Of which, the first step is catalyzed by β-ketoacyl-CoA synthase (KCS) encoded by the fatty acid elongase 1 (FAE1) gene in Brassica. Mutations in the coding region of the FAE1 lead to the loss of KCS activity and consequently a drastic reduction of erucic acid in the seeds. Molecular markers have been developed on the basis of variation available in the coding or promoter region(s) of the FAE1. However, majority of these markers are not breeder friendly and are rarely used in the breeding programs. Present studies were planned to develop robust kompetitive allele-specific PCR (KASPar) assays with high throughput and economics of scale. We first cloned and sequenced FAE1.1 and FAE1.2 from high and low erucic acid (<2%) genotypes of B. juncea (AABB) and its progenitor species, B. rapa (AA) and B. nigra (BB). Sequence comparisons of FAE1.1 and FAE1.2 genes for low and high erucic acid genotypes revealed single nucleotide polymorphisms (SNPs) at 8 and 3 positions. Of these, three SNPs for FAE1.1 and one SNPs for FAE1.2 produced missense mutations, leading to amino acid modifications and inactivation of KCS enzyme. We used SNPs at positions 735 and 1,476 for genes FAE1.1 and FAE1.2, respectively, to develop KASPar assays. These markers were validated on a collection of diverse genotypes and a segregating backcross progeny. KASPar assays developed in this study will be useful for marker-assisted breeding, as these can track recessive alleles in their heterozygous state with high reproducibility.
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Affiliation(s)
- Karanjot Singh Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Gurpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Gurpreet Kaur, ; orcid.org/0000-0002-0660-9592
| | - Gurdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jasmeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Simarjeet Kaur Sra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kawalpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kaur Gurpreet
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meha Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Ostrowska-Mazurek A, Kasprzak P, Kubala S, Zaborowska M, Sobieszczuk-Nowicka E. Epigenetic Landmarks of Leaf Senescence and Crop Improvement. Int J Mol Sci 2020; 21:ijms21145125. [PMID: 32698545 PMCID: PMC7404090 DOI: 10.3390/ijms21145125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/04/2023] Open
Abstract
This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding.
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Affiliation(s)
- Agnieszka Ostrowska-Mazurek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Piotr Kasprzak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Magdalena Zaborowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
- Correspondence: ; Tel.: +48-61-829-5892
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8
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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9
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Pontier D, Picart C, El Baidouri M, Roudier F, Xu T, Lahmy S, Llauro C, Azevedo J, Laudié M, Attina A, Hirtz C, Carpentier MC, Shen L, Lagrange T. The m 6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci Alliance 2019; 2:2/3/e201900393. [PMID: 31142640 PMCID: PMC6545605 DOI: 10.26508/lsa.201900393] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/24/2022] Open
Abstract
This study reveals that an m6A-assisted polyadenylation pathway comprising conserved m6A writer proteins and a plant-specific m6A reader contributes to transcriptome integrity in Arabidopsis thaliana by restricting RNA chimera formation at rearranged loci. Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.
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Affiliation(s)
- Dominique Pontier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Claire Picart
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Moaine El Baidouri
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Lyon, France
| | - Tao Xu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sylvie Lahmy
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Christel Llauro
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Jacinthe Azevedo
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Michèle Laudié
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Aurore Attina
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Christophe Hirtz
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Marie-Christine Carpentier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore
| | - Thierry Lagrange
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France .,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
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10
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Fambrini M, Bellanca M, Costa Muñoz M, Usai G, Cavallini A, Pugliesi C. Ligulate inflorescence of Helianthus × multiflorus, cv. Soleil d'Or, correlates with a mis-regulation of a CYCLOIDEA gene characterised by insertion of a transposable element. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:956-967. [PMID: 30022587 DOI: 10.1111/plb.12876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Members of CYCLOIDEA (CYC)/TEOSINTE BRANCHED1 (TB1) transcription factor family are essential to control flower symmetry and inflorescence architecture. In the Helianthus annuus genome, ten CYC/TB1 genes have been identified. Studies performed on mutants recognised HaCYC2c as one of the key players controlling zygomorphism in sunflower. We identified CYC2c genes in the diploid Helianthus decapetalus (HdCYC2c) and in the interspecific hybrid Helianthus × multiflorus (H × mCYC2cA and H × mCYC2cB), a triploid (2n = 3× = 51), originated from unreduced eggs of H. decapetalus fertilised by reduced H. annuus male gametes. Phylogenetic analysis showed that HdCYC2c and H × mCYC2c were placed within a CYC2 subclade together with HaCYC2c but distinct from it. The present data showed that in H. × multiflorus the allele derived from H. annuus is deleted or highly modified. The H. × multiflorus taxon exists as radiate and ligulate inflorescence types. We analysed CYC2c expression in H. decapetalus and in the cultivar 'Soleil d'Or' of H. × multiflorus, a ligulate inflorescence type with actinomorphic corolla of disk flowers transformed into a zygomorphic ray-like corolla. In H. decapetalus, the HdCYC2c gene showed differential expression between developing flower types, being up-regulated in the corolla of ray flowers in comparison to the disk flower corolla. In H. × multiflorus, an insertion of 865 bp, which is part of a CACTA transposable element, was found in the 5'-untranslated region (5'-UTR) of H × mCYC2cB. This insertion could promote, even with epigenetic mechanisms, ectopic expression of the gene throughout the inflorescence, resulting in the observed loss of actinomorphy and originating a ligulate head.
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Affiliation(s)
- M Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Bellanca
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - M Costa Muñoz
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - G Usai
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - A Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - C Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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11
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Sahebi M, Hanafi MM, van Wijnen AJ, Rice D, Rafii MY, Azizi P, Osman M, Taheri S, Bakar MFA, Isa MNM, Noor YM. Contribution of transposable elements in the plant's genome. Gene 2018; 665:155-166. [PMID: 29684486 DOI: 10.1016/j.gene.2018.04.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/04/2018] [Accepted: 04/18/2018] [Indexed: 12/26/2022]
Abstract
Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed M Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | | | - David Rice
- Department of Molecular Biology & Biotecnology, University of Sheffield, United Kingdom
| | - M Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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12
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El Baidouri M, Kim KD, Abernathy B, Li YH, Qiu LJ, Jackson SA. Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres. MOLECULAR PLANT 2018; 11:485-495. [PMID: 29476915 DOI: 10.1016/j.molp.2018.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
Most plants are polyploid due to whole-genome duplications (WGD) and can thus have duplicated genes. Following a WGD, paralogs are often fractionated (lost) and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high-resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of genetic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit particular genomic features as they are often associated with proximal transposable elements (TEs) and are preferentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.
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Affiliation(s)
- Moaine El Baidouri
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA.
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA; Corporate R&D, LG Chem, LG Science Park, 30 Magokjungang 10-ro, Gangseo-gu, Seoul 07796, Republic of Korea.
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA.
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13
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Li D, Lei Z, Xue J, Zhou G, Hang Y, Sun X. Regulation of FATTY ACID ELONGATION1 expression and production in Brassica oleracea and Capsella rubella. PLANTA 2017; 246:763-778. [PMID: 28674753 DOI: 10.1007/s00425-017-2731-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The contribution of variations in coding regions or promoters to the changes in FAE1 expression levels have be quantified and compared in parallel by specifically designed swapping constructs. FATTY ACID ELONGATION1 (FAE1) is a key gene in control of erucic acid synthesis in plant seeds. The expression of FAE1 genes in Brassica oleracea and Capsella rubella, representatives of high and low erucic acid species, respectively, was characterized to provide insight into the regulation of very long-chain fatty-acid biosynthesis in seeds. Virtually, no methylation was detected either in B. oleracea or in C. rubella, suggesting that modification of promoter methylation might not be a predominant mechanism. Swapping constructs were specifically designed to quantify and compare the contribution of variations in coding regions or promoters to the changes in FAE1 expression levels in parallel. A significantly higher fold change in erucic acid content was observed when swapping coding regions rather than when swapping promoters, indicating that the coding region is a major determinant of the catalytic power of β-ketoacyl-CoA synthase proteins. Common motifs have been proposed as essential for the preservation of basic gene expression patterns, such as seed-specific expression. However, the occurrence of variation in common cis-elements or the presence of species-specific cis-elements might be plausible mechanisms for changes in the expression levels in different organisms. In addition, conflicting observations in previous reports associated with FAE1 expression are discussed, and we suggest that caution should be taken when selecting a plant transformation vector and in interpreting the results obtained from vectors carrying the CaMV 35S promoter.
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Affiliation(s)
- Dinghong Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Zhao Lei
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Jiayu Xue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Guangcan Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Yueyu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China.
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14
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Mutations in the promoter, intron and CDS of two FAD2 generate multiple alleles modulating linoleic acid level in yellow mustard. Sci Rep 2017; 7:8284. [PMID: 28811544 PMCID: PMC5557838 DOI: 10.1038/s41598-017-08317-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/07/2017] [Indexed: 11/08/2022] Open
Abstract
Linoleic acid (C18:2) is an important polyunsaturated fatty acid in the seed oil of many crops. Here, we report that mutations in the promoter, intron and CDS of the FAD2 genes SalFAD2.LIA1 and SalFAD2.LIA2 generate three alleles LIA 1a , LIA 1b and lia 1 and two alleles LIA 2 and lia 2, respectively, controlling the C18:2 variation (4.4-32.7%) in yellow mustard. The allelic effect on increasing C18:2 content is LIA 1a > LIA 1b > lia 1 , LIA 2 > lia 2, and LIA 1a > LIA 2. The five FAD 2 alleles each contain two exons, one intron and a promoter adjacent to exon 1. LIA 1a has a 1152 bp CDS, a 1221 bp intron with promoter function and a 607 bp promoter. Compared with LIA 1a , the intron of LIA 1b has reduced promoter activity and that of LIA 2 and lia 2 has no promoter function due to extensive SNP and indel mutations. lia 1 differed from LIA 1b by having an insertion of 1223 bp retrotransposon in its intron. lia 2 with mutations in the promoter has reduced promoter activity compared with LIA 2 . This study revealed that complex quantitative variation of trait phenotype in plants could be modulated by multiple alleles of oligogenic loci resulting from mutations in the regulatory region and CDS.
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15
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16
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Fortes AM, Gallusci P. Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:82. [PMID: 28220131 PMCID: PMC5292615 DOI: 10.3389/fpls.2017.00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants. In this perspective, we discuss the contribution of epigenetic mechanisms to our understanding of plant responses to biotic and abiotic stresses. This regulation of gene expression in response to environment raises important biological questions for perennial species such as grapevine which is asexually propagated and grown worldwide in contrasting terroirs and environmental conditions. However, most species used for epigenomic studies are annual herbaceous plants, and epigenome dynamics has been poorly investigated in perennial woody plants, including grapevine. In this context, we propose grape as an essential model for epigenetic and epigenomic studies in perennial woody plants of agricultural importance.
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Affiliation(s)
- Ana M. Fortes
- Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas, Universidade de LisboaLisboa, Portugal
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du VinVillenave-d’Ornon, France
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17
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Hirsch CD, Springer NM. Transposable element influences on gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:157-165. [PMID: 27235540 DOI: 10.1016/j.bbagrm.2016.05.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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18
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Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. PLANTA 2016; 243:1083-95. [PMID: 26919983 DOI: 10.1007/s00425-016-2485-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 05/03/2023]
Abstract
The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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19
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Springer NM, Lisch D, Li Q. Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. THE PLANT CELL 2016; 28:314-25. [PMID: 26869701 PMCID: PMC4790878 DOI: 10.1105/tpc.15.00911] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.
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Affiliation(s)
- Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
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20
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Wei L, Cao X. The effect of transposable elements on phenotypic variation: insights from plants to humans. SCIENCE CHINA-LIFE SCIENCES 2016; 59:24-37. [PMID: 26753674 DOI: 10.1007/s11427-015-4993-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.
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Affiliation(s)
- Liya Wei
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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21
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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Yan G, Li D, Cai M, Gao G, Chen B, Xu K, Li J, Li F, Wang N, Qiao J, Li H, Zhang T, Wu X. Characterization of FAE1 in the zero erucic acid germplasm of Brassica rapa L. BREEDING SCIENCE 2015; 65:257-64. [PMID: 26175623 PMCID: PMC4482176 DOI: 10.1270/jsbbs.65.257] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/01/2015] [Indexed: 05/07/2023]
Abstract
The modification of erucic acid content in seeds is one of the major goals for quality breeding in oil-yielding Brassica species. However, few low erucic acid (LEA) resources are available, and novel LEA genetic resources are being sought. Fatty acid elongase 1 (FAE1) is the key gene that controls erucic acid synthesis. However, the mechanism for erucic acid synthesis in B. rapa lacks systematic study. Here, we isolated zero erucic acid lines from 1981 Chinese landraces of B. rapa and found that the formation of LEA is not attributable to variations in FAE1 coding sequences, as reported for B. napus, but may be attributable to the decrease in FAE1 expression. Moreover, the FAE1 promoter sequences of LEA and high erucic acid materials shared 95% similarity. Twenty-eight bases deletions (containing a 24-base AT-rich region) were identified approximately 1300 bp upstream from the FAE1 start codon in the LEA accessions. The genotype with the deletions co-segregated with the LEA trait in the segregating population. This study isolated an LEA B. rapa resource that can be exploited in Brassica cultivation. The promoter variations might modify the expression level of FAE1, and the results shed light on novel regulation mechanisms for erucic acid synthesis.
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