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Mandáková T, Krumpolcová A, Matyášek R, Volkov R, Lysak MA, Kovařík A. Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38838061 DOI: 10.1111/tpj.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high-throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids.
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Affiliation(s)
- Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Alice Krumpolcová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Matyášek
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
| | - Roman Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, 58012, Chernivtsi, Ukraine
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Ales Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 00, Brno, Czech Republic
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Chen G, Stepanenko A, Borisjuk N. Contrasting patterns of 5S rDNA repeats in European and Asian ecotypes of greater duckweed, Spirodela polyrhiza (Lemnaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1378683. [PMID: 38711607 PMCID: PMC11070557 DOI: 10.3389/fpls.2024.1378683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
Ribosomal DNA (rDNA) contains highly conserved, specifically organized sequences encoding ribosomal RNAs (rRNAs) separated by variable non-transcribed intergenic spacers (NTSs) and is abundant in eukaryotic genomes. These characteristics make the rDNA an informative molecular target to study genome organization, molecular evolution, and phylogenetics. In this study, we characterized the 5S rDNA repeats in the greater duckweed Spiroldela polyrhiza, a species known for its small size, rapid growth, highly conserved genome organization, and low mutation rate. Sequence analysis of at least 12 individually cloned PCR fragments containing the 5S rDNA units for each of six ecotypes that originated from Europe (Ukraine) and Asia (China) revealed two distinct types of 5S rDNA repeats containing NTSs of different lengths and nucleotide compositions. The shorter 5S rDNA repeat units had a highly homogeneous 400-bp NTS, with few ecotype- or region-specific single-nucleotide polymorphisms (SNPs). The longer 5S rDNA units had NTSs of 1056-1084 bp with characteristic intra- and inter-genomic variants due to specific SNPs and insertions/deletions of 4-15-bp DNA elements. We also detected significant variability in the ratio of short/long 5S rDNA variants between ecotypes of S. polyrhiza. The contrasting dynamics of the two types of 5S rDNA units, combined with the unusually low repeat copy number (for plants) in S. polyrhiza (46-220 copies per genome), shows that this species could serve as an excellent model for examining the mechanisms of concerted evolution and functional significance of rDNA variability.
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Affiliation(s)
- Guimin Chen
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Anton Stepanenko
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Molecular Genetics, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Nikolai Borisjuk
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
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3
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Aviña-Padilla K, Zambada-Moreno O, Herrera-Oropeza GE, Jimenez-Limas MA, Abrahamian P, Hammond RW, Hernández-Rosales M. Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches. Int J Mol Sci 2022; 23:5983. [PMID: 35682662 PMCID: PMC9181013 DOI: 10.3390/ijms23115983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 01/25/2023] Open
Abstract
Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
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Affiliation(s)
- Katia Aviña-Padilla
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Octavio Zambada-Moreno
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
| | - Gabriel Emilio Herrera-Oropeza
- Center for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London WC2R 2LS, UK;
| | - Marco A. Jimenez-Limas
- Centro de Investigación en Computación, Instituto Politécnico Nacional, Mexico City 07738, Mexico;
| | - Peter Abrahamian
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Rosemarie W. Hammond
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
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Matoušek J, Steger G. The Splicing Variant TFIIIA-7ZF of Viroid-Modulated Transcription Factor IIIA Causes Physiological Irregularities in Transgenic Tobacco and Transient Somatic Depression of "Degradome" Characteristic for Developing Pollen. Cells 2022; 11:784. [PMID: 35269406 PMCID: PMC8909551 DOI: 10.3390/cells11050784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from Nicotiana benthamiana in tobacco (Nicotiana tabacum) where it caused morphological and physiological deviations like plant stunting, splitting of leaf petioles, pistils or apexes, irregular branching of shoots, formation of double-blade leaves, deformation of main stems, and modification of glandular trichomes. Plant aging and senescence was dramatically delayed in transgenic lines. Factors potentially involved in viroid degradation and elimination in pollen were transiently depressed in transgenic leaves. This depressed "degradome" in young plants involved NtTudor S-like nuclease, dicers, argonoute 5, and pollen extracellular nuclease I showing expression in tobacco anthers and leaves. Analysis of the "degradome" in tobacco leaves transformed with either of two hop viroids confirmed modifications of the "degradome" and TFIIIA expression. Thus, the regulatory network connected to TFIIIA-7ZF could be involved in plant pathogenesis as well as in viroid adaptation to avoid its degradation. These results support the hypothesis on a significant impact of limited TFIIIA-7ZF on viroid elimination in pollen.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic;
| | - Gerhard Steger
- Institutfür Pysikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
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Mudiyanselage SDD, Wang Y. Fluorescein-Based Electrophoretic Mobility Shift Assay. Methods Mol Biol 2022; 2316:133-140. [PMID: 34845691 DOI: 10.1007/978-1-0716-1464-8_12] [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] [Indexed: 06/13/2023]
Abstract
RNA-protein complexes are functionally important in biology. Electrophoretic mobility shift assays (EMSA) have been widely used to study the molecular basis of protein-RNA interactions. Previous methods for EMSA mostly relied on radioactive RNA substrates, raising health and environmental concerns. Here, we describe a method based on fluorescein-labeled RNA for EMSA. In addition, we simplified the protocol to efficiently purify RNA-binding proteins from bacterial expression systems.
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Affiliation(s)
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA.
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Wang Y. Current view and perspectives in viroid replication. Curr Opin Virol 2021; 47:32-37. [PMID: 33460914 DOI: 10.1016/j.coviro.2020.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. The noncoding nature indicates that viroids must harness their RNA genomes to redirect host machinery for infection. Therefore, the viroid model provides invaluable opportunities for delineating fundamental principles of RNA structure-function relationships and for dissecting the composition and mechanism of RNA-related cellular machinery. There are two viroid families, Pospiviroidae and Avsunviroidae. Members of both families replicate via the RNA-based rolling-circle mechanism with some variations. Viroid replication is generally divided into three steps: transcription, cleavage, and ligation. Decades of studies have uncovered numerous viroid RNA structures with a regulatory role in replication and multiple enzymes critical for the three replication steps. This review discusses these findings and highlights the latest discoveries. Future studies will continue to elucidate regulatory factors and mechanism of host machinery exploited by viroids and provide new insights into host-viroid interactions in the context of pathogenesis.
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Affiliation(s)
- Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA.
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Fan K, Yuan S, Chen J, Chen Y, Li Z, Lin W, Zhang Y, Liu J, Lin W. Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays. PLANTA 2019; 250:1521-1538. [PMID: 31346803 DOI: 10.1007/s00425-019-03243-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
97 ZmPP2Cs were clustered into 10 subfamilies with biased subfamily evolution and lineage-specific expansion. Segmental duplication after the divergence of maize and sorghum might have led to primary expansion of ZmPP2Cs. The protein phosphatase 2C (PP2C) enzymes control many stress responses and developmental processes in plants. In Zea mays, a comprehensive understanding of the evolution and expansion of the PP2C family is still lacking. In the current study, 97 ZmPP2Cs were identified and clustered into 10 subfamilies. Through the analysis of the PP2C family in monocots, the ZmPP2C subfamilies displayed biased subfamily molecular evolution and lineage-specific expansion, as evidenced by their differing numbers of member genes, expansion and evolutionary rates, conserved subdomains, chromosomal distributions, expression levels, responsive-regulatory elements and regulatory networks. Moreover, while segmental duplication events have caused the primary expansion of the ZmPP2Cs, the majority of their diversification occurred following the additional whole-genome duplication that took place after the divergence of maize and sorghum (Sorghum bicolor). After this event, the PP2C subfamilies showed asymmetric evolutionary rates, with the D, F2 and H subfamily likely the most closely to resemble its ancestral subfamily's genes. These findings could provide novel insights into the molecular evolution and expansion of the PP2C family in maize, and lay the foundation for the functional analysis of these enzymes in maize and related monocots.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Shuna Yuan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences/Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou, 571737, China
| | - Jie Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yunrui Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Zhaowei Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yongqiang Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Jianping Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Wenxiong Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China.
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Simon L, Rabanal FA, Dubos T, Oliver C, Lauber D, Poulet A, Vogt A, Mandlbauer A, Le Goff S, Sommer A, Duborjal H, Tatout C, Probst AV. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana. Nucleic Acids Res 2019. [PMID: 29518237 PMCID: PMC5887818 DOI: 10.1093/nar/gky163] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.
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Affiliation(s)
- Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Fernando A Rabanal
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tristan Dubos
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Damien Lauber
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Andreas Sommer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hervé Duborjal
- Plant Engineering Platform, BIOGEMMA, Route d'Ennezat Centre de Recherche de Chappes, 63720 Chappes, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
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Potato Spindle Tuber Viroid RNA-Templated Transcription: Factors and Regulation. Viruses 2018; 10:v10090503. [PMID: 30227597 PMCID: PMC6164485 DOI: 10.3390/v10090503] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 12/14/2022] Open
Abstract
Viroids are circular noncoding RNAs that infect plants. Without encoding any protein, these noncoding RNAs contain the necessary genetic information for propagation in hosts. Nuclear-replicating viroids employ DNA-dependent RNA polymerase II (Pol II) for replication, a process that makes a DNA-dependent enzyme recognize RNA templates. Recently, a splicing variant of transcription factor IIIA (TFIIIA-7ZF) was identified as essential for Pol II to replicate potato spindle tuber viroid (PSTVd). The expression of TFIIIA-7ZF, particularly the splicing event, is regulated by a ribosomal protein (RPL5). PSTVd modulates its expression through a direct interaction with RPL5 resulting in optimized expression of TFIIIA-7ZF. This review summarizes the recent discoveries of host factors and regulatory mechanisms underlying PSTVd-templated transcription processes and raises new questions that may help future exploration in this direction. In addition, it briefly compares the machinery and the regulatory mechanism for PSTVd with the replication/transcription system of human hepatitis delta virus.
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Capote T, Barbosa P, Usié A, Ramos AM, Inácio V, Ordás R, Gonçalves S, Morais-Cecílio L. ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber). BMC PLANT BIOLOGY 2018; 18:198. [PMID: 30223777 PMCID: PMC6142680 DOI: 10.1186/s12870-018-1403-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 08/30/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy. RESULTS Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly. CONCLUSION To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.
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Affiliation(s)
- Tiago Capote
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Pedro Barbosa
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Ricardo Ordás
- Departamento BOS, Escuela Politécnica de Mieres, Oviedo University, Oviedo, Spain
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Present Address: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB101SA UK
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
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Iñiguez LP, Ramírez M, Barbazuk WB, Hernández G. Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max. BMC Genomics 2017; 18:650. [PMID: 28830361 PMCID: PMC5568362 DOI: 10.1186/s12864-017-4054-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/11/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed. RESULTS We identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5'UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species. CONCLUSIONS The identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15-20 MY of divergence, and may point to the biological relevance of AS.
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Affiliation(s)
- Luis P. Iñiguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | | | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
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Wang Y, Qu J, Ji S, Wallace AJ, Wu J, Li Y, Gopalan V, Ding B. A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II. THE PLANT CELL 2016; 28:1094-107. [PMID: 27113774 PMCID: PMC4904678 DOI: 10.1105/tpc.16.00100] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/11/2016] [Accepted: 04/22/2016] [Indexed: 05/05/2023]
Abstract
Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP PSTVd replication in the nucleoplasm generates (-)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (-)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes.
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Affiliation(s)
- Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210
| | - Jie Qu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210
| | - Shaoyi Ji
- College of Life Sciences, Peking University, Beijing, China
| | - Andrew J Wallace
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Jian Wu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Yi Li
- College of Life Sciences, Peking University, Beijing, China
| | - Venkat Gopalan
- The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Biao Ding
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
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Martinez G, Castellano M, Tortosa M, Pallas V, Gomez G. A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants. Nucleic Acids Res 2013; 42:1553-62. [PMID: 24178032 PMCID: PMC3919566 DOI: 10.1093/nar/gkt968] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Viroids are plant-pathogenic non-coding RNAs able to interfere with as yet poorly known host-regulatory pathways and to cause alterations recognized as diseases. The way in which these RNAs coerce the host to express symptoms remains to be totally deciphered. In recent years, diverse studies have proposed a close interplay between viroid-induced pathogenesis and RNA silencing, supporting the belief that viroid-derived small RNAs mediate the post-transcriptional cleavage of endogenous mRNAs by acting as elicitors of symptoms expression. Although the evidence supporting the role of viroid-derived small RNAs in pathogenesis is robust, the possibility that this phenomenon can be a more complex process, also involving viroid-induced alterations in plant gene expression at transcriptional levels, has been considered. Here we show that plants infected with the ‘Hop stunt viroid’ accumulate high levels of sRNAs derived from ribosomal transcripts. This effect was correlated with an increase in the transcription of ribosomal RNA (rRNA) precursors during infection. We observed that the transcriptional reactivation of rRNA genes correlates with a modification of DNA methylation in their promoter region and revealed that some rRNA genes are demethylated and transcriptionally reactivated during infection. This study reports a previously unknown mechanism associated with viroid (or any other pathogenic RNA) infection in plants providing new insights into aspects of host alterations induced by the viroid infectious cycle.
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Affiliation(s)
- German Martinez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-UPV, CPI, Edificio 8 E, Avenida de los Naranjos s/n, 46022 Valencia, Spain
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Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:274-82. [DOI: 10.1016/j.bbagrm.2012.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 12/14/2022]
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Benoit M, Layat E, Tourmente S, Probst AV. Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci. Gene 2013; 526:39-45. [PMID: 23410919 DOI: 10.1016/j.gene.2013.01.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 01/01/2023]
Abstract
The Arabidopsis chromosomes contain conspicuous heterochromatin domains comprising the repetitive 45S and 5S ribosomal DNA loci as well as centromeric and pericentromeric repeats that organize into chromocenters during interphase. During developmental phase transitions such as seed maturation, germination, seedling growth and flowering that require large-scale reprogramming of gene expression patterns, the organization of repetitive sequences into chromocenters dynamically changes. Here we illustrate recent studies that shed light on the heterochromatin dynamics in cotyledons, the first aerial tissues preformed in the embryo, and in true leaves. We will summarize available data for the 5S rDNA repeat loci, in particular their chromatin organization and expression dynamics during the first days of post-germination development, and discuss how the plant accommodates 5S rRNA transcription during large-scale chromatin reorganization events.
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Affiliation(s)
- Matthias Benoit
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, 63171 Aubière Cedex, France.
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