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Hussain SS, Abbas M, Abbas S, Wei M, El-Sappah AH, Sun Y, Li Y, Ragauskas AJ, Li Q. Alternative splicing: transcriptional regulatory network in agroforestry. Front Plant Sci 2023; 14:1158965. [PMID: 37123829 PMCID: PMC10132464 DOI: 10.3389/fpls.2023.1158965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Sammar Abbas
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mingke Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Arthur J. Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
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Lippolis R, Rossi C, De Angelis M, Minervini F, Paparella A, Chaves-lópez C. Adaptive remodelling of blue pigmenting Pseudomonas fluorescens pf59 proteome in response to different environmental conditions. Food Control 2021; 127:108105. [DOI: 10.1016/j.foodcont.2021.108105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. New Phytol 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Wang R, Yin P, Ruixia Y, Liu X, Luo L, Xu J. Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves. PLoS One 2020; 15:e0241914. [PMID: 33206683 PMCID: PMC7673502 DOI: 10.1371/journal.pone.0241914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.
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Affiliation(s)
- Ruixue Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Peng Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Yang Ruixia
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Xiao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Lie Luo
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jichen Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- * E-mail:
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Arias C, Obudulu O, Zhao X, Ansolia P, Zhang X, Paul S, Bygdell J, Pirmoradian M, Zubarev RA, Samuelsson G, Wingsle G, Bajhaiya AK. Nuclear proteome analysis of Chlamydomonas with response to CO2 limitation. ALGAL RES 2020; 46:101765. [DOI: 10.1016/j.algal.2019.101765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Tai HH, Lagüe M, Thomson S, Aurousseau F, Neilson J, Murphy A, Bizimungu B, Davidson C, Deveaux V, Bègue Y, Wang HY, Xiong X, Jacobs JME. Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage. Plant Physiol Biochem 2020; 146:163-176. [PMID: 31756603 DOI: 10.1016/j.plaphy.2019.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 05/19/2023]
Abstract
Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2-4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.
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Affiliation(s)
- Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada.
| | - Martin Lagüe
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - Frédérique Aurousseau
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Jonathan Neilson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Agnes Murphy
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Benoit Bizimungu
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Charlotte Davidson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Virginie Deveaux
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Yves Bègue
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Hui Ying Wang
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Xingyao Xiong
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Jeanne M E Jacobs
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
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Paudel JR, Davidson C, Song J, Maxim I, Aharoni A, Tai HH. Pathogen and Pest Responses Are Altered Due to RNAi-Mediated Knockdown of GLYCOALKALOID METABOLISM 4 in Solanum tuberosum. Mol Plant Microbe Interact 2017; 30:876-885. [PMID: 28786312 DOI: 10.1094/mpmi-02-17-0033-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are major secondary metabolites constitutively produced in cultivated potato Solanum tuberosum, and α-solanine and α-chaconine are the most abundant SGAs. SGAs are toxic to humans at high levels but their role in plant protection against pests and pathogens is yet to be established. In this study, levels of SGAs in potato were reduced by RNA interference (RNAi)-mediated silencing of GLYCOALKALOID METABOLISM 4 (GAME4)-a gene encoding cytochrome P450, involved in an oxidation step in the conversion of cholesterol to SGA aglycones. Two GAME4 RNAi lines, T8 and T9, were used to investigate the effects of manipulation of the SGA biosynthetic pathway in potato. Growth and development of an insect pest, Colorado potato beetle (CPB), were affected in these lines. While no effect on CPB leaf consumption or weight gain was observed, early instar larval death and accelerated development of the insect was found while feeding on leaves of GAME4 RNAi lines. Modulation of SGA biosynthetic pathway in GAME4 RNAi plants was associated with a larger alteration to the metabolite profile, including increased levels of one or both the steroidal saponins or phytoecdysteroids, which could affect insect mortality as well as development time. Colonization by Verticillium dahliae on GAME4 RNAi plants was also tested. There were increased pathogen levels in the T8 GAME4 RNAi line but not in the T9. Metabolite differences between T8 and T9 were found and may have contributed to differences in V. dahliae infection. Drought responses created by osmotic stress were not affected by modulation of SGA biosynthetic pathway in potato.
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Affiliation(s)
- Jamuna Risal Paudel
- 1 Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, NB, Canada
| | - Charlotte Davidson
- 1 Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, NB, Canada
| | - Jun Song
- 2 Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS, Canada
| | | | - Asaph Aharoni
- 4 Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Helen H Tai
- 1 Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, NB, Canada
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An C, Gao Y, Li J, Liu X, Gao F, Gao H. Alternative splicing affects the targeting sequence of peroxisome proteins in Arabidopsis. Plant Cell Rep 2017; 36:1027-1036. [PMID: 28352967 DOI: 10.1007/s00299-017-2131-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
A systematic analysis of the Arabidopsis genome in combination with localization experiments indicates that alternative splicing affects the peroxisomal targeting sequence of at least 71 genes in Arabidopsis. Peroxisomes are ubiquitous eukaryotic cellular organelles that play a key role in diverse metabolic functions. All peroxisome proteins are encoded by nuclear genes and target to peroxisomes mainly through two types of targeting signals: peroxisomal targeting signal type 1 (PTS1) and PTS2. Alternative splicing (AS) is a process occurring in all eukaryotes by which a single pre-mRNA can generate multiple mRNA variants, often encoding proteins with functional differences. However, the effects of AS on the PTS1 or PTS2 and the targeting of the protein were rarely studied, especially in plants. Here, we systematically analyzed the genome of Arabidopsis, and found that the C-terminal targeting sequence PTS1 of 66 genes and the N-terminal targeting sequence PTS2 of 5 genes are affected by AS. Experimental determination of the targeting of selected protein isoforms further demonstrated that AS at both the 5' and 3' region of a gene can affect the inclusion of PTS2 and PTS1, respectively. This work underscores the importance of AS on the global regulation of peroxisome protein targeting.
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Affiliation(s)
- Chuanjing An
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuefang Gao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinyu Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaomin Liu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fuli Gao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongbo Gao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Valledor L, Furuhashi T, Hanak AM, Weckwerth W. Systemic cold stress adaptation of Chlamydomonas reinhardtii. Mol Cell Proteomics 2013; 12:2032-47. [PMID: 23564937 PMCID: PMC3734567 DOI: 10.1074/mcp.m112.026765] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/15/2013] [Indexed: 11/06/2022] Open
Abstract
Chlamydomonas reinhardtii is one of the most important model organisms nowadays phylogenetically situated between higher plants and animals (Merchant et al. 2007). Stress adaptation of this unicellular model algae is in the focus because of its relevance to biomass and biofuel production. Here, we have studied cold stress adaptation of C. reinhardtii hitherto not described for this algae whereas intensively studied in higher plants. Toward this goal, high throughput mass spectrometry was employed to integrate proteome, metabolome, physiological and cell-morphological changes during a time-course from 0 to 120 h. These data were complemented with RT-qPCR for target genes involved in central metabolism, signaling, and lipid biosynthesis. Using this approach dynamics in central metabolism were linked to cold-stress dependent sugar and autophagy pathways as well as novel genes in C. reinhardtii such as CKIN1, CKIN2 and a hitherto functionally not annotated protein named CKIN3. Cold stress affected extensively the physiology and the organization of the cell. Gluconeogenesis and starch biosynthesis pathways are activated leading to a pronounced starch and sugar accumulation. Quantitative lipid profiles indicate a sharp decrease in the lipophilic fraction and an increase in polyunsaturated fatty acids suggesting this as a mechanism of maintaining membrane fluidity. The proteome is completely remodeled during cold stress: specific candidates of the ribosome and the spliceosome indicate altered biosynthesis and degradation of proteins important for adaptation to low temperatures. Specific proteasome degradation may be mediated by the observed cold-specific changes in the ubiquitinylation system. Sparse partial least squares regression analysis was applied for protein correlation network analysis using proteins as predictors and Fv/Fm, FW, total lipids, and starch as responses. We applied also Granger causality analysis and revealed correlations between proteins and metabolites otherwise not detectable. Twenty percent of the proteins responsive to cold are uncharacterized proteins. This presents a considerable resource for new discoveries in cold stress biology in alga and plants.
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Affiliation(s)
- Luis Valledor
- ‡From the Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria, Althanstrasse 14, A-1090, Vienna, Austria
| | - Takeshi Furuhashi
- ‡From the Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria, Althanstrasse 14, A-1090, Vienna, Austria
| | - Anne-Mette Hanak
- ‡From the Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria, Althanstrasse 14, A-1090, Vienna, Austria
| | - Wolfram Weckwerth
- ‡From the Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria, Althanstrasse 14, A-1090, Vienna, Austria
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Tai HH, Goyer C, Bud Platt HW, De Koeyer D, Murphy A, Uribe P, Halterman D. Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato. Funct Integr Genomics 2013. [PMID: 23842988 DOI: 10.1007/s10142‐013‐0329‐0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Verticillium dahliae Kleb., a soil-borne fungus that colonizes vascular tissues, induces wilting, chlorosis and early senescence in potato. Difference in senescence timing found in two diploid potato clones, 07506-01 and 12120-03, was studied and genetic variation in response to V. dahliae infection was identified as a causal factor. The clone, 07506-01, was infected with V. dahliae but did not develop symptoms, indicating tolerance to the pathogen. The other diploid clone, 12120-03 had low levels of pathogen with infection and moderate symptoms indicating partial resistance. 07506-01 was found to carry two susceptible alleles of the Ve2 gene and 12120-03 carried one Ve2 resistant and one susceptible allele. Infected leaves of the two clones were compared using gene expression profiling with the Potato Oligonucleotide Chip Initiative (POCI) microrarray. The results provide further evidence for differences in response of the two clones to infection with V. dahliae. Chlorophyll biosynthesis was higher in the tolerant 07506-01 compared to partially resistant 12120-03. On the other hand, expression of fungal defense genes, Ve resistance genes and defense phytohormone biosynthetic enzyme genes was decreased in 07506-01 compared to 12120-03 suggesting defense responses were suppressed in tolerance compared to resistance. Transcription factor gene expression differences pointed to the WRKY family as potential regulators of V. dahliae responses in potato.
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Affiliation(s)
- Helen H Tai
- Potato Research Centre, Agriculture and Agri-Food Canada, PO Box 20280, Fredericton, NB E3B 4Z7, Canada.
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Tai HH, Goyer C, Bud Platt HW, De Koeyer D, Murphy A, Uribe P, Halterman D. Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato. Funct Integr Genomics 2013; 13:367-78. [PMID: 23842988 DOI: 10.1007/s10142-013-0329-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/03/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
Verticillium dahliae Kleb., a soil-borne fungus that colonizes vascular tissues, induces wilting, chlorosis and early senescence in potato. Difference in senescence timing found in two diploid potato clones, 07506-01 and 12120-03, was studied and genetic variation in response to V. dahliae infection was identified as a causal factor. The clone, 07506-01, was infected with V. dahliae but did not develop symptoms, indicating tolerance to the pathogen. The other diploid clone, 12120-03 had low levels of pathogen with infection and moderate symptoms indicating partial resistance. 07506-01 was found to carry two susceptible alleles of the Ve2 gene and 12120-03 carried one Ve2 resistant and one susceptible allele. Infected leaves of the two clones were compared using gene expression profiling with the Potato Oligonucleotide Chip Initiative (POCI) microrarray. The results provide further evidence for differences in response of the two clones to infection with V. dahliae. Chlorophyll biosynthesis was higher in the tolerant 07506-01 compared to partially resistant 12120-03. On the other hand, expression of fungal defense genes, Ve resistance genes and defense phytohormone biosynthetic enzyme genes was decreased in 07506-01 compared to 12120-03 suggesting defense responses were suppressed in tolerance compared to resistance. Transcription factor gene expression differences pointed to the WRKY family as potential regulators of V. dahliae responses in potato.
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12
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Rosloski SM, Singh A, Jali SS, Balasubramanian S, Weigel D, Grbic V. Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana. Plant Mol Biol 2013; 81:57-69. [PMID: 23111501 PMCID: PMC3527738 DOI: 10.1007/s11103-012-9982-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 10/19/2012] [Indexed: 05/19/2023]
Abstract
The MADS-AFFECTING FLOWERING 2 (MAF2) gene of Arabidopsis thaliana has been characterized as a repressor of flowering. The molecular basis of MAF2 gene function and role of alternative MAF2 transcripts in flowering time modulation is not understood. MAF2 splice variant expression was quantified in cold-acclimated plants by quantitative RT-PCR. Cold influenced the abundance of splice variants and prompted a functional study of splice forms. Individual variants were overexpressed in the Col background and were assayed for their ability to delay flowering. Overexpression of MAF2 variants 2 and 4 had limited effect on flowering time. Overexpression of MAF2 splice variant 1 resulted in early flowering and affected the expression of the endogenous MAF2 gene and its paralogues, confounding functional assessment. In the Ll-2 Arabidopsis accession, a MAF2, MAF3, MAF4 and FLC null line, MAF2 var1 was consistent in its effect on reproductive delay under ambient and reduced temperatures, indicating that it acts as a repressor of flowering.
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Affiliation(s)
| | - Anandita Singh
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Present Address: Department of Biotechnology, Faculty of Applied Science, TERI University, 10 Institutional Area, Vasant Kunj, New Delhi, 110070 India
| | | | - Sureshkumar Balasubramanian
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Present Address: School of Biological Sciences, Monash University, Clayton, VIC 3800 Australia
| | - Detlef Weigel
- Department of Molecular Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Vojislava Grbic
- Department of Biology, Western University, London, ON N6A 5B8 Canada
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Abstract
Members of the SR (serine/arginine-rich) protein gene family are key players in the regulation of alternative splicing, an important means of generating proteome diversity and regulating gene expression. In plants, marked changes in alternative splicing are induced by a wide variety of abiotic stresses, suggesting a role for this highly versatile gene regulation mechanism in the response to environmental cues. In support of this notion, the expression of plant SR proteins is stress-regulated at multiple levels, with environmental signals controlling their own alternative splicing patterns, phosphorylation status and subcellular distribution. Most importantly, functional links between these RNA-binding proteins and plant stress tolerance are beginning to emerge, including a role in the regulation of abscisic acid (ABA) signaling. Future identification of the physiological mRNA targets of plant SR proteins holds much promise for the elucidation of the molecular mechanisms underlying their role in the response to abiotic stress.
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Affiliation(s)
- Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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Abstract
A substantial fraction (approximately 30%) of plant genes is alternatively spliced, but how alternative splicing is regulated remains unknown. Many plant genes undergo alternative splicing in response to a variety of stresses. Large-scale computational analyses and experimental approaches focused on select genes are beginning to reveal that alternative splicing constitutes an integral part of gene regulation in stress responses. Based on the studies discussed in this chapter, it appears that alternative splicing generates transcriptome/proteome complexity that is likely to be important for stress adaptation. However, the signaling pathways that relay stress conditions to splicing machinery and if and how the alternative spliced products confer adaptive advantages to plants are poorly understood.
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Kurmangaliyev YZ, Gelfand MS. Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics 2008; 9:13. [PMID: 18194514 PMCID: PMC2234086 DOI: 10.1186/1471-2164-9-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 01/14/2008] [Indexed: 01/10/2023] Open
Abstract
Background Most retained introns found in human cDNAs generated by high-throughput sequencing projects seem to result from underspliced transcripts, and thus they capture intermediate steps of pre-mRNA splicing. On the other hand, mutations in splice sites cause exon skipping of the respective exon or activation of pre-existing cryptic sites. Both types of events reflect properties of the splicing mechanism. Results The retained introns were significantly shorter than constitutive ones, and skipped exons are shorter than exons with cryptic sites. Both donor and acceptor splice sites of retained introns were weaker than splice sites of constitutive introns. The authentic acceptor sites affected by mutations were significantly weaker in exons with activated cryptic sites than in skipped exons. The distance from a mutated splice site to the nearest equivalent site is significantly shorter in cases of activated cryptic sites compared to exon skipping events. The prevalence of retained introns within genes monotonically increased in the 5'-to-3' direction (more retained introns close to the 3'-end), consistent with the model of co-transcriptional splicing. The density of exonic splicing enhancers was higher, and the density of exonic splicing silencers lower in retained introns compared to constitutive ones and in exons with cryptic sites compared to skipped exons. Conclusion Thus the analysis of retained introns in human cDNA, exons skipped due to mutations in splice sites and exons with cryptic sites produced results consistent with the intron definition mechanism of splicing of short introns, co-transcriptional splicing, dependence of splicing efficiency on the splice site strength and the density of candidate exonic splicing enhancers and silencers. These results are consistent with other, recently published analyses.
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Affiliation(s)
- Yerbol Z Kurmangaliyev
- Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia.
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