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Joshi K, Ahmed S, Ge L, Avestakh A, Oloyede B, Phuntumart V, Kalinoski A, Morris PF. Spatial organization of putrescine synthesis in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112232. [PMID: 39214468 DOI: 10.1016/j.plantsci.2024.112232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Three plant pathways for the synthesis of putrescine have been described to date. These are the synthesis of putrescine from ornithine, by ornithine decarboxylase (ODC); the synthesis of putrescine from arginine by arginine decarboxylase, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NLP1); and arginine decarboxylase and agmatinase. To address how these pathways are organized in plants, we have used transient expression analysis of these genes in the leaves of Nicotiana benthamiana. Brassicas do not have ODC, but the single ODC gene from rice and one of the soybean genes, were localized to the ER. Transient expression of the rice agmatinase gene showed that it was localized to the mitochondria. In A. thaliana there are five isoforms of AIH and three isoforms of NLP1. Stable GFP-tagged transformants of the longest isoforms of AIH and NLP1 showed that both proteins were localized to the ER, but in tissues with chloroplasts, the localization was concentrated to lamellae adjacent to chloroplasts. Transient expression analyses showed that four of the isoforms of AIH and all of the isoforms of NLP1 were localized to the ER. However, AIH.4 was localized to the chloroplast. Combining these results with other published data, reveal that putrescine synthesis is excluded from the cytoplasm and is spatially localized to the chloroplast, ER, and likely the mitochondria. Synthesis of putrescine in the ER may facilitate cell to cell transport via plasmodesmata, or secretion via vesicles. Differential expression of these pathways may enable putrescine-mediated activation of hormone-responsive genes.
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Affiliation(s)
- Kumud Joshi
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Sheaza Ahmed
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Lingxiao Ge
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Arefeh Avestakh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Babatunde Oloyede
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Andrea Kalinoski
- Department of Surgery, University of Toledo, 3000 Arlington Ave., Toledo, USA
| | - Paul F Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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2
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Yu Y, He RR, Yang L, Feng YZ, Xue J, Liu Q, Zhou YF, Lei MQ, Zhang YC, Lian JP, Chen YQ. A transthyretin-like protein acts downstream of miR397 and LACCASE to regulate grain yield in rice. THE PLANT CELL 2024; 36:2893-2907. [PMID: 38735686 PMCID: PMC11289628 DOI: 10.1093/plcell/koae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Increasing grain yield is a major goal of breeders due to the rising global demand for food. We previously reported that the miR397-LACCASE (OsLAC) module regulates brassinosteroid (BR) signaling and grain yield in rice (Oryza sativa). However, the precise roles of laccase enzymes in the BR pathway remain unclear. Here, we report that OsLAC controls grain yield by preventing the turnover of TRANSTHYRETIN-LIKE (OsTTL), a negative regulator of BR signaling. Overexpressing OsTTL decreased BR sensitivity in rice, while loss-of-function of OsTTL led to enhanced BR signaling and increased grain yield. OsLAC directly binds to OsTTL and regulates its phosphorylation-mediated turnover. The phosphorylation site Ser226 of OsTTL is essential for its ubiquitination and degradation. Overexpressing the dephosphorylation-mimic form of OsTTL (OsTTLS226A) resulted in more severe defects than did overexpressing OsTTL. These findings provide insight into the role of an ancient laccase in BR signaling and suggest that the OsLAC-OsTTL module could serve as a target for improving grain yield.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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Araguirang GE, Venn B, Kelber NM, Feil R, Lunn J, Kleine T, Leister D, Mühlhaus T, Richter AS. Spliceosomal complex components are critical for adjusting the C:N balance during high-light acclimation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:153-175. [PMID: 38593295 DOI: 10.1111/tpj.16751] [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: 10/27/2023] [Revised: 01/25/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Plant acclimation to an ever-changing environment is decisive for growth, reproduction, and survival. Light availability limits biomass production on both ends of the intensity spectrum. Therefore, the adjustment of plant metabolism is central to high-light (HL) acclimation, and the accumulation of photoprotective anthocyanins is commonly observed. However, mechanisms and factors regulating the HL acclimation response are less clear. Two Arabidopsis mutants of spliceosome components exhibiting a pronounced anthocyanin overaccumulation in HL were isolated from a forward genetic screen for new factors crucial for plant acclimation. Time-resolved physiological, transcriptome, and metabolome analysis revealed a vital function of the spliceosome components for rapidly adjusting gene expression and metabolism. Deficiency of INCREASED LEVEL OF POLYPLOIDY1 (ILP1), NTC-RELATED PROTEIN1 (NTR1), and PLEIOTROPIC REGULATORY LOCUS1 (PRL1) resulted in a marked overaccumulation of carbohydrates and strongly diminished amino acid biosynthesis in HL. While not generally limited in N-assimilation, ilp1, ntr1, and prl1 showed higher glutamate levels and reduced amino acid biosynthesis in HL. The comprehensive analysis reveals a function of the spliceosome components in the conditional regulation of the carbon:nitrogen balance and the accumulation of anthocyanins during HL acclimation. The importance of gene expression, metabolic regulation, and re-direction of carbon towards anthocyanin biosynthesis for HL acclimation are discussed.
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Affiliation(s)
| | - Benedikt Venn
- Computational Systems Biology, RPTU Kaiserslautern, Kaiserslautern, Germany
| | | | - Regina Feil
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - John Lunn
- Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU Kaiserslautern, Kaiserslautern, Germany
| | - Andreas S Richter
- Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
- Department Life, Light and Matter, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
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Zhong Z, Wu M, Yang T, Nan X, Zhang S, Zhang L, Jin L. Integrated transcriptomic and proteomic analyses uncover the early response mechanisms of Catharanthus roseus under ultraviolet-B radiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 252:112862. [PMID: 38330691 DOI: 10.1016/j.jphotobiol.2024.112862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Catharanthus roseus produces a large array of terpenoid indole alkaloids (TIAs) that are important natural source for many drugs. Ultraviolet B (UVB) radiation have been proved to have regulatory effect towards biosynthesis of TIAs, which were meaningful for boost of TIA production. To decipher more comprehensive molecular characteristics in C. roseus under UVB radiation, integrated analysis of the nuclear proteome together with the transcriptome data under UVB radiation were performed. Expression of genes related to transmembrane transporters gradually increased during the prolonged exposure to UVB radiation. Some of known TIA transporters were affected by UVB. Abundance of proteins associated with spliceosome and nucleocytoplasmic transport increased. Homologs belonging to ORCA and CrWRKY transcription factors family increased at both transcriptomic and proteomic levels. At the same time, the numbers of differential alternative splicing events between UVB-radiated and white-light-treated plants continuously increased. These results suggest that the nucleus participated in early response of C. roseus under UVB radiation, where alternative splicing events occurred and might regulate multiple pathways. Furthermore, integrative omics analysis indicates that expression of enzymes at the terminal stages of seco-iridoid pathway decreased with the prolonged radiation exposure, potentially inhibiting further rise of TIA synthesis under extended UVB exposure.
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Affiliation(s)
- Zhuoheng Zhong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Mengmin Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Tiancai Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xiaoyue Nan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Shuyao Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Lin Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
| | - Limin Jin
- Clinical Laboratory, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing 314001, PR China.
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5
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Raihan MRH, Rahman M, Rastogi A, Fujita M, Hasanuzzaman M. Exogenous Allantoin Confers Rapeseed ( Brassica campestris) Tolerance to Simulated Drought by Improving Antioxidant Metabolism and Physiology. Antioxidants (Basel) 2023; 12:1508. [PMID: 37627503 PMCID: PMC10451791 DOI: 10.3390/antiox12081508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Allantoin is an emerging plant metabolite, but its role in conferring drought-induced oxidative stress is still elusive. Therefore, an experiment was devised to explore the role of allantoin (0.5 and 1.0 mM; foliar spray) in rapeseed (Brassica campestris cv. BARI Sarisha-17) under drought. Seedlings at fifteen days of age were subjected to drought, maintaining soil moisture levels at 50% and 25% field capacities, while well-irrigated plants served as the control group. Drought-stressed plants exhibited increased levels of lipid peroxidation and hydrogen peroxide, electrolyte leakage, and impaired glyoxalase systems. Thus, the growth, biomass, and yield attributes of rapeseed were significantly impaired under drought. However, the allantoin-supplemented plants showed a notable increase in their contents of ascorbate and glutathione and decreased dehydroascorbate and glutathione disulfide contents under drought. Moreover, the activity of antioxidant enzymes such as ascorbate peroxidase, dehydroascorbate reductase, glutathione reductase, glutathione peroxidase, and catalase were accelerated with the allantoin spray and the glyoxalase system was also enhanced under drought. Moreover, the improvement in water balance with reduction in proline and potassium ion contents was also observed when allantoin was applied to the plants. Overall, the beneficial effects of allantoin supplementation resulted in the improved plant growth, biomass, and yield of rapeseed under drought conditions. These findings suggest that allantoin acts as an efficient metabolite in mitigating the oxidative stress caused by reactive oxygen species by enhancing antioxidant defense mechanisms and the glyoxalase system.
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Affiliation(s)
- Md. Rakib Hossain Raihan
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
- Laboratory of Bioclimatology, Department of Ecology and Environmental Protection, Poznań University of Life Sciences, Piątkowska 94, 60-649 Poznan, Poland
| | - Mira Rahman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
| | - Anshu Rastogi
- Laboratory of Bioclimatology, Department of Ecology and Environmental Protection, Poznań University of Life Sciences, Piątkowska 94, 60-649 Poznan, Poland
| | - Masayuki Fujita
- Faculty of Agriculture, Kagawa University, Kita-Gun, Kagawa, Miki-cho 761-0795, Japan
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
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Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. THE NEW PHYTOLOGIST 2023; 238:1722-1732. [PMID: 36751910 PMCID: PMC10952736 DOI: 10.1111/nph.18799] [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: 12/09/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Understanding the evolutionary conservation of complex eukaryotic transcriptomes significantly illuminates the physiological relevance of alternative splicing (AS). Examining the evolutionary depth of a given AS event with ordinary homology searches is generally challenging and time-consuming. Here, we present Catsnap, an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by AS. It employs a machine learning approach following a database search with the provided pair of protein sequences. We used the Catsnap algorithm for analyzing the conservation of emerging experimentally characterized alternative proteins from plants and animals. Indeed, most of them are conserved among other species. Catsnap can detect the conserved functional protein isoforms regardless of the AS type by which they are generated. Notably, we found that while the primary amino acid sequence is maintained, the type of AS determining the inclusion or exclusion of protein regions varies throughout plant phylogenetic lineages in these proteins. We also document that this phenomenon is less seen among animals. In sum, our algorithm highlights the presence of unexpectedly frequent hotspots where protein isoforms recurrently arise to carry physiologically relevant functions. The user web interface is available at https://catsnap.cesnet.cz/.
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Affiliation(s)
- Ksenia Timofeyenko
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental BotanyCzech Academy of Sciences165 02Prague 6Czech Republic
- Functional Genomics and Proteomics of Plants and National Centre for Biomolecular ResearchMasaryk University625 00BrnoCzech Republic
| | | | - Panagiotis Alexiou
- Central European Institute of TechnologyMasaryk University625 00BrnoCzech Republic
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, Institute of Molecular Plant BiologyUniversity of Natural Resources and Life Sciences (BOKU)1190ViennaAustria
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental BotanyCzech Academy of Sciences165 02Prague 6Czech Republic
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Zhan C, Zhu P, Chen Y, Chen X, Liu K, Chen S, Hu J, He Y, Xie T, Luo S, Yang Z, Chen S, Tang H, Zhang H, Cheng J. Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:58. [PMID: 36912929 PMCID: PMC10011300 DOI: 10.1007/s00122-023-04252-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Two causal OsTTL and OsSAPK1 genes of the key locus qNL3.1 significantly associated with seed germination under salt stress were identified via a genome-wide association study, which could improve rice seed germination under salt stress. Rice is a salt-sensitive crop, and its seed germination determines subsequent seedling establishment and yields. In this study, 168 accessions were investigated for the genetic control of seed germination under salt stress based on the germination rate (GR), germination index (GI), time at which 50% germination was achieved (T50) and mean level (ML). Extensive natural variation in seed germination was observed among accessions under salt stress. Correlation analysis showed significantly positive correlations among GR, GI and ML and a negative correlation with T50 during seed germination under salt stress. Forty-nine loci significantly associated with seed germination under salt stress were identified, and seven of these were identified in both years. By comparison, 16 loci were colocated with the previous QTLs, and the remaining 33 loci might be novel. qNL3.1, colocated with qLTG-3, was simultaneously identified with the four indices in two years and might be a key locus for seed germination under salt stress. Analysis of candidate genes showed that two genes, the similar to transthyretin-like protein OsTTL and the serine/threonine protein kinase OsSAPK1, were the causal genes of qNL3.1. Germination tests indicated that both Osttl and Ossapk1 mutants significantly reduced seed germination under salt stress compared to the wild type. Haplotype analysis showed that Hap.1 of OsTTL and Hap.1 of OsSAPK1 genes were excellent alleles, and their combination resulted in high seed germination under salt stress. Eight accessions with elite performance of seed germination under salt stress were identified, which could improve rice seed germination under salt stress.
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Affiliation(s)
- Chengfang Zhan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Peiwen Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yongji Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Kexin Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shanshan Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jiaxiao Hu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ying He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ting Xie
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shasha Luo
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zeyuan Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sunlu Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Haijuan Tang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongsheng Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Jinping Cheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, China.
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8
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Enzymes and cellular interplay required for flux of fixed nitrogen to ureides in bean nodules. Nat Commun 2022; 13:5331. [PMID: 36088455 PMCID: PMC9464200 DOI: 10.1038/s41467-022-33005-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/29/2022] [Indexed: 11/27/2022] Open
Abstract
Tropical legumes transport fixed nitrogen in form of ureides (allantoin and allantoate) over long distances from the nodules to the shoot. Ureides are formed in nodules from purine mononucleotides by a partially unknown reaction network that involves bacteroid-infected and uninfected cells. Here, we demonstrate by metabolic analysis of CRISPR mutant nodules of Phaseolus vulgaris defective in either xanthosine monophosphate phosphatase (XMPP), guanosine deaminase (GSDA), the nucleoside hydrolases 1 and 2 (NSH1, NSH2) or xanthine dehydrogenase (XDH) that nodule ureide biosynthesis involves these enzymes and requires xanthosine and guanosine but not inosine monophosphate catabolism. Interestingly, promoter reporter analyses revealed that XMPP, GSDA and XDH are expressed in infected cells, whereas NSH1, NSH2 and the promoters of the downstream enzymes urate oxidase (UOX) and allantoinase (ALN) are active in uninfected cells. The data suggest a complex cellular organization of ureide biosynthesis with three transitions between infected and uninfected cells. Tropical legumes export fixed nitrogen from nodules as ureides. Here, the authors describe how ureides are produced by several biosynthetic enzymes in different nodule cell types and provide explanations for metabolic compartmentation.
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9
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Alternative Splicing and Its Roles in Plant Metabolism. Int J Mol Sci 2022; 23:ijms23137355. [PMID: 35806361 PMCID: PMC9266299 DOI: 10.3390/ijms23137355] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/02/2023] Open
Abstract
Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.
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10
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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11
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Kashkan I, Timofeyenko K, Růžička K. How alternative splicing changes the properties of plant proteins. QUANTITATIVE PLANT BIOLOGY 2022; 3:e14. [PMID: 37077961 PMCID: PMC10095807 DOI: 10.1017/qpb.2022.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 05/03/2023]
Abstract
Most plant primary transcripts undergo alternative splicing (AS), and its impact on protein diversity is a subject of intensive investigation. Several studies have uncovered various mechanisms of how particular protein splice isoforms operate. However, the common principles behind the AS effects on protein function in plants have rarely been surveyed. Here, on the selected examples, we highlight diverse tissue expression patterns, subcellular localization, enzymatic activities, abilities to bind other molecules and other relevant features. We describe how the protein isoforms mutually interact to underline their intriguing roles in altering the functionality of protein complexes. Moreover, we also discuss the known cases when these interactions have been placed inside the autoregulatory loops. This review is particularly intended for plant cell and developmental biologists who would like to gain inspiration on how the splice variants encoded by their genes of interest may coordinately work.
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Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Ksenia Timofeyenko
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Author for correspondence: K. Růžička, E-mail:
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12
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Bosse MA, Silva MBD, Oliveira NGRMD, Araujo MAD, Rodrigues C, Azevedo JPD, Reis ARD. Physiological impact of flavonoids on nodulation and ureide metabolism in legume plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:512-521. [PMID: 34171572 DOI: 10.1016/j.plaphy.2021.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 05/20/2023]
Abstract
Legume plants from Fabaceae family (phylogenetic group composed by three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae) can fix atmospheric nitrogen (N2) into ammonia (NH3) by the symbiotic relationship with rhizobia bacteria. These bacteria respond chemotactically to certain compounds released by plants such as sugars, amino acids and organic acids. Root secretion of isoflavonoids acts as inducers for nod genes in rhizobia and ABC transporters and ICHG (isoflavone conjugates hydrolyzing beta-glucosidase) at apoplast are related to the exudation of genistein and daidzein in soybean roots. Biological nitrogen fixation (BNF) occurs inside the nodule by the action of nitrogenase enzyme, which fixes N2 into NH3, which is converted into ureides (allantoin and allantoic acid). In this review, we bring together the latest findings on flavonoids biosynthesis and ureide metabolism in several legume plant species. We emphasize how flavonoids induce nod genes in rhizobia, affecting chemotaxis, nodulation, ureide production, growth and yield of legume plants. Mainly, isoflavonoids daidzein and genistein are responsible for nod genes activation in the rhizobia bacteria. Flavonoids also play an important role during nodule organogenesis by acting as auxin transporter inhibitors in root cells, especially in indeterminate nodules. The ureides are the main N transport form in tropical legumes and they are catabolized in leaves and other sink tissues to produce amino acids and proteins needed for plant growth and yield.
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Affiliation(s)
- Marco Antônio Bosse
- São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Postal Code 14884-900, Brazil
| | | | | | | | - Cleverson Rodrigues
- São Paulo State University (UNESP), Postal Code 15385-000, Ilha Solteira, SP, Brazil
| | | | - André Rodrigues Dos Reis
- São Paulo State University (UNESP), Rua Domingos da Costa Lopes 780, Postal Code 17602-496, Tupã, SP, Brazil.
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13
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Costello R, Emms DM, Kelly S. Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles. Mol Biol Evol 2021; 37:969-981. [PMID: 31750917 PMCID: PMC7086175 DOI: 10.1093/molbev/msz275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.
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Affiliation(s)
- Rona Costello
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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14
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Kechasov D, de Grahl I, Endries P, Reumann S. Evolutionary Maintenance of the PTS2 Protein Import Pathway in the Stramenopile Alga Nannochloropsis. Front Cell Dev Biol 2020; 8:593922. [PMID: 33330478 PMCID: PMC7710942 DOI: 10.3389/fcell.2020.593922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The stramenopile alga Nannochloropsis evolved by secondary endosymbiosis of a red alga by a heterotrophic host cell and emerged as a promising organism for biotechnological applications, such as the production of polyunsaturated fatty acids and biodiesel. Peroxisomes play major roles in fatty acid metabolism but experimental analyses of peroxisome biogenesis and metabolism in Nannochloropsis are not reported yet. In fungi, animals, and land plants, soluble proteins of peroxisomes are targeted to the matrix by one of two peroxisome targeting signals (type 1, PTS1, or type 2, PTS2), which are generally conserved across kingdoms and allow the prediction of peroxisomal matrix proteins from nuclear genome sequences. Because diatoms lost the PTS2 pathway secondarily, we investigated its presence in the stramenopile sister group of diatoms, the Eustigmatophyceae, represented by Nannochloropsis. We detected a full-length gene of a putative PEX7 ortholog coding for the cytosolic receptor of PTS2 proteins and demonstrated its expression in Nannochloropsis gaditana. The search for predicted PTS2 cargo proteins in N. gaditana yielded several candidates. In vivo subcellular targeting analyses of representative fusion proteins in different plant expression systems demonstrated that two predicted PTS2 domains were indeed functional and sufficient to direct a reporter protein to peroxisomes. Peroxisome targeting of the predicted PTS2 cargo proteins was further confirmed in Nannochloropsis oceanica by confocal and transmission electron microscopy. Taken together, the results demonstrate for the first time that one group of stramenopile algae maintained the import pathway for PTS2 cargo proteins. To comprehensively map and model the metabolic capabilities of Nannochloropsis peroxisomes, in silico predictions needs to encompass both the PTS1 and the PTS2 matrix proteome.
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Affiliation(s)
- Dmitry Kechasov
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Pierre Endries
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
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15
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Lescano I, Devegili AM, Martini C, Tessi TM, González CA, Desimone M. Ureide metabolism in Arabidopsis thaliana is modulated by C:N balance. JOURNAL OF PLANT RESEARCH 2020; 133:739-749. [PMID: 32740857 DOI: 10.1007/s10265-020-01215-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Plants can respond and adapt to changes in the internal content of carbon and nitrogen by using organic compounds that widely differ in their carbon/nitrogen ratio. Among them, the amides asparagine and glutamine are believed to be preferred by most plants, including Arabidopsis. However, increases in the ureides allantoin and/or allantoate concentrations have been observed in different plant species under several environmental conditions. In this work, changes in the ratio between carbon skeletons and reduced nitrogen were investigated by varying the concentrations of nitrogen and sucrose in the growth media. Allantoin accumulation was observed when plants were grown in media with high ammonia concentrations. This increase was reverted by adding sucrose as additional carbon source. Moreover, mutant plants with a decreased capability to degrade allantoin showed a compromised growth compared to WT in ammonia supplemented media. Together, our results indicate that allantoin accumulation is induced by low carbon/nitrogen ratio and suggest that its degradation is critical for proper plant growth and development.
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Affiliation(s)
- Ignacio Lescano
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina.
| | - Andrés Matías Devegili
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
| | - Carolina Martini
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology. Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
| | - Tomás María Tessi
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
| | - Claudio Alejandro González
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology. Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
| | - Marcelo Desimone
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology. Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA, Córdoba, Argentina
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16
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Chen T, Zhang W, Yang G, Chen JH, Chen BX, Sun R, Zhang H, An LZ. TRANSTHYRETIN-LIKE and BYPASS1-LIKE co-regulate growth and cold tolerance in Arabidopsis. BMC PLANT BIOLOGY 2020; 20:332. [PMID: 32664862 PMCID: PMC7362626 DOI: 10.1186/s12870-020-02534-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/28/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cold stress inhibits normal physiological metabolism in plants, thereby seriously affecting plant development. Meanwhile, plants also actively adjust their metabolism and development to adapt to changing environments. Several cold tolerance regulators have been found to participate in the regulation of plant development. Previously, we reported that BYPASS1-LIKE (B1L), a DUF793 family protein, participates in the regulation of cold tolerance, at least partly through stabilizing C-REPEAT BINDING FACTORS (CBFs). In this study, we found that B1L interacts with TRANSTHYRETIN-LIKE (TTL) protein, which is involved in brassinosteroid (BR)-mediated plant growth and catalyses the synthesis of S-allantoin, and both proteins participate in modulating plant growth and cold tolerance. RESULTS The results obtained with yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that B1L directly interacted with TTL. Similar to the ttl-1 and ttl-2 mutants, the b1l mutant displayed a longer hypocotyl and greater fresh weight than wild type, whereas B1L-overexpressing lines exhibited a shorter hypocotyl and reduced fresh weight. Moreover, ttl-1 displayed freezing tolerance to cold treatment compared with WT, whereas the b1l mutant and TTL-overexpressing lines were freezing-sensitive. The b1l ttl double mutant had a developmental phenotype and freezing tolerance that were highly similar to those of ttl-1 compared to b1l, indicating that TTL is important for B1L function. Although low concentrations of brassinolide (0.1 or 1 nM) displayed similarly promoted hypocotyl elongation of WT and b1l under normal temperature, it showed less effect to the hypocotyl elongation of b1l than to that of WT under cold conditions. In addition, the b1l mutant also contained less amount of allantoin than Col-0. CONCLUSION Our results indicate that B1L and TTL co-regulate development and cold tolerance in Arabidopsis, and BR and allantoin may participate in these processes through B1L and TTL.
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Affiliation(s)
- Tao Chen
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Wei Zhang
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Gang Yang
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jia-Hui Chen
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Bi-Xia Chen
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Rui Sun
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hua Zhang
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| | - Li-Zhe An
- The Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
- School of Forestry, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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17
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Lescano I, Bogino MF, Martini C, Tessi TM, González CA, Schumacher K, Desimone M. Ureide Permease 5 (AtUPS5) Connects Cell Compartments Involved in Ureide Metabolism. PLANT PHYSIOLOGY 2020; 182:1310-1325. [PMID: 31862838 PMCID: PMC7054880 DOI: 10.1104/pp.19.01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/12/2019] [Indexed: 05/28/2023]
Abstract
Allantoin is a purine oxidative product involved in long distance transport of organic nitrogen in nodulating legumes and was recently shown to play a role in stress tolerance in other plants. The subcellular localization of enzymes that catalyze allantoin synthesis and degradation indicates that allantoin is produced in peroxisomes and degraded in the endoplasmic reticulum (ER). Although it has been determined that allantoin is mostly synthesized in roots and transported to shoots either for organic nitrogen translocation in legumes or for plant protection during stress in Arabidopsis (Arabidopsis thaliana), the mechanism and molecular components of allantoin export from root cells are still unknown. AtUPS5 (Arabidopsis UREIDE PERMEASE 5) is a transmembrane protein that transports allantoin with high affinity when expressed in yeast. The subcellular fate of splicing variants AtUPS5L (long) and AtUPS5S (short) was studied by tagging them with fluorescent proteins in their cytosolic loops. The capability of these fusion proteins to complement the function of the native proteins was demonstrated by nutritional and salt stress experiments. Both variants localized to the ER, but the AtUPS5L variant was also detected in the trans-Golgi network/early endosome and at the plasma membrane. AtUPS5L and AtUPS5S localization indicates that they could have different roles in allantoin distribution between subcellular compartments. Our data suggest that under nonstress conditions UPS5L and UPS5S may function in allantoin degradation for nutrient recycling, whereas under stress, both genes may be involved in vesicular export allowing allantoin translocation from roots to shoots.
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Affiliation(s)
- Ignacio Lescano
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
| | - María Florencia Bogino
- Plant Physiology Chair, Department of Physiology, Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
| | - Carolina Martini
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology, Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
| | - Tomás María Tessi
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
| | - Claudio Alejandro González
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology, Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
| | - Karin Schumacher
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Marcelo Desimone
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
- Plant Physiology Chair, Department of Physiology, Faculty of Exact, Physical and Natural Sciences, National University of Córdoba, Vélez Sarsfield Av. 299, X5000HUA Córdoba, Argentina
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18
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Maynard D, Kumar V, Sproï J, Dietz KJ. 12-Oxophytodienoic Acid Reductase 3 (OPR3) Functions as NADPH-Dependent α,β-Ketoalkene Reductase in Detoxification and Monodehydroascorbate Reductase in Redox Homeostasis. PLANT & CELL PHYSIOLOGY 2020; 61:584-595. [PMID: 31834385 DOI: 10.1093/pcp/pcz226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) 12-oxophytodienoic acid reductase isoform 3 (OPR3) is involved in the synthesis of jasmonic acid (JA) by reducing the α,β-unsaturated double bond of the cyclopentenone moiety in 12-oxophytodienoic acid (12-OPDA). Recent research revealed that JA synthesis is not strictly dependent on the peroxisomal OPR3. The ability of OPR3 to reduce trinitrotoluene suggests that the old yellow enzyme homolog OPR3 has additional functions. Here, we show that OPR3 catalyzes the reduction of a wide spectrum of electrophilic species that share a reactivity toward the major redox buffers glutathione (GSH) and ascorbate (ASC). Furthermore, we show that 12-OPDA reacts with ASC to form an ASC-12-OPDA adduct, but in addition OPR3 has the ability to regenerate ASC from monodehydroascorbate. The presented data characterize OPR3 as a bifunctional enzyme with NADPH-dependent α,β-ketoalkene double-bond reductase and monodehydroascorbate reductase activities (MDHAR). opr3 mutants showed a slightly less-reduced ASC pool in leaves in line with the MDHAR activity of OPR3 in vitro. These functions link redox homeostasis as mediated by ASC and GSH with OPR3 activity and metabolism of reactive electrophilic species.
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Affiliation(s)
- Daniel Maynard
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Universit�tsstr. 25, Bielefeld 33615, Germany
| | - Vijay Kumar
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Universit�tsstr. 25, Bielefeld 33615, Germany
| | - Jens Sproï
- Department of Chemistry, Industrial Organic Chemistry and Biotechnology, University of Bielefeld, Universit�tsstra�e 25, D-33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Universit�tsstr. 25, Bielefeld 33615, Germany
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19
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Witte CP, Herde M. Nucleotide Metabolism in Plants. PLANT PHYSIOLOGY 2020; 182:63-78. [PMID: 31641078 PMCID: PMC6945853 DOI: 10.1104/pp.19.00955] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 05/14/2023]
Abstract
Nucleotide metabolism is an essential function in plants.
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Affiliation(s)
- Claus-Peter Witte
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marco Herde
- Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419 Hannover, Germany
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20
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Gericó TG, Tavanti RFR, de Oliveira SC, Lourenzani AEBS, de Lima JP, Ribeiro RP, dos Santos LCC, dos Reis AR. Bradyrhizobium sp. enhance ureide metabolism increasing peanuts yield. Arch Microbiol 2019; 202:645-656. [DOI: 10.1007/s00203-019-01778-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/06/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
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21
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Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
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Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
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22
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Fahad S, Khan FA, Pandupuspitasari N, Hussain S, Khan IA, Saeed M, Saud S, Hassan S, Adnan M, Arif M, Alam M, Ullah H, Hakeem KR, Alharby H, Riaz M, Sameeullah M, Hammad HM, Nasim W, Ahmad S, Afzal M, Alghamdi SS, Bamagoos AA, Abd Allah EF, Huang J. Suppressing photorespiration for the improvement in photosynthesis and crop yields: A review on the role of S-allantoin as a nitrogen source. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:644-651. [PMID: 30870683 DOI: 10.1016/j.jenvman.2019.02.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 02/12/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Environmental variations resulting in biotic and abiotic stresses demand adaptive changes in the photosynthetic machinery. To cope with these challenges, plant scientists are constantly striving to enhance photosynthetic activity. The photorespiration pathway, which fixes O2 and releases CO2 in C3 plants, competes with photosynthesis. One method to increase yield would be to enhance photosynthesis by engineering the photorespiratory pathway. To date, three engineered photorespiratory pathways have been produced, of which two have been proven experimentally in the model plant, Arabidopsis thaliana. These approaches might be helpful in enhancing crop resilience to future environmental challenges. In partially photorespiratory suppressed plants, it is hypothesized that a gene cluster may have formed between bacterial glycolate dehydrogenase (GDH), glyoxylate carboligase (GCL), and tartronic semi aldehyde (TSR) genes with Arabidopsis allantoin degradation genes like Arabidopsis allantoinase (AtALN) to utilize S-allantoin as a source of nitrogen. Observations of the use of allantoin as an exclusive source of nitrogen or energy by Arabidopsis and Escherichia coli led us to propose a genetic switch control model between nitrogen assimilation and energy producing pathways in partially photorespiratory suppressed plants.
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Affiliation(s)
- Shah Fahad
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Department of Agriculture, The University of Swabi, Pakistan.
| | - Faheem Ahmed Khan
- Molecular Biotechnology Laboratory for Triticeae Crops, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Imtiaz Ali Khan
- Department of Agriculture, The University of Swabi, Pakistan
| | - Muhammad Saeed
- Department of Agriculture, The University of Swabi, Pakistan
| | - Shah Saud
- Department of Horticultural, Northeast Agricultural University, Harbin, 150030, China
| | - Shah Hassan
- Agriculture Extension Department, The University of Agriculture, Peshawar, 25000, Pakistan
| | - Muhammad Adnan
- Department of Agriculture, The University of Swabi, Pakistan
| | - Muhammad Arif
- Department of Agronomy, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25000, Pakistan
| | - Mukhtar Alam
- Department of Agriculture, The University of Swabi, Pakistan
| | - Hidayat Ullah
- Department of Agriculture, The University of Swabi, Pakistan
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Hesham Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Riaz
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, Pakistan
| | - Muhammad Sameeullah
- Department of Horticulture, Faculty of Agricultural and Natural Sciences, Abant Izzet Baysal University, Bolu, Turkey
| | - Hafiz Mohkum Hammad
- Department of Environmental Sciences, COMSATS University Islamabad, 61100, Vehari Campus, Pakistan
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS University Islamabad, 61100, Vehari Campus, Pakistan
| | - Shakeel Ahmad
- Bahauddin Zakariya University Multan, 60800, Pakistan
| | - Muhammad Afzal
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem Safer Alghamdi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Atif A Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud-123, Oman
| | - Jianliang Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Hubei, China.
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23
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Allantoin reduces cell death induced by cisplatin: possible implications for tumor lysis syndrome management. J Biol Inorg Chem 2019; 24:547-562. [PMID: 31030325 DOI: 10.1007/s00775-019-01661-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Abstract
Massive lysis of tumor mass in cancer patients under chemotherapy regimens generates high levels of uric acid, leading to what is known as tumor lysis syndrome (TLS). Rasburicase, a recombinant urate oxidase, converts urate to allantoin, which is readily excreted by the kidneys. Even though there is a high production of allantoin from urate in cancer patients following rasburicase treatment, there are no studies on how allantoin excess could interfere with chemotherapy. We have evaluated allantoin interference with cisplatin efficiency on the lung cancer cell line H460 in vitro. The cells were treated with cisplatin (33 µM), with or without allantoin, for 48 h, in the presence or absence of UV light, and N-acetyl-L-cysteine (NAC) for 24 h. Cell viability, cell cycle, ROS production, apoptosis and immunoblot assays were performed. We showed that allantoin reduced the apoptosis induced by cisplatin in the H460 cell line. However, the activity of carboplatin and oxaliplatin, betulinic acid, TIBA, UV and H2O2 was not affected by allantoin. NMR spectroscopy showed that allantoin reduces cisplatin activity through direct interaction with cisplatin.
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24
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Baccolini C, Witte CP. AMP and GMP Catabolism in Arabidopsis Converge on Xanthosine, Which Is Degraded by a Nucleoside Hydrolase Heterocomplex. THE PLANT CELL 2019; 31:734-751. [PMID: 30787180 PMCID: PMC6482636 DOI: 10.1105/tpc.18.00899] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/28/2019] [Accepted: 02/14/2019] [Indexed: 05/17/2023]
Abstract
Plants can fully catabolize purine nucleotides. A firmly established central intermediate is the purine base xanthine. In the current widely accepted model of plant purine nucleotide catabolism, xanthine can be generated in various ways involving either inosine and hypoxanthine or guanosine and xanthosine as intermediates. In a comprehensive mutant analysis involving single and multiple mutants of urate oxidase, xanthine dehydrogenase, nucleoside hydrolases, guanosine deaminase, and hypoxanthine guanine phosphoribosyltransferase, we demonstrate that purine nucleotide catabolism in Arabidopsis (Arabidopsis thaliana) mainly generates xanthosine, but not inosine and hypoxanthine, and that xanthosine is derived from guanosine deamination and a second source, likely xanthosine monophosphate dephosphorylation. Nucleoside hydrolase 1 (NSH1) is known to be essential for xanthosine hydrolysis, but the in vivo function of a second cytosolic nucleoside hydrolase, NSH2, is unclear. We demonstrate that NSH1 activates NSH2 in vitro and in vivo, forming a complex with almost two orders of magnitude higher catalytic efficiency for xanthosine hydrolysis than observed for NSH1 alone. Remarkably, an inactive NSH1 point mutant can activate NSH2 in vivo, fully preventing purine nucleoside accumulation in nsh1 background. Our data lead to an altered model of purine nucleotide catabolism that includes an NSH heterocomplex as a central component.
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Affiliation(s)
- Chiara Baccolini
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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25
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Casartelli A, Melino VJ, Baumann U, Riboni M, Suchecki R, Jayasinghe NS, Mendis H, Watanabe M, Erban A, Zuther E, Hoefgen R, Roessner U, Okamoto M, Heuer S. Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. PLANT MOLECULAR BIOLOGY 2019; 99:477-497. [PMID: 30721380 DOI: 10.1007/s11103-019-00831-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/24/2019] [Indexed: 05/06/2023]
Abstract
Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH4+) thereby preventing N losses. On the other hand, under N deficiency, increasing the NH4+ liberated via allantoin catabolism contributes towards the maintenance of N homeostasis.
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Affiliation(s)
- Alberto Casartelli
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Strube Research GmbH & Co. KG, 38387, Söllingen, Germany
| | - Vanessa J Melino
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- School of Agriculture and Food, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Nirupama S Jayasinghe
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Himasha Mendis
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mutsumi Watanabe
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alexander Erban
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ellen Zuther
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Rainer Hoefgen
- Max Plank Institute of Molecular Plant Physiology, 14476, Potsdam, Golm, Germany
| | - Ute Roessner
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mamoru Okamoto
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
- Rothamsted Research, Plant Science Department, Harpenden, Hertfordshire, AL5 2JQ, UK.
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26
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Nourimand M, Todd CD. There is a direct link between allantoin concentration and cadmium tolerance in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:441-449. [PMID: 30473421 DOI: 10.1016/j.plaphy.2018.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 05/17/2023]
Abstract
Allantoin, an important intermediate of ureide metabolism, has been the subject of investigation recently due to its dual function in nitrogen recycling and abiotic stress response in plants. Allantoin appears to be the dominant ureide accumulating in response to different abiotic stresses, and mutants containing elevated allantoin concentrations exhibit a stress-tolerant phenotype due to limited reactive oxygen species (ROS) generation. Here we describe the involvement of allantoin in stress response and attempt to explain the regulatory mechanism(s) underlying allantoin function in plants. Growth of wild type Col-0 seedlings in the presence of exogenous allantoin improved root elongation in response to Cd treatment. Allantoin treatment of Col-0 seeds increases superoxide dismutase activity causing an enhanced seed germination and seedling growth following Cd exposure. Additionally, allantoinase-overexpressed (ALNox) lines, with lower levels of allantoin, exhibited more susceptibility to Cd treatment than Col-0 Arabidopsis, implying that there is a positive correlation between allantoin concentration and Cd resistance in plants. Growing ABA-insensitive (abi) mutants on allantoin-containing media and comparison between abi mutants and their wild-type backgrounds demonstrated that the potential regulatory function of allantoin does not require ABA at germination but may be ABA-dependent at later stages of seedling growth, suggesting a potential crosstalk between allantoin-mediated stress response and ABA signalling pathway in plants.
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Affiliation(s)
- Maryam Nourimand
- Department of Biology, University of Saskatchewan, Saskatoon, S7N 5E2, Canada
| | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon, S7N 5E2, Canada.
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27
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Takagi H, Watanabe S, Tanaka S, Matsuura T, Mori IC, Hirayama T, Shimada H, Sakamoto A. Disruption of ureide degradation affects plant growth and development during and after transition from vegetative to reproductive stages. BMC PLANT BIOLOGY 2018; 18:287. [PMID: 30458716 PMCID: PMC6245725 DOI: 10.1186/s12870-018-1491-2] [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: 07/03/2018] [Accepted: 10/19/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The ureides allantoin and allantoate are major metabolic intermediates of purine catabolism with high nitrogen-to-carbon ratios. Ureides play a key role in nitrogen utilization in ureide-type legumes, but their effects on growth and development in non-legume plants are poorly understood. Here, we examined the effects of knocking out genes encoding ureide-degrading enzymes, allantoinase (ALN) and allantoate amidohydrolase (AAH), on the vegetative-to-reproductive transition and subsequent growth of Arabidopsis plants. RESULTS The ureide-degradation mutants (aln and aah) showed symptoms similar to those of nitrogen deficiency: early flowering, reduced size at maturity, and decreased fertility. Consistent with these phenotypes, carbon-to-nitrogen ratios and nitrogen-use efficiencies were significantly decreased in ureide-degradation mutants; however, adding nitrogen to irrigation water did not alleviate the reduced growth of these mutants. In addition to nitrogen status, levels of indole-3-acetic acid and gibberellin in five-week-old plants were also affected by the aln mutations. To test the possibility that ureides are remobilized from source to sink organs, we measured ureide levels in various organs. In wild-type plants, allantoate accumulated predominantly in inflorescence stems and siliques; this accumulation was augmented by disruption of its catabolism. Mutants lacking ureide transporters, ureide permeases 1 and 2 (UPS1 and UPS2), exhibited phenotypes similar to those of the ureide-degradation mutants, but had decreased allantoate levels in the reproductive organs. Transcript analysis in wild-type plants suggested that genes involved in allantoate synthesis and ureide transport were coordinately upregulated in senescing leaves. CONCLUSIONS This study demonstrates that ureide degradation plays an important role in supporting healthy growth and development in non-legume Arabidopsis during and after transition from vegetative to reproductive stages.
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Affiliation(s)
- Hiroshi Takagi
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
- Present Address: Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108 USA
| | - Shunsuke Watanabe
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
- Present Address: Center for Sustainable Resource Science, RIKEN, Yokohama, 230-0045 Japan
| | - Shoma Tanaka
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Izumi C. Mori
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Hiroshi Shimada
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
| | - Atsushi Sakamoto
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
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28
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Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation. G3-GENES GENOMES GENETICS 2018; 8:3093-3108. [PMID: 30049745 PMCID: PMC6118316 DOI: 10.1534/g3.118.200573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The complex is structurally divided into four modules known as the head, middle, tail and kinase modules, and in Arabidopsis thaliana, comprises 28-34 subunits. Here, we explore the functions of four Arabidopsis Mediator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits affect both unique and overlapping sets of genes, providing insight into the functional and structural relationships between them. The mutants primarily exhibit changes in the expression of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for MED23, as well as in the production of alternative transcripts. Together, our data help disentangle the individual contributions of these MED subunits to global gene expression and suggest new avenues for future research into their functions.
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29
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Oh J, Liuzzi A, Ronda L, Marchetti M, Corsini R, Folli C, Bettati S, Rhee S, Percudani R. Diatom Allantoin Synthase Provides Structural Insights into Natural Fusion Protein Therapeutics. ACS Chem Biol 2018; 13:2237-2246. [PMID: 29874034 DOI: 10.1021/acschembio.8b00404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Humans have lost the ability to convert urate into the more soluble allantoin with the evolutionary inactivation of three enzymes of the uricolytic pathway. Restoration of this function through enzyme replacement therapy can treat severe hyperuricemia and Lesch-Nyhan disease. Through a genomic exploration of natural gene fusions, we found that plants and diatoms independently evolved a fusion protein (allantoin synthase) complementing two human pseudogenes. The 1.85-Å-resolution crystal structure of allantoin synthase from the diatom Phaeodactylum tricornutum provides a rationale for the domain combinations observed in the metabolic pathway, suggesting that quaternary structure is key to the evolutionary success of protein domain fusions. Polyethylene glycol (PEG) conjugation experiments indicate that a PEG-modified form of the natural fusion protein provides advantages over separate enzymes in terms of activity maintenance and manufacturing of the bioconjugate. These results suggest that the combination of different activities in a single molecular unit can simplify the production and chemical modification of recombinant proteins for multifunctional enzyme therapy.
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Affiliation(s)
- Juntaek Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
- National Institute of Biostructures and Biosystems, 00136, Rome, Italy
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
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Abstract
Plant peroxisomes are required for a number of fundamental physiological processes, such as primary and secondary metabolism, development and stress response. Indexing the dynamic peroxisome proteome is prerequisite to fully understanding the importance of these organelles. Mass Spectrometry (MS)-based proteome analysis has allowed the identification of novel peroxisomal proteins and pathways in a relatively high-throughput fashion and significantly expanded the list of proteins and biochemical reactions in plant peroxisomes. In this chapter, we summarize the experimental proteomic studies performed in plants, compile a list of ~200 confirmed Arabidopsis peroxisomal proteins, and discuss the diverse plant peroxisome functions with an emphasis on the role of Arabidopsis MS-based proteomics in discovering new peroxisome functions. Many plant peroxisome proteins and biochemical pathways are specific to plants, substantiating the complexity, plasticity and uniqueness of plant peroxisomes. Mapping the full plant peroxisome proteome will provide a knowledge base for the improvement of crop production, quality and stress tolerance.
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Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
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31
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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 REPORTS 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] [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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32
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Uric acid in plants and microorganisms: Biological applications and genetics - A review. J Adv Res 2017; 8:475-486. [PMID: 28748114 PMCID: PMC5512154 DOI: 10.1016/j.jare.2017.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 11/23/2022] Open
Abstract
Uric acid increased accumulation and/or reduced excretion in human bodies is closely related to pathogenesis of gout and hyperuricemia. It is highly affected by the high intake of food rich in purine. Uric acid is present in both higher plants and microorganisms with species dependent concentration. Urate-degrading enzymes are found both in plants and microorganisms but the mechanisms by which plant degrade uric acid was found to be different among them. Higher plants produce various metabolites which could inhibit xanthine oxidase and xanthine oxidoreductase, so prohibit the oxidation of hypoxanthine to xanthine then to uric acid in the purine metabolism. However, microorganisms produce group of degrading enzymes uricase, allantoinase, allantoicase and urease, which catalyze the degradation of uric acid to the ammonia. In humans, researchers found that several mutations caused a pseudogenization (silencing) of the uricase gene in ancestral apes which exist as an insoluble crystalloid in peroxisomes. This is in contrast to microorganisms in which uricases are soluble and exist either in cytoplasm or peroxisomes. Moreover, many recombinant uricases with higher activity than the wild type uricases could be induced successfully in many microorganisms. The present review deals with the occurrence of uric acid in plants and other organisms specially microorganisms in addition to the mechanisms by which plant extracts, metabolites and enzymes could reduce uric acid in blood. The genetic and genes encoding for uric acid in plants and microorganisms are also presented.
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33
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Irani S, Todd CD. Ureide metabolism under abiotic stress in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2016; 199:87-95. [PMID: 27302009 DOI: 10.1016/j.jplph.2016.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/21/2023]
Abstract
Ureides are nitrogenous compounds derived from purine catabolism which contribute to nitrogen recycling in plants. Accumulation of ureide compounds has been reported in a number of plant species under stress conditions, suggesting their involvement in plants' response to stress. In this research a biochemical and molecular approach was applied to address the ureide accumulation under abiotic stress conditions in Arabidopsis thaliana. Ureide concentration and changes in expression of ureide metabolic genes were examined in response to drought, NaCl and mannitol treatments. Additionally, an Arabidopsis allantoinase (ALN) mutant with constitutive accumulation of a ureide compound, allantoin, was used to investigate the impact of high levels of this compound on drought and NaCl stress responses. In the leaf tissue of adult plants allantoin accumulated in response to soil drying. Transcription of urate oxidase (UO), involved in allantoin production, was highly up-regulated under the same conditions. Allantoin and allantoate also accumulated in seedlings following treatment with NaCl or mannitol. aln mutants with enhanced levels of allantoin exhibited higher tolerance to drought and NaCl. Hydrogen peroxide and superoxide did not accumulate in the aln mutant leaves to the same degree in response to drought when compared to the wild-type. Our results suggest that ureide metabolism and accumulation contribute to the abiotic stress response which is regulated, at least in part, at the transcriptional level. Higher concentrations of allantoin in the mutant elevates abiotic stress tolerance, possibly by reducing oxidative damage.
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Affiliation(s)
- Solmaz Irani
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada.
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Lescano CI, Martini C, González CA, Desimone M. Allantoin accumulation mediated by allantoinase downregulation and transport by Ureide Permease 5 confers salt stress tolerance to Arabidopsis plants. PLANT MOLECULAR BIOLOGY 2016; 91:581-95. [PMID: 27209043 DOI: 10.1007/s11103-016-0490-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/10/2016] [Indexed: 05/19/2023]
Abstract
Allantoin, a metabolite generated in the purine degradation pathway, was primarily considered an intermediate for recycling of the abundant nitrogen assimilated in plant purines. More specifically, tropical legumes utilize allantoin and allantoic acid as major nodule-to-shoot nitrogen transport compounds. In other species, an increase in allantoin content was observed under different stress conditions, but the underlying molecular mechanisms remain poorly understood. In this work, Arabidopsis thaliana was used as a model system to investigate the effects of salt stress on allantoin metabolism and to know whether its accumulation results in plant protection. Plant seedlings treated with NaCl at different concentrations showed higher allantoin and lower allantoic acid contents. Treatments with NaCl favored the expression of genes involved in allantoin synthesis, but strongly repressed the unique gene encoding allantoinase (AtALN). Due to the potential regulatory role of this gene for allantoin accumulation, AtALN promoter activity was studied using a reporter system. GUS mediated coloration was found in specific plant tissues and was diminished with increasing salt concentrations. Phenotypic analysis of knockout, knockdown and stress-inducible mutants for AtALN revealed that allantoin accumulation is essential for salt stress tolerance. In addition, the possible role of allantoin transport was investigated. The Ureide Permease 5 (UPS5) is expressed in the cortex and endodermis of roots and its transcription is enhanced by salt treatment. Ups5 knockout plants under salt stress presented a susceptible phenotype and altered allantoin root-to-shoot content ratios. Possible roles of allantoin as a protectant compound in oxidative events or signaling are discussed.
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Affiliation(s)
- Carlos Ignacio Lescano
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, FCEFyN, Vélez Sarsfield Av. 299, 5000, Córdoba, Argentina
| | - Carolina Martini
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, FCEFyN, Vélez Sarsfield Av. 299, 5000, Córdoba, Argentina
| | - Claudio Alejandro González
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, FCEFyN, Vélez Sarsfield Av. 299, 5000, Córdoba, Argentina
| | - Marcelo Desimone
- Multidisciplinary Institute of Plant Biology, National University of Córdoba, CONICET, FCEFyN, Vélez Sarsfield Av. 299, 5000, Córdoba, Argentina.
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Baral B, Teixeira da Silva JA, Izaguirre-Mayoral ML. Early signaling, synthesis, transport and metabolism of ureides. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:97-109. [PMID: 26967003 DOI: 10.1016/j.jplph.2016.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/04/2015] [Accepted: 01/11/2016] [Indexed: 05/26/2023]
Abstract
The symbiosis between α nitrogen (N2)-fixing Proteobacteria (family Rhizobiaceae) and legumes belonging to the Fabaceae (a single phylogenetic group comprising three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae) results in the formation of a novel root structure called a nodule, where atmospheric N2 is fixed into NH3(+). In the determinate type of nodules harbored by Rhizobium-nodulated Fabaceae species, newly synthesized NH3(+) is finally converted into allantoin (C4H6N4O3) and allantoic acid (C4H8N4O4) (ureides) through complex pathways involving at least 20 different enzymes that act synchronously in two types of nodule cells with contrasting ultrastructure, including the tree nodule cell organelles. Newly synthesized ureides are loaded into the network of nodule-root xylem vessels and transported to aerial organs by the transpirational water current. Once inside the leaves, ureides undergo an enzymatically driven reverse process to yield NH4(+) that is used for growth. This supports the role of ureides as key nitrogen (N)-compounds for the growth and yield of legumes nodulated by Rhizobium that grow in soils with a low N content. Thus, a concrete understanding of the mechanisms underlying ureide biogenesis and catabolism in legumes may help agrobiologists to achieve greater agricultural discoveries. In this review we focus on the transmembranal and transorganellar symplastic and apoplastic movement of N-precursors within the nodules, as well as on the occurrence, localization and properties of enzymes and genes involved in the biogenesis and catabolism of ureides. The synthesis and transport of ureides are not unique events in Rhizobium-nodulated N2-fixing legumes. Thus, a brief description of the synthesis and catabolism of ureides in non-legumes was included for comparison. The establishment of the symbiosis, nodule organogenesis and the plant's control of nodule number, synthesis and translocation of ureides via feed-back inhibition mechanisms are also reviewed.
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Affiliation(s)
- Bikash Baral
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, Latokartanonkaari 7, FIN-00014 Helsinki, Finland.
| | | | - Maria Luisa Izaguirre-Mayoral
- Biological Nitrogen Fixation Laboratory, Chemistry Department, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa.
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Nicolas M, Rodríguez-Buey ML, Franco-Zorrilla JM, Cubas P. A Recently Evolved Alternative Splice Site in the BRANCHED1a Gene Controls Potato Plant Architecture. Curr Biol 2015; 25:1799-809. [PMID: 26119747 DOI: 10.1016/j.cub.2015.05.053] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
Amplification and diversification of transcriptional regulators that control development is a driving force of morphological evolution. A major source of protein diversity is alternative splicing, which leads to the generation of different isoforms from a single gene. The mechanisms and timing of intron evolution nonetheless remain unclear, and the functions of alternative splicing-generated protein isoforms are rarely studied. In Solanum tuberosum, the BRANCHED1a (BRC1a) gene encodes a TCP transcription factor that controls lateral shoot outgrowth. Here, we report the recent evolution in Solanum of an alternative splice site in BRC1a that leads to the generation of two BRC1a protein isoforms with distinct C-terminal regions, BRC1a(Long) and BRC1a(Short), encoded by unspliced and spliced mRNA, respectively. The BRC1a(Long) C-terminal region has a strong activation domain, whereas that of BRC1a(S) lacks an activation domain and is predicted to form an amphipathic helix, the H domain, which prevents protein nuclear targeting. BRC1a(Short) is thus mainly cytoplasmic, while BRC1a(Long) is mainly nuclear. BRC1a(Long) functions as a transcriptional activator, whereas BRC1a(Short) appears to have no transcriptional activity. Moreover, BRC1a(Short) can heterodimerize with BRC1a(Long) and act as a dominant-negative factor; it increases BRC1a(Long) concentration in cytoplasm and reduces its transcriptional activity. This alternative splicing mechanism is regulated by hormones and external stimuli that control branching. The evolution of a new alternative splicing site and a novel protein domain in Solanum BRC1a led to a multi-level mechanism of post-transcriptional and post-translational BRC1a regulation that effectively modulates its branch suppressing activity in response to environmental and endogenous cues.
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Affiliation(s)
- Michael Nicolas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María Luisa Rodríguez-Buey
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José Manuel Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología/CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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Du H, Kim S, Hur YS, Lee MS, Lee SH, Cheon CI. A cytosolic thioredoxin acts as a molecular chaperone for peroxisome matrix proteins as well as antioxidant in peroxisome. Mol Cells 2015; 38:187-94. [PMID: 26013260 PMCID: PMC4332030 DOI: 10.14348/molcells.2015.2255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022] Open
Abstract
Thioredoxin (TRX) is a disulfide reductase present ubiquitously in all taxa and plays an important role as a regulator of cellular redox state. Recently, a redox-independent, chaperone function has also been reported for some thioredoxins. We previously identified nodulin-35, the subunit of soybean uricase, as an interacting target of a cytosolic soybean thioredoxin, GmTRX. Here we report the further characterization of the interaction, which turns out to be independent of the disulfide reductase function and results in the co-localization of GmTRX and nodulin-35 in peroxisomes, suggesting a possible function of GmTRX in peroxisomes. In addition, the chaperone function of GmTRX was demonstrated in in vitro molecular chaperone activity assays including the thermal denaturation assay and malate dehydrogenase aggregation assay. Our results demonstrate that the target of GmTRX is not only confined to the nodulin-35, but many other peroxisomal proteins, including catalase (AtCAT), transthyretin-like protein 1 (AtTTL1), and acyl-coenzyme A oxidase 4 (AtACX4), also interact with the GmTRX. Together with an increased uricase activity of nodulin-35 and reduced ROS accumulation observed in the presence of GmTRX in our results, especially under heat shock and oxidative stress conditions, it appears that GmTRX represents a novel thioredoxin that is co-localized to the peroxisomes, possibly providing functional integrity to peroxisomal proteins.
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Affiliation(s)
- Hui Du
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Sunghan Kim
- Department of Plant Science, Seoul National University, Seoul 151-742, Korea
| | - Yoon-Sun Hur
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Myung-Sok Lee
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National University, Seoul 151-742, Korea
| | - Choong-Ill Cheon
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
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Geigenberger P, Fernie AR. Metabolic control of redox and redox control of metabolism in plants. Antioxid Redox Signal 2014; 21:1389-421. [PMID: 24960279 PMCID: PMC4158967 DOI: 10.1089/ars.2014.6018] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. RECENT ADVANCES The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. CRITICAL ISSUES It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. FUTURE DIRECTIONS Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.
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Affiliation(s)
- Peter Geigenberger
- 1 Department of Biology I, Ludwig Maximilian University Munich , Planegg-Martinsried, Germany
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Xu P, Kong Y, Song D, Huang C, Li X, Li L. Conservation and functional influence of alternative splicing in wood formation of Populus and Eucalyptus. BMC Genomics 2014; 15:780. [PMID: 25209012 PMCID: PMC4287496 DOI: 10.1186/1471-2164-15-780] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 09/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wood formation in tree species is regulated by multiple factors at various layers. Alternative splicing (AS) occurs within a large number of genes in wood formation. However, the functional implications and conservation of the AS occurrence are not well understood. RESULTS In this study, we profiled AS events in wood-forming tissues of Populus and Eucalyptus, and analyzed their functional implications as well as inter-species conservation. 28.3% and 20.7% of highly expressed transcripts in the developing xylem of Populus and Eucalyptus respectively were affected by AS events. Around 42% of the AS events resulted in changes to the original reading frame. 25.0% (in Populus) and 26.8% (in Eucalyptus) of the AS events may cause protein domain modification. In the process of wood formation, about 28% of AS-occurring genes were putative orthologs and 71 conserved AS events were identified in the two species. CONCLUSION Through analysis of AS events in developing xylem of two tree species, this study reveals an array of new information regarding AS occurrence and function in tree development.
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Affiliation(s)
| | | | | | | | | | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032, China.
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Hauck OK, Scharnberg J, Escobar NM, Wanner G, Giavalisco P, Witte CP. Uric acid accumulation in an Arabidopsis urate oxidase mutant impairs seedling establishment by blocking peroxisome maintenance. THE PLANT CELL 2014; 26:3090-100. [PMID: 25052714 PMCID: PMC4145134 DOI: 10.1105/tpc.114.124008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/30/2014] [Accepted: 07/04/2014] [Indexed: 05/21/2023]
Abstract
Purine nucleotides can be fully catabolized by plants to recycle nutrients. We have isolated a urate oxidase (uox) mutant of Arabidopsis thaliana that accumulates uric acid in all tissues, especially in the developing embryo. The mutant displays a reduced germination rate and is unable to establish autotrophic growth due to severe inhibition of cotyledon development and nutrient mobilization from the lipid reserves in the cotyledons. The uox mutant phenotype is suppressed in a xanthine dehydrogenase (xdh) uox double mutant, demonstrating that the underlying cause is not the defective purine base catabolism, or the lack of UOX per se, but the elevated uric acid concentration in the embryo. Remarkably, xanthine accumulates to similar levels in the xdh mutant without toxicity. This is paralleled in humans, where hyperuricemia is associated with many diseases whereas xanthinuria is asymptomatic. Searching for the molecular cause of uric acid toxicity, we discovered a local defect of peroxisomes (glyoxysomes) mostly confined to the cotyledons of the mature embryos, which resulted in the accumulation of free fatty acids in dry seeds. The peroxisomal defect explains the developmental phenotypes of the uox mutant, drawing a novel link between uric acid and peroxisome function, which may be relevant beyond plants.
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Affiliation(s)
- Oliver K Hauck
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany
| | - Jana Scharnberg
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany
| | - Nieves Medina Escobar
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany
| | - Gerhard Wanner
- Biozentrum der Ludwig-Maximillians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Patrick Giavalisco
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Claus-Peter Witte
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany
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Coleto I, Pineda M, Rodiño AP, De Ron AM, Alamillo JM. Comparison of inhibition of N2 fixation and ureide accumulation under water deficit in four common bean genotypes of contrasting drought tolerance. ANNALS OF BOTANY 2014; 113:1071-82. [PMID: 24638821 PMCID: PMC3997645 DOI: 10.1093/aob/mcu029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/12/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Drought is the principal constraint on world production of legume crops. There is considerable variability among genotypes in sensitivity of nitrogen fixation to drought, which has been related to accumulation of ureides in soybean. The aim of this study was to search for genotypic differences in drought sensitivity and ureide accumulation in common bean (Phaseolus vulgaris) germplasm that may be useful in the improvement of tolerance to water deficit in common bean. METHODS Changes in response to water deficit of nitrogen fixation rates, ureide content and the expression and activity of key enzymes for ureide metabolism were measured in four P. vulgaris genotypes differing in drought tolerance. KEY RESULTS A variable degree of drought-induced nitrogen fixation inhibition was found among the bean genotypes. In addition to inhibition of nitrogen fixation, there was accumulation of ureides in stems and leaves of sensitive and tolerant genotypes, although this was higher in the leaves of the most sensitive ones. In contrast, there was no accumulation of ureides in the nodules or roots of stressed plants. In addition, the level of ureides in the most sensitive genotype increased after inhibition of nitrogen fixation, suggesting that ureides originate in vegetative tissues as a response to water stress, probably mediated by the induction of allantoinase. CONCLUSIONS Variability of drought-induced inhibition of nitrogen fixation among the P. vulgaris genotypes was accompanied by subsequent accumulation of ureides in stems and leaves, but not in nodules. The results indicate that shoot ureide accumulation after prolonged exposure to drought could not be the cause of inhibition of nitrogen fixation, as has been suggested in soybean. Instead, ureides seem to be produced as part of a general response to stress, and therefore higher accumulation might correspond to higher sensitivity to the stressful conditions.
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Affiliation(s)
- I. Coleto
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas del Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus Rabanales, Edif. Severo Ochoa, 1 planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - M. Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas del Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus Rabanales, Edif. Severo Ochoa, 1 planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - A. P. Rodiño
- Departamento de Recursos Fitogenéticos, Grupo de Biología de Agrosistemas, Misión Biológica de Galicia-CSIC, El Palacio-Salcedo, 36143 Pontevedra, Spain
| | - A. M. De Ron
- Departamento de Recursos Fitogenéticos, Grupo de Biología de Agrosistemas, Misión Biológica de Galicia-CSIC, El Palacio-Salcedo, 36143 Pontevedra, Spain
| | - J. M. Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas del Campus de Excelencia Internacional Agroalimentario, CEIA3, Campus Rabanales, Edif. Severo Ochoa, 1 planta, Universidad de Córdoba, 14071 Córdoba, Spain
- For correspondence. E-mail
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Quan S, Yang P, Cassin-Ross G, Kaur N, Switzenberg R, Aung K, Li J, Hu J. Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. PLANT PHYSIOLOGY 2013; 163:1518-38. [PMID: 24130194 PMCID: PMC3850190 DOI: 10.1104/pp.113.223453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
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Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E. Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. BIOLOGY 2013; 2:1311-37. [PMID: 24833227 PMCID: PMC4009788 DOI: 10.3390/biology2041311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/06/2013] [Accepted: 11/12/2013] [Indexed: 12/17/2022]
Abstract
Developing soybean seeds accumulate oils, proteins, and carbohydrates that are used as oxidizable substrates providing metabolic precursors and energy during seed germination. The accumulation of these storage compounds in developing seeds is highly regulated at multiple levels, including at transcriptional and post-transcriptional regulation. RNA sequencing was used to provide comprehensive information about transcriptional and post-transcriptional events that take place in developing soybean embryos. Bioinformatics analyses lead to the identification of different classes of alternatively spliced isoforms and corresponding changes in their levels on a global scale during soybean embryo development. Alternative splicing was associated with transcripts involved in various metabolic and developmental processes, including central carbon and nitrogen metabolism, induction of maturation and dormancy, and splicing itself. Detailed examination of selected RNA isoforms revealed alterations in individual domains that could result in changes in subcellular localization of the resulting proteins, protein-protein and enzyme-substrate interactions, and regulation of protein activities. Different isoforms may play an important role in regulating developmental and metabolic processes occurring at different stages in developing oilseed embryos.
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Affiliation(s)
- Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Mahdi Nabiyouni
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Yihui Fang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Curtis Klumas
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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Werner AK, Medina-Escobar N, Zulawski M, Sparkes IA, Cao FQ, Witte CP. The ureide-degrading reactions of purine ring catabolism employ three amidohydrolases and one aminohydrolase in Arabidopsis, soybean, and rice. PLANT PHYSIOLOGY 2013; 163:672-81. [PMID: 23940254 PMCID: PMC3793049 DOI: 10.1104/pp.113.224261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/11/2013] [Indexed: 05/19/2023]
Abstract
Several ureides are intermediates of purine base catabolism, releasing nitrogen from the purine nucleotides for reassimilation into amino acids. In some legumes like soybean (Glycine max), ureides are used for nodule-to-shoot translocation of fixed nitrogen. Four enzymes of Arabidopsis (Arabidopsis thaliana), (1) allantoinase, (2) allantoate amidohydrolase (AAH), (3) ureidoglycine aminohydrolase, and (4) ureidoglycolate amidohydrolase (UAH), catalyze the complete hydrolysis of the ureide allantoin in vitro. However, the metabolic route in vivo remains controversial. Here, in growth and metabolite analyses of Arabidopsis mutants, we demonstrate that these enzymes are required for allantoin degradation in vivo. Orthologous enzymes are present in soybean, encoded by one to four gene copies. All isoenzymes are active in vitro, while some may be inefficiently translated in vivo. Surprisingly, transcript and protein amounts are not significantly regulated by nitrogen fixation or leaf ureide content. A requirement for soybean AAH and UAH for ureide catabolism in leaves has been demonstrated by the use of virus-induced gene silencing. Functional AAH, ureidoglycine aminohydrolase, and UAH are also present in rice (Oryza sativa), and orthologous genes occur in all other plant genomes sequenced to date, indicating that the amidohydrolase route of ureide degradation is universal in plants, including mosses (e.g. Physcomitrella patens) and algae (e.g. Chlamydomomas reinhardtii).
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Affiliation(s)
| | | | - Monika Zulawski
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany (A.K.W., N.M.-E., M.Z., F.-Q.C., C.-P.W.); and
- Oxford Brookes University, School of Life Sciences, Oxford OX3 0BP, United Kingdom (I.A.S.)
| | | | - Feng-Qiu Cao
- Freie Universität Berlin, Dahlem Centre of Plant Sciences, Department of Plant Biochemistry, 14195 Berlin, Germany (A.K.W., N.M.-E., M.Z., F.-Q.C., C.-P.W.); and
- Oxford Brookes University, School of Life Sciences, Oxford OX3 0BP, United Kingdom (I.A.S.)
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46
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Darracq A, Adams KL. Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. THE NEW PHYTOLOGIST 2013; 199:252-263. [PMID: 23551259 DOI: 10.1111/nph.12238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/18/2013] [Indexed: 06/02/2023]
Abstract
Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. The evolutionary conservation of AS events in plants is largely unexplored and only a small number of AS events have been identified as conserved between divergent species. We performed a large-scale analysis of cDNA data from Brassica and Arabidopsis to identify and further characterize conserved AS events. We identified 537 conserved AS events in 485 genes. Alternative donor and acceptor events are significantly overrepresented among conserved events, whereas intron retention and exon skipping events are underrepresented. Conserved AS events are significantly shorter, less likely to be in the 3'UTR, and they are enriched for genes whose products function in the chloroplast. AS modified a functional domain for about half of the genes with conserved events. We further characterized three genes with conserved AS events. This study identifies many AS events that are conserved between Brassica and Arabidopsis, revealing features of conserved AS events. Many of the conserved AS events may have important, but uncharacterized, functions.
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Affiliation(s)
- Aude Darracq
- Department of Botany, and UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, and UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Bao H, Li E, Mansfield SD, Cronk QCB, El-Kassaby YA, Douglas CJ. The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics 2013; 14:359. [PMID: 23718132 PMCID: PMC3680236 DOI: 10.1186/1471-2164-14-359] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 05/23/2013] [Indexed: 11/13/2022] Open
Abstract
Background Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-woody plants such as Arabidopsis thaliana (Arabidopsis) and rice. However, little is known about AS patterns in wood-forming tissues and how much AS variation exists within plant populations. Results Here we used high-throughput RNA sequencing to analyze the Populus trichocarpa (P. trichocarpa) xylem transcriptome in 20 individuals from different populations across much of its range in western North America. Deep transcriptome sequencing and mapping of reads to the P. trichocarpa reference genome identified a suite of xylem-expressed genes common to all accessions. Our analysis suggests that at least 36% of the xylem-expressed genes in P. trichocarpa are alternatively spliced. Extensive AS was observed in cell-wall biosynthesis related genes such as glycosyl transferases and C2H2 transcription factors. 27902 AS events were documented and most of these events were not conserved across individuals. Differences in isoform-specific read densities indicated that 7% and 13% of AS events showed significant differences between individuals within geographically separated southern and northern populations, a level that is in general agreement with AS variation in human populations. Conclusions This genome-wide analysis of alternative splicing reveals high levels of AS in P. trichocarpa and extensive inter-individual AS variation. We provide the most comprehensive analysis of AS in P. trichocarpa to date, which will serve as a valuable resource for the plant community to study transcriptome complexity and AS regulation during wood formation.
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Affiliation(s)
- Hua Bao
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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48
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Linka N, Theodoulou FL. Metabolite transporters of the plant peroxisomal membrane: known and unknown. Subcell Biochem 2013; 69:169-194. [PMID: 23821149 DOI: 10.1007/978-94-007-6889-5_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Tremendous progress in plant peroxisome research has revealed unexpected metabolic functions for plant peroxisomes. Besides photorespiration and lipid metabolism, plant peroxisomes play a key role in many metabolic and signaling pathways, such as biosynthesis of phytohormones, pathogen defense, senescence-associated processes, biosynthesis of biotin and isoprenoids, and metabolism of urate, polyamines, sulfite, phylloquinone, volatile benzenoids, and branched chain amino acids. These peroxisomal pathways require an interplay with other cellular compartments, including plastids, mitochondria, and the cytosol. Consequently, a considerable number of substrates, intermediates, end products, and cofactors have to shuttle across peroxisome membranes. However, our knowledge of their membrane passage is still quite limited. This review describes the solute transport processes required to connect peroxisomes with other cell compartments. Furthermore, we discuss the known and yet-to-be-defined transport proteins that mediate these metabolic exchanges across the peroxisomal bilayer.
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Affiliation(s)
- Nicole Linka
- Department of Plant Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany,
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49
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Bussell JD, Behrens C, Ecke W, Eubel H. Arabidopsis peroxisome proteomics. FRONTIERS IN PLANT SCIENCE 2013; 4:101. [PMID: 23630535 PMCID: PMC3633942 DOI: 10.3389/fpls.2013.00101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/02/2013] [Indexed: 05/08/2023]
Abstract
The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, peroxisomes are lagging considerably behind chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review, we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.
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Affiliation(s)
- John D. Bussell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western AustraliaCrawley, WA, Australia
- *Correspondence: John D. Bussell, Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia. e-mail: ; Holger Eubel, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany. e-mail:
| | - Christof Behrens
- Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Wiebke Ecke
- Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
| | - Holger Eubel
- Institute for Plant Genetics, Leibniz Universität HannoverHannover, Germany
- *Correspondence: John D. Bussell, Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia. e-mail: ; Holger Eubel, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany. e-mail:
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50
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James AB, Syed NH, Brown JWS, Nimmo HG. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. PLANT SIGNALING & BEHAVIOR 2012; 7:1219-23. [PMID: 22902701 PMCID: PMC3493400 DOI: 10.4161/psb.21491] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the March 2012 issue of The Plant Cell we describe extensive alternative splicing (AS) of Arabidopsis circadian clock genes. Notably these distinct post-transcriptional events associate with different steady-state temperatures and also with plants undergoing temperature transitions leading us to propose that temperature-associated AS is an additional mechanism involved in the operation and control of the plant circadian clock. Here we show that temperature associated AS also extends to REVEILLE 8 (RVE8), demonstrating a hitherto unrecognized link between the expression of this clock associated gene and temperature. Finally we discuss our observations of the plastic nature of clock gene expression at the post-transcriptional level in the context of the ongoing fascination of how plants respond to temperature.
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Affiliation(s)
- Allan B James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland.
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