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Zhang Y, Jia R, Hui T, Hu Y, Wang W, Wang Y, Wang Y, Zhu Y, Yang L, Xiang B. Transcriptomic and physiological analysis of the response of Spirodela polyrrhiza to sodium nitroprusside. BMC PLANT BIOLOGY 2024; 24:95. [PMID: 38331719 PMCID: PMC10851477 DOI: 10.1186/s12870-024-04766-6] [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: 12/12/2022] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Spirodela polyrrhiza is a simple floating aquatic plant with great potential in synthetic biology. Sodium nitroprusside (SNP) stimulates plant development and increases the biomass and flavonoid content in some plants. However, the molecular mechanism of SNP action is still unclear. RESULTS To determine the effect of SNP on growth and metabolic flux in S. polyrrhiza, the plants were treated with different concentrations of SNP. Our results showed an inhibition of growth, an increase in starch, soluble protein, and flavonoid contents, and enhanced antioxidant enzyme activity in plants after 0.025 mM SNP treatment. Differentially expressed transcripts were analysed in S. polyrrhiza after 0.025 mM SNP treatment. A total of 2776 differentially expressed genes (1425 upregulated and 1351 downregulated) were identified. The expression of some genes related to flavonoid biosynthesis and NO biosynthesis was upregulated, while the expression of some photosynthesis-related genes was downregulated. Moreover, SNP stress also significantly influenced the expression of transcription factors (TFs), such as ERF, BHLH, NAC, and WRKY TFs. CONCLUSIONS Taken together, these findings provide novel insights into the mechanisms of underlying the SNP stress response in S. polyrrhiza and show that the metabolic flux of fixed CO2 is redirected into the starch synthesis and flavonoid biosynthesis pathways after SNP treatment.
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Affiliation(s)
- Yamei Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Rong Jia
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Tanyue Hui
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Yue Hu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Wenjing Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Yi Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China
| | - Yong Wang
- College of Life Science, Nankai University, Tianjin, 300071, China
| | - Yerong Zhu
- College of Life Science, Nankai University, Tianjin, 300071, China
| | - Lin Yang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Beibei Xiang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, P. R. China.
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Dainelli M, Castellani MB, Pignattelli S, Falsini S, Ristori S, Papini A, Colzi I, Coppi A, Gonnelli C. Growth, physiological parameters and DNA methylation in Spirodela polyrhiza (L.) Schleid exposed to PET micro-nanoplastic contaminated waters. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108403. [PMID: 38290343 DOI: 10.1016/j.plaphy.2024.108403] [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: 09/22/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
The effects of polyethylene terephthalate micro-nanoplastics (PET-MNPs) were tested on the model freshwater species Spirodela polyrhiza (L.) Schleid., with focus on possible particle-induced epigenetic effects (i.e. alteration of DNA methylation status). MNPs (size ∼ 200-300 nm) were produced as water dispersions from PET bottles through repeated cycles of homogenization and used to prepare N-medium at two environmentally relevant concentrations (∼0.05 g L-1 and ∼0.1 g L-1 of MNPs). After 10 days of exposure, a reduction in fresh and dry weight was observed in treated plants, even if the average specific growth rate for both frond number and area was not altered. Impaired growth was coupled with a MNP-induced decrease of chlorophyll fluorescence parameters (i.e. ΨETo and Piabs, indicators of photochemical efficiency) and starch concentration, as well as with alterations in plant ionomic profile and oxidative status. The methylation-sensitive amplification polymorphism (MSAP) technique was used to assess possible changes in DNA methylation levels induced by plastic particles. The analysis showed unusual hypermethylation in 5'-CCGG sites that could be implicated in DNA protection from dangerous agents (i.e. reactive oxygen species) or in the formation of new epialleles. This work represents the first evidence of MNP-induced epigenetic modifications in the plant world.
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Affiliation(s)
- Marco Dainelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Maria Beatrice Castellani
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Pignattelli
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Falsini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Sandra Ristori
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Firenze, Italy
| | - Alessio Papini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Ilaria Colzi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy.
| | - Andrea Coppi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Cristina Gonnelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
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3
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Wang L, Kuang Y, Zheng S, Tong Y, Zhu Y, Wang Y. Overexpression of the Phosphoserine Phosphatase-Encoding Gene ( AtPSP1) Promotes Starch Accumulation in Lemna turionifera 5511 under Sulfur Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:1012. [PMID: 36903873 PMCID: PMC10005638 DOI: 10.3390/plants12051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Duckweeds are well known for their high accumulation of starch under stress conditions, along with inhibited growth. The phosphorylation pathway of serine biosynthesis (PPSB) was reported as playing a vital role in linking the carbon, nitrogen, and sulfur metabolism in this plant. The overexpression of AtPSP1, the last key enzyme of the PPSB pathway in duckweed, was found to stimulate the accumulation of starch under sulfur-deficient conditions. The growth- and photosynthesis-related parameters were higher in the AtPSP1 transgenic plants than in the WT. The transcriptional analysis showed that the expression of several genes in starch synthesis, TCA, and sulfur absorption, transportation, and assimilation was significantly up- or downregulated. The study suggests that PSP engineering could improve starch accumulation in Lemna turionifera 5511 by coordinating the carbon metabolism and sulfur assimilation under sulfur-deficient conditions.
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Affiliation(s)
- Lei Wang
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yingying Kuang
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Siyu Zheng
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yana Tong
- Tianjin Academy of Agricultural Sciences, Tianjin 300192, China
| | - Yerong Zhu
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yong Wang
- College of Life Science, Nankai University, Tianjin 300071, China
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4
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Efficient Accumulation of Amylopectin and Its Molecular Mechanism in the Submerged Duckweed Mutant. Int J Mol Sci 2023; 24:ijms24032934. [PMID: 36769258 PMCID: PMC9917893 DOI: 10.3390/ijms24032934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Large-scale use of fossil fuels has brought about increasingly serious problems of environmental pollution, development and utilization of renewable energy is one of the effective solutions. Duckweed has the advantages of fast growth, high starch content and no occupation of arable land, so it is a promising starchy energy plant. A new submerged duckweed mutant (sub-1) with abundant starch accumulation was obtained, whose content of amylopectin accounts for 84.04% of the starch granules. Compared with the wild type (Lemna aequinoctialis), the branching degree of starch in sub-1 mutant was significantly increased by 19.6%. Chain length DP 6-12, DP 25-36 and DP > 36 of amylopectin significantly decreased, while chain length DP 13-24 significantly increased. Average chain length of wild-type and sub-1 mutant starches were greater than DP 22. Moreover, the crystal structure and physical properties of starch have changed markedly in sub-1 mutant. For example, the starch crystallinity of sub-1 mutant was only 8.94%, while that of wild-type was 22.3%. Compared with wild type, water solubility of starch was significantly reduced by 29.42%, whereas swelling power significantly increased by 97.07% in sub-1 mutant. In order to further analyze the molecular mechanism of efficient accumulation of amylopectin in sub-1 mutant, metabolome and transcriptome were performed. The results showed that glucose accumulated in sub-1 mutant, then degradation of starch to glucose mainly depends on α-amylase. At night, the down-regulated β-amylase gene resulted in the inhibition of starch degradation. The starch and sucrose metabolism pathways were significantly enriched. Up-regulated expression of SUS, AGPase2, AGPase3, PYG, GPI and GYS provide sufficient substrate for starch synthesis in sub-1 mutant. From the 0H to 16H light treatment, granule-bound starch synthase (GBSS1) gene was inhibited, on the contrary, the starch branching enzyme (SBE) gene was induced. Differential expression of GBSS1 and SBE may be an important reason for the decrease ratio of amylose/amylopectin in sub-1 mutant. Taken together, our results indicated that the sub-1 mutant can accumulate the amylopectin efficiently, potentially through altering the differential expression of AGPase, GBSS1, SBE, and BAM. This study also provides theoretical guidance for creating crop germplasm with high amylopectin by means of synthetic biology in the future.
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5
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Yang GL. Duckweed Is a Promising Feedstock of Biofuels: Advantages and Approaches. Int J Mol Sci 2022; 23:ijms232315231. [PMID: 36499555 PMCID: PMC9740428 DOI: 10.3390/ijms232315231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
With the growing scarcity of traditional sources of energy and the accompanying acute environmental challenges, biofuels based on biomass are favored as the most promising alternative. As one of the core raw materials for biomass energy, research on its production methods and synthesis mechanisms is emerging. In recent years, duckweed has been used as a high-quality new biomass feedstock for its advantages, including fast biomass accumulation, high starch content, high biomass conversion efficiency, and sewage remediation. This study provides a systematic review of the growth characteristics, starch metabolism pathways, and methods to improve starch accumulation in the new energy plant, duckweed. The study also presents a prospect that might be used as a reference for the development of duckweed as a new energy-providing plant.
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Affiliation(s)
- Gui-Li Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China;
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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6
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Wang X, Jin Y, Cheng L, Li Z, Li C, Ban X, Gu Z, Hong Y. Pasting properties and multi-scale structures of Spirodela starch and its comparison with normal corn and rice starch. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Over-Expression of Phosphoserine Aminotransferase-Encoding Gene ( AtPSAT1) Prompts Starch Accumulation in L. turionifera under Nitrogen Starvation. Int J Mol Sci 2022; 23:ijms231911563. [PMID: 36232863 PMCID: PMC9570139 DOI: 10.3390/ijms231911563] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the energy plant duckweed (strain Lemna turionifera 5511) as the research object and used a stable genetic transformation system to heterologously over-expressing Arabidopsis AtPSAT1 (the gene encoding phosphoserine aminotransferase, the second enzyme of PPSB). Our results showed that, under nitrogen starvation, the transgenic plants grew faster, with higher values of Fv/Fm, rETR, and Y(II), as well as fresh and dry weight, than the wild-type. More promisingly, the accumulation of starch was also found to be significantly improved when over-expressing AtPSAT1 in the transgenic plants. qRT-PCR analysis results showed that the expression of genes related to nitrogen assimilation, carbon metabolism, and starch biosynthesis was up-regulated, while the expression of starch degradation-related genes was down-regulated by AtPSAT1 over-expression. We propose that the increased starch accumulation caused by AtPSAT1 over-expression may result from both elevated photosynthetic capacity and nitrogen utilization efficiency. This research sheds new light on the mechanism underlying the ability of PPSB to coordinate nitrogen and carbon metabolism, and provides a feasible way to improve starch production, that is, through engineering PPSB in crops.
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Li G, Chen Y, Zhao X, Yang J, Wang X, Li X, Hu S, Hou H. Genome-Wide Analysis of the Growth-Regulating Factor (GRF) Family in Aquatic Plants and Their Roles in the ABA-Induced Turion Formation of Spirodela polyrhiza. Int J Mol Sci 2022; 23:ijms231810485. [PMID: 36142399 PMCID: PMC9499638 DOI: 10.3390/ijms231810485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/16/2023] Open
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: (J.Y.); (H.H.)
| | - Xiaoyu Wang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shiqi Hu
- Zhejiang Marine Development Research Institute, Zhoushan 316021, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.Y.); (H.H.)
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9
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Mallu TS, Irafasha G, Mutinda S, Owuor E, Githiri SM, Odeny DA, Runo S. Mechanisms of pre-attachment Striga resistance in sorghum through genome-wide association studies. Mol Genet Genomics 2022; 297:751-762. [PMID: 35305146 DOI: 10.1007/s00438-022-01882-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/26/2022] [Indexed: 11/30/2022]
Abstract
Witchweeds (Striga spp.) greatly limit production of Africa's most staple crops. These parasitic plants use strigolactones (SLs)-chemical germination stimulants, emitted from host's roots to germinate, and locate their hosts for invasion. This information exchange provides opportunities for controlling the parasite by either stimulating parasite seed germination without a host (suicidal germination) or by inhibiting parasite seed germination (pre-attachment resistance). We sought to determine genetic factors that underpin Striga pre-attachment resistance in sorghum using the genome wide association study (GWAS) approach. Results revealed that Striga germination was associated with genes encoding hormone signaling functions, e.g., the Novel interactor of jaz (NINJA) and, Abscisic acid-insensitive 5 (ABI5). This pointed toward abscisic acid (ABA) and gibberellic acid (GA) as probable determinants of Striga germination. To test this hypothesis, we conditioned Striga using: ABA, ABA + its inhibitor fluridone (FLU), GA or water. Unexpectedly, Striga conditioned with FLU germinated after 4 days without SL. Upon germination stimulation using sorghum root exudate or the synthetic SL GR24, we found that ABA conditioned seeds had above 20-fold reduction in germination. Conversely, FLU conditioned seeds recorded above 20-fold increase in germination. Conditioning with GA reduced Striga seed germination 1.5-fold only in the GR24 treatment. Germination assays using seeds of a related parasitic plant (Alectra vogelii) showed similar degrees of stimulation and reduction of germination by the hormones further affirming the hormonal crosstalk. Our findings have far-reaching implications in the control of some of the most noxious pathogens of crops in Africa.
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Affiliation(s)
- Tesfamichael S Mallu
- Pan African University Institute for Basic Sciences, Technology and Innovation, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya.,Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Gilles Irafasha
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Sylvia Mutinda
- Pan African University Institute for Basic Sciences, Technology and Innovation, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya.,Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Erick Owuor
- International Crops Research Institute for the Semi-Arid Tropics, P. O. Box 39063-00623, Nairobi, Kenya
| | - Stephen M Githiri
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, P. O. Box 39063-00623, Nairobi, Kenya.
| | - Steven Runo
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya.
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Characterization of Various Subunit Combinations of ADP-Glucose Pyrophosphorylase in Duckweed (Landoltia punctata). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5455593. [PMID: 35309169 PMCID: PMC8927976 DOI: 10.1155/2022/5455593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022]
Abstract
Background Landoltia punctata can be used as renewable and sustainable biofuel feedstock because it can quickly accumulate high starch levels. ADP-glucose pyrophosphorylase (AGPase) catalyzes the first committed step during starch biosynthesis in higher plants. The heterotetrameric structure of plant AGPases comprises pairs of large subunits (LSs) and small subunits (SSs). Although several studies have reported on the high starch accumulation capacity of duckweed, no study has explored the underlying molecular accumulation mechanisms and their linkage with AGPase. Therefore, this study focused on characterizing the roles of different L. punctate AGPases. Methodology. Expression patterns of LpAGPs were determined through comparative transcriptome analyses, followed by coexpressing their coding sequences in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana tabacum. Results Comparative transcriptome analyses showed that there are five AGPase subunits encoding cDNAs in L. punctata (LpAGPS1, LpAGPS2, LpAGPL1, LpAGPL2, and LpAGPL3). Nutrient starvation (distilled water treatment) significantly upregulated the expression of LpAGPS1, LpAGPL2, and LpAGPL3. Coexpression of LpAGPSs and LpAGPLs in Escherichia coli generated six heterotetramers, but only four (LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3) exhibited AGPase activities and displayed a brownish coloration upon exposure to iodine staining. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays validated the interactions between LpAGPS1/LpAGPL2, LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3. All the five LpAGPs were fusion-expressed with hGFP in Arabidopsis protoplasts, and their green fluorescence signals were uniformly localized in the chloroplast, indicating that they are plastid proteins. Conclusions This study uncovered the cDNA sequences, structures, subunit interactions, expression patterns, and subcellular localization of AGPase. Collectively, these findings provide new insights into the molecular mechanism of fast starch accumulation in L. punctata.
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11
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Appenroth KJ, Ziegler P, Sree KS. Accumulation of starch in duckweeds (Lemnaceae), potential energy plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2621-2633. [PMID: 34924714 PMCID: PMC8639912 DOI: 10.1007/s12298-021-01100-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/23/2021] [Accepted: 11/05/2021] [Indexed: 06/12/2023]
Abstract
Starch can accumulate in both actively growing vegetative fronds and over-wintering propagules, or turions of duckweeds, small floating aquatic plants belonging to the family of the Lemnaceae. The starch synthesizing potential of 36 duckweed species varies enormously, and the starch contents actually occurring in the duckweed tissues are determined by growth conditions, various types of stress and the action of growth regulators. The present review examines the effects of phytohormones and growth retardants, heavy metals, nutrient deficiency and salinity on the accumulation of starch in duckweeds with a view to obtaining high yields of starch as a feedstock for biofuel production. Biotechnological approaches to degrading duckweed starch to its component sugars and the fermentation of these sugars to bio-alcohols are also discussed.
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Affiliation(s)
- Klaus-J. Appenroth
- Matthias Schleiden Institute – Plant Physiology, University of Jena, Jena, Germany
| | - Paul Ziegler
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - K. Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periye, 671320 India
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12
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Zhu Y, Li X, Gao X, Sun J, Ji X, Feng G, Shen G, Xiang B, Wang Y. Molecular mechanism underlying the effect of maleic hydrazide treatment on starch accumulation in S. polyrrhiza 7498 fronds. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:99. [PMID: 33874980 PMCID: PMC8056677 DOI: 10.1186/s13068-021-01932-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/19/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Duckweed is considered a promising feedstock for bioethanol production due to its high biomass and starch production. The starch content can be promoted by plant growth regulators after the vegetative reproduction being inhibited. Maleic hydrazide (MH) has been reported to inhibit plant growth, meantime to increase biomass and starch content in some plants. However, the molecular explanation on the mechanism of MH action is still unclear. RESULTS To know the effect and action mode of MH on the growth and starch accumulation in Spirodela polyrrhiza 7498, the plants were treated with different concentrations of MH. Our results showed a substantial inhibition of the growth in both fronds and roots, and increase in starch contents of plants after MH treatment. And with 75 µg/mL MH treatment and on the 8th day of the experiment, starch content was the highest, about 40 mg/g fresh weight, which is about 20-fold higher than the control. The I2-KI staining and TEM results confirmed that 75 µg/mL MH-treated fronds possessed more starch and big starch granules than that of the control. No significant difference for both in the photosynthetic pigment content and the chlorophyll fluorescence parameters of PII was found. Differentially expressed transcripts were analyzed in S. polyrrhiza 7498 after 75 µg/mL MH treatment. The results showed that the expression of some genes related to auxin response reaction was down-regulated; while, expression of some genes involved in carbon fixation, C4 pathway of photosynthesis, starch biosynthesis and ABA signal transduction pathway was up-regulated. CONCLUSION The results provide novel insights into the underlying mechanisms of growth inhibition and starch accumulation by MH treatment, and provide a selective way for the improvement of starch production in duckweed.
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Affiliation(s)
- Yerong Zhu
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Xiaoxue Li
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Xuan Gao
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Jiqi Sun
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Xiaoyuan Ji
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Guodong Feng
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Guangshuang Shen
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Beibei Xiang
- School of Chinese Material Medica, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Yong Wang
- College of Life Science, Nankai University, Weijin Road 94, Tianjin, 300071, China.
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13
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Baek G, Saeed M, Choi HK. Duckweeds: their utilization, metabolites and cultivation. APPLIED BIOLOGICAL CHEMISTRY 2021; 64:73. [PMID: 34693083 PMCID: PMC8525856 DOI: 10.1186/s13765-021-00644-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 05/21/2023]
Abstract
Duckweeds are floating plants of the family Lemnaceae, comprising 5 genera and 36 species. They typically live in ponds or lakes and are found worldwide, except the polar regions. There are two duckweed subfamilies-namely Lemnoidea and Wolffioideae, with 15 and 21 species, respectively. Additionally, they have characteristic reproduction methods. Several metabolites have also been reported in various duckweeds. Duckweeds have a wide range of adaptive capabilities and are particularly suitable for experiments requiring high productivity because of their speedy growth and reproduction rates. Duckweeds have been studied for their use as food/feed resources and pharmaceuticals, as well as for phytoremediation and industrial applications. Because there are numerous duckweed species, culture conditions should be optimized for industrial applications. Here, we review and summarize studies on duckweed species and their utilization, metabolites, and cultivation methods to support the extended application of duckweeds in future.
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Affiliation(s)
- GahYoung Baek
- College of Pharmacy, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Maham Saeed
- College of Pharmacy, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, 06974 Republic of Korea
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Płachno BJ, Strzemski M, Dresler S, Adamec L, Wojas-Krawczyk K, Sowa I, Danielewicz A, Miranda VFO. A Chemometry of Aldrovanda vesiculosa L. (Waterwheel, Droseraceae) Populations. Molecules 2020; 26:E72. [PMID: 33375725 PMCID: PMC7795913 DOI: 10.3390/molecules26010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
The genus Aldrovanda is a Palaeogene element containing a single extant species, Aldrovanda vesiculosa L. This aquatic carnivorous herb has a very wide range of distribution, natively covering four continents; however, it is a critically endangered aquatic plant species worldwide. Previous studies revealed that A. vesiculosa had an extremely low genetic variation. The main aim of the present paper is to explore, using chemometric tools, the diversity of 16 A. vesiculosa populations from various sites from four continents (Eurasia, Africa, Australia). Using chemometric data as markers for genetic diversity, we show the relationships of 16 A. vesiculosa populations from various sites, including four continents. Phytochemical markers allowed the identification of five well-supported (bootstrap > 90%) groups among the 16 populations sampled. The principal component analysis data support the idea that the strongly related African (Botswana) and Australian (Kimberley, NT, NW Australia) populations are the most distant ones, separated from the European and Asian ones. However, considering the five Australian populations sampled, three are nested within the Eurasian group. The chemometric data are correlated positively with the geographical distances between the samples, which suggests a tendency toward isolation for the most distant populations.
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Affiliation(s)
- Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St. 30-387 Cracow, Poland
| | - Maciej Strzemski
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland;
| | - Sławomir Dresler
- Department of Plant Physiology and Biophysics, Institute of Biological Science, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Lubomír Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic;
| | - Kamila Wojas-Krawczyk
- Department of Pneumology, Oncology and Allergology, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Ireneusz Sowa
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland;
| | - Anna Danielewicz
- Department of Paediatric Orthopaedics, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Vitor F. O. Miranda
- Laboratory of Plant Systematics, Department of Applied Biology, Campus Jaboticabal, School of Agricultural and Veterinarian Sciences, UNESP-São Paulo State University, São Paulo CEP 14884-900, Brazil;
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Hitsman HW, Simons AM. Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza. J Evol Biol 2020; 33:1405-1416. [PMID: 32656868 DOI: 10.1111/jeb.13678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022]
Abstract
Variable environments may result in the evolution of adaptive phenotypic plasticity when cues reliably indicate an appropriate phenotype-environment match. Although adaptive plasticity is well established for phenological traits expressed across environments, local differentiation in norms of reaction is less well studied. The switch from the production of regular fronds to overwintering 'turions' in the greater duckweed Spirodela polyrhiza is vital to fitness and is expressed as a norm of reaction induced by falling temperatures associated with the onset of winter. However, the optimal norm of reaction to temperature is expected to differ across latitudes. Here, we test the hypothesis that a gradient in the length and predictability of growing seasons across latitudes results in the evolution of reaction norms characterized by earlier turion production at higher latitudes. We test this by collecting S. polyrhiza from replicate populations across seven latitudes from Ontario to Florida and then assessing differentiation in thermal reaction norms of turion production along a common temperature gradient. As predicted, northern populations produce turions at a lower birth order and earlier; a significant latitude-by-temperature interaction suggests that reaction norm differentiation has occurred. Our results provide evidence of differentiation in reaction norms across latitudes in a phenological trait, and we discuss how the adaptive significance of this plasticity might be further tested.
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Affiliation(s)
- Harry W Hitsman
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrew M Simons
- Department of Biology, Carleton University, Ottawa, ON, Canada
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Differential effects of synthetic media on long-term growth, starch accumulation and transcription of ADP-glucosepyrophosphorylase subunit genes in Landoltia punctata. Sci Rep 2019; 9:15310. [PMID: 31653895 PMCID: PMC6814796 DOI: 10.1038/s41598-019-51677-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/04/2019] [Indexed: 01/20/2023] Open
Abstract
Murashige & Skoog (MS) and Hoagland's media were previously used for in vitro culture of Landoltia punctata. During subsequent ex vitro culture, the use of MS medium resulted in a higher growth rate, compared to Hoagland's medium. Thus, a higher starch content of L. punctata in MS medium was previously hypothesized. Here, L. punctata strain 5632 was isolated and characterized using morphological characteristics and the atpF-atpH intergenic region. During early cultivation stage, fresh weight and relative growth rate in MS medium were lower than Hoagland's medium. Conversely, starch content in MS medium was considerably higher than in Hoagland's medium. Medium effects on expression of genes coding for starch-biosynthesis ADP-glucosepyrophosphorylase (AGPase) were determined. Genomic fragments of small (LeAPS) and large (LeAPL1) AGPase subunits were characterized. Differential expression between each AGPase subunit genes was observed in both media. Additionally, in MS medium, the highest correlation coefficients between starch content and gene expression was found with LeAPS (0.81) and followed by LeAPL3 (0.67), LeAPL2 (0.65) and LeAPL1 (0.28). In Hoagland's medium, the coefficients of LeAPL3 (0.83) and LeAPL2 (0.62) were higher than LeAPS (0.18) and LeAPL1 (-0.62). This suggested different levels of contributions of these genes in starch biosynthesis in both media.
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Chen G, Huang J, Fang Y, Zhao Y, Tian X, Jin Y, Zhao H. Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin. BIORESOURCE TECHNOLOGY 2019; 276:8-17. [PMID: 30602128 DOI: 10.1016/j.biortech.2018.12.102] [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: 10/16/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Carriers strengthened duckweed treatment system (CDW), duckweed treatment system (DW) and water hyacinth treatment system (WH) were developed to treat rural wastewater in Dianchi Lake basin. Results showed that adding microbial carrier did not affect the growth and biomass components of duckweed. The following features were discovered in the CDW system. First, the NO3--N and TN removal efficiencies were the highest among three systems, reaching 80.02% and 56.42%, respectively. Secondly, Illumina sequencing revealed the highest microbial diversity. Thirdly, a distinct succession of microbial community was observed. Rhodobacter, Bacteria vadinCA02, C39 and Flavobacterium dominated in the start-up stage, and contributed to biofilm formation and pollutants degradation. Acinetobacter, Planctomyces and Methylibium significantly increased in the stable stage, and contributed to nitrogen removal. Finally, highly abundant plant growth-promoting bacteria were found. Comprehensive analysis indicated that the functional bacteria community was closely related to the pollutant removals, plant growth and system operating status.
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Affiliation(s)
- Guoke Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Jun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
| | - Yonggui Zhao
- Institute of Environmental Sciences and Ecological Restoration, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Xueping Tian
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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18
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Chu P, Wilson GM, Michael TP, Vaiciunas J, Honig J, Lam E. Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. PLANT MOLECULAR BIOLOGY 2018; 98:219-231. [PMID: 30191440 DOI: 10.1007/s11103-018-0774-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/23/2018] [Indexed: 05/13/2023]
Abstract
Leveraging the heightened levels of polymorphism in NB-ARC-related protein encoding genes in higher plants, a bioinformatic pipeline was created to identify regions in this gene family from sequenced plant genomes that exhibit fragment length or single nucleotide differences in different accessions of the same species. Testing this approach with the aquatic plant Spirodela polyrhiza demonstrated its superior performance in comparison with currently available genotyping technologies based on PCR amplification. Rapid and economical genotyping tools that can reliably distinguish species and intraspecific variations in plants can be powerful tools for biogeographical and ecological studies. Clones of the cosmopolitan duckweed species, Spirodela polyrhiza, are difficult to distinguish morphologically due to their highly abbreviated architecture and inherently low levels of sequence variation. The use of plastidic markers and generic Amplification Fragment Length Polymorphism approaches have met with limited success in resolving clones of S. polyrhiza from diverse geographical locales. Using whole genome sequencing data from nine S. polyrhiza clones as a training set, we created an informatic pipeline to identify and rank polymorphic regions from nuclear-encoded NB-ARC-related genes to design markers for PCR, Sanger sequencing (barcoding), and fragment length analysis. With seven primer sets, we found 21 unique fingerprints from a set of 23 S. polyrhiza clones. However, three of these clones share the same fingerprint and are indistinguishable by these markers. These primer sets can also be used as interspecific barcoding tools to rapidly resolve S. polyrhiza from the closely related S. intermedia species without the need for DNA sequencing. Our work demonstrates a general approach of using hyper-polymorphic loci within genomes as a resource to produce facile tools that can have high resolving power for genotyping applications.
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Affiliation(s)
- Philomena Chu
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Glen M Wilson
- Department of Mathematics, University of Oslo, Postboks 1053, 0316 OSLO, Blindern, Norway
| | | | - Jennifer Vaiciunas
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Joshua Honig
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA.
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19
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Liu Y, Chen X, Wang X, Fang Y, Huang M, Guo L, Zhang Y, Zhao H. Improving biomass and starch accumulation of bioenergy crop duckweed (Landoltia punctata) by abscisic acid application. Sci Rep 2018; 8:9544. [PMID: 29934519 PMCID: PMC6015002 DOI: 10.1038/s41598-018-27944-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/05/2018] [Indexed: 12/03/2022] Open
Abstract
Duckweed is a valuable feedstock for bioethanol production due to its high biomass and starch accumulation. In our preliminary experiment, we found that abscisic acid (ABA) could simultaneously increase starch and biomass accumulation of duckweed, but the mechanisms are still unclear. The results showed that the biomass production of duckweed reached up to 59.70 and 63.93 g m−2 in 6 days, respectively, with an increase of 7% (P < 0.05) compared to the control. The starch percentage increased from 2.29% up to 46.18% after 14 days of treatment, with a total of starch level 2.6-fold higher than that of the control. Moreover, the level of endogenous ABA, zeatin-riboside (ZR) and indole-3-acetic acid (IAA) increased, while gibberellins (GAs) decreased. Notably, ABA content in treated samples reached 336.5 mg/kg (fresh weight), which was 7.5-fold greater than that of the control. Importantly, the enzyme activities involved in starch biosynthesis increased while those catalyzing starch degradation decreased after ABA application. Taken together, these results indicated that ABA can promote biomass and starch accumulation by regulating endogenous hormone levels and the activity of starch metabolism related key enzymes. These results will provide an operable method for high starch accumulation in duckweed for biofuels production.
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Affiliation(s)
- Yang Liu
- School of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Xiaoyi Chen
- School of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Xinhui Wang
- School of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China
| | - Mengjun Huang
- Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences, 402160, Chongqing, China
| | - Ling Guo
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China
| | - Yin Zhang
- School of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, 610106, China.,Meat Processing Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610106, China
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China.
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20
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Liu C, Feng Q, Yang J, Qi X. Catalytic production of levulinic acid and ethyl levulinate from uniconazole-induced duckweed (Lemna minor). BIORESOURCE TECHNOLOGY 2018; 255:50-57. [PMID: 29414172 DOI: 10.1016/j.biortech.2018.01.087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Duckweed (Lemna minor) with a high starch content of 50.4% was cultivated by uniconazole-induction method. The cultivated duckweed was used to produce value-added chemicals such as glucose, levulinic acid and formic acid in diluted HCl aqueous solution. A high glucose yield of 93.4% (471 g/kg based on loading duckweed mass) could be achieved at 180 °C in short reaction time, and the generated glucose was converted into levulinic acid and formic acid with yields of 52.0% and 34.1%, respectively, for 150 min, corresponding to 262 g/kg levulinic acid yield and 171 g/kg formic acid yield based on the mass of loading duckweed, respectively. Moreover, the duckweed was efficiently converted to ethyl levulinate with 55.2% yield (400.6 g/kg) at 200 °C in ethanol. This work provides a promising strategy for the production of value-added chemicals from phytoplankton that is able to purify the wastewater containing high content of P and N.
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Affiliation(s)
- Chunguang Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin 300350, China
| | - Qingna Feng
- Agro-Environmental Protection Institute, Chinese Academy of Agricultural Sciences, Tianjin 300191, China; Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin 300350, China
| | - Jirui Yang
- Agro-Environmental Protection Institute, Chinese Academy of Agricultural Sciences, Tianjin 300191, China
| | - Xinhua Qi
- Agro-Environmental Protection Institute, Chinese Academy of Agricultural Sciences, Tianjin 300191, China.
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21
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Chen G, Fang Y, Huang J, Zhao Y, Li Q, Lai F, Xu Y, Tian X, He K, Jin Y, Tan L, Zhao H. Duckweed systems for eutrophic water purification through converting wastewater nutrients to high-starch biomass: comparative evaluation of three different genera (Spirodela polyrhiza, Lemna minor and Landoltia punctata) in monoculture or polyculture. RSC Adv 2018; 8:17927-17937. [PMID: 35542060 PMCID: PMC9080494 DOI: 10.1039/c8ra01856a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/23/2018] [Indexed: 11/21/2022] Open
Abstract
This study provides a new insight into the application of duckweed in eutrophic water advanced treatment and starch production.
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22
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Yu C, Zhao X, Qi G, Bai Z, Wang Y, Wang S, Ma Y, Liu Q, Hu R, Zhou G. Integrated analysis of transcriptome and metabolites reveals an essential role of metabolic flux in starch accumulation under nitrogen starvation in duckweed. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:167. [PMID: 28670341 PMCID: PMC5485579 DOI: 10.1186/s13068-017-0851-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/16/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Duckweed is considered a promising source of energy due to its high starch content and rapid growth rate. Starch accumulation in duckweed involves complex processes that depend on the balanced expression of genes controlled by various environmental and endogenous factors. Previous studies showed that nitrogen starvation induces a global stress response and results in the accumulation of starch in duckweed. However, relatively little is known about the mechanisms underlying the regulation of starch accumulation under conditions of nitrogen starvation. RESULTS In this study, we used next-generation sequencing technology to examine the transcriptome responses of Lemna aequinoctialis 6000 at three stages (0, 3, and 7 days) during nitrogen starvation in the presence of exogenously applied sucrose. Overall, 2522, 628, and 1832 differentially expressed unigenes (DEGs) were discovered for the treated and control samples. Clustering and enrichment analysis of DEGs revealed several biological processes occurring under nitrogen starvation. Genes involved in nitrogen metabolism showed the earliest responses to nitrogen starvation, whereas genes involved in carbohydrate biosynthesis were responded subsequently. The expression of genes encoding nitrate reductase, glutamine synthetase, and glutamate synthase was down-regulated under nitrogen starvation. The expression of unigenes encoding enzymes involved in gluconeogenesis was up-regulated, while the majority of unigenes involved in glycolysis were down-regulated. The metabolite results showed that more ADP-Glc was accumulated and lower levels of UDP-Glc were accumulated under nitrogen starvation, the activity of AGPase was significantly increased while the activity of UGPase was dramatically decreased. These changes in metabolite levels under nitrogen starvation are roughly consistent with the gene expression changes in the transcriptome. CONCLUSIONS Based on these results, it can be concluded that the increase of ADP-glucose and starch contents under nitrogen starvation is a consequence of increased output from the gluconeogenesis and TCA pathways, accompanied with the reduction of lipids and pectin biosynthesis. The results provide novel insights into the underlying mechanisms of starch accumulation during nitrogen starvation, which provide a foundation for the improvement of advanced bioethanol production in duckweed.
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Affiliation(s)
- Changjiang Yu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Xiaowen Zhao
- College of Life Sciences, China Agricultural University, Beijing, 100094 People’s Republic of China
| | - Guang Qi
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Zetao Bai
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Yu Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Shumin Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Yubin Ma
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qian Liu
- Guangzhou Genedenovo Biotechnology Co., Ltd, Guangzhou, 510006 China
| | - Ruibo Hu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Gongke Zhou
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
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23
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Wang W, Wu Y, Messing J. Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant. PLANTA 2016; 244:893-899. [PMID: 27306450 DOI: 10.1007/s00425-016-2555-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
A large proportion of genes in plant genomes are organized as gene families. Whereas most gene families in the aquative plant Spirodela are reduced in their copy number, the PPR gene family is expanded, which match the RNA editing sites in organelles, providing us with new insights in the evolution of flowering plants. Pentatricopeptide-repeat proteins (PPRs) are nuclear-encoded proteins that are targeted to mitochondria and plastids to stabilize and edit mRNA transcribed from organellar genomes. They have been described for many terrestrial plant species from a diverse spectrum of sequenced genomes. To further increase our understanding of the evolution of this gene family across angiosperms, we analyzed the PPR genes in the aquatic species Spirodela polyrhiza in the order of the Alismatales (monocotyledonous plants). Because we had generated next generation sequencing data from transcripts and had sequenced the genome of Spirodela polyrhiza, we were able to identify its PPR genes and determine the level of their expression. In total, we could identify 556 PPR proteins, of which 238 members belong to the P (P motif) subfamily that is mainly involved in RNA stabilization and 318 ones to the PLS (P, Longer P, shorter P motif) subfamily responsible for RNA editing. Compared to other angiosperms, this is a large increase in the copy number of the PLS-PPRs subfamily and the expansion correlates with the increase of the number of RNA editing sites of organellar transcripts. Expression of PPR was generally stable even during growing and dormant stages, indicating that their function was critical throughout development. However, PPRs, especially those of the PLS subfamily, were expressed at relatively low levels, suggesting a delicate fine-tuning of its trans-acting function in the post-transcriptional regulation of gene expression. Thus, understanding PPR evolution and expression will help decipher the PPR code for their binding sites, which could genetically engineer RNA-binding proteins toward desired sequence.
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Affiliation(s)
- Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Yongrui Wu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KFX, Messing J. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 2015; 5:3311. [PMID: 24548928 PMCID: PMC3948053 DOI: 10.1038/ncomms4311] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/24/2014] [Indexed: 11/30/2022] Open
Abstract
The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications. Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.
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Affiliation(s)
- W Wang
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - G Haberer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - H Gundlach
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - C Gläßer
- 1] MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany [2]
| | - T Nussbaumer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - M C Luo
- Department of Plant Sciences, University of California, 265 Hunt Hall, One Shields Avenue, Davis, California 95616, USA
| | - A Lomsadze
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - M Borodovsky
- Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332, USA
| | - R A Kerstetter
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - J Shanklin
- Brookhaven National Laboratory, 50 Bell Ave, Upton, New York 11973, USA
| | - D W Byrant
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - T C Mockler
- Donald Danforth Plant Science Center, 975N Warson Road, St. Louis, Missouri 63132, USA
| | - K J Appenroth
- Department of Plant Physiology, University of Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - J Grimwood
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - J Chow
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Choi
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - C Adam
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - X-H Cao
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - J Fuchs
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - I Schubert
- Department of Cytogenetics and Genome Analysis, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - D Rokhsar
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - J Schmutz
- 1] DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - T P Michael
- 1] Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA [2]
| | - K F X Mayer
- MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - J Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
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RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species. PLoS One 2015; 10:e0140285. [PMID: 26517707 PMCID: PMC4627657 DOI: 10.1371/journal.pone.0140285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022] Open
Abstract
RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
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Huang M, Fang Y, Liu Y, Jin Y, Sun J, Tao X, Ma X, He K, Zhao H. Using proteomic analysis to investigate uniconazole-induced phytohormone variation and starch accumulation in duckweed (Landoltia punctata). BMC Biotechnol 2015; 15:81. [PMID: 26369558 PMCID: PMC4570701 DOI: 10.1186/s12896-015-0198-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Duckweed (Landoltia punctata) has the potential to remediate wastewater and accumulate enormous amounts of starch for bioethanol production. Using systematical screening, we determined that the highest biomass and starch percentage of duckweed was obtained after uniconazole application. Uniconazole contributes to starch accumulation of duckweed, but the molecular mechanism is still unclear. RESULTS To elucidate the mechanisms of high starch accumulation, in the study, the responses of L. punctata to uniconazole were investigated using a quantitative proteomic approach combined with physiological and biochemical analysis. A total of 3327 proteins were identified. Among these identified proteins, a large number of enzymes involved in endogenous hormone synthetic and starch metabolic pathways were affected. Notably, most of the enzymes involved in abscisic acid (ABA) biosynthesis showed up-regulated expression, which was consistent with the content variation. The increased endogenous ABA may up-regulate expression of ADP-glucose pyrophosphorylase to promote starch biosynthesis. Importantly, the expression levels of several key enzymes in the starch biosynthetic pathway were up-regulated, which supported the enzymatic assay results and may explain why there is increased starch accumulation. CONCLUSIONS These generated data linked uniconazole with changes in expression of enzymes involved in hormone biosynthesis and starch metabolic pathways and elucidated the effect of hormones on starch accumulation. Thus, this study not only provided insights into the molecular mechanisms of uniconazole-induced hormone variation and starch accumulation but also highlighted the potential for duckweed to be feedstock for biofuel as well as for sewage treatment.
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Affiliation(s)
- Mengjun Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yang Fang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yang Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yanling Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Jiaolong Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xinrong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Kaize He
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
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Wang W, Messing J. Status of duckweed genomics and transcriptomics. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:10-5. [PMID: 24995947 DOI: 10.1111/plb.12201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/28/2014] [Indexed: 05/06/2023]
Abstract
Duckweeds belong to the smallest flowering plants that undergo fast vegetative growth in an aquatic environment. They are commonly used in wastewater treatment and animal feed. Whereas duckweeds have been studied at the biochemical level, their reduced morphology and wide environmental adaption had not been subjected to molecular analysis until recently. Here, we review the progress that has been made in using a DNA barcode system and the sequences of chloroplast and mitochondrial genomes to identify duckweed species at the species or population level. We also review analysis of the nuclear genome sequence of Spirodela that provides new insights into fundamental biological questions. Indeed, reduced gene families and missing genes are consistent with its compact morphogenesis, aquatic floating and suppression of juvenile-to-adult transition. Furthermore, deep RNA sequencing of Spirodela at the onset of dormancy and Landoltia in exposure of nutrient deficiency illustrate the molecular network for environmental adaption and stress response, constituting major progress towards a post-genome sequencing phase, where further functional genomic details can be explored. Rapid advances in sequencing technologies could continue to promote a proliferation of genome sequences for additional ecotypes as well as for other duckweed species.
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Affiliation(s)
- W Wang
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Zhao Z, Shi HJ, Wang ML, Cui L, Zhao H, Zhao Y. Effect of nitrogen and phosphorus deficiency on transcriptional regulation of genes encoding key enzymes of starch metabolism in duckweed (Landoltia punctata). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 86:72-81. [PMID: 25438139 DOI: 10.1016/j.plaphy.2014.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/13/2014] [Indexed: 06/04/2023]
Abstract
The production of starch by plants influences their use as biofuels. Nitrogen (N) and phosphorus (P) regulate starch gene expression during plant growth and development, yet the role of key enzymes such as ADP-glucose pyrophosphorylase (E.C. 2.7.7.27 AGPase) in starch metabolism during N- and P-deficiency remains unknown. We investigated the effect of N- and P-deficiency on the expression of large (LeAPL1, LeAPL2, and LeAPL3) and small (LeAPS) subunits of AGPase in duckweed (Landoltia punctata) and their correlation with starch content. We first isolated the full-length cDNA encoding LeAPL1 (GenBank Accession No. KJ603244) and LeAPS (GenBank Accession No. KJ603243); they contained open reading frames of 1554 bp (57.7-kDa polypeptide of 517 amino acids) and 1578 bp (57.0 kDa polypeptide of 525 amino acids), respectively. Real-time PCR analysis revealed that LeAPL1 and LeAPL3 were highly expressed during early stages of N-deficiency, while LeAPL2 was only expressed during late stage. However, in response to P-deficiency, LeAPL1 and LeAPL2 were upregulated during early stages and LeAPL3 was primarily expressed in the late stage. Interestingly, LeAPS was highly expressed following N-deficiency during both stages, but was only upregulated in the early stage after P-deficiency. The activities of AGPase and soluble starch synthesis enzyme (SSS EC 2.4.1.21) were positively correlated with changes in starch content. Furthermore, LeAPL3 and LeSSS (SSS gene) were positively correlated with changes in starch content during N-deficiency, while LeAPS and LeSSS were correlated with starch content in response to P-deficiency. These results elevate current knowledge of the molecular mechanisms underlying starch synthesis.
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Affiliation(s)
- Zhao Zhao
- School of Basic Medical Sciences, Guiyang Medical University, 550000 Guiyang, Guizhou, China; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, 610064 Chengdu, Sichuan, China; Chengdu Institute of Biology, Chinese Academy of Sciences, 610064 Chengdu, Sichuan, China.
| | - Hui-Juan Shi
- School of Basic Medical Sciences, Guiyang Medical University, 550000 Guiyang, Guizhou, China.
| | - Mao-Lin Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, 610064 Chengdu, Sichuan, China.
| | - Long Cui
- Livzon Pharmaceutical Group Co., Ltd, Zhuhai, Guangdong, China.
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610064 Chengdu, Sichuan, China.
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, 610064 Chengdu, Sichuan, China.
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29
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Liu Y, Fang Y, Huang M, Jin Y, Sun J, Tao X, Zhang G, He K, Zhao Y, Zhao H. Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) II: transcriptome alterations of pathways involved in carbohydrate metabolism and endogenous hormone crosstalk. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:64. [PMID: 25873998 PMCID: PMC4396169 DOI: 10.1186/s13068-015-0245-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/24/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Landoltia punctata is a widely distributed duckweed species with great potential to accumulate enormous amounts of starch for bioethanol production. We found that L. punctata can accumulate starch rapidly accompanied by alterations in endogenous hormone levels after uniconazole application, but the relationship between endogenous hormones and starch accumulation is still unclear. RESULTS After spraying fronds with 800 mg/L uniconazole, L. punctata can accumulate starch quickly, with a dry weight starch content of up to 48% after 240 h of growth compared to 15.7% in the control group. Electron microscopy showed that the starch granule content was elevated after uniconazole application. The activities of key enzymes involved in starch synthesis were also significantly increased. Moreover, the expression of regulatory elements of the cytokinin (CK), abscisic acid (ABA) and gibberellin (GA) signaling pathways that are involved in chlorophyll and starch metabolism also changed correspondingly. Importantly, the expression levels of key enzymes involved in starch biosynthesis were up-regulated, while transcript-encoding enzymes involved in starch degradation and other carbohydrate metabolic branches were down-regulated. CONCLUSION The increase of endogenous ABA and CK levels positively promoted the activity of ADP-glucose pyrophosphorylase (AGPase) and chlorophyll content, while the decrease in endogenous GA levels inactivated α-amylase. Thus, the alterations of endogenous hormone levels resulted in starch accumulation due to regulation of the expression of genes involved in the starch metabolism pathway.
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Affiliation(s)
- Yang Liu
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />University of Chinese Academy of Sciences, No.19A Yuquan Road, 100049 Beijing, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Yang Fang
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Mengjun Huang
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />University of Chinese Academy of Sciences, No.19A Yuquan Road, 100049 Beijing, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Yanling Jin
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Jiaolong Sun
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Xiang Tao
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Guohua Zhang
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Kaize He
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
| | - Yun Zhao
- />Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, N0.24 South Section 1, Yihuan Road, 610064 Chengdu, China
| | - Hai Zhao
- />Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
- />Environmental Microbiology Key Laboratory of Sichuan Province, No.9 Section 4, Renmin Nan Road, 610041 Chengdu, China
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Płachno BJ, Adamec L, Kozieradzka-Kiszkurno M, Swiątek P, Kamińska I. Cytochemical and ultrastructural aspects of aquatic carnivorous plant turions. PROTOPLASMA 2014; 251:1449-54. [PMID: 24770880 PMCID: PMC4209241 DOI: 10.1007/s00709-014-0646-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/08/2014] [Indexed: 05/04/2023]
Abstract
Turions, which are modified shoot apices, are vegetative, dormant overwintering organs produced by perennial aquatic plants. In this study, the turion cytochemistry and ultrastructure of Aldrovanda vesiculosa, Utricularia vulgaris and U. stygia were compared with particular emphasis placed on storage substances. These three aquatic, rootless carnivorous plant species were studied at the end of their winter dormancy. At this stage, the turions of all species had starch as their main storage material. In contrast with A. vesiculosa, Utricularia turions were rich in protein storage vacuoles, and proteins were also accumulated as crystalline inclusions in the nuclei. All examined species accumulated lipid droplets in cells of epidermal glands.
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Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University Kraków, 9 Gronostajowa St, 30-387, Cracow, Poland,
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Structural comparison, substrate specificity, and inhibitor binding of AGPase small subunit from monocot and dicot: present insight and future potential. BIOMED RESEARCH INTERNATIONAL 2014; 2014:583606. [PMID: 25276800 PMCID: PMC4167649 DOI: 10.1155/2014/583606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Accepted: 04/21/2014] [Indexed: 11/18/2022]
Abstract
ADP-glucose pyrophosphorylase (AGPase) is the first rate limiting enzyme of starch biosynthesis pathway and has been exploited as the target for greater starch yield in several plants. The structure-function analysis and substrate binding specificity of AGPase have provided enormous potential for understanding the role of specific amino acid or motifs responsible for allosteric regulation and catalytic mechanisms, which facilitate the engineering of AGPases. We report the three-dimensional structure, substrate, and inhibitor binding specificity of AGPase small subunit from different monocot and dicot crop plants. Both monocot and dicot subunits were found to exploit similar interactions with the substrate and inhibitor molecule as in the case of their closest homologue potato tuber AGPase small subunit. Comparative sequence and structural analysis followed by molecular docking and electrostatic surface potential analysis reveal that rearrangements of secondary structure elements, substrate, and inhibitor binding residues are strongly conserved and follow common folding pattern and orientation within monocot and dicot displaying a similar mode of allosteric regulation and catalytic mechanism. The results from this study along with site-directed mutagenesis complemented by molecular dynamics simulation will shed more light on increasing the starch content of crop plants to ensure the food security worldwide.
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32
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Wang W, Wu Y, Messing J. RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction. BMC Genomics 2014; 15:60. [PMID: 24456086 PMCID: PMC3933069 DOI: 10.1186/1471-2164-15-60] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/15/2014] [Indexed: 11/17/2022] Open
Abstract
Background Higher plants exhibit a remarkable phenotypic plasticity to adapt to adverse environmental changes. The Greater Duckweed Spirodela, as an aquatic plant, presents exceptional tolerance to cold winters through its dormant structure of turions in place of seeds. Abundant starch in turions permits them to sink and escape the freezing surface of waters. Due to their clonal propagation, they are the fastest growing biomass on earth, providing yet an untapped source for industrial applications. Results We used next generation sequencing technology to examine the transcriptome of turion development triggered by exogenous ABA. A total of 208 genes showed more than a 4-fold increase compared with 154 down-regulated genes in developing turions. The analysis of up-regulated differential expressed genes in response to dormancy exposed an enriched interplay among various pathways: signal transduction, seed dehydration, carbohydrate and secondary metabolism, and senescence. On the other side, the genes responsible for rapid growth and biomass accumulation through DNA assembly, protein synthesis and carbon fixation are repressed. Noticeably, three members of late embryogenesis abundant protein family are exclusively expressed during turion formation. High expression level of key genes in starch synthesis are APS1, APL3 and GBSSI, which could artificially be reduced for re-directing carbon flow from photosynthesis to create a higher energy biomass. Conclusions The identification and functional annotation of differentially expressed genes open a major step towards understanding the molecular network underlying vegetative frond dormancy. Moreover, genes have been identified that could be engineered in duckweeds for practical applications easing agricultural production of food crops.
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Affiliation(s)
| | | | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ, USA.
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Kuehdorf K, Jetschke G, Ballani L, Appenroth KJ. The clonal dependence of turion formation in the duckweed Spirodela polyrhiza--an ecogeographical approach. PHYSIOLOGIA PLANTARUM 2014; 150:46-54. [PMID: 23621650 DOI: 10.1111/ppl.12065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 05/13/2023]
Abstract
Formation of turions, the vegetative perennation organs, plays an important role in the survival strategy of Spirodela polyrhiza (L.) Schleiden. Turion formation [quantified as number of turions formed per frond; specific turion yield (SY)] was investigated in 27 clones collected from a wide geographical range. The Pearson correlation was tested with (1) duration of growing season (monthly average temperature of ≥10°C), (2) relative growth rate of the fronds, (3) longitude and latitude, and (4) several climatic parameters, in all possible single and multiple regressions. All single coefficients of determination were below 0.10. The highest correlation (R(2) = 0.61; adjusted for the number of explaining variables 0.54) was found in a multiple linear regression with the following five parameters: average temperatures over the year and during the growing season, duration of the growing season and precipitation over the year and during the growth period. All these parameters were shown to have significant contributions. This equation was used successfully to predict the SY of five newly isolated clones. Finally, on the basis of all 32 clones the following conclusions were drawn: The mean annual temperature has the highest impact. It is suggested that lower temperatures decrease the survival rate of turions and that adaptation refers to increasing SY. The different levels of SY in the clones (ranging from SY = 0.22 to 5.9) were detected even after several years of in vitro cultivation. It is therefore assumed that these adaptations to the climatic conditions are genetically determined.
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Affiliation(s)
- Katja Kuehdorf
- University of Jena, Institute of Plant Physiology, Jena, Germany
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