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Li M, Boisson-Dernier A, Bertoldi D, Ardini F, Larcher R, Grotti M, Varotto C. Elucidation of arsenic detoxification mechanism in Marchantia polymorpha: The role of ACR3. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134088. [PMID: 38555672 DOI: 10.1016/j.jhazmat.2024.134088] [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: 01/18/2024] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
The arsenic-specific ACR3 transporter plays pivotal roles in As detoxification in yeast and a group of ancient tracheophytes, the ferns. Despite putative ACR3 genes being present in the genomes of bryophytes, whether they have the same relevance also in this lineage is currently unknown. In this study, we characterized the MpACR3 gene from the bryophyte Marchantia polymorpha L. through a multiplicity of functional approaches ranging from phylogenetic reconstruction, expression analysis, loss- and gain-of-function as well as genetic complementation with an MpACR3 gene tagged with a fluorescent protein. Genetic complementation demonstrates that MpACR3 plays a pivotal role in As tolerance in M. polymorpha, with loss-of-function Mpacr3 mutants being hypersensitive and MpACR3 overexpressors more tolerant to As. Additionally, MpACR3 activity regulates intracellular As concentration, affects its speciation and controls the levels of intracellular oxidative stress. The MpACR3::3xCitrine appears to localize at the plasma membrane and possibly in other endomembrane systems. Taken together, these results demonstrate the pivotal function of ACR3 detoxification in both sister lineages of land plants, indicating that it was present in the common ancestor to all embryophytes. We propose that Mpacr3 mutants could be used in developing countries as low-cost and low-technology visual bioindicators to detect As pollution in water.
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Affiliation(s)
- Mingai Li
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, San Michele all'Adige, 38098 Trento, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| | - Aurélien Boisson-Dernier
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 400 Route des Chappes, BP167, 06903 Sophia Antipolis Cedex, France
| | - Daniela Bertoldi
- Department of Food and Transformation, Technology Transfer Centre of Fondazione Edmund Mach, E. Mach 1, San Michele all'Adige, 38098 TN, Italy
| | - Francisco Ardini
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, Genoa, Italy
| | - Roberto Larcher
- Department of Food and Transformation, Technology Transfer Centre of Fondazione Edmund Mach, E. Mach 1, San Michele all'Adige, 38098 TN, Italy
| | - Marco Grotti
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, Genoa, Italy
| | - Claudio Varotto
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, San Michele all'Adige, 38098 Trento, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
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2
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Smith KE, Zhou M, Flis P, Jones DH, Bishopp A, Yant L. The evolution of the duckweed ionome mirrors losses in structural complexity. ANNALS OF BOTANY 2024; 133:997-1006. [PMID: 38307008 PMCID: PMC11089258 DOI: 10.1093/aob/mcae012] [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: 12/14/2023] [Accepted: 02/03/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND AND AIMS The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown. METHODS We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. KEY RESULTS We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale. CONCLUSIONS These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.
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Affiliation(s)
- Kellie E Smith
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Min Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Paulina Flis
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Dylan H Jones
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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3
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Smith KE, Cowan L, Taylor B, McAusland L, Heatley M, Yant L, Murchie EH. Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2046-2063. [PMID: 38217537 DOI: 10.1093/jxb/erad499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.
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Affiliation(s)
- Kellie E Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Beth Taylor
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Lorna McAusland
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Matthew Heatley
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Erik H Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
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Li Q, Lan Y, Yang Y, Kang S, Wang X, Jiang J, Liu S, Wang Q, Zhang W, Zhang L. Effect of luminescent materials on the biochemistry, ultrastructure, and rhizobial microbiota of Spirodela polyrhiza. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108427. [PMID: 38367389 DOI: 10.1016/j.plaphy.2024.108427] [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: 11/04/2023] [Revised: 01/13/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024]
Abstract
Fluorescent materials and technologies have become widely used in scientific research, and due to the ability to convert light wavelengths, their application to photosynthetic organisms can affect their development by altering light quality. However, the impacts of fluorescent materials on aquatic plants and their environmental risks remain unclear. To assess the effects of luminescent materials on floating aquatic macrophytes and their rhizosphere microorganisms, 4-(di-p-tolylamino)benzaldehyde-A (DTB-A) and 4-(di-p-tolylamino)benzaldehyde-M (DTB-M) (emitting blue-green and orange-red light, respectively) were added individually and jointly to Spirodela polyrhiza cultures and set at different concentrations (1, 10, and 100 μM). Both DTB-A and DTB-M exhibited phytotoxicity, which increased with concentration under separate treatment. Moreover, the combined group exhibited obvious stress relief at 10 μM compared to the individually treated group. Fluorescence imaging showed that DTB-A and DTB-M were able to enter the cell matrix and organelles of plant leaves and roots. Peroxidation induced cellular damage, contributing to a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities and malondialdehyde (MDA) accumulation. Decomposition of organelle structures, starch accumulation in chloroplasts, and plasmolysis were observed under the ultrastructure, disrupting photosynthetic pigment content and photosynthesis. DTB-A and DTB-M exposure resulted in growth inhibition, dry weight loss, and leaf yellowing in S. polyrhiza. A total of 3519 Operational Taxonomic Units (OTUs) were identified in the rhizosphere microbiome. The microbial communities were dominated by Alphaproteobacteria, Oxyphotobacteria, and Gammaproteobacteria, with the abundance and diversity varied significantly among treatment groups according to Shannon, Simpson, and Chao1 indices. This study revealed the stress defense response of S. polyrhiza to DTB-A and DTB-M exposures, which provides a broader perspective for the bioremediation of pollutants using aquatic plants and supports the further development of fluorescent materials for applications.
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Affiliation(s)
- Qi Li
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China.
| | - Yiyang Lan
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Yixia Yang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Shiyun Kang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Xin Wang
- The Chinese University of Hong Kong, Shenzhen, 518172, PR China
| | - Jiarui Jiang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Shengyue Liu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | | | - Weizhen Zhang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Liping Zhang
- The Chinese University of Hong Kong, Shenzhen, 518172, PR China.
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5
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Subbaraman B, de Lange O, Ferguson S, Peek N. The Duckbot: A system for automated imaging and manipulation of duckweed. PLoS One 2024; 19:e0296717. [PMID: 38261570 PMCID: PMC10805289 DOI: 10.1371/journal.pone.0296717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 01/25/2024] Open
Abstract
Laboratory automation can boost precision and reproducibility of science workflows. However, current laboratory automation systems are difficult to modify for custom applications. Automating new experiment workflows therefore requires development of one-off research platforms, a process which requires significant time, resources, and experience. In this work, we investigate systems to lower the threshold to automation for plant biologists. Our approach establishes a direct connection with a generic motion platform to support experiment development and execution from a computational notebook environment. Specifically, we investigate the use of the open-source tool-changing motion platform Jubilee controlled using Jupyter notebooks. We present the Duckbot, a machine customized for automating laboratory research workflows with duckweed, a common multicellular plant. The Duckbot comprises (1) a set of end-effectors relevant for plant biology, (2) software modules which provide flexible control of these tools, and (3) computational notebooks which make use of these tools to automate duckweed experiments. We demonstrate the Duckbot's functionality by automating a particular laboratory research workflow, namely, duckweed growth assays. The Duckbot supports setting up sample plates with duckweed and growth media, gathering image data, and conducting relevant data analysis. We discuss the opportunities and limitations for developing custom laboratory automation with this platform and provide instructions on usage and customization.
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Affiliation(s)
- Blair Subbaraman
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Orlando de Lange
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
- Biology Department, Shoreline Community College, Shoreline, Washington, United States of America
| | - Sam Ferguson
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Nadya Peek
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
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Popržen T, Nikolić I, Krstić-Milošević D, Uzelac B, Trifunović-Momčilov M, Marković M, Radulović O. Characterization of the IAA-Producing and -Degrading Pseudomonas Strains Regulating Growth of the Common Duckweed ( Lemna minor L.). Int J Mol Sci 2023; 24:17207. [PMID: 38139036 PMCID: PMC10742903 DOI: 10.3390/ijms242417207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
The rhizosphere represents a center of complex and dynamic interactions between plants and microbes, resulting in various positive effects on plant growth and development. However, less is known about the effects of indole-3-acetic acid (IAA) on aquatic plants. In this study, we report the characterization of four Pseudomonas strains isolated from the rhizosphere of the common duckweed (Lemna minor) with IAA-degradation and -utilization ability. Our results confirm previous reports on the negative effect of IAA on aquatic plants, contrary to the effect on terrestrial plants. P. putida A3-104/5 demonstrated particularly beneficial traits, as it exhibited not only IAA-degrading and -producing activity but also a positive effect on the doubling time of duckweeds in the presence of IAA, positive chemotaxis in the presence of IAA, increased tolerance to oxidative stress in the presence of IAA and increased biofilm formation related to IAA. Similarly, P. gessardii C31-106/3 significantly shortened the doubling time of duckweeds in the presence of IAA, while having a neutral effect in the absence of IAA. These traits are important in the context of plant-bacteria interactions and highlight the role of IAA as a common metabolite in these interactions, especially in aquatic environments where plants are facing unique challenges compared to their terrestrial counterparts. We conclude that IAA-degrading and -producing strains presented in this study might regulate IAA effects on aquatic plants and confer evolutionary benefits under adverse conditions (e.g., under oxidative stress, excess of IAA or nutrient scarcity).
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Affiliation(s)
- Tatjana Popržen
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Ivan Nikolić
- Center for Biological Control and Plant Growth Promotion, Faculty of Biology, University of Belgrade, 16 Studentski Trg Street, 11000 Belgrade, Serbia;
| | - Dijana Krstić-Milošević
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Branka Uzelac
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Milana Trifunović-Momčilov
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Marija Marković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
| | - Olga Radulović
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana Street, 11060 Belgrade, Serbia; (T.P.); (D.K.-M.); (B.U.); (M.T.-M.); (M.M.)
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7
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Clark JW. Genome evolution in plants and the origins of innovation. THE NEW PHYTOLOGIST 2023; 240:2204-2209. [PMID: 37658677 DOI: 10.1111/nph.19242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.
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Affiliation(s)
- James W Clark
- School of Biological Sciences, University of Bristol, Tyndall Ave, Bristol, BS8 1TQ, UK
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8
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Liu L, Trendel J, Jiang G, Liu Y, Bruckmann A, Küster B, Sprunck S, Dresselhaus T, Bleckmann A. RBPome identification in egg-cell like callus of Arabidopsis. Biol Chem 2023; 404:1137-1149. [PMID: 37768858 DOI: 10.1515/hsz-2023-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.
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Affiliation(s)
- Liping Liu
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Guojing Jiang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Yanhui Liu
- College of Life Science, Longyan University, Longyan 364012, China
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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