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Nelson DR, Mystikou A, Jaiswal A, Rad-Menendez C, Preston MJ, De Boever F, El Assal DC, Daakour S, Lomas MW, Twizere JC, Green DH, Ratcliff WC, Salehi-Ashtiani K. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. MOLECULAR PLANT 2024; 17:747-771. [PMID: 38614077 DOI: 10.1016/j.molp.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.
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Affiliation(s)
- David R Nelson
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE; Biotechnology Research Center, Technology Innovation Institute, PO Box 9639, Masdar City, Abu Dhabi, UAE.
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Cecilia Rad-Menendez
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frederik De Boever
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jean-Claude Twizere
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - David H Green
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
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Rapin MN, Murray L, Sadler IH, Bothwell JH, Fry SC. Same but different - pseudo-pectin in the charophytic alga Chlorokybus atmophyticus. PHYSIOLOGIA PLANTARUM 2023; 175:e14079. [PMID: 38148229 PMCID: PMC10953000 DOI: 10.1111/ppl.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 12/28/2023]
Abstract
All land-plant cell walls possess hemicelluloses, cellulose and anionic pectin. The walls of their cousins, the charophytic algae, exhibit some similarities to land plants' but also major differences. Charophyte 'pectins' are extractable by conventional land-plant methods, although they differ significantly in composition. Here, we explore 'pectins' of an early-diverging charophyte, Chlorokybus atmophyticus, characterising the anionic polysaccharides that may be comparable to 'pectins' in other streptophytes. Chlorokybus 'pectin' was anionic and upon acid hydrolysis gave GlcA, GalA and sulphate, plus neutral sugars (Ara≈Glc>Gal>Xyl); Rha was undetectable. Most Gal was the l-enantiomer. A relatively acid-resistant disaccharide was characterised as β-d-GlcA-(1→4)-l-Gal. Two Chlorokybus 'pectin' fractions, separable by anion-exchange chromatography, had similar sugar compositions but different sulphate-ester contents. No sugars were released from Chlorokybus 'pectin' by several endo-hydrolases [(1,5)-α-l-arabinanase, (1,4)-β-d-galactanase, (1,4)-β-d-xylanase, endo-polygalacturonase] and exo-hydrolases [α- and β-d-galactosidases, α-(1,6)-d-xylosidase]. 'Driselase', which hydrolyses most land-plant cell wall polysaccharides to mono- and disaccharides, released no sugars except traces of starch-derived Glc. Thus, the Ara, Gal, Xyl and GalA of Chlorokybus 'pectin' were not non-reducing termini with configurations familiar from land-plant polysaccharides (α-l-Araf, α- and β-d-Galp, α- and β-d-Xylp and α-d-GalpA), nor mid-chain residues of α-(1→5)-l-arabinan, β-(1→4)-d-galactan, β-(1→4)-d-xylan or α-(1→4)-d-galacturonan. In conclusion, Chlorokybus possesses anionic 'pectic' polysaccharides, possibly fulfilling pectic roles but differing fundamentally from land-plant pectin. Thus, the evolution of land-plant pectin since the last common ancestor of Chlorokybus and land plants is a long and meandering path involving loss of sulphate, most l-Gal and most d-GlcA; re-configuration of Ara, Xyl and GalA; and gain of Rha.
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Affiliation(s)
- Marie N. Rapin
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
| | - Lorna Murray
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | - Ian H. Sadler
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | | | - Stephen C. Fry
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
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León-Ruiz JA, Cruz Ramírez A. Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1507-1524. [PMID: 36305297 DOI: 10.1111/tpj.16012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 05/16/2023]
Abstract
The colonization of land by a single streptophyte algae lineage some 450 million years ago has been linked to multiple key innovations such as three-dimensional growth, alternation of generations, the presence of stomata, as well as innovations inherent to the birth of major plant lineages, such as the origins of vascular tissues, roots, seeds and flowers. Multicellularity, which evolved multiple times in the Chloroplastida coupled with precise spatiotemporal control of proliferation and differentiation were instrumental for the evolution of these traits. RETINOBLASTOMA-RELATED (RBR), the plant homolog of the metazoan Retinoblastoma protein (pRB), is a highly conserved and multifunctional core cell cycle regulator that has been implicated in the evolution of multicellularity in the green lineage as well as in plant multicellularity-related processes such as proliferation, differentiation, stem cell regulation and asymmetric cell division. RBR fulfills these roles through context-specific protein-protein interactions with proteins containing the Leu-x-Cys-x-Glu (LxCxE) short-linear motif (SLiM); however, how RBR-LxCxE interactions have changed throughout major innovations in the Viridiplantae kingdom is a question that remains unexplored. Here, we employ an in silico evo-devo approach to predict and analyze potential RBR-LxCxE interactions in different representative species of key Chloroplastida lineages, providing a valuable resource for deciphering RBR-LxCxE multiple functions. Furthermore, our analyses suggest that RBR-LxCxE interactions are an important component of RBR functions and that interactions with chromatin modifiers/remodelers, DNA replication and repair machinery are highly conserved throughout the Viridiplantae, while LxCxE interactions with transcriptional regulators likely diversified throughout the water-to-land transition.
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Affiliation(s)
- Jesús A León-Ruiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
| | - Alfredo Cruz Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
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Thiriet-Rupert S, Gain G, Jadoul A, Vigneron A, Bosman B, Carnol M, Motte P, Cardol P, Nouet C, Hanikenne M. Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas. PLANT PHYSIOLOGY 2021; 187:1653-1678. [PMID: 34618070 PMCID: PMC8566208 DOI: 10.1093/plphys/kiab375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/17/2021] [Indexed: 05/06/2023]
Abstract
Increasing industrial and anthropogenic activities are producing and releasing more and more pollutants in the environment. Among them, toxic metals are one of the major threats for human health and natural ecosystems. Because photosynthetic organisms play a critical role in primary productivity and pollution management, investigating their response to metal toxicity is of major interest. Here, the green microalga Chlamydomonas (Chlamydomonas reinhardtii) was subjected to short (3 d) or chronic (6 months) exposure to 50 µM cadmium (Cd), and the recovery from chronic exposure was also examined. An extensive phenotypic characterization and transcriptomic analysis showed that the impact of Cd on biomass production of short-term (ST) exposed cells was almost entirely abolished by long-term (LT) acclimation. The underlying mechanisms were initiated at ST and further amplified after LT exposure resulting in a reversible equilibrium allowing biomass production similar to control condition. This included modification of cell wall-related gene expression and biofilm-like structure formation, dynamics of metal ion uptake and homeostasis, photosynthesis efficiency recovery and Cd acclimation through metal homeostasis adjustment. The contribution of the identified coordination of phosphorus and iron homeostasis (partly) mediated by the main phosphorus homeostasis regulator, Phosphate Starvation Response 1, and a basic Helix-Loop-Helix transcription factor (Cre05.g241636) was further investigated. The study reveals the highly dynamic physiological plasticity enabling algal cell growth in an extreme environment.
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Affiliation(s)
- Stanislas Thiriet-Rupert
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
- Present address: Unité de Génétique des Biofilms, Département Microbiologie, Institut Pasteur, Paris, France
| | - Gwenaëlle Gain
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, 4000 Liège, Belgium
| | - Alice Jadoul
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Amandine Vigneron
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Bernard Bosman
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, 4000 Liège, Belgium
| | - Monique Carnol
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, 4000 Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Pierre Cardol
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, 4000 Liège, Belgium
| | - Cécile Nouet
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
- Author for communication:
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Wang M, Yuan WQ, Chen S, Wang L, Zhao S, Li S. Algal Lysis by Sagittula stellata for the Production of Intracellular Valuables. Appl Biochem Biotechnol 2021; 193:2516-2533. [PMID: 33779932 DOI: 10.1007/s12010-021-03502-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/07/2021] [Indexed: 01/10/2023]
Abstract
The purpose of this study was to examine the efficacy of the algicidal bacterium Sagittula stellata on the cell lysis of Nannochloropsis oceanica, a microalga found in the marine environment, in order to extract intracellular valuables. Algicidal bacteria are capable of lysing algal cell walls while keeping lipids and proteins intact yet separated. We obtained these microbes from locations with consistent algae blooms and found that the bacterium Sagittula stellata displayed significant algicidal properties toward Nannochloropsis oceanica, achieving an algicidal rate of 80.1%. We detected a decrease of 66.2% in in vivo fluorescence intensity in algae cultures, obtained a recoverable crude lipid content of 23.3% and a polyunsaturated fatty acid (PUFA) ratio of 29.0% of bacteria-treated algae, and observed the lysis of the cell membrane and the structure of the nucleus of algae. We also identified the inhibited transcription of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene and proliferating cell nuclear antigen (PCNA)-related genes and the upregulated heat shock protein (hsp) gene in algal cells during bacterial exposure. Our results indicate that Sagittula stellata effectively lysed microalgae cells, allowing the recovery of intracellular valuables. The algicidal method of Sagittula stellata on Nannochloropsis oceanica cells was confirmed to be a direct attack (or predation), followed by an indirect attack through the secretion of extracellular algicidal compounds. This study provides an important framework for the broad application of algicidal microorganisms in algal cell disruption and the production of intracellular valuables.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Wen Qiao Yuan
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
| | - Lifu Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Shuwen Zhao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Shanshan Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
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González-Hourcade M, Del Campo EM, Casano LM. The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms. MICROBIAL ECOLOGY 2021; 81:437-453. [PMID: 32989484 DOI: 10.1007/s00248-020-01604-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.
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Affiliation(s)
| | - Eva M Del Campo
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain.
| | - Leonardo M Casano
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
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Krishnan S, Ghani NA, Aminuddin NF, Quraishi KS, Azman NS, Cravotto G, Leveque JM. Microwave-assisted lipid extraction from Chlorella vulgaris in water with 0.5%–2.5% of imidazolium based ionic liquid as additive. RENEWABLE ENERGY 2020; 149:244-252. [DOI: 10.1016/j.renene.2019.12.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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10
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Keeling PJ. Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190085. [PMID: 31587641 DOI: 10.1098/rstb.2019.0085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z4
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11
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Warren SD, Clair LL, Stark LR, Lewis LA, Pombubpa N, Kurbessoian T, Stajich JE, Aanderud ZT. Reproduction and Dispersal of Biological Soil Crust Organisms. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00344] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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12
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Evolution of the Auxin Response Factors from charophyte ancestors. PLoS Genet 2019; 15:e1008400. [PMID: 31553720 PMCID: PMC6797205 DOI: 10.1371/journal.pgen.1008400] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/17/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Auxin is a major developmental regulator in plants and the acquisition of a transcriptional response to auxin likely contributed to developmental innovations at the time of water-to-land transition. Auxin Response Factors (ARFs) Transcription Factors (TFs) that mediate auxin-dependent transcriptional changes are divided into A, B and C evolutive classes in land plants. The origin and nature of the first ARF proteins in algae is still debated. Here, we identify the most ‘ancient’ ARF homologue to date in the early divergent charophyte algae Chlorokybus atmophyticus, CaARF. Structural modelling combined with biochemical studies showed that CaARF already shares many features with modern ARFs: it is capable of oligomerization, interacts with the TOPLESS co-repressor and specifically binds Auxin Response Elements as dimer. In addition, CaARF possesses a DNA-binding specificity that differs from class A and B ARFs and that was maintained in class C ARF along plants evolution. Phylogenetic evidence together with CaARF biochemical properties indicate that the different classes of ARFs likely arose from an ancestral proto-ARF protein with class C-like features. The foundation of auxin signalling would have thus happened from a pre-existing hormone-independent transcriptional regulation together with the emergence of a functional hormone perception complex. Plants transition from water to land was determining for the history of our planet, since it led to atmospheric and soil condition changes that promoted the appearance of other life forms. This transition initiated around 1 billion years ago from a Charophyte algae lineage that acquired features allowing it to adapt to the very different terrestrial conditions. Land plants coordinate their development with external stimuli through signalling mechanisms triggered by plant hormones. Therefore, evolution of these molecules and their signalling pathways likely played an important role in the aquatic to terrestrial move. In this manuscript we study the origin of auxin signalling, a plant hormone implicated in all plant developmental steps. Our studies suggest that out of the three families of proteins originally proposed to trigger auxin signalling in land plants, only one existed in Charophyte ancestors as a likely transcriptional repressor independent of auxin. We show that despite millions of years of evolution, this family of proteins has conserved its biochemical and structural properties that are found today in land plants. The results presented here provide an insight on how hormone signalling pathways could have evolved by co-opting a pre-existing hormone-independent transcriptional regulatory mechanism.
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Polysaccharide associated protein (PSAP) from the green microalga Botryococcus braunii is a unique extracellular matrix hydroxyproline-rich glycoprotein. ALGAL RES 2018. [DOI: 10.1016/j.algal.2017.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Joo S, Nishimura Y, Cronmiller E, Hong RH, Kariyawasam T, Wang MH, Shao NC, El Akkad SED, Suzuki T, Higashiyama T, Jin E, Lee JH. Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2017; 175:314-332. [PMID: 28710131 PMCID: PMC5580766 DOI: 10.1104/pp.17.00731] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/12/2017] [Indexed: 05/20/2023]
Abstract
The sexual cycle of the unicellular Chlamydomonas reinhardtii culminates in the formation of diploid zygotes that differentiate into dormant spores that eventually undergo meiosis. Mating between gametes induces rapid cell wall shedding via the enzyme g-lysin; cell fusion is followed by heterodimerization of sex-specific homeobox transcription factors, GSM1 and GSP1, and initiation of zygote-specific gene expression. To investigate the genetic underpinnings of the zygote developmental pathway, we performed comparative transcriptome analysis of both pre- and post-fertilization samples. We identified 253 transcripts specifically enriched in early zygotes, 82% of which were not up-regulated in gsp1 null zygotes. We also found that the GSM1/GSP1 heterodimer negatively regulates the vegetative wall program at the posttranscriptional level, enabling prompt transition from vegetative wall to zygotic wall assembly. Annotation of the g-lysin-induced and early zygote genes reveals distinct vegetative and zygotic wall programs, supported by concerted up-regulation of genes encoding cell wall-modifying enzymes and proteins involved in nucleotide-sugar metabolism. The haploid-to-diploid transition in Chlamydomonas is masterfully controlled by the GSM1/GSP1 heterodimer, translating fertilization and gamete coalescence into a bona fide differentiation program. The fertilization-triggered integration of genes required to make related, but structurally and functionally distinct organelles-the vegetative versus zygote cell wall-presents a likely scenario for the evolution of complex developmental gene regulatory networks.
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Affiliation(s)
- Sunjoo Joo
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Evan Cronmiller
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Ran Ha Hong
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Thamali Kariyawasam
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Ming Hsiu Wang
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Nai Chun Shao
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Saif-El-Din El Akkad
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Takamasa Suzuki
- ERATO, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- ERATO, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Eonseon Jin
- Department Life Sciences, Research Institute for Natural Sciences, Hanyang University, 222 Wangsipri-ro, Sungdong-gu, Seoul 133-791, Republic of Korea
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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15
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In situ monitoring of molecular changes during cell differentiation processes in marine macroalgae through mass spectrometric imaging. Anal Bioanal Chem 2017; 409:4893-4903. [PMID: 28600691 DOI: 10.1007/s00216-017-0430-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/15/2017] [Accepted: 05/24/2017] [Indexed: 10/19/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) was employed to discriminate between cell differentiation processes in macroalgae. One of the key developmental processes in the algal life cycle is the production of germ cells (gametes and zoids). The gametogenesis of the marine green macroalga Ulva mutabilis (Chlorophyta) was monitored by metabolomic snapshots of the surface, when blade cells differentiate synchronously into gametangia and giving rise to gametes. To establish MSI for macroalgae, dimethylsulfoniopropionate (DMSP), a known algal osmolyte, was determined. MSI of the surface of U. mutabilis followed by chemometric data analysis revealed dynamic metabolomic changes during cell differentiation. DMSP and a total of 55 specific molecular biomarkers, which could be assigned to important stages of the gametogenesis, were detected. Our research contributes to the understanding of molecular mechanisms underlying macroalgal cell differentiation. Graphical abstract Molecular changes during cell differentiation of the marine macroalga Ulva were visualized by matrix assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI).
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Mravec J, Guo X, Hansen AR, Schückel J, Kračun SK, Mikkelsen MD, Mouille G, Johansen IE, Ulvskov P, Domozych DS, Willats WGT. Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics. PLANT PHYSIOLOGY 2017; 174:1051-1066. [PMID: 28400496 PMCID: PMC5462005 DOI: 10.1104/pp.16.00097] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/06/2017] [Indexed: 05/21/2023]
Abstract
The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases, though, plant cells are programmed to detach, and root cap-derived border cells are examples of this. Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immunocarbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy, quantitative reverse transcription-PCR of cell wall biosynthetic genes, analysis of hydrolytic activities, transmission electron microscopy, and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our findings provide a new level of detail about border cell maturation and enable us to develop a model of the separation process. We propose that loss of adhesion by the dissolution of homogalacturonan in the middle lamellae is augmented by an active biophysical process of cell curvature driven by the polarized distribution of xyloglucan and extensin epitopes.
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Affiliation(s)
- Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.);
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.);
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Aleksander Riise Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Julia Schückel
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Stjepan Krešimir Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Maria Dalgaard Mikkelsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Grégory Mouille
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - David S Domozych
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - William George Tycho Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.);
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.);
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
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Holzinger A, Pichrtová M. Abiotic Stress Tolerance of Charophyte Green Algae: New Challenges for Omics Techniques. FRONTIERS IN PLANT SCIENCE 2016; 7:678. [PMID: 27242877 PMCID: PMC4873514 DOI: 10.3389/fpls.2016.00678] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/02/2016] [Indexed: 05/20/2023]
Abstract
Charophyte green algae are a paraphyletic group of freshwater and terrestrial green algae, comprising the classes of Chlorokybophyceae, Coleochaetophyceae, Klebsormidiophyceae, Zygnematophyceae, Mesostigmatophyceae, and Charo- phyceae. Zygnematophyceae (Conjugating green algae) are considered to be closest algal relatives to land plants (Embryophyta). Therefore, they are ideal model organisms for studying stress tolerance mechanisms connected with transition to land, one of the most important events in plant evolution and the Earth's history. In Zygnematophyceae, but also in Coleochaetophyceae, Chlorokybophyceae, and Klebsormidiophyceae terrestrial members are found which are frequently exposed to naturally occurring abiotic stress scenarios like desiccation, freezing and high photosynthetic active (PAR) as well as ultraviolet (UV) irradiation. Here, we summarize current knowledge about various stress tolerance mechanisms including insight provided by pioneer transcriptomic and proteomic studies. While formation of dormant spores is a typical strategy of freshwater classes, true terrestrial groups are stress tolerant in vegetative state. Aggregation of cells, flexible cell walls, mucilage production and accumulation of osmotically active compounds are the most common desiccation tolerance strategies. In addition, high photophysiological plasticity and accumulation of UV-screening compounds are important protective mechanisms in conditions with high irradiation. Now a shift from classical chemical analysis to next-generation genome sequencing, gene reconstruction and annotation, genome-scale molecular analysis using omics technologies followed by computer-assisted analysis will give new insights in a systems biology approach. For example, changes in transcriptome and role of phytohormone signaling in Klebsormidium during desiccation were recently described. Application of these modern approaches will deeply enhance our understanding of stress reactions in an unbiased non-targeted view in an evolutionary context.
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Affiliation(s)
- Andreas Holzinger
- Unit of Functional Plant Biology, Institute of Botany, University of Innsbruck, InnsbruckAustria
- *Correspondence: Andreas Holzinger,
| | - Martina Pichrtová
- Unit of Functional Plant Biology, Institute of Botany, University of Innsbruck, InnsbruckAustria
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