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Lindsey CR, Rosenzweig F, Herron MD. Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae. BMC Biol 2021; 19:182. [PMID: 34465312 PMCID: PMC8408923 DOI: 10.1186/s12915-021-01087-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. RESULTS We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. CONCLUSIONS Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.
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Affiliation(s)
- Charles Ross Lindsey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, USA
| | - Matthew D Herron
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Pan L, Fonseca De Lima CF, Vu LD, De Smet I. A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. FRONTIERS IN PLANT SCIENCE 2021; 12:650171. [PMID: 34484252 PMCID: PMC8415026 DOI: 10.3389/fpls.2021.650171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.
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Affiliation(s)
- Lixia Pan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca De Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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de Vries S, Fürst-Jansen JMR, Irisarri I, Dhabalia Ashok A, Ischebeck T, Feussner K, Abreu IN, Petersen M, Feussner I, de Vries J. The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:975-1002. [PMID: 34165823 DOI: 10.1111/tpj.15387] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 05/20/2023]
Abstract
Land plants constantly respond to fluctuations in their environment. Part of their response is the production of a diverse repertoire of specialized metabolites. One of the foremost sources for metabolites relevant to environmental responses is the phenylpropanoid pathway, which was long thought to be a land-plant-specific adaptation shaped by selective forces in the terrestrial habitat. Recent data have, however, revealed that streptophyte algae, the algal relatives of land plants, have candidates for the genetic toolkit for phenylpropanoid biosynthesis and produce phenylpropanoid-derived metabolites. Using phylogenetic and sequence analyses, we here show that the enzyme families that orchestrate pivotal steps in phenylpropanoid biosynthesis have independently undergone pronounced radiations and divergence in multiple lineages of major groups of land plants; sister to many of these radiated gene families are streptophyte algal candidates for these enzymes. These radiations suggest a high evolutionary versatility in the enzyme families involved in the phenylpropanoid-derived metabolism across embryophytes. We suggest that this versatility likely translates into functional divergence, and may explain the key to one of the defining traits of embryophytes: a rich specialized metabolism.
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Affiliation(s)
- Sophie de Vries
- Population Genetics, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Ilka N Abreu
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtsr. 1, 37077, Goettingen, Germany
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Role and Evolution of the Extracellular Matrix in the Acquisition of Complex Multicellularity in Eukaryotes: A Macroalgal Perspective. Genes (Basel) 2021; 12:genes12071059. [PMID: 34356075 PMCID: PMC8307928 DOI: 10.3390/genes12071059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Multicellular eukaryotes are characterized by an expanded extracellular matrix (ECM) with a diversified composition. The ECM is involved in determining tissue texture, screening cells from the outside medium, development, and innate immunity, all of which are essential features in the biology of multicellular eukaryotes. This review addresses the origin and evolution of the ECM, with a focus on multicellular marine algae. We show that in these lineages the expansion of extracellular matrix played a major role in the acquisition of complex multicellularity through its capacity to connect, position, shield, and defend the cells. Multiple innovations were necessary during these evolutionary processes, leading to striking convergences in the structures and functions of the ECMs of algae, animals, and plants.
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Petroll R, Schreiber M, Finke H, Cock JM, Gould SB, Rensing SA. Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity. Genes (Basel) 2021; 12:1055. [PMID: 34356071 PMCID: PMC8304369 DOI: 10.3390/genes12071055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Red algae (Rhodophyta) belong to the superphylum Archaeplastida, and are a species-rich group exhibiting diverse morphologies. Theory has it that the unicellular red algal ancestor went through a phase of genome contraction caused by adaptation to extreme environments. More recently, the classes Porphyridiophyceae, Bangiophyceae, and Florideophyceae experienced genome expansions, coinciding with an increase in morphological complexity. Transcription-associated proteins (TAPs) regulate transcription, show lineage-specific patterns, and are related to organismal complexity. To better understand red algal TAP complexity and evolution, we investigated the TAP family complement of uni- and multi-cellular red algae. We found that the TAP family complement correlates with gain of morphological complexity in the multicellular Bangiophyceae and Florideophyceae, and that abundance of the C2H2 zinc finger transcription factor family may be associated with the acquisition of morphological complexity. An expansion of heat shock transcription factors (HSF) occurred within the unicellular Cyanidiales, potentially as an adaption to extreme environmental conditions.
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Affiliation(s)
- Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; (R.P.); (M.S.); (H.F.); (S.B.G.)
| | - Mona Schreiber
- Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; (R.P.); (M.S.); (H.F.); (S.B.G.)
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Hermann Finke
- Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; (R.P.); (M.S.); (H.F.); (S.B.G.)
| | - J. Mark Cock
- Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, CNRS, UPMC University Paris 06, CS 90074, 29688 Roscoff, France;
| | - Sven B. Gould
- Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; (R.P.); (M.S.); (H.F.); (S.B.G.)
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; (R.P.); (M.S.); (H.F.); (S.B.G.)
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79108 Freiburg, Germany
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56
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Blomme J, Liu X, Jacobs TB, De Clerck O. A molecular toolkit for the green seaweed Ulva mutabilis. PLANT PHYSIOLOGY 2021; 186:1442-1454. [PMID: 33905515 PMCID: PMC8260120 DOI: 10.1093/plphys/kiab185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/02/2021] [Indexed: 06/02/2023]
Abstract
The green seaweed Ulva mutabilis is an ecologically important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed U. mutabilis based on a Golden Gate cloning system. The toolkit presently contains 125 entry vectors, 26 destination vectors, and 107 functionally validated expression vectors. We demonstrate the importance of endogenous regulatory sequences for transgene expression and characterize three endogenous promoters suitable to drive transgene expression. We describe two vector architectures to express transgenes via two expression cassettes or a bicistronic approach. The majority of selected transformants (50%-80%) consistently give clear visual transgene expression. Furthermore, we made different marker lines for intracellular compartments after evaluating 13 transit peptides and 11 tagged endogenous Ulva genes. Our molecular toolkit enables the study of Ulva gain-of-function lines and paves the way for gene characterization and large-scale functional genomics studies in a green seaweed.
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Affiliation(s)
- Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
| | - Xiaojie Liu
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
| | - Thomas B Jacobs
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
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57
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Cai C, Gu K, Zhao H, Steinhagen S, He P, Wichard T. Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea. PLoS One 2021; 16:e0250968. [PMID: 34061855 PMCID: PMC8168861 DOI: 10.1371/journal.pone.0250968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/18/2021] [Indexed: 11/18/2022] Open
Abstract
Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.
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Affiliation(s)
- Chuner Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Gu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Hui Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
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58
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Vallet M, Kaftan F, Grabe V, Ghaderiardakani F, Fenizia S, Svatoš A, Pohnert G, Wichard T. A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry. Beilstein J Org Chem 2021; 17:1313-1322. [PMID: 34136011 PMCID: PMC8182680 DOI: 10.3762/bjoc.17.91] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.
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Affiliation(s)
- Marine Vallet
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Filip Kaftan
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Research Group Olfactory Coding, Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Fatemeh Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany
| | - Simona Fenizia
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Georg Pohnert
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, Jena, Germany.,Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Germany
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Fort A, Linderhof C, Coca-Tagarro I, Inaba M, McHale M, Cascella K, Potin P, Guiry MD, Sulpice R. A sequencing-free assay for foliose Ulva species identification, hybrid detection and bulk biomass characterisation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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60
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Patwary ZP, Paul NA, Nishitsuji K, Campbell AH, Shoguchi E, Zhao M, Cummins SF. Application of omics research in seaweeds with a focus on red seaweeds. Brief Funct Genomics 2021; 20:148-161. [PMID: 33907795 DOI: 10.1093/bfgp/elab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/01/2023] Open
Abstract
Targeted 'omics' research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed-microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.
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Affiliation(s)
| | | | - Koki Nishitsuji
- marine genomics unit in the Okinawa Institute of Science and Technology Graduate University
| | | | - Eiichi Shoguchi
- marine genomics unit in the Okinawa Institute of Science and Technology Graduate University
| | - Min Zhao
- University of the Sunshine Coast
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Přerovská T, Henke S, Bleha R, Spiwok V, Gillarová S, Yvin JC, Ferrières V, Nguema-Ona E, Lipovová P. Arabinogalactan-like Glycoproteins from Ulva lactuca (Chlorophyta) Show Unique Features Compared to Land Plants AGPs. JOURNAL OF PHYCOLOGY 2021; 57:619-635. [PMID: 33338254 DOI: 10.1111/jpy.13121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 05/21/2023]
Abstract
Arabinogalactan proteins (AGPs) encompass a diverse group of plant cell wall proteoglycans, which play an essential role in plant development, signaling, plant-microbe interactions, and many others. Although they are widely distributed throughout the plant kingdom and extensively studied, they remain largely unexplored in the lower plants, especially in seaweeds. Ulva species have high economic potential since various applications were previously described including bioremediation, biofuel production, and as a source of bioactive compounds. This article presents the first experimental confirmation of AGP-like glycoproteins in Ulva species and provides a simple extraction protocol of Ulva lactuca AGP-like glycoproteins, their partial characterization and unique comparison to scarcely described Solanum lycopersicum AGPs. The reactivity with primary anti-AGP antibodies as well as Yariv reagent showed a great variety between Ulva lactuca and Solanum lycopersicum AGP-like glycoproteins. While the amino acid analysis of the AGP-like glycoproteins purified by the β-d-glucosyl Yariv reagent showed a similarity between algal and land plant AGP-like glycoproteins, neutral saccharide analysis revealed unique glycosylation of the Ulva lactuca AGP-like glycoproteins. Surprisingly, arabinose and galactose were not the most prevalent monosaccharides and the most outstanding was the presence of 3-O-methyl-hexose, which has never been described in the AGPs. The exceptional structure of the Ulva lactuca AGP-like glycoproteins implies a specialized adaptation to the marine environment and might bring new insight into the evolution of the plant cell wall.
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Affiliation(s)
- Tereza Přerovská
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, Univ Rennes, 35000, Rennes, France
| | - Svatopluk Henke
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Roman Bleha
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Simona Gillarová
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Jean-Claude Yvin
- Centre Mondial de l'Innovation Roullier, Laboratoire de Nutrition Végétal, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Vincent Ferrières
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, Univ Rennes, 35000, Rennes, France
| | - Eric Nguema-Ona
- Centre Mondial de l'Innovation Roullier, Laboratoire de Nutrition Végétal, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
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Bucciarelli E, Stiger-Pouvreau V, Connan S. A New Protocol Using Acidification for Preserving DMSP in Macroalgae and Comparison with Existing Protocols. JOURNAL OF PHYCOLOGY 2021; 57:689-693. [PMID: 33295639 DOI: 10.1111/jpy.13113] [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: 06/25/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) plays many important physiological and ecological roles in macroalgae. The most common method to measure DMSP is by gas chromatography analysis of the dimethylsulfide (DMS) produced after NaOH hydrolysis (pH > 12). Storage of DMS, however, is not recommended for more than a week. We investigated if acidification can be a suitable method to preserve DMSP in macroalgal samples over three months of storage, compared to widely used protocols such as drying and freezing at -20°C. The DMSP content of green (Ulva sp. and Ulva compressa), red (Chondrus crispus), and brown (Bifurcaria bifurcata) macroalgae were analyzed: 24 h after NaOH addition (control values); and after acidification (0.2 mol · L HCl-1 ) for 24 h of fresh material, followed by NaOH addition for 24 h. These values were compared to measurements after 3-month storage of samples that had been either dried in a heater (60°C for a night, and storage at room temperature), or frozen at -20°C, or kept in 0.2 mol · L HCl-1 . There was no significant difference between DMSP measurements on freshly collected material and after acidification of the samples, whether 24 h later or after 3 months of storage. This was in contrast to 3-month storage protocols involving overnight drying at 60°C (75-98% DMSP loss), and to a lesser degree freezing at -20°C (37-80% DMSP loss). We thus advise to acidify macroalgal samples for preservation over long periods of time rather than drying or freezing, when assaying DMSP content.
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Affiliation(s)
- Eva Bucciarelli
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | | | - Solène Connan
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
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63
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Hanikenne M, Esteves SM, Fanara S, Rouached H. Coordinated homeostasis of essential mineral nutrients: a focus on iron. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2136-2153. [PMID: 33175167 DOI: 10.1093/jxb/eraa483] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/13/2020] [Indexed: 05/22/2023]
Abstract
In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.
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Affiliation(s)
- Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Sara M Esteves
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Steven Fanara
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Hatem Rouached
- BPMP, Univ. Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
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64
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Resemann HC, Herrfurth C, Feussner K, Hornung E, Ostendorf AK, Gömann J, Mittag J, van Gessel N, Vries JD, Ludwig-Müller J, Markham J, Reski R, Feussner I. Convergence of sphingolipid desaturation across over 500 million years of plant evolution. NATURE PLANTS 2021; 7:219-232. [PMID: 33495556 DOI: 10.1038/s41477-020-00844-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/18/2020] [Indexed: 05/16/2023]
Abstract
For plants, acclimation to low temperatures is fundamental to survival. This process involves the modification of lipids to maintain membrane fluidity. We previously identified a new cold-induced putative desaturase in Physcomitrium (Physcomitrella) patens. Lipid profiles of null mutants of this gene lack sphingolipids containing monounsaturated C24 fatty acids, classifying the new protein as sphingolipid fatty acid denaturase (PpSFD). PpSFD mutants showed a cold-sensitive phenotype as well as higher susceptibility to the oomycete Pythium, assigning functions in stress tolerance for PpSFD. Ectopic expression of PpSFD in the Atads2.1 (acyl coenzyme A desaturase-like 2) Arabidopsis thaliana mutant functionally complemented its cold-sensitive phenotype. While these two enzymes catalyse a similar reaction, their evolutionary origin is clearly different since AtADS2 is a methyl-end desaturase whereas PpSFD is a cytochrome b5 fusion desaturase. Altogether, we suggest that adjustment of membrane fluidity evolved independently in mosses and seed plants, which diverged more than 500 million years ago.
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Affiliation(s)
- Hanno Christoph Resemann
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Cornelia Herrfurth
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
- Goettingen Metabolomics and Lipidomics Laboratory, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Kirstin Feussner
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
- Goettingen Metabolomics and Lipidomics Laboratory, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Ellen Hornung
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Anna K Ostendorf
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jasmin Gömann
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Jennifer Mittag
- Institute of Botany, Technical University Dresden, Dresden, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jan de Vries
- Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
| | | | - Jennifer Markham
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| | - Ivo Feussner
- Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.
- Goettingen Metabolomics and Lipidomics Laboratory, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.
- Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.
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Fort A, McHale M, Cascella K, Potin P, Usadel B, Guiry MD, Sulpice R. Foliose Ulva Species Show Considerable Inter-Specific Genetic Diversity, Low Intra-Specific Genetic Variation, and the Rare Occurrence of Inter-Specific Hybrids in the Wild. JOURNAL OF PHYCOLOGY 2021; 57:219-233. [PMID: 32996142 PMCID: PMC7894351 DOI: 10.1111/jpy.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/24/2020] [Accepted: 09/19/2020] [Indexed: 05/22/2023]
Abstract
Foliose Ulva spp. have become increasingly important worldwide for their environmental and financial impacts. A large number of such Ulva species have rapid reproduction and proliferation habits, which explains why they are responsible for Ulva blooms, known as "green tides", having dramatic negative effects on coastal ecosystems, but also making them attractive for aquaculture applications. Despite the increasing interest in the genus Ulva, particularly on the larger foliose species for aquaculture, their inter- and intra-specific genetic diversity is still poorly described. We compared the cytoplasmic genome (chloroplast and mitochondrion) of 110 strains of large distromatic foliose Ulva from Ireland, Brittany (France), the Netherlands and Portugal. We found six different species, with high levels of inter-specific genetic diversity, despite highly similar or overlapping morphologies. Genetic variation was as high as 82 SNPs/kb between Ulva pseudorotundata and U. laetevirens, indicating considerable genetic diversity. On the other hand, intra-specific genetic diversity was relatively low, with only 36 variant sites (0.03 SNPs/kb) in the mitochondrial genome of the 29 Ulva rigida individuals found in this study, despite different geographical origins. The use of next-generation sequencing allowed for the detection of a single inter-species hybrid between two genetically closely related species, U. laetevirens, and U. rigida, among the 110 strains analyzed in this study. Altogether, this study represents an important advance in our understanding of Ulva biology and provides genetic information for genomic selection of large foliose strains in aquaculture.
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Affiliation(s)
- Antoine Fort
- Plant Systems Biology LabRyan Institute & MaREI Centre for MarineClimate and EnergySchool of Natural SciencesNational University of Ireland ‐ GalwayGalwayH91 TK33Ireland
| | - Marcus McHale
- Plant Systems Biology LabRyan Institute & MaREI Centre for MarineClimate and EnergySchool of Natural SciencesNational University of Ireland ‐ GalwayGalwayH91 TK33Ireland
| | - Kevin Cascella
- UMR 8227Integrative Biology of Marine ModelsCNRSSorbonne Université SciencesStation Biologique de Roscoff, CS 90074F‐29688RoscoffFrance
| | - Philippe Potin
- UMR 8227Integrative Biology of Marine ModelsCNRSSorbonne Université SciencesStation Biologique de Roscoff, CS 90074F‐29688RoscoffFrance
| | - Björn Usadel
- Institute for Biology IRWTH Aachen UniversityWorringer Weg 3Aachen52074Germany
| | - Michael D. Guiry
- AlgaeBaseRyan InstituteNational University of IrelandGalwayH91 TK33Ireland
| | - Ronan Sulpice
- Plant Systems Biology LabRyan Institute & MaREI Centre for MarineClimate and EnergySchool of Natural SciencesNational University of Ireland ‐ GalwayGalwayH91 TK33Ireland
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66
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Wang Y, Liu F, Liu M, Shi S, Bi Y, Chen N. Molecular cloning and transcriptional regulation of two γ-carbonic anhydrase genes in the green macroalga Ulva prolifera. Genetica 2021; 149:63-72. [PMID: 33449239 DOI: 10.1007/s10709-020-00112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 12/06/2020] [Indexed: 12/01/2022]
Abstract
Ulva prolifera O.F. Müller (Ulvophyceae, Chlorophyta) is well known as a typical green-tide forming macroalga which has caused the world's largest macroalgal blooms in the Yellow Sea of China. In this study, two full-length γ-carbonic anhydrase (γ-CA) genes (UpγCA1 and UpγCA2) were cloned from U. prolifera. UpγCA1 has three conserved histidine residues, which act as an active site for binding a zinc metal ion. In UpγCA2, two of the three histidine residues were replaced by serine and arginine, respectively. The two γ-CA genes are clustered together with other γ-CAs in Chlorophyta with strong support value (100% bootstrap) in maximum likelihood (ML) phylogenetic tree. Quantitative real-time PCR (qRT-PCR) analysis showed that stressful environmental conditions markedly inhibited transcription levels of these two γ-CA genes. Low pH value (pH 7.5) significantly increased transcription level of UpγCA2 not UpγCA1 at 12 h, whereas high pH value (pH 8.5) significantly inhibited the transcription of these two γ-CA genes at 6 h. These findings enhanced our understanding on transcriptional regulation of γ-CA genes in response to environmental factors in U. prolifera.
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Affiliation(s)
- Yu Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, People's Republic of China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, People's Republic of China. .,Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, Shandong, People's Republic of China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266400, Shandong, People's Republic of China.
| | - Manman Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, People's Republic of China
| | - Shitao Shi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, People's Republic of China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, People's Republic of China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, Shandong, People's Republic of China.,Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, Shandong, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266400, Shandong, People's Republic of China
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67
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Bowles AMC, Paps J, Bechtold U. Evolutionary Origins of Drought Tolerance in Spermatophytes. FRONTIERS IN PLANT SCIENCE 2021; 12:655924. [PMID: 34239520 PMCID: PMC8258419 DOI: 10.3389/fpls.2021.655924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/11/2021] [Indexed: 05/19/2023]
Abstract
It is commonly known that drought stress is a major constraint limiting crop production. Drought stress and associated drought tolerance mechanisms are therefore under intense investigation with the view to future production of drought tolerant crops. With an ever-growing population and variable climate, novel approaches need to be considered to sustainably feed future generations. In this context, definitions of drought tolerance are highly variable, which poses a major challenge for the systematic assessment of this trait across the plant kingdom. Furthermore, drought tolerance is a polygenic trait and understanding the evolution of this complex trait may inform us about patterns of gene gain and loss in relation to diverse drought adaptations. We look at the transition of plants from water to land, and the role of drought tolerance in enabling this transition, before discussing the first drought tolerant plant and common drought responses amongst vascular plants. We reviewed the distribution of a combined "drought tolerance" trait in very broad terms to encompass different experimental systems and definitions used in the current literature and assigned a binary trait "tolerance vs. sensitivity" in 178 extant plant species. By simplifying drought responses of plants into this "binary" trait we were able to explore the evolution of drought tolerance across the wider plant kingdom, compared to previous studies. We show how this binary "drought tolerance/sensitivity" trait has evolved and discuss how incorporating this information into an evolutionary genomics framework could provide insights into the molecular mechanisms underlying extreme drought adaptations.
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Affiliation(s)
| | - Jordi Paps
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Ulrike Bechtold
- School of Life Sciences, University of Essex, Colchester, United Kingdom
- *Correspondence: Ulrike Bechtold,
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68
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Han L, Yang GP, Liu CY, Jin YM, Liu T. Emissions of biogenic sulfur compounds and their regulation by nutrients during an Ulva prolifera bloom in the Yellow Sea. MARINE POLLUTION BULLETIN 2021; 162:111885. [PMID: 33302126 DOI: 10.1016/j.marpolbul.2020.111885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Three cruises were conducted during an Ulva prolifera bloom in 2018 off the Qingdao coast to observe early-, late-, and after-bloom characteristics. Spatio-temporal changes in dimethylsulfide (DMS), dimethylsulphoniopropionate (DMSP), and acrylic acid (AA) and their relationships with environmental parameters were examined. Mesocosm experiments tested the effect of nutrient on the release of biogenic sulfur compounds during the decline period. Biogenic sulfur concentrations contrasted with those in non-bloom regions and reached their highest values during the late-bloom period. The average sea-to-air DMS flux was about 5 times higher than those of non-bloom regions. The mean concentrations of DMS and DMSP in the enclosures were 3-5 times those of in-situ seawater. Biogenic sulfur release was promoted by the addition of high concentrations of nutrients as U. prolifera was declining. The contribution of the U. prolifera bloom to atmospheric DMS was estimated to be 125 kg S d-1.
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Affiliation(s)
- Lu Han
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Gui-Peng Yang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chun-Ying Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Yue-Mei Jin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Tao Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
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69
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Žárský J, Žárský V, Hanáček M, Žárský V. Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split. FRONTIERS IN PLANT SCIENCE 2021; 12:735020. [PMID: 35154170 PMCID: PMC8829067 DOI: 10.3389/fpls.2021.735020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/17/2021] [Indexed: 05/05/2023]
Abstract
For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.
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Affiliation(s)
- Jakub Žárský
- CryoEco Research Group, Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Jakub Žárský,
| | - Vojtěch Žárský
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Martin Hanáček
- Polar-Geo-Lab, Department of Geography, Faculty of Science, Masaryk University, Brno, Czechia
- Regional Museum in Jeseník, Jeseník, Czechia
| | - Viktor Žárský
- Laboratory of Cell Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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70
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Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet 2020; 36:915-925. [DOI: 10.1016/j.tig.2020.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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de Vries J, Ischebeck T. Ties between Stress and Lipid Droplets Pre-date Seeds. TRENDS IN PLANT SCIENCE 2020; 25:1203-1214. [PMID: 32921563 DOI: 10.1016/j.tplants.2020.07.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 05/12/2023]
Abstract
Seeds were a key evolutionary innovation. These durable structures provide a concerted solution to two challenges on land: dispersal and stress. Lipid droplets (LDs) that act as nutrient storage reservoirs are one of the main cell-biological reasons for seed endurance. Although LDs are key structures in spermatophytes and are especially abundant in seeds, they are found across plants and algae, and increase during stress. Further, the proteins that underpin their form and function often have deep homologs. We propose an evolutionary scenario in which (i) the generation of LDs arose as a mechanism to mediate general drought and desiccation resilience, and (ii) the required protein framework was co-opted by spermatophytes for a seed-specific program.
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Affiliation(s)
- Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstrasse 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidtstrasse 1, 37077 Goettingen, Germany.
| | - Till Ischebeck
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.
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72
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Nagy LG, Varga T, Csernetics Á, Virágh M. Fungi took a unique evolutionary route to multicellularity: Seven key challenges for fungal multicellular life. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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73
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Li L, Wang S, Wang H, Sahu SK, Marin B, Li H, Xu Y, Liang H, Li Z, Cheng S, Reder T, Çebi Z, Wittek S, Petersen M, Melkonian B, Du H, Yang H, Wang J, Wong GKS, Xu X, Liu X, Van de Peer Y, Melkonian M, Liu H. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nat Ecol Evol 2020; 4:1220-1231. [PMID: 32572216 PMCID: PMC7455551 DOI: 10.1038/s41559-020-1221-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/12/2020] [Indexed: 12/31/2022]
Abstract
Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.
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Affiliation(s)
- Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Birger Marin
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Haoyuan Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Tanja Reder
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Zehra Çebi
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
| | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany.
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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74
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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75
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Yoshida K, Horinouchi Y, Watanabe M, Togashi T. Estimation of the Genome Sizes of Males and Females in the Marine Green Alga Monostroma angicava Using Flow Cytometry. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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76
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Caisová L. Draparnaldia: a chlorophyte model for comparative analyses of plant terrestrialization. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3305-3313. [PMID: 32100007 DOI: 10.1093/jxb/eraa102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/25/2020] [Indexed: 05/22/2023]
Abstract
It is generally accepted that land plants evolved from streptophyte algae. However, there are also many chlorophytes (a sister group of streptophyte algae and land plants) that moved to terrestrial habitats and even resemble mosses. This raises the question of why no land plants evolved from chlorophytes. In order to better understand what enabled streptophyte algae to conquer the land, it is necessary to study the chlorophytes as well. This review will introduce the freshwater filamentous chlorophyte alga Draparnaldia sp. (Chaetophorales, Chlorophyceae) as a model for comparative analyses between these two lineages. It will also focus on current knowledge about the evolution of morphological complexity in chlorophytes versus streptophytes and their respective morphological/behavioural adaptations to semi-terrestrial habitats, and will show why Draparnaldia is needed as a new model system.
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Affiliation(s)
- Lenka Caisová
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, UK
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77
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Alsufyani T, Califano G, Deicke M, Grueneberg J, Weiss A, Engelen AH, Kwantes M, Mohr JF, Ulrich JF, Wichard T. Macroalgal-bacterial interactions: identification and role of thallusin in morphogenesis of the seaweed Ulva (Chlorophyta). JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3340-3349. [PMID: 32016363 PMCID: PMC7289720 DOI: 10.1093/jxb/eraa066] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 02/01/2020] [Indexed: 05/07/2023]
Abstract
Macroalgal microbiomes have core functions related to biofilm formation, growth, and morphogenesis of seaweeds. In particular, the growth and development of the sea lettuce Ulva spp. (Chlorophyta) depend on bacteria releasing morphogenetic compounds. Under axenic conditions, the macroalga Ulva mutabilis develops a callus-like phenotype with cell wall protrusions. However, co-culturing with Roseovarius sp. (MS2) and Maribacter sp. (MS6), which produce various stimulatory chemical mediators, completely recovers morphogenesis. This ecological reconstruction forms a tripartite community which can be further studied for its role in cross-kingdom interactions. Hence, our study sought to identify algal growth- and morphogenesis-promoting factors (AGMPFs) capable of phenocopying the activity of Maribacter spp. We performed bioassay-guided solid-phase extraction in water samples collected from U. mutabilis aquaculture systems. We uncovered novel ecophysiological functions of thallusin, a sesquiterpenoid morphogen, identified for the first time in algal aquaculture. Thallusin, released by Maribacter sp., induced rhizoid and cell wall formation at a concentration of 11 pmol l-1. We demonstrated that gametes acquired the iron complex of thallusin, thereby linking morphogenetic processes with intracellular iron homeostasis. Understanding macroalgae-bacteria interactions permits further elucidation of the evolution of multicellularity and cellular differentiation, and development of new applications in microbiome-mediated aquaculture systems.
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Affiliation(s)
- Taghreed Alsufyani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Algal Research Laboratory, Chemistry Department, Science Faculty, Taif University, Taif, Saudi Arabia
| | - Gianmaria Califano
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Michael Deicke
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Jan Grueneberg
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Jena, Germany
| | - Anne Weiss
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Jena, Germany
| | - Aschwin H Engelen
- Centre for Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Michiel Kwantes
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Jan Frieder Mohr
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Jena, Germany
| | - Johann F Ulrich
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Jena, Germany
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78
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Morffy N, Strader LC. Old Town Roads: routes of auxin biosynthesis across kingdoms. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:21-27. [PMID: 32199307 PMCID: PMC7540728 DOI: 10.1016/j.pbi.2020.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/28/2020] [Accepted: 02/09/2020] [Indexed: 05/04/2023]
Abstract
Auxin is an important signaling molecule synthesized in organisms from multiple kingdoms of life, including land plants, green algae, and bacteria. In this review, we highlight the similarities and differences in auxin biosynthesis among these organisms. Tryptophan-dependent routes to IAA are found in land plants, green algae and bacteria. Recent sequencing efforts show that the indole-3-pyruvic acid pathway, one of the primary biosynthetic pathways in land plants, is also found in the green algae. These similarities raise questions about the origin of auxin biosynthesis. Future studies comparing auxin biosynthesis across kingdoms will shed light on its origin and role outside of the plant lineage.
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Affiliation(s)
- Nicholas Morffy
- Department of Biology, Washington University, St. Louis, MO 63130, United States; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, United States.
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, United States; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, United States; Center for Engineering MechanoBiology, Washington University, St. Louis, MO 63130, United States.
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79
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Jiao C, Sørensen I, Sun X, Sun H, Behar H, Alseekh S, Philippe G, Palacio Lopez K, Sun L, Reed R, Jeon S, Kiyonami R, Zhang S, Fernie AR, Brumer H, Domozych DS, Fei Z, Rose JKC. The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants. Cell 2020; 181:1097-1111.e12. [PMID: 32442406 DOI: 10.1016/j.cell.2020.04.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/14/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
The evolutionary features and molecular innovations that enabled plants to first colonize land are not well understood. Here, insights are provided through our report of the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The genome has a high proportion of repeat sequences that are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with representatives of earlier diverging algal lineages, P. margaritaceum has expanded repertoires of gene families, signaling networks, and adaptive responses that highlight the evolutionary trajectory toward terrestrialization. These encompass a broad range of physiological processes and protective cellular features, such as flavonoid compounds and large families of modifying enzymes involved in cell wall biosynthesis, assembly, and remodeling. Transcriptome profiling further elucidated adaptations, responses, and selective pressures associated with the semi-terrestrial ecosystems of P. margaritaceum, where a simple body plan would be an advantage.
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Affiliation(s)
- Chen Jiao
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Hila Behar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Li Sun
- Skidmore College, Saratoga Springs, NY, USA
| | | | - Susan Jeon
- Skidmore College, Saratoga Springs, NY, USA
| | - Reiko Kiyonami
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA, USA
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada; Department of Botany, University of British Columbia, 3200-6270 University Blvd., Vancouver, BC V6H 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA; U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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80
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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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81
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The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty. Curr Biol 2020; 30:530-536.e2. [DOI: 10.1016/j.cub.2019.11.090] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022]
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82
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Liang Z, Geng Y, Ji C, Du H, Wong CE, Zhang Q, Zhang Y, Zhang P, Riaz A, Chachar S, Ding Y, Wen J, Wu Y, Wang M, Zheng H, Wu Y, Demko V, Shen L, Han X, Zhang P, Gu X, Yu H. Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901850. [PMID: 31921561 PMCID: PMC6947507 DOI: 10.1002/advs.201901850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/10/2019] [Indexed: 05/02/2023]
Abstract
The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
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Affiliation(s)
- Zhe Liang
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Yuke Geng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Changmian Ji
- Biomarker TechnologiesBeijing101300China
- Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou571101China
| | - Hai Du
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Chui Eng Wong
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Qian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Ye Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Pingxian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Adeel Riaz
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Sadaruddin Chachar
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Yike Ding
- Department of EntomologyUniversity of California RiversideRiversideCA92521USA
| | - Jing Wen
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Yunwen Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | | | | | - Yanmin Wu
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Viktor Demko
- Department of Plant PhysiologyFaculty of Natural SciencesComenius University in BratislavaBratislava84215Slovakia
| | - Lisha Shen
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
| | - Xiao Han
- College of Biological Science and EngineeringFuzhou UniversityFuzhou350108China
| | - Pengpeng Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaofeng Gu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Hao Yu
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
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83
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Abstract
Two genomes of the closest algal sisters to land plants were sequenced, providing potential evidence that bacterial genes were key in adapting to terrestrial stresses.
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Affiliation(s)
- Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.
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84
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ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes. Genes (Basel) 2019; 10:genes10120950. [PMID: 31757073 PMCID: PMC6969924 DOI: 10.3390/genes10120950] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to “public” or “restricted” mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user- friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.
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85
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Ichihara K, Yamazaki T, Miyamura S, Hiraoka M, Kawano S. Asexual thalli originated from sporophytic thalli via apomeiosis in the green seaweed Ulva. Sci Rep 2019; 9:13523. [PMID: 31534182 PMCID: PMC6751216 DOI: 10.1038/s41598-019-50070-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/05/2019] [Indexed: 11/09/2022] Open
Abstract
Apomixis is an asexual reproduction system without fertilization, which is an important proliferation strategy for plants and algae. Here, we report on the apomeiosis in the green seaweed Ulva prolifera, which has sexual and obligate asexual populations. Genomic PCR of mating type (MT)-locus genes revealed asexual thalli carrying both MT genomes. Observation of the chromosomes during the formation of each type of reproductive cell revealed that cells in asexual thalli performed apomeiosis without chromosome reduction. Moreover, genotyping revealed that laboratory-cultured sporophytic thalli produced not only each type of gametophyte but also diploid thalli carrying the mt- and mt+ genome (mt± thallus strains). The mt± thallus strain released diploid biflagellate zoids, with ultrastructure and behavior similar to mt+ gametes. Additionally, a transcriptomic analysis revealed that some meiosis-related genes (Mei2L and RAD1) were highly expressed in the quadriflagellate zoosporoids. Our results strongly suggest that asexual thalli originally evolved via apomeiosis in sporophytic thalli.
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Affiliation(s)
- Kensuke Ichihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562, Japan. .,Field Science Center for Northern Biosphere, Hokkaido University, 1-133-31, Funami-Cho, Muroran, 051-0013, Japan.
| | - Tomokazu Yamazaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562, Japan
| | - Shinichi Miyamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masanori Hiraoka
- Usa Marine Biological Institute, Kochi University, Inoshiri 194, Usa, Tosa, Kochi, 781-1164, Japan
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562, Japan. .,Future Center Initiative, The University of Tokyo, Wakashiba, Kashiwa, Chiba, 277-0871, Japan.
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86
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Abstract
Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.
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Affiliation(s)
- James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
| | - Susana Coelho
- Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, CS 90074, F-29688 Roscoff, France;
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87
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Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E. A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. DNA Res 2019; 26:183-192. [PMID: 30918953 PMCID: PMC6476727 DOI: 10.1093/dnares/dsz002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga.
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Affiliation(s)
- Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yoshimi Higa
- Onna Village Fisheries Cooperative, Onna, Okinawa, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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88
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Wu C, Zheng C, Ji G, Jiang P. Synergistic effects of HSE and LTR elements from hsp70 gene promoter of Ulva prolifera (Ulvophyceae, Chlorophyta) upon temperature induction 1. JOURNAL OF PHYCOLOGY 2019; 55:738-743. [PMID: 30843209 DOI: 10.1111/jpy.12854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Besides heat stress, the 70 kDa heat shock proteins (HSP70s) have been shown to respond to cold stress. However, the involved cis-acting elements remain unknown. The hsp70 gene from the green macroalga Ulva prolifera (Uphsp70) has been cloned, from which one heat shock element HSE and one low-temperature-responsive element LTR were found in the promoter. Using the established transient expression system and quantitative GUS assay, a series of element deletion experiments were performed to determine the functions of HSE and LTR in response to temperature stress. The results showed that under cold stress, both HSE and LTR were indispensable, since deletion leads to complete loss of promoter activity. Under heat stress, although the HSE could respond independently, coexistence with LTR was essential for high induced activity of the Uphsp70 promoter. Therefore, synergistic effects exist between HSE and LTR elements in response to temperature stress in Ulva, and extensive bioinformatics analysis showed that the mechanism is widespread in algae and plants, since LTR coexists widely with HSE in the promoter region of hsp70. Our findings provide important supplements to the knowledge of algal and plant HSP70s response to temperature stress. We speculated that for algal domestication and artificial breeding, HSE and LTR elements might serve as potential molecular targets to temperature acclimation.
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Affiliation(s)
- Chunhui Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Caiyun Zheng
- College of Biotechnology Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Gengsheng Ji
- College of Biotechnology Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Peng Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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89
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Beaulieu L. Insights into the Regulation of Algal Proteins and Bioactive Peptides Using Proteomic and Transcriptomic Approaches. Molecules 2019; 24:E1708. [PMID: 31052532 PMCID: PMC6539653 DOI: 10.3390/molecules24091708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/22/2019] [Accepted: 05/01/2019] [Indexed: 11/24/2022] Open
Abstract
Oceans abound in resources of various kinds for R&D and for commercial applications. Monitoring and bioprospecting allow the identification of an increasing number of key natural resources. Macroalgae are essential elements of marine ecosystems as well as a natural resource influenced by dynamic environmental factors. They are not only nutritionally attractive but have also demonstrated potential health benefits such as antioxidant, antihypertensive, and anti-inflammatory activities. Several bioactive peptides have been observed following enzymatic hydrolysis of macroalgal proteins. In addition, significant differences in protein bioactivities and peptide extracts of wild and cultivated macroalgae have been highlighted, but the metabolic pathways giving rise to these bioactive molecules remain largely elusive. Surprisingly, the biochemistry that underlies the environmental stress tolerance of macroalgae has not been well investigated and remains poorly understood. Proteomic and functional genomic approaches based on identifying precursor proteins and bioactive peptides of macroalgae through integrated multi-omics analysis can give insights into their regulation as influenced by abiotic factors. These strategies allow evaluating the proteomics profile of regulation of macroalgae in response to different growth conditions as well as establishing a comparative transcriptome profiling targeting structural protein-coding genes. Elucidation of biochemical pathways in macroalgae could provide an innovative means of enhancing the protein quality of edible macroalgae. This could be ultimately viewed as a powerful way to drive the development of a tailored production and extraction of high value molecules. This review provides an overview of algal proteins and bioactive peptide characterization using proteomics and transcriptomic analyses.
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Affiliation(s)
- Lucie Beaulieu
- Département des Sciences des Aliments, Institut sur la Nutrition et les Aliments Fonctionnels (INAF), 2425, rue de l'Agriculture, Université Laval, Québec, QC G1V 0A6, Canada.
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90
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Steinhagen S, Barco A, Wichard T, Weinberger F. Conspecificity of the model organism Ulva mutabilis and Ulva compressa (Ulvophyceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2019; 55:25-36. [PMID: 30367499 DOI: 10.1111/jpy.12804] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
As one of the most abundant and ubiquitous representatives of marine and brackish coastal macrophytobenthos communities, the genus Ulva is not only an important primary producer but also of ecological and morphogenetic interest to many scientists. Ulva mutabilis became an important model organism to study morphogenesis and mutualistic interactions of macroalgae and microorganisms. Here, we report that our collections of Ulva compressa Linnaeus (1753) from Germany are conspecific with the type strains of the model organism U. mutabilis Føyn (1958), which were originally collected at Olhão on the south coast of Portugal and have from that time on been maintained in culture as gametophytic and parthenogenetic lab strains. Different approaches were used to test conspecificity: (i) comparisons of vegetative and reproductive features of cultured material of U. mutabilis and German U. compressa demonstrated a shared morphological pattern; (ii) gametes of U. compressa and U. mutabilis successfully mated and developed into fertile sporophytic first-generation offspring; (iii) molecular phylogenetics and species delimitation analyses based on the Generalized Mixed Yule-Coalescent method showed that U. mutabilis isolates (sl-G[mt+]) and (wt-G[mt-]) and U. compressa belong to a unique Molecular Operational Taxonomic Unit. According to these findings, there is sufficient evidence that U. mutabilis and U. compressa should be regarded as conspecific.
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Affiliation(s)
- Sophie Steinhagen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Ecology Department, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Andrea Barco
- Deutsches Zentrum für Marine Biodiversitätsforschung, Senckenberg am Meer, Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Thomas Wichard
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Lessingstr.8, 07743, Jena, Germany
| | - Florian Weinberger
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Ecology Department, Düsternbrooker Weg 20, 24105, Kiel, Germany
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