1
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Godfroy O, Zheng M, Yao H, Henschen A, Peters AF, Scornet D, Colin S, Ronchi P, Hipp K, Nagasato C, Motomura T, Cock JM, Coelho SM. The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus. Development 2023; 150:dev201283. [PMID: 36786333 PMCID: PMC10112911 DOI: 10.1242/dev.201283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023]
Abstract
The first mitotic division of the initial cell is a key event in all multicellular organisms and is associated with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular generations: the sporophyte and the gametophyte. Each generation deploys a distinct developmental programme autonomously from an initial cell, the first cell division of which sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first cell division and subsequent failure to produce basal structures during both generations. BAS encodes a type B″ regulatory subunit of protein phosphatase 2A (PP2A), and transcriptomic analysis identified potential effector genes that may be involved in determining basal cell fate. The bas mutant phenotype is very similar to that observed in distag (dis) mutants, which lack a functional Tubulin-binding co-factor Cd1 (TBCCd1) protein, indicating that TBCCd1 and PP2A are two essential components of the cellular machinery that regulates the first cell division and mediates basal cell fate determination.
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Affiliation(s)
- Olivier Godfroy
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Min Zheng
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Haiqin Yao
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnes Henschen
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Delphine Scornet
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Sebastien Colin
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katharina Hipp
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - J. Mark Cock
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M. Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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2
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Soorni A, Karimi M, Al Sharif B, Habibi K. Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC PLANT BIOLOGY 2023; 23:3. [PMID: 36588159 PMCID: PMC9806901 DOI: 10.1186/s12870-022-04031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. RESULTS For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. CONCLUSION Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | | | - Batoul Al Sharif
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Khashayar Habibi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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3
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Cossard GG, Godfroy O, Nehr Z, Cruaud C, Cock JM, Lipinska AP, Coelho SM. Selection drives convergent gene expression changes during transitions to co-sexuality in haploid sexual systems. Nat Ecol Evol 2022; 6:579-589. [PMID: 35314785 PMCID: PMC9085613 DOI: 10.1038/s41559-022-01692-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022]
Abstract
Co-sexuality has evolved repeatedly from unisexual (dioicous) ancestors across a wide range of taxa. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red algae and brown algae. Here we explore four independent events of emergence of co-sexuality from unisexual ancestors in brown algal clades to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amounts of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in stark contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, some of their predicted functions were conserved across species. Transitions to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly for male-biased genes. Gene expression in co-sexual species was more similar to that in females rather than males of related dioicous species, suggesting that co-sexuality may have arisen from ancestral females. Finally, extensive convergent gene expression changes, driven by selection, were associated with the transition to co-sexuality. Together, our observations provide insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.
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Affiliation(s)
- Guillaume G Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Zofia Nehr
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France.
- Max Plank Institute for Biology Tübingen, Tübingen, Germany.
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4
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Gueno J, Borg M, Bourdareau S, Cossard G, Godfroy O, Lipinska A, Tirichine L, Cock J, Coelho S. Chromatin landscape associated with sexual differentiation in a UV sex determination system. Nucleic Acids Res 2022; 50:3307-3322. [PMID: 35253891 PMCID: PMC8989524 DOI: 10.1093/nar/gkac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.
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Affiliation(s)
- Josselin Gueno
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Simon Bourdareau
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Guillaume Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Agnieszka Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Leila Tirichine
- Nantes Universite, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
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5
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Coelho SM, Umen J. Switching it up: algal insights into sexual transitions. PLANT REPRODUCTION 2021; 34:287-296. [PMID: 34181073 PMCID: PMC8566403 DOI: 10.1007/s00497-021-00417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
While the process of meiosis is highly conserved across eukaryotes, the sexual systems that govern life cycle phase transitions are surprisingly labile. Switches between sexual systems have profound evolutionary and ecological consequences, in particular for plants, but our understanding of the fundamental mechanisms and ultimate causes underlying these transitions is still surprisingly incomplete. We explore here the idea that brown and green algae may be interesting comparative models that can increase our understanding of relevant processes in plant reproductive biology, from evolution of gamete dimorphism, gametogenesis, sex determination and transitions in sex-determining systems.
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Affiliation(s)
- Susana M Coelho
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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6
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Bringloe TT, Zaparenkov D, Starko S, Grant WS, Vieira C, Kawai H, Hanyuda T, Filbee-Dexter K, Klimova A, Klochkova TA, Krause-Jensen D, Olesen B, Verbruggen H. Whole-genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae). JOURNAL OF PHYCOLOGY 2021; 57:1721-1738. [PMID: 34510441 DOI: 10.1111/jpy.13212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/20/2021] [Accepted: 09/05/2021] [Indexed: 05/22/2023]
Abstract
The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.
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Affiliation(s)
- Trevor T Bringloe
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
| | - Dani Zaparenkov
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
| | - Samuel Starko
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 2Y2, Canada
| | - William Stewart Grant
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Christophe Vieira
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Kobe University, Rokkodai, Nada, Kobe, Japan
| | - Karen Filbee-Dexter
- ArcticNet, Québec Océan, Départment de biologie, Université Laval, Québec, Canada
- Institute of Marine Research, His, Norway
| | - Anna Klimova
- Kamchatka State Technical University, Petropavlovsk-Kamchatsky, 683003, Russia
| | - Tatyana A Klochkova
- Kamchatka State Technical University, Petropavlovsk-Kamchatsky, 683003, Russia
| | - Dorte Krause-Jensen
- Department of Bioscience, Aarhus University, Vejlsøvej 25, Silkeborg, DK-8600, Denmark
- Arctic Research Center, Aarhus University, Ole Worms Allé 1, Arhus C, DK-8000, Denmark
| | - Birgit Olesen
- Department of Biology, Aarhus University, Ole Worms Allé 1, Aarhus C, 8000, Denmark
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville Campus, Parkville, Victoria, 3010, Australia
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7
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Müller DG, Gaschet E, Godfroy O, Gueno J, Cossard G, Kunert M, Peters AF, Westermeier R, Boland W, Cock JM, Lipinska AP, Coelho SM. A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system. THE NEW PHYTOLOGIST 2021; 232:252-263. [PMID: 34166525 DOI: 10.1111/nph.17582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown alga Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental programme may occur by 'default'. Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental programme is however incomplete, because gametes of this feminized male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programmes, and show that the phenotypic feminization is associated with both feminization and de-masculinization of gene expression patterns. Importantly, the feminization phenotype was associated with dramatic downregulation of two V-specific genes including a candidate male-determining gene. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system, and contribute to disentangling the role of sex-linked and autosomal gene expression in the initiation of sex-specific developmental programmes. Overall, the data presented here imply that the U-specific region is not required to initiate the female developmental programme, but is critical to produce fully functional eggs, arguing against the idea that female is the 'default' sex in this species.
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Affiliation(s)
- Dieter G Müller
- Fachbereich Biologie der Universität Konstanz, Konstanz, 78457, Germany
| | - Enora Gaschet
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Olivier Godfroy
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Josselin Gueno
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Guillaume Cossard
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Maritta Kunert
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | | | - Renato Westermeier
- Instituto de Acuicultura, Universidad Austral de Chile, Casilla 1327, Puerto Montt, Chile
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - J Mark Cock
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Agnieszka P Lipinska
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
- Max Plank Institute for Developmental Biology, Tübingen, Germany
| | - Susana M Coelho
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
- Max Plank Institute for Developmental Biology, Tübingen, Germany
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8
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Constable GWA, Kokko H. Parthenogenesis and the Evolution of Anisogamy. Cells 2021; 10:2467. [PMID: 34572116 PMCID: PMC8467976 DOI: 10.3390/cells10092467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/10/2023] Open
Abstract
Recently, it was pointed out that classic models for the evolution of anisogamy do not take into account the possibility of parthenogenetic reproduction, even though sex is facultative in many relevant taxa (e.g., algae) that harbour both anisogamous and isogamous species. Here, we complement this recent analysis with an approach where we assume that the relationship between progeny size and its survival may differ between parthenogenetically and sexually produced progeny, favouring either the former or the latter. We show that previous findings that parthenogenesis can stabilise isogamy relative to the obligate sex case, extend to our scenarios. We additionally investigate two different ways for one mating type to take over the entire population. First, parthenogenesis can lead to biased sex ratios that are sufficiently extreme that one type can displace the other, leading to de facto asexuality for the remaining type that now lacks partners to fuse with. This process involves positive feedback: microgametes, being numerous, lack opportunities for syngamy, and should they proliferate parthenogenetically, the next generation makes this asexual route even more prominent for microgametes. Second, we consider mutations to strict asexuality in producers of micro- or macrogametes, and show that the prospects of asexual invasion depend strongly on the mating type in which the mutation arises. Perhaps most interestingly, we also find scenarios in which parthenogens have an intrinsic survival advantage yet facultatively sexual isogamous populations are robust to the invasion of asexuals, despite us assuming no genetic benefits of recombination. Here, equal contribution from both mating types to zygotes that are sufficiently well provisioned can outweigh the additional costs associated with syngamy.
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Affiliation(s)
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
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9
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Emelianova K, Martínez Martínez A, Campos-Dominguez L, Kidner C. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Sci Rep 2021; 11:17773. [PMID: 34493743 PMCID: PMC8423730 DOI: 10.1038/s41598-021-96854-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.
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Affiliation(s)
- Katie Emelianova
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988Dementia Research Institute at the University of Edinburgh, Edinburgh, UK
| | - Andrea Martínez Martínez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Lucia Campos-Dominguez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Catherine Kidner
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
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10
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Zhang J, Li Y, Luo S, Cao M, Zhang L, Li X. Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica. BMC PLANT BIOLOGY 2021; 21:335. [PMID: 34261451 PMCID: PMC8278619 DOI: 10.1186/s12870-021-03117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In brown algae, dioicy is the prevalent sexual system, and phenotypic differences between male and female gametophytes have been found in many dioicous species. Saccharina japonica show remarkable sexual dimorphism in gametophytes before gametogenesis. A higher level of phenotypic differentiation was also found in female and male gametes after gametogenesis. However, the patterns of differential gene expression throughout gametophyte development and how these changes might relate to sex-specific fitness at the gamete stage in S. japonica are not well known. RESULTS In this study, differences in gene expression between male and female gametophytes in different developmental stages were investigated using comparative transcriptome analysis. Among the 20,151 genes expressed in the haploid gametophyte generation, 37.53% were sex-biased. The abundance of sex-biased genes in mature gametophytes was much higher than that in immature gametophytes, and more male-biased than female-biased genes were observed in the mature stage. The predicted functions of most sex-biased genes were closely related to the sex-specific characteristics of gametes, including cell wall biosynthesis, sperm motility, and sperm and egg recognition. In addition, 51 genes were specifically expressed in males in both stages, showing great potential as candidate male sex-determining region (SDR) genes. CONCLUSIONS This study describes a thorough investigation into differential gene expression between male and female gametophytes in the dioicous kelp S. japonica. A large number of sex-biased genes in mature gametophytes may be associated with the divergence of phenotypic traits and physiological functions between female gametes (eggs) and male gametes (sperm) during sexual differentiation. These genes may mainly come from new sex-biased genes that have recently evolved in the S. japonica lineage. The duplication of sex-biased genes was detected, which may increase the number of sex-biased genes after gametogenesis in S. japonica to some extent. The excess of male-biased genes over female-biased genes in the mature stage may reflect the different levels of sexual selection across sexes. This study deepens our understanding of the regulation of sex development and differentiation in the dioicous kelp S. japonica.
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Affiliation(s)
- Jiaxun Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yan Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Shiju Luo
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
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11
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Heesch S, Serrano-Serrano M, Barrera-Redondo J, Luthringer R, Peters AF, Destombe C, Cock JM, Valero M, Roze D, Salamin N, Coelho SM. Evolution of life cycles and reproductive traits: Insights from the brown algae. J Evol Biol 2021; 34:992-1009. [PMID: 34096650 DOI: 10.1111/jeb.13880] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023]
Abstract
A vast diversity of types of life cycles exists in nature, and several theories have been advanced to explain how this diversity has evolved and how each type of life cycle is retained over evolutionary time. Here, we exploited the diversity of life cycles and reproductive traits of the brown algae (Phaeophyceae) to test several hypotheses on the evolution of life cycles. We investigated the evolutionary dynamics of four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assigned states to up to 77 representative species of the taxonomic diversity of the brown algal group, in a multi-gene phylogeny. We used maximum likelihood and Bayesian analyses of correlated evolution, while taking the phylogeny into account, to test for correlations between traits and to investigate the chronological sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth evolves when sexual reproduction is preferred over asexual reproduction, possibly because it allows the complementation of deleterious mutations. We also found that haploid sex determination is ancestral in relation to diploid sex determination. However, our results could not address whether increased zygotic and diploid growth are associated with increased sexual dimorphism. Our analyses suggest that in the brown algae, isogamous species evolved from anisogamous ancestors, contrary to the commonly reported pattern where evolution proceeds from isogamy to anisogamy.
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Affiliation(s)
- Svenja Heesch
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Applied Ecology & Phycology, Institute for Biosciences, University of Rostock, Rostock, Germany
| | | | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rémy Luthringer
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | | | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - J Mark Cock
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Susana M Coelho
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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12
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Bourdareau S, Tirichine L, Lombard B, Loew D, Scornet D, Wu Y, Coelho SM, Cock JM. Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biol 2021; 22:12. [PMID: 33397407 PMCID: PMC7784034 DOI: 10.1186/s13059-020-02216-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 12/02/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. RESULTS A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. CONCLUSIONS The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
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Affiliation(s)
- Simon Bourdareau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Leila Tirichine
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yue Wu
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
- Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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13
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Abstract
Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.
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Affiliation(s)
- Susana M Coelho
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
- Current affiliation: Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - J Mark Cock
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
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14
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Dittami SM, Corre E, Brillet-Guéguen L, Lipinska AP, Pontoizeau N, Aite M, Avia K, Caron C, Cho CH, Collén J, Cormier A, Delage L, Doubleau S, Frioux C, Gobet A, González-Navarrete I, Groisillier A, Hervé C, Jollivet D, KleinJan H, Leblanc C, Liu X, Marie D, Markov GV, Minoche AE, Monsoor M, Pericard P, Perrineau MM, Peters AF, Siegel A, Siméon A, Trottier C, Yoon HS, Himmelbauer H, Boyen C, Tonon T. The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga. Mar Genomics 2020; 52:100740. [PMID: 31937506 DOI: 10.1016/j.margen.2020.100740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/01/2020] [Indexed: 11/20/2022]
Abstract
Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France.
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Noé Pontoizeau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Meziane Aite
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Komlan Avia
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Université de Strasbourg, INRA, SVQV UMR-A 1131, F-68000 Colmar, France
| | - Christophe Caron
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Sylvie Doubleau
- IRD, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | | | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Irene González-Navarrete
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Agnès Groisillier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Cécile Hervé
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Hetty KleinJan
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Xi Liu
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - André E Minoche
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Misharl Monsoor
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Pierre Pericard
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Marie-Mathilde Perrineau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, United Kingdom
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Amandine Siméon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Camille Trottier
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France; Laboratory of Digital Sciences of Nantes (LS2N) - University of Nantes, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190 Vienna, Austria
| | - Catherine Boyen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Thierry Tonon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
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15
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Li S, Wang L, Jung S, Lee BS, He N, Lee MS. Biochemical Characterization of a New Oligoalginate Lyase and Its Biotechnological Application in Laminaria japonica Degradation. Front Microbiol 2020; 11:316. [PMID: 32210931 PMCID: PMC7076127 DOI: 10.3389/fmicb.2020.00316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022] Open
Abstract
Oligoalginate lyases catalyze the degradation of alginate polymers and oligomers into monomers, a prerequisite for biotechnological utilizing alginate. In this study, we report the cloning, expression and biochemical characterization of a new polysaccharide lyase (PL) family 17 oligoalginate lyase, OalV17, from the marine bacterium Vibrio sp. SY01. The recombinant OalV17 showed metal ion independent and detergent resistant properties. Furthermore, OalV17 is an exo-type enzyme that yields alginate monomers as the main product and recognizes alginate disaccharides as the minimal substrate. Site-directed mutagenesis followed by kinetic analysis indicates that the residue Arg231 plays a key role in substrate specificity. Furthermore, a rapid and efficient alginate monomer-producing method was developed directly from Laminaria japonica. These results suggest that OalV17 is a potential candidate for saccharification of alginate.
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Affiliation(s)
- Shangyong Li
- School of Basic Medicine, Qingdao University, Qingdao, China.,Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Linna Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Samil Jung
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Beom Suk Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Myeong-Sok Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Seoul, South Korea
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16
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Lipinska AP, Serrano-Serrano ML, Cormier A, Peters AF, Kogame K, Cock JM, Coelho SM. Correction to: Rapid turnover of life-cycle-related genes in the brown algae. Genome Biol 2019; 20:44. [PMID: 30795789 PMCID: PMC6385437 DOI: 10.1186/s13059-019-1657-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 11/10/2022] Open
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