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Hörandl E. Apomixis and the paradox of sex in plants. ANNALS OF BOTANY 2024; 134:1-18. [PMID: 38497809 PMCID: PMC11161571 DOI: 10.1093/aob/mcae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. SCOPE This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. CONCLUSIONS Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), University of Göttingen, Göttingen, Germany
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2
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 2024; 56:1018-1031. [PMID: 38693345 PMCID: PMC11096116 DOI: 10.1038/s41588-024-01737-3] [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: 04/21/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Zhejiang Lab, Hanzhou, China
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Yunnan, China
| | - Bo Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jaccoline M S Zegers
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora', Málaga, Spain
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Jeffrey P Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University, Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg and Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Xiyin Wang
- North China University of Science and Technology, Tangshan, China
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- University of Goettingen, Goettingen Center for Molecular Biosciences, Goettingen, Germany.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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3
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Mathieu D, Bryson AE, Hamberger B, Singan V, Keymanesh K, Wang M, Barry K, Mondo S, Pangilinan J, Koriabine M, Grigoriev IV, Bonito G, Hamberger B. Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long-standing interaction among land plants and fungi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:304-323. [PMID: 38265362 DOI: 10.1111/tpj.16605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/16/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.
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Affiliation(s)
- Davis Mathieu
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Abigail E Bryson
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Britta Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Keykhosrow Keymanesh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, 94720, USA
| | - Gregory Bonito
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Björn Hamberger
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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4
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Pri-Tal O, Sun Y, Dadras A, Fürst-Jansen JMR, Zimran G, Michaeli D, Wijerathna-Yapa A, Shpilman M, Merilo E, Yarmolinsky D, Efroni I, de Vries J, Kollist H, Mosquna A. Constitutive activation of ABA receptors in Arabidopsis reveals unique regulatory circuitries. THE NEW PHYTOLOGIST 2024; 241:703-714. [PMID: 37915144 DOI: 10.1111/nph.19363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Abscisic acid (ABA) is best known for regulating the responses to abiotic stressors. Thus, applications of ABA signaling pathways are considered promising targets for securing yield under stress. ABA levels rise in response to abiotic stress, mounting physiological and metabolic responses that promote plant survival under unfavorable conditions. ABA elicits its effects by binding to a family of soluble receptors found in monomeric and dimeric states, differing in their affinity to ABA and co-receptors. However, the in vivo significance of the biochemical differences between these receptors remains unclear. We took a gain-of-function approach to study receptor-specific functionality. First, we introduced activating mutations that enforce active ABA-bound receptor conformation. We then transformed Arabidopsis ABA-deficient mutants with the constitutive receptors and monitored suppression of the ABA deficiency phenotype. Our findings suggest that PYL4 and PYL5, monomeric ABA receptors, have differential activity in regulating transpiration and transcription of ABA biosynthesis and stress response genes. Through genetic and metabolic data, we demonstrate that PYR1, but not PYL5, is sufficient to activate the ABA positive feedback mechanism. We propose that ABA signaling - from perception to response - flows differently when triggered by different PYLs, due to tissue and transcription barriers, thus resulting in distinct circuitries.
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Affiliation(s)
- Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Yufei Sun
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Daphna Michaeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Akila Wijerathna-Yapa
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | | | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtsr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
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5
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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6
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Rieseberg TP, Dadras A, Bergschmidt LIN, Bierenbroodspot MJ, Fürst-Jansen JMR, Irisarri I, de Vries S, Darienko T, de Vries J. Divergent responses in desiccation experiments in two ecophysiologically different Zygnematophyceae. PHYSIOLOGIA PLANTARUM 2023; 175:e14056. [PMID: 38148198 DOI: 10.1111/ppl.14056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 12/28/2023]
Abstract
Water scarcity can be considered a major stressor on land, with desiccation being its most extreme form. Land plants have found two different solutions to this challenge: avoidance and tolerance. The closest algal relatives to land plants, the Zygnematophyceae, use the latter, and how this is realized is of great interest for our understanding of the conquest of land. Here, we worked with two representatives of the Zygnematophyceae, Zygnema circumcarinatum SAG 698-1b and Mesotaenium endlicherianum SAG 12.97, who differ in habitats and drought resilience. We challenged both algal species with severe desiccation in a laboratory setup until photosynthesis ceased, followed by a recovery period. We assessed their morphological, photophysiological, and transcriptomic responses. Our data pinpoint global differential gene expression patterns that speak of conserved responses, from calcium-mediated signaling to the adjustment of plastid biology, cell envelopes, and amino acid pathways, between Zygnematophyceae and land plants despite their strong ecophysiological divergence. The main difference between the two species appears to rest in a readjustment of the photobiology of Zygnema, while Mesotaenium experiences stress beyond a tipping point.
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Affiliation(s)
- Tim P Rieseberg
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Armin Dadras
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Luisa I N Bergschmidt
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute of Microbiology and Genetics, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
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7
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Arzac MI, Miranda-Apodaca J, Gasulla F, Arce-Guerrero M, Fernández-Marín B, García-Plazaola JI. Acquisition of Desiccation Tolerance Unveiled: Polar Lipid Profiles of Streptophyte Algae Offer Insights. PHYSIOLOGIA PLANTARUM 2023; 175:e14073. [PMID: 38148218 DOI: 10.1111/ppl.14073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Terrestrialization by photosynthetic eukaryotes took place in the two branches of green microalgae: Chlorophyta and Charophyta. Within the latter, the paraphyletic streptophytic algae divide into two clades. These are named Klebsormidiophyceae-Chlorokybophyceae-Mesostigmatophyceae (KCM), which is the oldest, and Zygnematophyceae-Coleochaetophyceae-Charophyceae (ZCC), which contains the closest relatives of vascular plants. Terrestrialization required the emergence of adaptations in response to new challenges, such as irradiance, temperature oscillations and water deprivation. In this study, we evaluated lipid composition in species representative of distinct phylogenetic clusters within Charophyta and Chlorophyta. We aim to study whether the inherent thylakoid lipid composition, as well as its adaptability in response to desiccation, were fundamental factors for the evolutionary history of terrestrial plants. The results showed that the lipid composition was similar to that found in flowering land plants, differing only in betaine lipids. Likewise, the largest constitutive pool of oligogalactolipids (OGL) was found only in the fully desiccation-tolerant species Klebsormidium nitens. After desiccation, the content of polar lipids decreased in all species. Conversely, the content of OGL increased, particularly trigalactosyldiacylglycerol and tetragalactosyldiacylglycerol in the ZCC clade. The analysis of the molecular species composition of the newly formed OGL may suggest a different biosynthetic route for the KCM and ZCC clades. We speculate that the appearance of a new OGL synthesis pathway, which eventually arose during the streptophyte evolutionary process, endowed algae with a much more dynamic regulation of thylakoid composition in response to stress, which ultimately contributed to the colonization of terrestrial habitats.
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Affiliation(s)
- Miren Irati Arzac
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jon Miranda-Apodaca
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - María Arce-Guerrero
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Beatriz Fernández-Marín
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Botany, Ecology and Plant Physiology, University of La Laguna (ULL), La Laguna, Canary Islands, Spain
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8
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Van de Poel B, de Vries J. Evolution of ethylene as an abiotic stress hormone in streptophytes. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2023; 214:105456. [PMID: 37780400 PMCID: PMC10518463 DOI: 10.1016/j.envexpbot.2023.105456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 10/03/2023]
Abstract
All land plants modulate their growth and physiology through intricate signaling cascades. The majority of these are at least modulated-and often triggered-by phytohormones. Over the past decade, it has become apparent that some phytohormones have an evolutionary origin that runs deeper than plant terrestrialization-many emerged in the streptophyte algal progenitors of land plants. Ethylene is such a case. Here we synthesize the current knowledge on the evolution of the phytohormone ethylene and speculate about its deeply conserved role in adjusting stress responses of streptophytes for more than half a billion years of evolution.
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Affiliation(s)
- Bram Van de Poel
- Molecular Plant Hormone Physiology lab, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute (LPI), University of Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
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9
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Heß D, Holzhausen A, Hess WR. Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276. PHYSIOLOGIA PLANTARUM 2023; 175:e14025. [PMID: 37882314 DOI: 10.1111/ppl.14025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023]
Abstract
Charophyceae are the most complex streptophyte algae, possessing tissue-like structures, rhizoids and a cellulose-pectin-based cell wall akin to embryophytes. Together with the Zygnematophyceae and the Coleochaetophycae, the Charophyceae form a grade in which the Zygnematophyceae share a last common ancestor with land plants. The availability of genomic data, its short life cycle, and the ease of non-sterile cultivation in the laboratory have made the species Chara braunii an emerging model system for streptophyte terrestrialization and early land plant evolution. In this study, tissue containing nodal cells was prepared under the stereomicroscope, and an RNA-seq dataset was generated and compared to transcriptome data from whole plantlets. In both samples, transcript coverage was high for genes encoding ribosomal proteins and a homolog of the putative PAX3- and PAX7-binding protein 1. Gene ontology was used to classify the putative functions of the differently expressed genes. In the nodal cell sample, main upregulated molecular functions were related to protein, nucleic acid, ATP- and DNA binding. Looking at specific genes, several signaling-related genes and genes encoding sugar-metabolizing enzymes were found to be expressed at a higher level in the nodal cell sample, while photosynthesis-and chloroplast-related genes were expressed at a comparatively lower level. We detected the transcription of 21 different genes encoding DUF4360-containing cysteine-rich proteins. The data contribute to the growing understanding of Charophyceae developmental biology by providing a first insight into the transcriptome composition of Chara nodal cells.
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Affiliation(s)
- Daniel Heß
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Anja Holzhausen
- Plant Cell Biology, Department of Biology, Philipps University Marburg, Marburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
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10
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Dadras A, Fürst-Jansen JMR, Darienko T, Krone D, Scholz P, Sun S, Herrfurth C, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Feussner I, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs pre-dating plant terrestrialization. NATURE PLANTS 2023; 9:1419-1438. [PMID: 37640935 PMCID: PMC10505561 DOI: 10.1038/s41477-023-01491-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravelled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here we used fine-combed RNA sequencing in tandem with a photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study the combinatory effects of stress response using clustering along gradients. Mesotaenium shares with land plants major hubs in genetic networks underpinning stress response and acclimation. Our data suggest that lipid droplet formation and plastid and cell wall-derived signals have denominated molecular programmes since more than 600 million years of streptophyte evolution-before plants made their first steps on land.
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Affiliation(s)
- Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Denis Krone
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Patricia Scholz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Siqi Sun
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Cornelia Herrfurth
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Rasmus Steinkamp
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Hansen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Henrik Buschmann
- Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Oliver Valerius
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Ivo Feussner
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Till Ischebeck
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Lorenz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Experimental Phycology and SAG Culture Collection of Algae, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- Goettingen Center for Molecular Biosciences, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
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11
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Kurepa J, Smalle JA. Plant Hormone Modularity and the Survival-Reproduction Trade-Off. BIOLOGY 2023; 12:1143. [PMID: 37627027 PMCID: PMC10452219 DOI: 10.3390/biology12081143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Biological modularity refers to the organization of living systems into separate functional units that interact in different combinations to promote individual well-being and species survival. Modularity provides a framework for generating and selecting variations that can lead to adaptive evolution. While the exact mechanisms underlying the evolution of modularity are still being explored, it is believed that the pressure of conflicting demands on limited resources is a primary selection force. One prominent example of conflicting demands is the trade-off between survival and reproduction. In this review, we explore the available evidence regarding the modularity of plant hormones within the context of the survival-reproduction trade-off. Our findings reveal that the cytokinin module is dedicated to maximizing reproduction, while the remaining hormone modules function to ensure reproduction. The signaling mechanisms of these hormone modules reflect their roles in this survival-reproduction trade-off. While the cytokinin response pathway exhibits a sequence of activation events that aligns with the developmental robustness expected from a hormone focused on reproduction, the remaining hormone modules employ double-negative signaling mechanisms, which reflects the necessity to prevent the excessive allocation of resources to survival.
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Affiliation(s)
| | - Jan A. Smalle
- Plant Physiology, Biochemistry, Molecular Biology Program, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA;
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12
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Fichman Y, Rowland L, Oliver MJ, Mittler R. ROS are evolutionary conserved cell-to-cell stress signals. Proc Natl Acad Sci U S A 2023; 120:e2305496120. [PMID: 37494396 PMCID: PMC10400990 DOI: 10.1073/pnas.2305496120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
Cell-to-cell communication is fundamental to multicellular organisms and unicellular organisms living in a microbiome. It is thought to have evolved as a stress- or quorum-sensing mechanism in unicellular organisms. A unique cell-to-cell communication mechanism that uses reactive oxygen species (ROS) as a signal (termed the "ROS wave") was identified in flowering plants. This process is essential for systemic signaling and plant acclimation to stress and can spread from a small group of cells to the entire plant within minutes. Whether a similar signaling process is found in other organisms is however unknown. Here, we report that the ROS wave can be found in unicellular algae, amoeba, ferns, mosses, mammalian cells, and isolated hearts. We further show that this process can be triggered in unicellular and multicellular organisms by a local stress or H2O2 treatment and blocked by the application of catalase or NADPH oxidase inhibitors and that in unicellular algae it communicates important stress-response signals between cells. Taken together, our findings suggest that an active process of cell-to-cell ROS signaling, like the ROS wave, evolved before unicellular and multicellular organisms diverged. This mechanism could have communicated an environmental stress signal between cells and coordinated the acclimation response of many different cells living in a community. The finding of a signaling process, like the ROS wave, in mammalian cells further contributes to our understanding of different diseases and could impact the development of drugs that target for example cancer or heart disease.
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Affiliation(s)
- Yosef Fichman
- Division of Plant Sciences and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Linda Rowland
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Melvin J. Oliver
- Division of Plant Sciences and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Ron Mittler
- Division of Plant Sciences and Technology, College of Agriculture Food and Natural Resources and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
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13
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Liao J, Wei X, Tao K, Deng G, Shu J, Qiao Q, Chen G, Wei Z, Fan M, Saud S, Fahad S, Chen S. Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants. HORTICULTURE RESEARCH 2023; 10:uhad102. [PMID: 37786731 PMCID: PMC10541563 DOI: 10.1093/hr/uhad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/16/2023] [Accepted: 05/05/2023] [Indexed: 10/04/2023]
Abstract
Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.
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Affiliation(s)
- Jugou Liao
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, Yunnan Province, 671003, China
| | - Keliang Tao
- School of Life Science, Yunnan University, Yunnan Province, Kunming 650091, China
| | - Gang Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Yunnan Province, Kunming 650091, China
| | - Jie Shu
- School of Life Science, Yunnan University, Yunnan Province, Kunming 650091, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Yunnan Province, Kunming 650091, China
| | - Gonglin Chen
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Zhuo Wei
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Meihui Fan
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
| | - Shah Saud
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Shah Fahad
- Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan
| | - Suiyun Chen
- School of Ecology and Environmental Sciences, Yunnan University; Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Kunming 650091, China
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14
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Powell AE, Heyl A. The origin and early evolution of cytokinin signaling. FRONTIERS IN PLANT SCIENCE 2023; 14:1142748. [PMID: 37457338 PMCID: PMC10338860 DOI: 10.3389/fpls.2023.1142748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023]
Abstract
Angiosperms, especially Arabidopsis and rice, have long been at the center of plant research. However, technological advances in sequencing have led to a dramatic increase in genome and transcriptome data availability across land plants and, more recently, among green algae. These data allowed for an in-depth study of the evolution of different protein families - including those involved in the metabolism and signaling of phytohormones. While most early studies on phytohormone evolution were phylogenetic, those studies have started to be complemented by genetic and biochemical studies in recent years. Examples of such functional analyses focused on ethylene, jasmonic acid, abscisic acid, and auxin. These data have been summarized recently. In this review, we will focus on the progress in our understanding of cytokinin biology. We will use these data to synthesize key points about the evolution of cytokinin metabolism and signaling, which might apply to the evolution of other phytohormones as well.
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15
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Chini A, Monte I, Zamarreño AM, García-Mina JM, Solano R. Evolution of the jasmonate ligands and their biosynthetic pathways. THE NEW PHYTOLOGIST 2023; 238:2236-2246. [PMID: 36942932 DOI: 10.1111/nph.18891] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 05/04/2023]
Abstract
Different plant species employ different jasmonates to activate a conserved signalling pathway in land plants, where (+)-7-iso-JA-Ile (JA-Ile) is the ligand for the COI1/JAZ receptor in angiosperms and dn-cis-OPDA, dn-iso-OPDA and Δ4 -dn-iso-OPDA act as ligands in Marchantia polymorpha. In addition, some jasmonates play a COI1-independent role. To understand the distribution of bioactive jasmonates in the green lineage and how their biosynthetic pathways evolved, we performed phylogenetic analyses and systematic jasmonates profiling in representative species from different lineages. We found that both OPDA and dn-OPDA are ubiquitous in all tested land plants and present also in charophyte algae, underscoring their importance as ancestral signalling molecules. By contrast, JA-Ile biosynthesis emerged within lycophytes coincident with the evolutionary appearance of JAR1 function. We identified that the OPR3-independent JA biosynthesis pathway is ancient and predates the evolutionary appearance of the OPR3-dependent pathway. Moreover, we identified a negative correlation between dn-iso-OPDA and JA-Ile in land plants, which supports that in bryophytes and lycophytes dn-iso-OPDA represents the analogous hormone to JA-Ile in other vascular plants.
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Affiliation(s)
- Andrea Chini
- Plant Molecular Genetics Department, Centro Nacional de Biotecnologia-CSIC (CNB-CSIC), 28049, Madrid, Spain
| | - Isabel Monte
- Plant Molecular Genetics Department, Centro Nacional de Biotecnologia-CSIC (CNB-CSIC), 28049, Madrid, Spain
| | - Angel M Zamarreño
- Department of Environmental Biology, Bioma Institute, University of Navarra, Navarra, 31008, Spain
| | - José M García-Mina
- Department of Environmental Biology, Bioma Institute, University of Navarra, Navarra, 31008, Spain
| | - Roberto Solano
- Plant Molecular Genetics Department, Centro Nacional de Biotecnologia-CSIC (CNB-CSIC), 28049, Madrid, Spain
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16
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Sanyal SK, Sharma K, Bisht D, Sharma S, Kateriya S, Pandey GK. Role of calcium sensor protein module CBL-CIPK in abiotic stress and light signaling responses in green algae. Int J Biol Macromol 2023; 237:124163. [PMID: 36965564 DOI: 10.1016/j.ijbiomac.2023.124163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
Ca2+ signaling is an important biological process that enable to perceive and communicate information in the cell. Our current understanding of the signaling system suggests that plants and animals have certain differences in signal-sensing mechanisms. The Ca2+-mediated CBL-CIPK module has emerged as a major sensor responder network for Ca2+ signaling and has been speculated to be involved in plant terrestrial life adaptation. This module has previously been reported in Archaeplastids, Chromalveolates, and Excavates. In our experimental analysis of Chlamydomonas reinhardtii CBLs, we proved that the CrCBL1 protein interacts with Phototropin and Channelrhodopsin, and the expression of CrCBLs is modulated by light. Further analysis using chlorophyte and streptophyte algal sequences allowed us to identify the differences that have evolved in CBL and CIPK proteins since plants have progressed from aquatic to terrestrial habitats. Moreover, an investigation of Klebsormidium CBL and CIPK genes led us to know that they are abiotic stress stimuli-responsive, indicating that their role was defined very early during terrestrial adaptations. Structure-based prediction and Ca2+-binding assays indicated that the KnCBL1 protein in Klebsormidium showed a typical Ca2+-binding pocket. In summary, the results of this study suggest that these stress-responsive proteins enable crosstalk between Ca2+ and light signaling pathways very early during plant adaptation from aquatic to terrestrial habitats.
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Affiliation(s)
- Sibaji K Sanyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India; Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Komal Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India; Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Diksha Bisht
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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17
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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18
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Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, de Vries J. Crossroads in the evolution of plant specialized metabolism. Semin Cell Dev Biol 2023; 134:37-58. [PMID: 35292191 DOI: 10.1016/j.semcdb.2022.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022]
Abstract
The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.
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Affiliation(s)
- Tim P Rieseberg
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtsr. 1, 37077 Goettingen, Germany.
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19
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Leong R, Tan JJ, Koh SS, Wu TY, Ishizaki K, Urano D. G protein signaling and metabolic pathways as evolutionarily conserved mechanisms to combat calcium deficiency. THE NEW PHYTOLOGIST 2023; 237:615-630. [PMID: 36266966 DOI: 10.1111/nph.18561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Calcium (Ca) deficiency causes necrotic symptoms of foliar edges known as tipburn; however, the underlying cellular mechanisms have been poorly understood due to the lack of an ideal plant model and research platform. Using a phenotyping system that quantitates growth and tipburn traits in the model bryophyte Marchantia polymorpha, we evaluated metabolic compounds and the Gβ-null mutant (gpb1) that modulate the occurrence and expansion of the tipburn. Transcriptomic comparisons between wild-type and gpb1 plants revealed the phenylalanine/phenylpropanoid biosynthesis pathway and reactive oxygen species (ROS) important for Ca deficiency responses. gpb1 plants reduced ROS production possibly through transcriptomic regulations of class III peroxidases and induced the expression of phenylpropanoid pathway enzymes without changing downstream lignin contents. Supplementation of intermediate metabolites and chemical inhibitors further confirmed the cell-protective mechanisms of the phenylpropanoid and ROS pathways. Marchantia polymorpha, Arabidopsis thaliana, and Lactuca sativa showed comparable transcriptomic changes where genes related to phenylpropanoid and ROS pathways were enriched in response to Ca deficiency. In conclusion, our study demonstrated unresolved signaling and metabolic pathways of Ca deficiency response. The phenotyping platform can speed up the discovery of chemical and genetic pathways, which could be widely conserved between M. polymorpha and angiosperms.
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Affiliation(s)
- Richalynn Leong
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
| | - Javier Jingheng Tan
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
| | - Sally Shuxian Koh
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
| | - Ting-Ying Wu
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore City, Singapore
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20
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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21
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Pettinari G, Finello J, Plaza Rojas M, Liberatore F, Robert G, Otaiza-González S, Velez P, Theumer M, Agudelo-Romero P, Enet A, González C, Lascano R, Saavedra L. Autophagy modulates growth and development in the moss Physcomitrium patens. FRONTIERS IN PLANT SCIENCE 2022; 13:1052358. [PMID: 36600927 PMCID: PMC9807217 DOI: 10.3389/fpls.2022.1052358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Physcomitrium patens apical growing protonemal cells have the singularity that they continue to undergo cell divisions as the plant develops. This feature provides a valuable tool to study autophagy in the context of a multicellular apical growing tissue coupled to development. Herein, we showed that the core autophagy machinery is present in the moss P. patens, and characterized the 2D and 3D growth and development of atg5 and atg7 loss-of-function mutants under optimal and nutrient-deprived conditions. Our results showed that 2D growth of the different morphological and functional protonemata apical growing cells, chloronema and caulonema, is differentially modulated by this process. These differences depend on the protonema cell type and position along the protonemal filament, and growth condition. As a global plant response, the absence of autophagy favors the spread of the colony through protonemata growth at the expense of a reduction of the 3D growth, such as the buds and gametophore development, and thus the adult gametophytic and reproductive phases. Altogether this study provides valuable information suggesting that autophagy has roles during apical growth with differential responses within the cell types of the same tissue and contributes to life cycle progression and thus the growth and development of the 2D and 3D tissues of P. patens.
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Affiliation(s)
- Georgina Pettinari
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan Finello
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Macarena Plaza Rojas
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Franco Liberatore
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
| | - Germán Robert
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Pilar Velez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Universidad Nacional de Córdoba-CONICET, Córdoba, Argentina
| | - Martin Theumer
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Universidad Nacional de Córdoba-CONICET, Córdoba, Argentina
| | | | - Alejandro Enet
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
| | - Claudio González
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ramiro Lascano
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Laura Saavedra
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
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22
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Wu TY, Krishnamoorthi S, Boonyaves K, Al-Darabsah I, Leong R, Jones AM, Ishizaki K, Liao KL, Urano D. G protein controls stress readiness by modulating transcriptional and metabolic homeostasis in Arabidopsis thaliana and Marchantia polymorpha. MOLECULAR PLANT 2022; 15:1889-1907. [PMID: 36321200 DOI: 10.1016/j.molp.2022.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The core G protein signaling module, which consists of Gα and extra-large Gα (XLG) subunits coupled with the Gβγ dimer, is a master regulator of various stress responses. In this study, we compared the basal and salt stress-induced transcriptomic, metabolomic and phenotypic profiles in Gα, Gβ, and XLG-null mutants of two plant species, Arabidopsis thaliana and Marchantia polymorpha, and showed that G protein mediates the shift of transcriptional and metabolic homeostasis to stress readiness status. We demonstrated that such stress readiness serves as an intrinsic protection mechanism against further stressors through enhancing the phenylpropanoid pathway and abscisic acid responses. Furthermore, WRKY transcription factors were identified as key intermediates of G protein-mediated homeostatic shifts. Statistical and mathematical model comparisons between A. thaliana and M. polymorpha revealed evolutionary conservation of transcriptional and metabolic networks over land plant evolution, whereas divergence has occurred in the function of plant-specific atypical XLG subunit. Taken together, our results indicate that the shifts in transcriptional and metabolic homeostasis at least partially act as the mechanisms of G protein-coupled stress responses that are conserved between two distantly related plants.
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Affiliation(s)
- Ting-Ying Wu
- Temasek Life Sciences Laboratory, Singapore, Singapore.
| | | | - Kulaporn Boonyaves
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Isam Al-Darabsah
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| | - Richalynn Leong
- Temasek Life Sciences Laboratory, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Alan M Jones
- Departments of Biology and Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kang-Ling Liao
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada.
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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23
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Davies KM, Landi M, van Klink JW, Schwinn KE, Brummell DA, Albert NW, Chagné D, Jibran R, Kulshrestha S, Zhou Y, Bowman JL. Evolution and function of red pigmentation in land plants. ANNALS OF BOTANY 2022; 130:613-636. [PMID: 36070407 PMCID: PMC9670752 DOI: 10.1093/aob/mcac109] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments. SCOPE In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues; theories on the functions of stress-induced pigmentation; the evolution of the biosynthetic pathways; and structure-function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants. CONCLUSIONS The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.
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Affiliation(s)
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - John W van Klink
- The New Zealand Institute for Plant and Food Research Limited, Department of Chemistry, Otago University, Dunedin, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Samarth Kulshrestha
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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24
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Koshimizu S, Minamino N, Nishiyama T, Yoro E, Sato M, Wakazaki M, Toyooka K, Ebine K, Sakakibara K, Ueda T, Yano K. Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis. THE NEW PHYTOLOGIST 2022; 236:1182-1196. [PMID: 35842793 DOI: 10.1111/nph.18385] [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: 05/18/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Land plant spermatozoids commonly possess characteristic structures such as the spline, which consists of a microtubule array, the multilayered structure (MLS) in which the uppermost layer is a continuum of the spline, and multiple flagella. However, the molecular mechanisms underpinning spermatogenesis remain to be elucidated. We successfully identified candidate genes involved in spermatogenesis, deeply divergent BLD10s, by computational analyses combining multiple methods and omics data. We then examined the functions of BLD10s in the liverwort Marchantia polymorpha and the moss Physcomitrium patens. MpBLD10 and PpBLD10 are required for normal basal body (BB) and flagella formation. Mpbld10 mutants exhibited defects in remodeling of the cytoplasm and nucleus during spermatozoid formation, and thus MpBLD10 should be involved in chromatin reorganization and elimination of the cytoplasm during spermiogenesis. We identified orthologs of MpBLD10 and PpBLD10 in diverse Streptophyta and found that MpBLD10 and PpBLD10 are orthologous to BLD10/CEP135 family proteins, which function in BB assembly. However, BLD10s evolved especially quickly in land plants and MpBLD10 might have acquired additional functions in spermatozoid formation through rapid molecular evolution.
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Affiliation(s)
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan
| | - Emiko Yoro
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kazuo Ebine
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
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25
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Hess S, Williams SK, Busch A, Irisarri I, Delwiche CF, de Vries S, Darienko T, Roger AJ, Archibald JM, Buschmann H, von Schwartzenberg K, de Vries J. A phylogenomically informed five-order system for the closest relatives of land plants. Curr Biol 2022; 32:4473-4482.e7. [PMID: 36055238 PMCID: PMC9632326 DOI: 10.1016/j.cub.2022.08.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
The evolution of streptophytes had a profound impact on life on Earth. They brought forth those photosynthetic eukaryotes that today dominate the macroscopic flora: the land plants (Embryophyta).1 There is convincing evidence that the unicellular/filamentous Zygnematophyceae-and not the morphologically more elaborate Coleochaetophyceae or Charophyceae-are the closest algal relatives of land plants.2-6 Despite the species richness (>4,000), wide distribution, and key evolutionary position of the zygnematophytes, their internal phylogeny remains largely unresolved.7,8 There are also putative zygnematophytes with interesting body plan modifications (e.g., filamentous growth) whose phylogenetic affiliations remain unknown. Here, we studied a filamentous green alga (strain MZCH580) from an Austrian peat bog with central or parietal chloroplasts that lack discernible pyrenoids. It represents Mougeotiopsis calospora PALLA, an enigmatic alga that was described more than 120 years ago9 but never subjected to molecular analyses. We generated transcriptomic data of M. calospora strain MZCH580 and conducted comprehensive phylogenomic analyses (326 nuclear loci) for 46 taxonomically diverse zygnematophytes. Strain MZCH580 falls in a deep-branching zygnematophycean clade together with some unicellular species and thus represents a formerly unknown zygnematophycean lineage with filamentous growth. Our well-supported phylogenomic tree lets us propose a new five-order system for the Zygnematophyceae and provides evidence for at least five independent origins of true filamentous growth in the closest algal relatives of land plants. This phylogeny provides a robust and comprehensive framework for performing comparative analyses and inferring the evolution of cellular traits and body plans in the closest relatives of land plants.
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Affiliation(s)
- Sebastian Hess
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany.
| | - Shelby K Williams
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - Anna Busch
- Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Charles F Delwiche
- Cell Biology and Molecular Genetics, University of Maryland-College Park, College Park, MD, USA
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax NS B3H 4R2, Canada
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
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26
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Niemeyer PW, Irisarri I, Scholz P, Schmitt K, Valerius O, Braus GH, Herrfurth C, Feussner I, Sharma S, Carlsson AS, de Vries J, Hofvander P, Ischebeck T. A seed-like proteome in oil-rich tubers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:518-534. [PMID: 36050843 DOI: 10.1111/tpj.15964] [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: 03/12/2021] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
There are numerous examples of plant organs or developmental stages that are desiccation-tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation-tolerant. One example are the tubers of yellow nutsedge (Cyperus esculentus), which also store large amounts of lipids similar to seeds. Interestingly, the closest known relative, purple nutsedge (Cyperus rotundus), generates tubers that do not accumulate oil and are not desiccation-tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the close relative purple nutsedge (C. rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid droplet-enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homologous to ABSCISIC ACID INSENSITIVE3, WRINKLED1, and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.
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Affiliation(s)
- Philipp William Niemeyer
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Kerstin Schmitt
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Oliver Valerius
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Gerhard H Braus
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Shrikant Sharma
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Anders S Carlsson
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Jan de Vries
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Per Hofvander
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
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27
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Guo D, Wang H, Zhang S, Lan T. The type III polyketide synthase supergene family in plants: complex evolutionary history and functional divergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:414-428. [PMID: 36004534 DOI: 10.1111/tpj.15953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Type III polyketide synthases (PKSs) are key enzymes involved in the biosynthesis of a variety of plant specialized metabolites, including flavonoids, stilbenes, and sporopollenin, to name a few. These enzymes likely played vital roles in plant adaptation during their transition from aquatic to terrestrial habitats and their colonization of specific ecological environments. Members of this supergene family have diverse functions, but how type III PKSs and their functions have evolved remains poorly understood. Here, we conducted comprehensive phylogenomics analysis of the type III PKS supergene family in 60 species representing the major plant lineages and elucidated the classification, origin, and evolutionary history of each class. Molecular evolutionary analysis of the typical chalcone synthase and stilbene synthase types revealed evidence for strong positive natural selection in both the Pinaceae and Fabaceae lineages. The positively selected sites of these proteins include residues at the catalytic tunnel entrance and homodimer interface, which might have driven the functional divergence between the two types. Our results also suggest that convergent evolution of enzymes involved in plant flavonoid biosynthesis is quite common. The results of this study provide new insights into the origin, evolution, and functional diversity of plant type III PKSs. In addition, they serve as a guide for the enzymatic engineering of plant polyketides.
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Affiliation(s)
- Dongmei Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Hanyan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Shumin Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Ting Lan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
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28
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Fürst-Jansen JM, de Vries S, Lorenz M, von Schwartzenberg K, Archibald JM, de Vries J. Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with core metabolism and photosynthesis. PROTOPLASMA 2022; 259:1157-1174. [PMID: 34939169 PMCID: PMC9385824 DOI: 10.1007/s00709-021-01730-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/06/2021] [Indexed: 06/01/2023]
Abstract
The streptophyte algal class Zygnematophyceae is the closest algal sister lineage to land plants. In nature, Zygnematophyceae can grow in both terrestrial and freshwater habitats and how they do this is an important unanswered question. Here, we studied what happens to the zygnematophyceaen alga Mougeotia sp., which usually occurs in permanent and temporary freshwater bodies, when it is shifted to liquid growth conditions after growth on a solid substrate. Using global differential gene expression profiling, we identified changes in the core metabolism of the organism interlinked with photosynthesis; the latter went hand in hand with measurable impact on the photophysiology as assessed via pulse amplitude modulation (PAM) fluorometry. Our data reveal a pronounced change in the overall physiology of the alga after submergence and pinpoint candidate genes that play a role. These results provide insight into the importance of photophysiological readjustment when filamentous Zygnematophyceae transition between terrestrial and aquatic habitats.
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Affiliation(s)
- Janine M.R. Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, University of Goettingen, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, University of Goettingen, 37077 Goettingen, Germany
| | - Maike Lorenz
- Department of Experimental Phycology and SAG Culture Collection of Algae, Albrecht-von-Haller Institute for Plant Science, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Klaus von Schwartzenberg
- Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Universität Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, University of Goettingen, 37077 Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstr. 1, 37077 Goettingen, Germany
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29
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Schreiber M, Rensing SA, Gould SB. The greening ashore. TRENDS IN PLANT SCIENCE 2022; 27:847-857. [PMID: 35739050 DOI: 10.1016/j.tplants.2022.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.
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Affiliation(s)
- Mona Schreiber
- Plant Cell Biology, University of Marburg, 35043 Marburg, Germany.
| | - Stefan A Rensing
- Plant Cell Biology, University of Marburg, 35043 Marburg, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany.
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University (HHU) Düsseldorf, 40225 Düsseldorf, Germany.
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30
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Puginier C, Keller J, Delaux PM. Plant-microbe interactions that have impacted plant terrestrializations. PLANT PHYSIOLOGY 2022; 190:72-84. [PMID: 35642902 PMCID: PMC9434271 DOI: 10.1093/plphys/kiac258] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 05/30/2023]
Abstract
Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
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31
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Acclimation Strategy of Masson Pine (Pinus massoniana) by Limiting Flavonoid and Terpenoid Production under Low Light and Drought. Int J Mol Sci 2022; 23:ijms23158441. [PMID: 35955577 PMCID: PMC9368996 DOI: 10.3390/ijms23158441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 12/10/2022] Open
Abstract
Low light and drought often limit the growth and performance of Masson pines (Pinus massoniana) in the subtropical forest ecosystem of China. We speculated that stress-induced defensive secondary metabolites, such as flavonoids and terpenoids, might influence the growth of Masson pines, considering the existence of tradeoffs between growth and defense. However, the mechanisms of Masson pines responsive to low light and drought at the levels of these two metabolites remain unclear. In the present work, the compositions of flavonoids and terpenoids, as well as their biosynthetic pathways, were revealed through metabolome and transcriptome analyses, respectively, coupled with a study on carbon allocation using a 13CO2-pulse-labeling experiment in two-year-old seedlings under low light (LL), drought (DR), and their combined stress (DL) compared to a control (CK). A total of 35 flavonoids and derivatives (LL vs. CK: 18; DR vs. CK: 20; and DL vs. CK: 18), as well as 29 terpenoids and derivatives (LL vs. CK: 23; DR vs. CK: 13; and DL vs. CK: 7), were differentially identified in the leaves. Surprisingly, most of them were decreased under all three stress regimes. At the transcriptomic level, most or all of the detected DEGs (differentially expressed genes) involved in the biosynthetic pathways of flavonoids and terpenoids were downregulated in phloem and xylem under stress treatments. This indicated that stress treatments limited the production of flavonoids and terpenoids. The reduction in the 13C allocation to stems might suggest that it is necessary for maintaining the growth of Masson pine seedlings at the whole-plant level by attenuating energetic resources to the biosynthetic pathways of flavonoids and terpenoids when facing the occurrence of adverse environments. Our results provide new insight into understanding the acclimation strategy of Masson pines or other conifers in adverse environments.
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32
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Degola F, Sanità di Toppi L, Petraglia A. Bryophytes: how to conquer an alien planet and live happily (ever after). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4267-4272. [PMID: 35849121 DOI: 10.1093/jxb/erac252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Francesca Degola
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | | | - Alessandro Petraglia
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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33
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Reboledo G, Agorio A, Ponce De León I. Moss transcription factors regulating development and defense responses to stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4546-4561. [PMID: 35167679 DOI: 10.1093/jxb/erac055] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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34
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Martínez-Abaigar J, Núñez-Olivera E. Bryophyte ultraviolet-omics: from genes to the environment. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4412-4426. [PMID: 35274697 DOI: 10.1093/jxb/erac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Ultraviolet (UV) radiation has contributed to the evolution of organisms since the origins of life. Bryophytes also have evolutionary importance as the first clearly identified lineage of land plants (embryophytes) colonizing the terrestrial environment, thus facing high UV and water scarcity, among other new challenges. Here we review bryophyte UV-omics, the discipline relating bryophytes and UV, with an integrative perspective from genes to the environment. We consider species and habitats investigated, methodology, response variables, protection mechanisms, environmental interactions, UV biomonitoring, molecular and evolutionary aspects, and applications. Bryophyte UV-omics shows convergences and divergences with the UV-omics of other photosynthetic organisms, from algae to tracheophytes. All these organisms converge in that UV damage may be limited under realistic UV levels, due to structural protection and/or physiological acclimation capacity. Nevertheless, bryophytes diverge because they have a unique combination of vegetative and reproductive characteristics to cope with high UV and other concomitant adverse processes, such as desiccation. This interaction has both evolutionary and ecological implications. In addition, UV effects on bryophytes depend on the species and the evolutionary lineage considered, with mosses more UV-tolerant than liverworts. Thus, bryophytes do not constitute a homogeneous functional type with respect to their UV tolerance.
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Affiliation(s)
- Javier Martínez-Abaigar
- Faculty of Science and Technology, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
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35
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Kulshrestha S, Jibran R, van Klink JW, Zhou Y, Brummell DA, Albert NW, Schwinn KE, Chagné D, Landi M, Bowman JL, Davies KM. Stress, senescence, and specialized metabolites in bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4396-4411. [PMID: 35259256 PMCID: PMC9291361 DOI: 10.1093/jxb/erac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
Life on land exposes plants to varied abiotic and biotic environmental stresses. These environmental drivers contributed to a large expansion of metabolic capabilities during land plant evolution and species diversification. In this review we summarize knowledge on how the specialized metabolite pathways of bryophytes may contribute to stress tolerance capabilities. Bryophytes are the non-tracheophyte land plant group (comprising the hornworts, liverworts, and mosses) and rapidly diversified following the colonization of land. Mosses and liverworts have as wide a distribution as flowering plants with regard to available environments, able to grow in polar regions through to hot desert landscapes. Yet in contrast to flowering plants, for which the biosynthetic pathways, transcriptional regulation, and compound function of stress tolerance-related metabolite pathways have been extensively characterized, it is only recently that similar data have become available for bryophytes. The bryophyte data are compared with those available for angiosperms, including examining how the differing plant forms of bryophytes and angiosperms may influence specialized metabolite diversity and function. The involvement of stress-induced specialized metabolites in senescence and nutrient response pathways is also discussed.
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Affiliation(s)
- Samarth Kulshrestha
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - John W van Klink
- The New Zealand Institute for Plant and Food Research Limited, Department of Chemistry, Otago University, Dunedin, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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36
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Oliveira MF, Maciel-Silva AS. Biological soil crusts and how they might colonize other worlds: insights from these Brazilian ecosystem engineers. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4362-4379. [PMID: 35522077 DOI: 10.1093/jxb/erac162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
When bryophytes, lichens, eukaryotic algae, cyanobacteria, bacteria, and fungi live interacting intimately with the most superficial particles of the soil, they form a complex community of organisms called the biological soil crust (BSC or biocrust). These biocrusts occur predominantly in drylands, where they provide important ecological services such as soil aggregation, moisture retention, and nitrogen fixation. Unfortunately, many BSC communities remain poorly explored, especially in the tropics. This review summarizes studies about BSCs in Brazil, a tropical megadiverse country, and shows the importance of ecological, physiological, and taxonomic knowledge of biocrusts. We also compare Brazilian BSC communities with others around the world, describe why BSCs can be considered ecosystem engineers, and propose their use in the colonization of other worlds.
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Affiliation(s)
- Mateus Fernandes Oliveira
- Universidade Federal de Minas Gerais, Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Adaíses Simone Maciel-Silva
- Universidade Federal de Minas Gerais, Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
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37
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Bowles AMC, Paps J, Bechtold U. Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. THE NEW PHYTOLOGIST 2022; 235:732-742. [PMID: 35048381 PMCID: PMC9303528 DOI: 10.1111/nph.17981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/25/2021] [Indexed: 05/26/2023]
Abstract
The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
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Affiliation(s)
- Alexander M. C. Bowles
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Geographical SciencesUniversity of BristolUniversity RoadBristolBS8 1RLUK
| | - Jordi Paps
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ulrike Bechtold
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Present address:
Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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38
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Fürst-Jansen JMR, de Vries S, Irisarri I. Different patterns of gene evolution underpin water-related innovations in land plants. THE NEW PHYTOLOGIST 2022; 235:380-383. [PMID: 35593660 DOI: 10.1111/nph.18176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Sophie de Vries
- 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
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstr. 1, 37077, Goettingen, Germany
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39
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA,Corresponding author.
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40
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Barthlott W, Büdel B, Mail M, Neumann KM, Bartels D, Fischer E. Superhydrophobic Terrestrial Cyanobacteria and Land Plant Transition. FRONTIERS IN PLANT SCIENCE 2022; 13:880439. [PMID: 35685010 PMCID: PMC9173694 DOI: 10.3389/fpls.2022.880439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Plants and other organisms have evolved structures and mechanisms for colonizing land since the Early Ordovician. In this context, their surfaces, the crucial physical interface with the environment, are mainly considered barriers against water loss. It is suggested that extreme water repellency (superhydrophobicity) was an additional key innovation for the transition of algae from water to land some 400 mya. Superhydrophobicity enhances gas exchange on land and excludes aquatic competitors in water films. In a different context, in material science and surface technology, superhydrophobicity has also become one of the most important bioinspired innovations enabling the avoidance of water films and contamination. Here, we present data for an extremely water-repellent cyanobacterial biofilm of the desiccation tolerant Hassallia byssoidea providing evidence for a much earlier prokaryotic Precambrian (ca. 1-2 bya) origin of superhydrophobicity and chemical heterogeneities associated with land transition. The multicellular cyanobacterium is functionally differentiated in a submerged basal hydrophilic absorbing portion like a "rhizoid" and an upright emersed superhydrophobic "phyllocauloid" filament for assimilation, nitrogen fixation, and splash dispersed diaspores. Additional data are provided for superhydrophobic surfaces in terrestrial green algae and in virtually all ancestral land plants (Bryophytes, ferns and allies, Amborella, Nelumbo), slime molds, and fungi. Rethinking of superhydrophobicity as an essential first step for life in terrestrial environments is suggested.
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Affiliation(s)
- Wilhelm Barthlott
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Burkhard Büdel
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Matthias Mail
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
- Karlsruhe Nano Micro Facility and Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Dorothea Bartels
- Institute of Molecular Biology and Biochemistry of Plants, University of Bonn, Bonn, Germany
| | - Eberhard Fischer
- Department of Biology, University of Koblenz-Landau, Koblenz, Germany
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Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization. Int J Mol Sci 2022; 23:ijms23095284. [PMID: 35563675 PMCID: PMC9101737 DOI: 10.3390/ijms23095284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile “defense compounds”, essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.
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42
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Ma J, Wang S, Zhu X, Sun G, Chang G, Li L, Hu X, Zhang S, Zhou Y, Song CP, Huang J. Major episodes of horizontal gene transfer drove the evolution of land plants. MOLECULAR PLANT 2022; 15:857-871. [PMID: 35235827 DOI: 10.1016/j.molp.2022.02.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/10/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
How horizontal gene transfer (HGT) has contributed to the evolution of animals and plants remains a major puzzle. Despite recent progress, defining the overall scale and pattern of HGT events in land plants has been largely elusive. In this study, we performed systematic analyses for acquired genes in different plant groups and throughout land plant evolution. We found that relatively recent HGT events occurred in charophytes and all major land plant groups, but their frequency declined rapidly in seed plants. Two major episodes of HGT events occurred in land plant evolution, corresponding to the early evolution of streptophytes and the origin of land plants, respectively. Importantly, a vast majority of the genes acquired in the two episodes have been retained in descendant groups, affecting numerous activities and processes of land plants. We analyzed some of the acquired genes involved in stress responses, ion and metabolite transport, growth and development, and specialized metabolism, and further assessed the cumulative effects of HGT in land plants.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Shuanghua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiaojing Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Guiling Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Guanxiao Chang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Linhong Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shouzhou Zhang
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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43
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Irisarri I, de Vries J. Punctuated ancestral gene gains in streptophyte evolution. MOLECULAR PLANT 2022; 15:799-801. [PMID: 35342001 DOI: 10.1016/j.molp.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, Germany; Campus Institute Data Science (CIDAS), Göttingen, Germany.
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, Germany; Campus Institute Data Science (CIDAS), Göttingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
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44
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Naumann C, Heisters M, Brandt W, Janitza P, Alfs C, Tang N, Toto Nienguesso A, Ziegler J, Imre R, Mechtler K, Dagdas Y, Hoehenwarter W, Sawers G, Quint M, Abel S. Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. Curr Biol 2022; 32:2189-2205.e6. [PMID: 35472311 PMCID: PMC9168544 DOI: 10.1016/j.cub.2022.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 02/21/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022]
Abstract
Access to inorganic phosphate (Pi), a principal intermediate of energy and nucleotide metabolism, profoundly affects cellular activities and plant performance. In most soils, antagonistic Pi-metal interactions restrict Pi bioavailability, which guides local root development to maximize Pi interception. Growing root tips scout the essential but immobile mineral nutrient; however, the mechanisms monitoring external Pi status are unknown. Here, we show that Arabidopsis LOW PHOSPHATE ROOT 1 (LPR1), one key determinant of Fe-dependent Pi sensing in root meristems, encodes a novel ferroxidase of high substrate specificity and affinity (apparent KM ∼ 2 μM Fe2+). LPR1 typifies an ancient, Fe-oxidizing multicopper protein family that evolved early upon bacterial land colonization. The ancestor of streptophyte algae and embryophytes (land plants) acquired LPR1-type ferroxidase from soil bacteria via horizontal gene transfer, a hypothesis supported by phylogenomics, homology modeling, and biochemistry. Our molecular and kinetic data on LPR1 regulation indicate that Pi-dependent Fe substrate availability determines LPR1 activity and function. Guided by the metabolic lifestyle of extant sister bacterial genera, we propose that Arabidopsis LPR1 monitors subtle concentration differentials of external Fe availability as a Pi-dependent cue to adjust root meristem maintenance via Fe redox signaling and cell wall modification. We further hypothesize that the acquisition of bacterial LPR1-type ferroxidase by embryophyte progenitors facilitated the evolution of local Pi sensing and acquisition during plant terrestrialization. Arabidopsis thaliana LPR1 multicopper oxidase typifies a novel ferroxidase cohort Fe availability tunes LPR1-dependent root responses to phosphate (Pi) limitation LPR1 specificity links Fe-Pi interactions to root Pi sensing via redox cycling Streptophyte ancestors acquired LPR1-type ferroxidase from soil bacteria by HGT
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45
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Kwantes M, Wichard T. The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants. PLANTA 2022; 255:76. [PMID: 35235070 PMCID: PMC8891106 DOI: 10.1007/s00425-022-03851-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/07/2022] [Indexed: 06/02/2023]
Abstract
We advance Ulva's genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily.
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Affiliation(s)
- Michiel Kwantes
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
- Jena School for Microbial Communication, 07743, Jena, Germany.
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46
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Schumacher I, Menghini D, Ovinnikov S, Hauenstein M, Fankhauser N, Zipfel C, Hörtensteiner S, Aubry S. Evolution of chlorophyll degradation is associated with plant transition to land. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1473-1488. [PMID: 34931727 PMCID: PMC9306834 DOI: 10.1111/tpj.15645] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 05/27/2023]
Abstract
Chlorophyll, the central pigment of photosynthesis, is highly photo‐active and degraded enzymatically during leaf senescence. Merging comparative genomics and metabolomics, we evaluate the extent to which the chlorophyll detoxification pathway has evolved in Viridiplantae. We argue that cytosolic detoxification of phyllobilins in particular was a critical process to the green lineage’s transition to land.
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Affiliation(s)
- Isabel Schumacher
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Damian Menghini
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Serguei Ovinnikov
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Mareike Hauenstein
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Niklaus Fankhauser
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Cyril Zipfel
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Stefan Hörtensteiner
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Sylvain Aubry
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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47
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Lee WK, Ho CL. Ecological and evolutionary diversification of sulphated polysaccharides in diverse photosynthetic lineages: A review. Carbohydr Polym 2022; 277:118764. [PMID: 34893214 DOI: 10.1016/j.carbpol.2021.118764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/02/2022]
Abstract
Sulphated polysaccharides (SPs) are carbohydrate macromolecules with sulphate esters that are found among marine algae, seagrasses, mangroves and some terrestrial plants. The sulphate concentration in the ocean (28 mM) since ancient time could have driven the production of SPs in marine algae. SPs have a gelatinous property that can protect marine algae against desiccation and salinity stress. Agar and carrageenan are red algal SPs that are widely used as gelling agents in the food and pharmaceutical industries. The information on the SPs from freshwater and land plants are limited. In this review, we reviewed the taxonomic distribution and composition of SPs in different photosynthetic lineages, and explored the association of SP production in these diversified photosynthetic organisms with evolution history and environmental stresses. We also reviewed the genes/proteins involved in SP biosynthesis. Insights into SP biosynthetic machinery may shed light on the evolution that accompanied adaptation to life on earth.
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Affiliation(s)
- Wei-Kang Lee
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia; Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Chai-Ling Ho
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia.
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48
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Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. QUANTITATIVE PLANT BIOLOGY 2022; 3:e5. [PMID: 37077982 PMCID: PMC10095996 DOI: 10.1017/qpb.2021.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
Abstract
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.
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Affiliation(s)
- Boas Pucker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
- Author for correspondence: Boas Pucker E-mail:
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB), University of Goettingen, Göttingen, Germany
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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49
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Arif MA, Top O, Csicsely E, Lichtenstern M, Beheshti H, Adjabi K, Frank W. DICER-LIKE1a autoregulation based on intronic microRNA processing is required for stress adaptation in Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:227-240. [PMID: 34743365 DOI: 10.1111/tpj.15570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/27/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
The Physcomitrium patens DICER-LIKE1a (PpDCL1a) mRNA encoding the essential Dicer protein for microRNA (miRNA) biogenesis harbors an intronic miRNA (miR1047). An autoregulatory mechanism to control PpDCL1a abundance that is based on competitive processing of the intronic miRNA and proper PpDCL1a mRNA splicing has previously been proposed. If intron splicing occurs first the mRNA can be translated into the functional PpDCL1a protein, whereas the processing of the intronic miRNA catalyzed by PpDCL1a itself, prior to pre-mRNA splicing, generates a truncated transcript unable to produce a functional protein. This proposed autoregulation of DCL1 has not been functionally analyzed in any plant species, and the existence of this autoregulatory control is expected to have a general impact on the overall miRNA biogenesis pathway and the transcriptome that is under miRNA control. We abolished PpDCL1a autoregulatory feedback control by the precise deletion of the MIR1047-containing intron. The generated line displayed hypersensitivity to salt stress and hyposensitivity to the plant hormone ABA, accompanied by the disturbed expression of miRNAs and mRNAs, revealed by transcriptome analyses. The feedback control together with the phenotypic abnormalities and molecular changes in the intron-less line can be rescued by the re-insertion of a modified intron harboring a sequence-unrelated artificial miRNA. Our findings indicate the physiological importance of miR1047-based feedback control of PpDCL1a transcript abundance, which controls the expression of miRNAs, and their cognate target RNAs during salt stress adaptation, and suggests a key role for this autoregulation in the molecular adaptation of land plants to terrestrial habitats.
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Affiliation(s)
- M Asif Arif
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Oguz Top
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Erika Csicsely
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Myriam Lichtenstern
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Hossein Beheshti
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Kaoutar Adjabi
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
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50
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Bhar A, Chakraborty A, Roy A. Plant Responses to Biotic Stress: Old Memories Matter. PLANTS (BASEL, SWITZERLAND) 2021; 11:84. [PMID: 35009087 PMCID: PMC8747260 DOI: 10.3390/plants11010084] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 05/20/2023]
Abstract
Plants are fascinating organisms present in most ecosystems and a model system for studying different facets of ecological interactions on Earth. In the environment, plants constantly encounter a multitude of abiotic and biotic stresses. The zero-avoidance phenomena make them more resilient to such environmental odds. Plants combat biotic stress or pathogenic ingression through a complex orchestration of intracellular signalling cascades. The plant-microbe interaction primarily relies on acquired immune response due to the absence of any specialised immunogenic cells for adaptive immune response. The generation of immune memory is mainly carried out by T cells as part of the humoral immune response in animals. Recently, prodigious advancements in our understanding of epigenetic regulations in plants invoke the "plant memory" theory afresh. Current innovations in cutting-edge genomic tools have revealed stress-associated genomic alterations and strengthened the idea of transgenerational memory in plants. In plants, stress signalling events are transferred as genomic imprints in successive generations, even without any stress. Such immunogenic priming of plants against biotic stresses is crucial for their eco-evolutionary success. However, there is limited literature capturing the current knowledge of the transgenerational memory of plants boosting biotic stress responses. In this context, the present review focuses on the general concept of memory in plants, recent advancements in this field and comprehensive implications in biotic stress tolerance with future perspectives.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, West Bengal, India
| | - Amrita Chakraborty
- EVA4.0-Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Amit Roy
- EVA4.0-Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, 16500 Prague, Czech Republic
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