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Han S, Wei Q, Liu J, Li L, Xu T, Cao L, Liu J, Liu X, Chen P, Liu H, Ma Y, Lei B, Lin Y. Naturally Occurring Dehydrocostus Lactone Covalently Binds to KARRIKIN INSENSITIVE 2 by Dual Serine Modifications in Orobanche cumana and Arabidopsis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19920-19930. [PMID: 39213540 DOI: 10.1021/acs.jafc.4c06359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Parasitic weeds, such as Orobanche and Striga, threaten crops globally. Contiguous efforts on the discovery and development of structurally novel seed germination stimulants targeting HYPOSENSITIVE TO LIGHT/KARRIKIN INSENSITIVE 2 (HTL/KAI2) have been made with the goal of weed control. Here, we demonstrate that a natural compound dehydrocostus lactone (DCL) exhibits effective "suicide germination" activity against Orobanche cumana and covalently binds to OcKAI2d2 on two catalytic serine sites with the second modification dependent on the first one. The same interactions and covalent modifications of DCL are also confirmed in AtKAI2. Further in-depth evolution analysis indicates that the proposed two catalytic sites are present throughout the streptophyte algae, hornworts, lycophytes, and seed plants. This discovery is particularly noteworthy as it signifies the first confirmation of a plant endogenous molecule directly binding to KAI2, which is valuable for unraveling the elusive identity of the KAI2 ligand and for targeting KAI2 paralogues for the development of novel germination stimulants.
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Affiliation(s)
- Siqi Han
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Qiannan Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Jiaxi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Linrui Li
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Tengqi Xu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Lin Cao
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Jiyuan Liu
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Xiayan Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Peng Chen
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Huawei Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Yongqing Ma
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Beilei Lei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Center of Bioinformatics, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China
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2
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Fortin JP, Friedman WE. A stomate by any other name? The open question of hornwort gametophytic pores, their homology, and implications for the evolution of stomates. THE NEW PHYTOLOGIST 2024. [PMID: 39256934 DOI: 10.1111/nph.20094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/14/2024] [Indexed: 09/12/2024]
Abstract
Advances in bryophyte genomics and the phylogenetic recovery of hornworts, mosses, and liverworts as a clade have spurred considerable recent interest in character evolution among early embryophytes. Discussion of stomatal evolution, however, has been incomplete; the result of the neglect of certain potential stomate homologues, namely the two-celled epidermal gametophytic pores of hornworts (typically referred to as 'mucilage clefts'). Confusion over the potential homology of these structures is the consequence of a relatively recent consensus that hornwort gametophytic pores ('HGPs' - our term) are not homologous to stomates. We explore the occurrence and diverse functions of stomates throughout the evolutionary history and diversity of extinct and extant embryophytes. We then address arguments for and against homology between known sporophyte- and gametophyte-borne stomates and HGPs and conclude that there is little to no evidence that contradicts the hypothesis of homology. We propose that 'intergenerational heterotopy' might well account for the novel expression of stomates in gametophytes of hornworts, if stomates first evolved in the sporophyte generation of embryophytes. We then explore phylogenetically based hypotheses for the evolution of stomates in both the gametophyte and sporophyte generations of early lineages of embryophytes.
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Affiliation(s)
- James Paul Fortin
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA
| | - William E Friedman
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
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3
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Frangedakis E, Yelina NE, Billakurthi K, Hua L, Schreier T, Dickinson PJ, Tomaselli M, Haseloff J, Hibberd JM. MYB-related transcription factors control chloroplast biogenesis. Cell 2024; 187:4859-4876.e22. [PMID: 39047726 DOI: 10.1016/j.cell.2024.06.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Chloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors. However, glk mutants contain residual chlorophyll, indicating that other proteins must be involved. Here, we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwort Marchantia polymorpha and angiosperm Arabidopsis thaliana. In both species, double-mutant alleles in MYB-related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in GLK mutants. Genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins, whereas those allowing CO2 fixation, photorespiration, and photosystem assembly and repair require MYB-related proteins. Regulation between the MYB-related and GLK transcription factors appears more extensive in A. thaliana than in M. polymorpha. Thus, MYB-related and GLK genes have overlapping as well as distinct targets. We conclude that MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.
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Affiliation(s)
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Kumari Billakurthi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Lei Hua
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Tina Schreier
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Patrick J Dickinson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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4
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Yelina NE, Frangedakis E, Wang Z, Schreier TB, Rever J, Tomaselli M, Forestier ECF, Billakurthi K, Ren S, Bai Y, Stewart-Wood J, Haseloff J, Zhong S, Hibberd JM. Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha. Cell Rep 2024; 43:114696. [PMID: 39235940 DOI: 10.1016/j.celrep.2024.114696] [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: 02/02/2024] [Revised: 07/23/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024] Open
Abstract
Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Zhemin Wang
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tina B Schreier
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Kumari Billakurthi
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Sibo Ren
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yahui Bai
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julia Stewart-Wood
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK.
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5
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Jeon HW, Iwakawa H, Naramoto S, Herrfurth C, Gutsche N, Schlüter T, Kyozuka J, Miyauchi S, Feussner I, Zachgo S, Nakagami H. Contrasting and conserved roles of NPR pathways in diverged land plant lineages. THE NEW PHYTOLOGIST 2024; 243:2295-2310. [PMID: 39056290 DOI: 10.1111/nph.19981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
The NPR proteins function as salicylic acid (SA) receptors in Arabidopsis thaliana. AtNPR1 plays a central role in SA-induced transcriptional reprogramming whereby positively regulates SA-mediated defense. NPRs are found in the genomes of nearly all land plants. However, we know little about the molecular functions and physiological roles of NPRs in most plant species. We conducted phylogenetic and alignment analyses of NPRs from 68 species covering the significant lineages of land plants. To investigate NPR functions in bryophyte lineages, we generated and characterized NPR loss-of-function mutants in the liverwort Marchantia polymorpha. Brassicaceae NPR1-like proteins have characteristically gained or lost functional residues identified in AtNPRs, pointing to the possibility of a unique evolutionary trajectory for the Brassicaceae NPR1-like proteins. We find that the only NPR in M. polymorpha, MpNPR, is not the master regulator of SA-induced transcriptional reprogramming and negatively regulates bacterial resistance in this species. The Mpnpr transcriptome suggested roles of MpNPR in heat and far-red light responses. We identify both Mpnpr and Atnpr1-1 display enhanced thermomorphogenesis. Interspecies complementation analysis indicated that the molecular properties of AtNPR1 and MpNPR are partially conserved. We further show that MpNPR has SA-binding activity. NPRs and NPR-associated pathways have evolved distinctively in diverged land plant lineages to cope with different terrestrial environments.
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Affiliation(s)
- Hyung-Woo Jeon
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hidekazu Iwakawa
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Cornelia Herrfurth
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Nora Gutsche
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Titus Schlüter
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Shingo Miyauchi
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ivo Feussner
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Hirofumi Nakagami
- Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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6
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Lafferty DJ, Robison TA, Gunadi A, Schafran PW, Gunn LH, Van Eck J, Li FW. Biolistics-mediated transformation of hornworts and its application to study pyrenoid protein localization. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4760-4771. [PMID: 38779949 DOI: 10.1093/jxb/erae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Hornworts are a deeply diverged lineage of bryophytes and a sister lineage to mosses and liverworts. Hornworts have an array of unique features that can be leveraged to illuminate not only the early evolution of land plants, but also alternative paths for nitrogen and carbon assimilation via cyanobacterial symbiosis and a pyrenoid-based CO2-concentrating mechanism (CCM), respectively. Despite this, hornworts are one of the few plant lineages with limited available genetic tools. Here we report an efficient biolistics method for generating transient expression and stable transgenic lines in the model hornwort, Anthoceros agrestis. An average of 569 (±268) cells showed transient expression per bombardment, with green fluorescent protein expression observed within 48-72 h. A total of 81 stably transformed lines were recovered across three separate experiments, averaging six lines per bombardment. We followed the same method to transiently transform nine additional hornwort species, and obtained stable transformants from one. This method was further used to verify the localization of Rubisco and Rubisco activase in pyrenoids, which are central proteins for CCM function. Together, our biolistics approach offers key advantages over existing methods as it enables rapid transient expression and can be applied to widely diverse hornwort species.
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Affiliation(s)
| | - Tanner A Robison
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Laura H Gunn
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Plant Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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7
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Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T, de Vries J. Phylogeny and evolution of streptophyte algae. ANNALS OF BOTANY 2024; 134:385-400. [PMID: 38832756 PMCID: PMC11341676 DOI: 10.1093/aob/mcae091] [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: 03/02/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors.
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Affiliation(s)
- Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Thomas Pröschold
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Research Department for Limnology, University of Innsbruck, Mondseestr. 9, 5310 Mondsee, Austria
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- Section of Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Department of Experimental Phycology and Culture Collection of Algae, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstraße 1, 37077 Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
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8
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Wu JJ, Deng QW, Qiu YY, Liu C, Lin CF, Ru YL, Sun Y, Lai J, Liu LX, Shen XX, Pan R, Zhao YP. Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants. THE NEW PHYTOLOGIST 2024. [PMID: 39166427 DOI: 10.1111/nph.20040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024]
Abstract
Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.
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Affiliation(s)
- Jun-Jie Wu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Wen Deng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Yi-Yang Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chao Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Chen-Feng Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ya-Lu Ru
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yue Sun
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jun Lai
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Xian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Xing-Xing Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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9
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Knosp S, Kriegshauser L, Tatsumi K, Malherbe L, Erhardt M, Wiedemann G, Bakan B, Kohchi T, Reski R, Renault H. An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development. EMBO J 2024:10.1038/s44318-024-00181-7. [PMID: 39090438 DOI: 10.1038/s44318-024-00181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t-cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species-the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis-consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p-coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology.
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Affiliation(s)
- Samuel Knosp
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Lucie Kriegshauser
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Amatera Biosciences, Pépinière Genopole Entreprise, 91000, Evry, France
| | - Kanade Tatsumi
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Ludivine Malherbe
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Mathieu Erhardt
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Inselspital, University of Bern, 3010, Bern, Switzerland
| | - Bénédicte Bakan
- INRAE, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière, Nantes, France
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Hugues Renault
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France.
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10
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Meleshko O, Martin M, Flatberg K, Stenøien H, Korneliussen T, Szövényi P, Hassel K. Linked Selection and Gene Density Shape Genome-Wide Patterns of Diversification in Peatmosses. Evol Appl 2024; 17:e13767. [PMID: 39165607 PMCID: PMC11333200 DOI: 10.1111/eva.13767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/22/2024] [Accepted: 07/29/2024] [Indexed: 08/22/2024] Open
Abstract
Genome evolution under speciation is poorly understood in nonmodel and nonvascular plants, such as bryophytes-the largest group of nonvascular land plants. Their genomes are structurally different from angiosperms and likely subjected to stronger linked selection pressure, which may have profound consequences on genome evolution in diversifying lineages, even more so when their genome architecture is conserved. We use the highly diverse, rapidly radiated group of peatmosses (Sphagnum) to characterize the processes affecting genome diversification in bryophytes. Using whole-genome sequencing data from populations of 12 species sampled at different phylogenetic and geographical scales, we describe high correlation of the genomic landscapes of differentiation, divergence, and diversity in Sphagnum. Coupled with evidence from the patterns of covariation among different measures of genetic diversity, phylogenetic discordance, and gene density, this provides strong support that peatmoss genome evolution has been shaped by the long-term effects of linked selection, constrained by distribution of selection targets in the genome. Thus, peatmosses join the growing number of animal and plant groups where functional features of the genome, such as gene density, and linked selection drive genome evolution along predetermined and highly similar routes in different species. Our findings demonstrate the great potential of bryophytes for studying the genomics of speciation and highlight the urgent need to expand the genomic resources in this remarkable group of plants.
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Affiliation(s)
- Olena Meleshko
- Department of Natural History, NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael D. Martin
- Department of Natural History, NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Kjell Ivar Flatberg
- Department of Natural History, NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Hans K. Stenøien
- Department of Natural History, NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
| | - Kristian Hassel
- Department of Natural History, NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
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11
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Sgroi M, Hoey D, Medina Jimenez K, Bowden SL, Hope M, Wallington EJ, Schornack S, Bravo A, Paszkowski U. The receptor-like kinase ARK controls symbiotic balance across land plants. Proc Natl Acad Sci U S A 2024; 121:e2318982121. [PMID: 39012828 PMCID: PMC11287157 DOI: 10.1073/pnas.2318982121] [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: 11/06/2023] [Accepted: 05/14/2024] [Indexed: 07/18/2024] Open
Abstract
The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.
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Affiliation(s)
- Mara Sgroi
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, CambridgeCB3 0LE, United Kingdom
| | - David Hoey
- Sainsbury Laboratory, University of Cambridge, CambridgeCB2 1LR, United Kingdom
| | | | - Sarah L. Bowden
- National Institute of Agricultural Botany, CambridgeCB3 0LE, United Kingdom
| | - Matthew Hope
- National Institute of Agricultural Botany, CambridgeCB3 0LE, United Kingdom
| | - Emma J. Wallington
- National Institute of Agricultural Botany, CambridgeCB3 0LE, United Kingdom
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, CambridgeCB2 1LR, United Kingdom
| | - Armando Bravo
- Donald Danforth Plant Science Center, St. Louis, MO63132
| | - Uta Paszkowski
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, CambridgeCB3 0LE, United Kingdom
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12
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Kaji T, Nishizato Y, Yoshimatsu H, Yoda A, Liang W, Chini A, Fernández-Barbero G, Nozawa K, Kyozuka J, Solano R, Ueda M. Δ 4-dn- iso-OPDA, a bioactive plant hormone of Marchantia polymorpha. iScience 2024; 27:110191. [PMID: 38974968 PMCID: PMC11225365 DOI: 10.1016/j.isci.2024.110191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/09/2024] [Accepted: 06/03/2024] [Indexed: 07/09/2024] Open
Abstract
Significant progress has been recently made in our understanding of the evolution of jasmonates biosynthesis and signaling. The bioactive jasmonate activating COI1-JAZ co-receptor differs in bryophytes and vascular plants. Dinor-iso-12-oxo-phytodienoic acid (dn-iso-OPDA) is the bioactive hormone in bryophytes and lycophytes. However, further studies showed that the full activation of hormone signaling in Marchantia polymorpha requires additional unidentified hormones. Δ4-dn-OPDAs were previously identified as novel bioactive jasmonates in M. polymorpha. In this paper, we describe the major bioactive isomer of Δ4-dn-OPDAs as Δ4-dn-iso-OPDA through chemical synthesis, receptor binding assay, and biological activity in M. polymorpha. In addition, we disclosed that Δ4-dn-cis-OPDA is a biosynthetic precursor of Δ4-dn-iso-OPDA. We demonstrated that in planta cis-to-iso conversion of Δ4-dn-cis-OPDA occurs in the biosynthesis of Δ4-dn-iso-OPDA, defining a key biosynthetic step in the chemical evolution of hormone structure. We predict that these findings will facilitate further understanding of the molecular evolution of plant hormone signaling.
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Affiliation(s)
- Takuya Kaji
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Yuho Nishizato
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Hidenori Yoshimatsu
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Akiyoshi Yoda
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Wenting Liang
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049 Madrid, Spain
| | - Andrea Chini
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049 Madrid, Spain
| | - Gemma Fernández-Barbero
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049 Madrid, Spain
| | - Kei Nozawa
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Roberto Solano
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049 Madrid, Spain
| | - Minoru Ueda
- Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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13
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De Agostini A, Cortis P, Robustelli Della Cuna FS, Soddu F, Sottani C, Tangredi DN, Guarino F, Cogoni A, Vacca A, Sanna C. Surviving adversity: Exploring the presence of Lunularia cruciata (L.) Dum. on metal-polluted mining waste. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38970643 DOI: 10.1111/plb.13686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/09/2024] [Indexed: 07/08/2024]
Abstract
The tailings dump of Barraxiutta (Sardinia, Italy) contains considerable concentrations of heavy metals and, consequently, is scarcely colonized by plants. However, wild populations of the liverwort Lunularia cruciata (L.) Dum. form dense and healthy-looking carpets on this tailing dump. L. cruciata colonizing the tailing dump was compared with a control population growing in a pristine environment in terms of: (i) pollutant content, (ii) photochemical efficiency, and (iii) volatile secondary metabolites in thalli extracts. L. cruciata maintained optimal photosynthesis despite containing considerable amounts of soil pollutants in its thalli and had higher sesquiterpene content compared to control plants. Sesquiterpenes have a role in plant stress resistance and adaptation to adverse environments. In the present study, we propose enhanced sesquiterpenes featuring Contaminated L. cruciata as a defence strategy implemented in the post-mining environment.
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Affiliation(s)
- A De Agostini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - P Cortis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - F Soddu
- Neuroimmunology Laboratory, IRCCS Mondino Foundation, Pavia, Italy
| | - C Sottani
- Environmental Research Center, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - D N Tangredi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano, Italy
- NBFC National Biodiversity Future Center, Palermo, Italy
| | - F Guarino
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano, Italy
- NBFC National Biodiversity Future Center, Palermo, Italy
| | - A Cogoni
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - A Vacca
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - C Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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14
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Wegner L, Ehlers K. Plasmodesmata dynamics in bryophyte model organisms: secondary formation and developmental modifications of structure and function. PLANTA 2024; 260:45. [PMID: 38965075 PMCID: PMC11224097 DOI: 10.1007/s00425-024-04476-1] [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: 03/25/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
MAIN CONCLUSION Developing bryophytes differentially modify their plasmodesmata structure and function. Secondary plasmodesmata formation via twinning appears to be an ancestral trait. Plasmodesmata networks in hornwort sporophyte meristems resemble those of angiosperms. All land-plant taxa use plasmodesmata (PD) cell connections for symplasmic communication. In angiosperm development, PD networks undergo an extensive remodeling by structural and functional PD modifications, and by postcytokinetic formation of additional secondary PD (secPD). Since comparable information on PD dynamics is scarce for the embryophyte sister groups, we investigated maturating tissues of Anthoceros agrestis (hornwort), Physcomitrium patens (moss), and Marchantia polymorpha (liverwort). As in angiosperms, quantitative electron microscopy revealed secPD formation via twinning in gametophytes of all model bryophytes, which gives rise to laterally adjacent PD pairs or to complex branched PD. This finding suggests that PD twinning is an ancient evolutionary mechanism to adjust PD numbers during wall expansion. Moreover, all bryophyte gametophytes modify their existing PD via taxon-specific strategies resembling those of angiosperms. Development of type II-like PD morphotypes with enlarged diameters or formation of pit pairs might be required to maintain PD transport rates during wall thickening. Similar to angiosperm leaves, fluorescence redistribution after photobleaching revealed a considerable reduction of the PD permeability in maturating P. patens phyllids. In contrast to previous reports on monoplex meristems of bryophyte gametophytes with single initials, we observed targeted secPD formation in the multi-initial basal meristems of A. agrestis sporophytes. Their PD networks share typical features of multi-initial angiosperm meristems, which may hint at a putative homologous origin. We also discuss that monoplex and multi-initial meristems may require distinct types of PD networks, with or without secPD formation, to control maintenance of initial identity and positional signaling.
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Affiliation(s)
- Linus Wegner
- Institute of Botany, Justus-Liebig University, 35392, Giessen, Germany.
| | - Katrin Ehlers
- Institute of Botany, Justus-Liebig University, 35392, Giessen, Germany.
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15
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Dhabalia Ashok A, de Vries S, Darienko T, Irisarri I, de Vries J. Evolutionary assembly of the plant terrestrialization toolkit from protein domains. Proc Biol Sci 2024; 291:20240985. [PMID: 39081174 PMCID: PMC11289646 DOI: 10.1098/rspb.2024.0985] [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: 08/15/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.
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Affiliation(s)
- Amra Dhabalia Ashok
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, Hamburg20146, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, Goettingen37077, Germany
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16
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Tsuda K. Evolution of the sporophyte shoot axis and functions of TALE HD transcription factors in stem development. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102594. [PMID: 38943830 DOI: 10.1016/j.pbi.2024.102594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
The stem is one of the major organs in seed plants and is important for plant survival as well as in agriculture. However, due to the lack of clear external landmarks in many species, its developmental and evolutionary processes are understudied compared to other organs. Recent approaches tackling these problems, especially those focused on KNOX1 and BLH transcription factors belonging to the TALE homeodomain superfamily have started unveiling the patterning process of nodes and internodes by connecting previously accumulated knowledge on lateral organ regulators. Fossil records played crucial roles in understanding the evolutionary process of the stem. The aim of this review is to introduce how the stem evolved from ancestorial sporophyte axes and to provide frameworks for future efforts in understanding the developmental process of this elusive but pivotal organ.
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Affiliation(s)
- Katsutoshi Tsuda
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan.
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17
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Jibran R, Tahir J, Andre CM, Janssen BJ, Drummond RSM, Albert NW, Zhou Y, Davies KM, Snowden KC. DWARF27 and CAROTENOID CLEAVAGE DIOXYGENASE 7 genes regulate release, germination and growth of gemma in Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2024; 15:1358745. [PMID: 38984156 PMCID: PMC11231376 DOI: 10.3389/fpls.2024.1358745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/07/2024] [Indexed: 07/11/2024]
Abstract
Strigolactones (SLs), a class of carotenoid-derived hormones, play a crucial role in flowering plants by regulating underground communication with symbiotic arbuscular mycorrhizal fungi (AM) and controlling shoot and root architecture. While the functions of core SL genes have been characterized in many plants, their roles in non-tracheophyte plants like liverworts require further investigation. In this study, we employed the model liverwort species Marchantia polymorpha, which lacks detectable SL production and orthologs of key SL biosynthetic genes, including CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8) and MORE AXILLARY GROWTH 1 (MAX1). However, it retains some SL pathway components, including DWARF27 (D27) and CCD7. To help elucidate the function of these remaining components in M. polymorpha, knockout mutants were generated for MpD27-1, MpD27-2 and MpCCD7. Phenotypic comparisons of these mutants with the wild-type control revealed a novel role for these genes in regulating the release of gemmae from the gemma cup and the germination and growth of gemmae in the dark. Mpd27-1, Mpd27-2, and Mpccd7 mutants showed lower transcript abundance of genes involved in photosynthesis, such as EARLY LIGHT INDUCED (ELI), and stress responses such as LATE EMBRYOGENESIS ABUNDANT (LEA) but exhibited higher transcript levels of ETHYLENE RESPONSE FACTORS (ERFs) and SL and carotenoid related genes, such as TERPENE SYNTHASE (TS), CCD7 and LECITHIN-RETINAL ACYL TRANSFERASE (LRAT). Furthermore, the mutants of M. polymorpha in the SL pathway exhibited increased contents of carotenoid. This unveils a previously unrecognized role for MpD27-1, MpD27-2 and MpCCD7 in controlling release, germination, and growth of gemmae in response to varying light conditions. These discoveries enhance our comprehension of the regulatory functions of SL biosynthesis genes in non-flowering plants.
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Affiliation(s)
- Rubina Jibran
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Jibran Tahir
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Christelle M Andre
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Bart J Janssen
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Revel S M Drummond
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Nick W Albert
- Metabolite Traits in Plants, The New Zealand Institute for Plant and Food Research Limited, Palmerston, North, New Zealand
| | - Yanfei Zhou
- Metabolite Traits in Plants, The New Zealand Institute for Plant and Food Research Limited, Palmerston, North, New Zealand
| | - Kevin M Davies
- Metabolite Traits in Plants, The New Zealand Institute for Plant and Food Research Limited, Palmerston, North, New Zealand
| | - Kimberley C Snowden
- Plant Development, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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18
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Ambrose BA, Stevenson DW. The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102563. [PMID: 38838582 DOI: 10.1016/j.pbi.2024.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.
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Affiliation(s)
- Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, USA.
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19
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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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20
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Arnoux-Courseaux M, Coudert Y. Re-examining meristems through the lens of evo-devo. TRENDS IN PLANT SCIENCE 2024; 29:413-427. [PMID: 38040554 DOI: 10.1016/j.tplants.2023.11.003] [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: 07/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.
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Affiliation(s)
- Moïra Arnoux-Courseaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France; Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des Martyrs, F-38054, Grenoble, France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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21
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Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, Sun Y, Wu D, Ye C, Zhu QH, Fan L. Technology-enabled great leap in deciphering plant genomes. NATURE PLANTS 2024; 10:551-566. [PMID: 38509222 DOI: 10.1038/s41477-024-01655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Affiliation(s)
- Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Xiaojiao Gong
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Kun Yang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Shiyu Zhang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Leti Shen
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Yanqing Sun
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China.
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22
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Dhabalia Ashok A, Freitag JN, Irisarri I, de Vries S, de Vries J. Sequence similarity networks bear out hierarchical relationships of green cytochrome P450. PHYSIOLOGIA PLANTARUM 2024; 176:e14244. [PMID: 38480467 DOI: 10.1111/ppl.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.
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Affiliation(s)
- Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jella N Freitag
- 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
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, 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 (CIDAS), University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettinzgen, Goettingen, Germany
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23
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Hembach L, Niemeyer PW, Schmitt K, Zegers JMS, Scholz P, Brandt D, Dabisch JJ, Valerius O, Braus GH, Schwarzländer M, de Vries J, Rensing SA, Ischebeck T. Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1466-1486. [PMID: 38059656 DOI: 10.1111/tpj.16574] [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: 08/07/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.
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Affiliation(s)
- Lea Hembach
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Philipp W 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
| | - 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
| | - Jaccoline M S Zegers
- 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
- Laboratoire Reproduction et Développement des Plantes (RDP), UCB Lyon 1, CNRS, INRAE, Université de Lyon, ENS de Lyon, Lyon, France
| | - Dennis Brandt
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Janis J Dabisch
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, 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
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - 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
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Till Ischebeck
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
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24
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Zhang Z, Diao R, Sun J, Liu Y, Zhao M, Wang Q, Xu Z, Zhong B. Diversified molecular adaptations of inorganic nitrogen assimilation and signaling machineries in plants. THE NEW PHYTOLOGIST 2024; 241:2108-2123. [PMID: 38155438 DOI: 10.1111/nph.19508] [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: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Plants evolved sophisticated machineries to monitor levels of external nitrogen supply, respond to nitrogen demand from different tissues and integrate this information for coordinating its assimilation. Although roles of inorganic nitrogen in orchestrating developments have been studied in model plants and crops, systematic understanding of the origin and evolution of its assimilation and signaling machineries remains largely unknown. We expanded taxon samplings of algae and early-diverging land plants, covering all main lineages of Archaeplastida, and reconstructed the evolutionary history of core components involved in inorganic nitrogen assimilation and signaling. Most components associated with inorganic nitrogen assimilation were derived from the ancestral Archaeplastida. Improvements of assimilation machineries by gene duplications and horizontal gene transfers were evident during plant terrestrialization. Clusterization of genes encoding nitrate assimilation proteins might be an adaptive strategy for algae to cope with changeable nitrate availability in different habitats. Green plants evolved complex nitrate signaling machinery that was stepwise improved by domains shuffling and regulation co-option. Our study highlights innovations in inorganic nitrogen assimilation and signaling machineries, ranging from molecular modifications of proteins to genomic rearrangements, which shaped developmental and metabolic adaptations of plants to changeable nutrient availability in environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zilong Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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25
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Nomura T, Seto Y, Kyozuka J. Unveiling the complexity of strigolactones: exploring structural diversity, biosynthesis pathways, and signaling mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1134-1147. [PMID: 37877933 DOI: 10.1093/jxb/erad412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
Strigolactone is the collective name for compounds containing a butenolide as a part of their structure, first discovered as compounds that induce seed germination of root parasitic plants. They were later found to be rhizosphere signaling molecules that induce hyphal branching of arbuscular mycorrhizal fungi, and, finally, they emerged as a class of plant hormones. Strigolactones are found in root exudates, where they display a great variability in their chemical structure. Their structure varies among plant species, and multiple strigolactones can exist in one species. Over 30 strigolactones have been identified, yet the chemical structure of the strigolactone that functions as an endogenous hormone and is found in the above-ground parts of plants remains unknown. We discuss our current knowledge of the synthetic pathways of diverse strigolactones and their regulation, as well as recent progress in identifying strigolactones as plant hormones. Strigolactone is perceived by the DWARF14 (D14), receptor, an α/β hydrolase which originated by gene duplication of KARRIKIN INSENSITIVE 2 (KAI2). D14 and KAI2 signaling pathways are partially overlapping paralogous pathways. Progress in understanding the signaling mechanisms mediated by two α/β hydrolase receptors as well as remaining challenges in the field of strigolactone research are reviewed.
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Affiliation(s)
- Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Yoshiya Seto
- School of Agriculture, Meiji University, Kawasaki, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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26
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Poveda J. Analysis of Marchantia polymorpha-microorganism interactions: basis for understanding plant-microbe and plant-pathogen interactions. FRONTIERS IN PLANT SCIENCE 2024; 15:1301816. [PMID: 38384768 PMCID: PMC10879820 DOI: 10.3389/fpls.2024.1301816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024]
Abstract
Marchantia polymorpha is a bryophyte gaining significance as a model plant in evolutionary studies in recent years. This is attributed to its small-sequenced genome, standardized transformation methodology, global distribution, and easy and rapid in vitro culturing. As an evolutionary model, M. polymorpha contributes to our understanding of the evolution of plant defensive responses and the associated hormonal signaling pathways. Through its interaction with microorganisms, M. polymorpha serves as a valuable source of knowledge, yielding insights into new microbial species and bioactive compounds. Bibliographic analysis involved collecting, reading, and categorizing documents obtained from the Scopus and Web of Science databases using different search terms. The review was based on 30 articles published between 1995 and 2023, with Japanese and Spanish authors emerging as the most prolific contributors in this field. These articles have been grouped into four main themes: antimicrobial metabolites produced by M. polymorpha; identification and characterization of epiphytic, endophytic, and pathogenic microorganisms; molecular studies of the direct interaction between M. polymorpha and microorganisms; and plant transformation using bacterial vectors. This review highlights the key findings from these articles and identifies potential future research directions.
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Affiliation(s)
- Jorge Poveda
- Recognised Research Group AGROBIOTECH, UIC-370 (JCyL), Department of Plant Production and Forest Resources, Higher Technical School of Agricultural Engineering of Palencia, University Institute for Research in Sustainable Forest Management (iuFOR), University of Valladolid, Palencia, Spain
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27
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Bierenbroodspot MJ, Darienko T, de Vries S, Fürst-Jansen JMR, Buschmann H, Pröschold T, Irisarri I, de Vries J. Phylogenomic insights into the first multicellular streptophyte. Curr Biol 2024; 34:670-681.e7. [PMID: 38244543 PMCID: PMC10849092 DOI: 10.1016/j.cub.2023.12.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1,2,3,4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.5,6 Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.
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Affiliation(s)
- Maaike J Bierenbroodspot
- 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
| | - Janine M R Fürst-Jansen
- 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
| | - 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
| | - Thomas Pröschold
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Innsbruck, Research Department for Limnology, 5310 Mondsee, Austria
| | - 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; Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 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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28
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A L, J K. At the root of plant symbioses: Untangling the genetic mechanisms behind mutualistic associations. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102448. [PMID: 37758591 DOI: 10.1016/j.pbi.2023.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
Mutualistic interactions between plants and microorganisms shape the continuous evolution and adaptation of plants such as to the terrestrial environment that was a founding event of subsequent life on land. Such interactions also play a central role in the natural and agricultural ecosystems and are of primary importance for a sustainable future. To boost plant's productivity and resistance to biotic and abiotic stresses, new approaches involving associated symbiotic organisms have recently been explored. New discoveries on mutualistic symbioses evolution and the interaction between partners will be key steps to enhance plant potential.
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Affiliation(s)
- Lebreton A
- INRAE, Aix-Marseille Université, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, UMR 7257, 13288 Marseille, France.
| | - Keller J
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
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29
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Gutsche N, Koczula J, Trupp M, Holtmannspötter M, Appelfeller M, Rupp O, Busch A, Zachgo S. MpTGA, together with MpNPR, regulates sexual reproduction and independently affects oil body formation in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1559-1573. [PMID: 38095258 DOI: 10.1111/nph.19472] [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: 08/30/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
In angiosperms, basic leucine-zipper (bZIP) TGACG-motif-binding (TGA) transcription factors (TFs) regulate developmental and stress-related processes, the latter often involving NON EXPRESSOR OF PATHOGENESIS-RELATED GENES (NPR) coregulator interactions. To gain insight into their functions in an early diverging land-plant lineage, the single MpTGA and sole MpNPR genes were investigated in the liverwort Marchantia polymorpha. We generated Marchantia MpTGA and MpNPR knockout and overexpression mutants and conducted morphological, transcriptomic and expression studies. Furthermore, we investigated MpTGA interactions with wild-type and mutagenized MpNPR and expanded our analyses including TGA TFs from two streptophyte algae. Mptga mutants fail to induce the switch from vegetative to reproductive development and lack gametangiophore formation. MpTGA and MpNPR proteins interact and Mpnpr mutant analysis reveals a novel coregulatory NPR role in sexual reproduction. Additionally, MpTGA acts independently of MpNPR as a repressor of oil body (OB) formation and can thereby affect herbivory. The single MpTGA TF exerts a dual role in sexual reproduction and OB formation in Marchantia. Common activities of MpTGA/MpNPR in sexual development suggest that coregulatory interactions were established after emergence of land-plant-specific NPR genes and contributed to the diversification of TGA TF functions during land-plant evolution.
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Affiliation(s)
- Nora Gutsche
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Jens Koczula
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Melanie Trupp
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | | | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Andrea Busch
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
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30
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Ponce de León I. Evolution of immunity networks across embryophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102450. [PMID: 37704543 DOI: 10.1016/j.pbi.2023.102450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
Land plants (embryophytes), including vascular (tracheophytes) and non-vascular plants (bryophytes), co-evolved with microorganisms since descendants of an algal ancestor colonized terrestrial habitats around 500 million years ago. To cope with microbial pathogen infections, embryophytes evolved a complex immune system for pathogen perception and activation of defenses. With the growing number of sequenced genomes and transcriptome datasets from algae, bryophytes, tracheophytes, and available plant models, comparative analyses are increasing our understanding of the evolution of molecular mechanisms underpinning immune responses in different plant lineages. In this review, recent progress on plant immunity networks is highlighted with emphasis on the identification of key components that shaped immunity against pathogens in bryophytes compared to angiosperms during plant evolution.
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Affiliation(s)
- Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600, Montevideo, Uruguay.
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31
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Valeeva LR, Sannikova AV, Shafigullina NR, Abdulkina LR, Sharipova MR, Shakirov EV. Telomere Length Variation in Model Bryophytes. PLANTS (BASEL, SWITZERLAND) 2024; 13:387. [PMID: 38337920 PMCID: PMC10856949 DOI: 10.3390/plants13030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The ends of linear chromosomes of most eukaryotes consist of protein-bound DNA arrays called telomeres, which play essential roles in protecting genome integrity. Despite general evolutionary conservation in function, telomeric DNA is known to drastically vary in length and sequence between different eukaryotic lineages. Bryophytes are a group of early diverging land plants that include mosses, liverworts, and hornworts. This group of ancient land plants recently emerged as a new model for important discoveries in genomics and evolutionary biology, as well as for understanding plant adaptations to a terrestrial lifestyle. We measured telomere length in different ecotypes of model bryophyte species, including Physcomitrium patens, Marchantia polymorpha, Ceratodon purpureus, and in Sphagnum isolates. Our data indicate that all analyzed moss and liverwort genotypes have relatively short telomeres. Furthermore, all analyzed ecotypes and isolates of model mosses and liverworts display evidence of substantial natural variation in telomere length. Interestingly, telomere length also differs between male and female strains of the dioecious liverwort M. polymorpha and dioecious moss C. purpureus. Given that bryophytes are extraordinarily well adapted to different ecological niches from polar to tropical environments, our data will contribute to understanding the impact of natural telomere length variation on evolutionary adaptations in this ancient land plant lineage.
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Affiliation(s)
- Liia R. Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Anastasia V. Sannikova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - Nadiya R. Shafigullina
- Institute of Environmental Sciences, Department of General Ecology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Liliia R. Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - Eugene V. Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
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Li C, Wickell D, Kuo LY, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, Shu S, Plott C, Barry K, Rajasekar S, Grimwood J, Han X, Sun S, Hou Z, He W, Dai G, Sun C, Schmutz J, Leebens-Mack JH, Li FW, Wang L. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proc Natl Acad Sci U S A 2024; 121:e2312607121. [PMID: 38236735 PMCID: PMC10823260 DOI: 10.1073/pnas.2312607121] [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: 07/31/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.
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Affiliation(s)
- Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - David Wickell
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Mellissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ85721
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Weijun He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Yanji133000, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing100048, China
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing100700, China
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Alisha A, Szweykowska-Kulinska Z, Sierocka I. Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes. Sci Rep 2024; 14:1611. [PMID: 38238367 PMCID: PMC10796333 DOI: 10.1038/s41598-024-51626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.
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Affiliation(s)
- Alisha Alisha
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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MacLeod AI, Knopp MR, Gould SB. A mysterious cloak: the peptidoglycan layer of algal and plant plastids. PROTOPLASMA 2024; 261:173-178. [PMID: 37603062 PMCID: PMC10784329 DOI: 10.1007/s00709-023-01886-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/23/2023] [Indexed: 08/22/2023]
Abstract
The plastids of algae and plants originated on a single occasion from an endosymbiotic cyanobacterium at least a billion years ago. Despite the divergent evolution that characterizes the plastids of different lineages, many traits such as membrane organization and means of fission are universal-they pay tribute to the cyanobacterial origin of the organelle. For one such trait, the peptidoglycan (PG) layer, the situation is more complicated. Our view on its distribution keeps on changing and little is known regarding its molecular relevance, especially for land plants. Here, we investigate the extent of PG presence across the Chloroplastida using a phylogenomic approach. Our data support the view of a PG layer being present in the last common ancestor of land plants and its remarkable conservation across bryophytes that are otherwise characterized by gene loss. In embryophytes, the occurrence of the PG layer biosynthetic toolkit becomes patchier and the availability of novel genome data questions previous predictions regarding a functional coevolution of the PG layer and the plastid division machinery-associated gene FtsZ3. Furthermore, our data confirm the presence of penicillin-binding protein (PBP) orthologs in seed plants, which were previously thought to be absent from this clade. The 5-7 nm thick, and seemingly unchanged, PG layer armoring the plastids of glaucophyte algae might still provide the original function of structural support, but the same can likely not be said about the only recently identified PG layer of bryophyte and tracheophyte plastids. There are several issues to be explored regarding the composition, exact function, and biosynthesis of the PG layer in land plants. These issues arise from the fact that land plants seemingly lack certain genes that are believed to be crucial for PG layer production, even though they probably synthesize a PG layer.
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Affiliation(s)
- Alexander I MacLeod
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany.
| | - Michael R Knopp
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
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Castel B, El Mahboubi K, Jacquet C, Delaux PM. Immunobiodiversity: Conserved and specific immunity across land plants and beyond. MOLECULAR PLANT 2024; 17:92-111. [PMID: 38102829 DOI: 10.1016/j.molp.2023.12.005] [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: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.
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Affiliation(s)
- Baptiste Castel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Karima El Mahboubi
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
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36
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Takahashi G, Kiyosue T, Hirakawa Y. Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha. Curr Biol 2023; 33:5121-5131.e6. [PMID: 37977139 DOI: 10.1016/j.cub.2023.10.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Land plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations. In the sporophyte of the flowering plant Arabidopsis thaliana, the apical meristems are located at the shoot and root tips in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes, even though genomic studies have revealed that the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants. Here, we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLAVATA3 (CLV3)/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwort Marchantia polymorpha. In the meristem, strong MpJIN expression was associated with the periclinal cell division at the periphery of the stem cell zone (SCZ), whereas faint MpJIN expression was found at the center of the SCZ. Time course observation indicates that the MpJIN-negative cells are lost from the SCZ and respecified de novo at two separate positions during the dichotomous branching event. Consistently, the induction of MpJIN results in ectopic periclinal cell division in the SCZ and meristem termination. Based on the comparative expression data, we speculate that the function of JIN/FEZ subfamily genes was shared among the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages, including the flowering plant A. thaliana.
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Affiliation(s)
- Go Takahashi
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Tomohiro Kiyosue
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan
| | - Yuki Hirakawa
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Tokyo 171-8588, Japan.
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37
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Hisanaga T, Wu S, Schafran P, Axelsson E, Akimcheva S, Dolan L, Li F, Berger F. The ancestral chromatin landscape of land plants. THE NEW PHYTOLOGIST 2023; 240:2085-2101. [PMID: 37823324 PMCID: PMC10952607 DOI: 10.1111/nph.19311] [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: 06/28/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023]
Abstract
Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss Physcomitrium patens and the liverwort Marchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants. We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwort Anthoceros agrestis. We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants. Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Shuangyang Wu
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | | | - Elin Axelsson
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Svetlana Akimcheva
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Liam Dolan
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
| | - Fay‐Wei Li
- Boyce Thompson InstituteIthacaNY14853USA
- Plant Biology SectionCornell UniversityIthacaNY14853USA
| | - Frédéric Berger
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BioCenterDr. Bohr‐Gasse 3Vienna1030Austria
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Prigge MJ, Morffy N, de Neve A, Szutu W, Abraham-Juárez MJ, Johnson K, Do N, Lavy M, Hake S, Strader L, Estelle M, Richardson AE. Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566459. [PMID: 38014308 PMCID: PMC10680667 DOI: 10.1101/2023.11.09.566459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A major challenge in plant biology is to understand how the plant hormone auxin regulates diverse transcriptional responses throughout development, in different environments, and in different species. The answer may lie in the specific complement of auxin signaling components in each cell. The balance between activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) is particularly important. It is unclear how this balance is achieved. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens , we have discovered a ∼500-million-year-old mechanism of class-B ARF protein level regulation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.
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Hisanaga T, Romani F, Wu S, Kowar T, Wu Y, Lintermann R, Fridrich A, Cho CH, Chaumier T, Jamge B, Montgomery SA, Axelsson E, Akimcheva S, Dierschke T, Bowman JL, Fujiwara T, Hirooka S, Miyagishima SY, Dolan L, Tirichine L, Schubert D, Berger F. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 2023; 33:4367-4380.e9. [PMID: 37738971 DOI: 10.1016/j.cub.2023.08.073] [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: 10/28/2022] [Revised: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Teresa Kowar
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Ruth Lintermann
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Arie Fridrich
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chung Hyun Cho
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Liam Dolan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Daniel Schubert
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Chahar N, Dangwal M, Das S. Complex origin, evolution, and diversification of non-canonically organized OVATE-OFP and OVATE-Like OFP gene pair across Embryophyta. Gene 2023; 883:147685. [PMID: 37536399 DOI: 10.1016/j.gene.2023.147685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Ovate Family Proteins (OFP) is a plant-specific gene family of negative transcriptional regulators. Till-date, a handful of in-silico studies have provided glimpses into family size, expansion patterns, and genic features across all major plant lineages. A major lacuna exists in understanding origin of organisation complexity of members such as those arranged in a head-to-head manner which may lead to transcriptional co-regulation via a common bi-directional promoter. To address this gap, we investigated the origin, organization and evolution of two head-to-head arranged gene pairs of homologs of AtOFP2-AtOFP17, and, AtOFP4-AtOFP20 across Archaeplastida. The ancestral forms of AtOFP2, AtOFP4, AtOFP17, and AtOFP20 are likely to have evolved in last common ancestors of Embryophyta (land plants) given their complete absence in Rhodophyta and Chlorophyta. The OFP gene family originated and expanded in Bryophyta, including protein variants with complete (OVATE-OFP) or partial (OVATE-Like OFP) OVATE domain; with head-to-head organization present only in Spermatophyta (gymnosperms and angiosperms). Ancestral State Reconstruction revealed the origin of head-to-head organized gene pair in gymnosperms, with both genes being OVATE-OFP (homologs of AtOFP2/4). Phylogenetic reconstruction and copy number analysis suggests the presence of a single copy of the head-to-head arranged pair of OFP2/4 (OVATE)-OFP17/20 (OVATE-Like) in all angiosperms except Brassicaceae, and a duplication event in last common ancestor of core Brassicaceae approximately 32-54 MYA leading to origin of AtOFP2-AtOFP17 and AtOFP4-AtOFP20 as paralogs. Synteny analysis of genomic regions harbouring homologs of AtOFP2-AtOFP17, AtOFP4-AtOFP20 and AtOFP2/4-AtOFP17/20 across angiosperms suggested ancestral nature of AtOFP2-AtOFP17 gene pair. The present study thus establishes the orthology and evolutionary history of two non-canonically organised gene pairs with variation in their OVATE domain. The non-canonical organisation, atleast in Brassicaceae, has the potential of generating complex transcriptional regulation mediated via a common bi-directional promoter. The study thus lays down a framework to understand evolution of gene and protein structure, transcriptional regulation and function across a phylogenetic lineage through comparative analyses.
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Affiliation(s)
- Nishu Chahar
- Department of Botany, University of Delhi, Delhi 110 007, India.
| | | | - Sandip Das
- Department of Botany, University of Delhi, Delhi 110 007, India.
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Flores-Téllez D, Tankmar MD, von Bülow S, Chen J, Lindorff-Larsen K, Brodersen P, Arribas-Hernández L. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet 2023; 19:e1010980. [PMID: 37816028 PMCID: PMC10617740 DOI: 10.1371/journal.pgen.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/31/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023] Open
Abstract
YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.
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Affiliation(s)
- Daniel Flores-Téllez
- University of Copenhagen, Biology Department. Copenhagen, Denmark
- Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales. Pozuelo de Alarcón (Madrid), Spain
| | | | - Sören von Bülow
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | - Junyu Chen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | | - Peter Brodersen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
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42
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Caygill S, Dolan L. ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation. PLoS One 2023; 18:e0287356. [PMID: 37733747 PMCID: PMC10513242 DOI: 10.1371/journal.pone.0287356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.
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Affiliation(s)
- Samuel Caygill
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Liam Dolan
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
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43
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Yotsui I, Matsui H, Miyauchi S, Iwakawa H, Melkonian K, Schlüter T, Michavila S, Kanazawa T, Nomura Y, Stolze SC, Jeon HW, Yan Y, Harzen A, Sugano SS, Shirakawa M, Nishihama R, Ichihashi Y, Ibanez SG, Shirasu K, Ueda T, Kohchi T, Nakagami H. LysM-mediated signaling in Marchantia polymorpha highlights the conservation of pattern-triggered immunity in land plants. Curr Biol 2023; 33:3732-3746.e8. [PMID: 37619565 DOI: 10.1016/j.cub.2023.07.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Pattern-recognition receptor (PRR)-triggered immunity (PTI) wards off a wide range of pathogenic microbes, playing a pivotal role in angiosperms. The model liverwort Marchantia polymorpha triggers defense-related gene expression upon sensing components of bacterial and fungal extracts, suggesting the existence of PTI in this plant model. However, the molecular components of the putative PTI in M. polymorpha and the significance of PTI in bryophytes have not yet been described. We here show that M. polymorpha has four lysin motif (LysM)-domain-containing receptor homologs, two of which, LysM-receptor-like kinase (LYK) MpLYK1 and LYK-related (LYR) MpLYR, are responsible for sensing chitin and peptidoglycan fragments, triggering a series of characteristic immune responses. Comprehensive phosphoproteomic analysis of M. polymorpha in response to chitin treatment identified regulatory proteins that potentially shape LysM-mediated PTI. The identified proteins included homologs of well-described PTI components in angiosperms as well as proteins whose roles in PTI are not yet determined, including the blue-light receptor phototropin MpPHOT. We revealed that MpPHOT is required for negative feedback of defense-related gene expression during PTI. Taken together, this study outlines the basic framework of LysM-mediated PTI in M. polymorpha and highlights conserved elements and new aspects of pattern-triggered immunity in land plants.
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Affiliation(s)
- Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Department of BioScience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hidenori Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Okinawa, Japan
| | - Hidekazu Iwakawa
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan
| | | | - Titus Schlüter
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Santiago Michavila
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | | | - Hyung-Woo Jeon
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yijia Yan
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Anne Harzen
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shigeo S Sugano
- Bioproduction Research Institute, The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Nara, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510, Chiba, Japan
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
| | - Selena Gimenez Ibanez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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44
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He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
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45
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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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46
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Kameoka H, Shimazaki S, Mashiguchi K, Watanabe B, Komatsu A, Yoda A, Mizuno Y, Kodama K, Okamoto M, Nomura T, Yamaguchi S, Kyozuka J. DIENELACTONE HYDROLASE LIKE PROTEIN1 negatively regulates the KAI2-ligand pathway in Marchantia polymorpha. Curr Biol 2023; 33:3505-3513.e5. [PMID: 37480853 DOI: 10.1016/j.cub.2023.06.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/25/2023] [Accepted: 06/29/2023] [Indexed: 07/24/2023]
Abstract
Karrikins are smoke-derived butenolides that induce seed germination and photomorphogenesis in a wide range of plants.1,2,3 KARRIKIN INSENSITIVE2 (KAI2), a paralog of a strigolactone receptor, perceives karrikins or their metabolized products in Arabidopsis thaliana.4,5,6,7 Furthermore, KAI2 is thought to perceive an unidentified plant hormone, called KAI2 ligand (KL).8,9 KL signal is transduced via the interaction between KAI2, MORE AXILLARY GROWTH2 (MAX2), and SUPPRESSOR of MORE AXILLARY GROWTH2 1 LIKE family proteins (SMXLs), followed by the degradation of SMXLs.4,7,10,11,12,13,14 This signaling pathway is conserved both in A. thaliana and the bryophyte Marchantia polymorpha.14 Although the KL signaling pathway is well characterized, the KL metabolism pathways remain poorly understood. Here, we show that DIENELACTONE HYDROLASE LIKE PROTEIN1 (DLP1) is a negative regulator of the KL pathway in M. polymorpha. The KL signal induces DLP1 expression. DLP1 overexpression lines phenocopied the Mpkai2a and Mpmax2 mutants, while dlp1 mutants phenocopied the Mpsmxl mutants. Mutations in the KL signaling genes largely suppressed these phenotypes, indicating that DLP1 acts upstream of the KL signaling pathway, although DLP1 also has KL pathway-independent functions. DLP1 exhibited enzymatic activity toward a potential substrate, suggesting the possibility that DLP1 works through KL inactivation. Investigation of DLP1 homologs in A. thaliana revealed that they do not play a major role in the KL pathway, suggesting different mechanisms for the KL signal regulation. Our findings provide new insights into the regulation of the KL signal in M. polymorpha and the evolution of the KL pathway in land plants.
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Affiliation(s)
- Hiromu Kameoka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan; PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.
| | - Shota Shimazaki
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kiyoshi Mashiguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bunta Watanabe
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Aino Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Akiyoshi Yoda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Yohei Mizuno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Kyoichi Kodama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Shinjiro Yamaguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan.
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47
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Hu R, Li X, Hu Y, Zhang R, Lv Q, Zhang M, Sheng X, Zhao F, Chen Z, Ding Y, Yuan H, Wu X, Xing S, Yan X, Bao F, Wan P, Xiao L, Wang X, Xiao W, Decker EL, van Gessel N, Renault H, Wiedemann G, Horst NA, Haas FB, Wilhelmsson PKI, Ullrich KK, Neumann E, Lv B, Liang C, Du H, Lu H, Gao Q, Cheng Z, You H, Xin P, Chu J, Huang CH, Liu Y, Dong S, Zhang L, Chen F, Deng L, Duan F, Zhao W, Li K, Li Z, Li X, Cui H, Zhang YE, Ma C, Zhu R, Jia Y, Wang M, Hasebe M, Fu J, Goffinet B, Ma H, Rensing SA, Reski R, He Y. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 2023; 186:3558-3576.e17. [PMID: 37562403 DOI: 10.1016/j.cell.2023.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/23/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.
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Affiliation(s)
- Ruoyang Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xuedong Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yong Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Runjie Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Qiang Lv
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Min Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xianyong Sheng
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Feng Zhao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Zhijia Chen
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yuhan Ding
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Huan Yuan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaofeng Wu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Shuang Xing
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaoyu Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Fang Bao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Ping Wan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Lihong Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Xiaoqin Wang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hugues Renault
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Inselspital, University of Bern, 3010 Bern, Switzerland
| | - Nelly A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; MetaSystems Hard & Software GmbH, 68804 Altlussheim, Germany
| | - Fabian B Haas
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | | | - Kristian K Ullrich
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Eva Neumann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Bin Lv
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
| | - Chengzhi Liang
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Hongwei Lu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Qiang Gao
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhukuan Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hanli You
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010031, China
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA; Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518085, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fei Chen
- Sanya Nanfan Research Institute from Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Lei Deng
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Fuzhou Duan
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Wenji Zhao
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Kai Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Zhongfeng Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Xingru Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Hengjian Cui
- School of Mathematical Sciences, CNU, Beijing 100048, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Ma
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruiliang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meizhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan A Rensing
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
| | - Yikun He
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China.
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48
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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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49
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Furudate H, Manabe M, Oshikiri H, Matsushita A, Watanabe B, Waki T, Nakayama T, Kubo H, Takanashi K. A Polyphenol Oxidase Catalyzes Aurone Synthesis in Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2023; 64:637-645. [PMID: 36947436 DOI: 10.1093/pcp/pcad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 03/21/2023] [Indexed: 06/16/2023]
Abstract
Aurones constitute one of the major classes of flavonoids, with a characteristic furanone structure that acts as the C-ring of flavonoids. Members of various enzyme families are involved in aurone biosynthesis in different higher plants, suggesting that during evolution plants acquired the ability to biosynthesize aurones independently and convergently. Bryophytes also produce aurones, but the biosynthetic pathways and enzymes involved have not been determined. The present study describes the identification and characterization of a polyphenol oxidase (PPO) that acts as an aureusidin synthase (MpAS1) in the model liverwort, Marchantia polymorpha. Crude enzyme assays using an M. polymorpha line overexpressing MpMYB14 with high accumulation of aureusidin showed that aureusidin was biosynthesized from naringenin chalcone and converted to riccionidin A. This activity was inhibited by N-phenylthiourea, an inhibitor specific to enzymes of the PPO family. Of the six PPOs highly induced in the line overexpressing MpMyb14, one, MpAS1, was found to biosynthesize aureusidin from naringenin chalcone when expressed in Saccharomyces cerevisiae. MpAS1 also recognized eriodictyol chalcone, isoliquiritigenin and butein, showing the highest activity for eriodictyol chalcone. Members of the PPO family in M. polymorpha evolved independently from PPOs in higher plants, indicating that aureusidin synthases evolved in parallel in land plants.
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Affiliation(s)
- Hiraku Furudate
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Misaki Manabe
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Haruka Oshikiri
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Ayako Matsushita
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Bunta Watanabe
- Chemistry Laboratory, The Jikei University School of Medicine, Kokuryo 8-3-1, Chofu, Tokyo, 182-8570 Japan
| | - Toshiyuki Waki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-11, Aramaki, Aoba, Sendai, Miyagi, 980-8579 Japan
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-11, Aramaki, Aoba, Sendai, Miyagi, 980-8579 Japan
| | - Hiroyoshi Kubo
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Kojiro Takanashi
- Department of Science, Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
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50
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Tounosu N, Sesoko K, Hori K, Shimojima M, Ohta H. Cis-regulatory elements and transcription factors related to auxin signaling in the streptophyte algae Klebsormidium nitens. Sci Rep 2023; 13:9635. [PMID: 37322074 PMCID: PMC10272232 DOI: 10.1038/s41598-023-36500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
The phytohormone auxin affects numerous processes in land plants. The central auxin signaling machinery, called the nuclear auxin pathway, is mediated by its pivotal receptor named TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB). The nuclear auxin pathway is widely conserved in land plants, but auxin also accumulates in various algae. Although auxin affects the growth of several algae, the components that mediate auxin signaling have not been identified. We previously reported that exogenous auxin suppresses cell proliferation in the Klebsormidium nitens that is a member of streptophyte algae, a paraphyletic group sharing the common ancestor with land plants. Although K. nitens lacks TIR1/AFB, auxin affects the expression of numerous genes. Thus, elucidation of the mechanism of auxin-inducible gene expression in K. nitens would provide important insights into the evolution of auxin signaling. Here, we show that some motifs are enriched in the promoter sequences of auxin-inducible genes in K. nitens. We also found that the transcription factor KnRAV activates several auxin-inducible genes and directly binds the promoter of KnLBD1, a representative auxin-inducible gene. We propose that KnRAV has the potential to regulate auxin-responsive gene expression in K. nitens.
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Affiliation(s)
- Noriaki Tounosu
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Kanami Sesoko
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Koichi Hori
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
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