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Garcias-Morales D, Palomar VM, Charlot F, Nogué F, Covarrubias AA, Reyes JL. N 6 -Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:7-22. [PMID: 36794900 DOI: 10.1111/tpj.16149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Plants colonized the land approximately 470 million years ago, coinciding with the development of apical cells that divide in three planes. The molecular mechanisms that underly the development of the 3D growth pattern are poorly understood, mainly because 3D growth in seed plants starts during embryo development. In contrast, the transition from 2D to 3D growth in the moss Physcomitrium patens has been widely studied, and it involves a large turnover of the transcriptome to allow the establishment of stage-specific transcripts that facilitate this developmental transition. N6 -Methyladenosine (m6 A) is the most abundant, dynamic and conserved internal nucleotide modification present on eukaryotic mRNA and serves as a layer of post-transcriptional regulation directly affecting several cellular processes and developmental pathways in many organisms. In Arabidopsis, m6 A has been reported to be essential for organ growth and determination, embryo development and responses to environmental signals. In this study, we identified the main genes of the m6 A methyltransferase complex (MTC), MTA, MTB and FIP37, in P. patens and demonstrate that their inactivation leads to the loss of m6 A in mRNA, a delay in the formation of gametophore buds and defects in spore development. Genome-wide analysis revealed several transcripts affected in the Ppmta background. We demonstrate that the PpAPB1-PpAPB4 transcripts, encoding central factors orchestrating the transition from 2D to 3D growth in P. patens, are modified by m6 A, whereas in the Ppmta mutant the lack of the m6 A marker is associated with a corresponding decrease in transcript accumulation. Overall, we suggest that m6 A is essential to enable the proper accumulation of these and other bud-specific transcripts directing the turnover of stage-specific transcriptomes, and thus promoting the transition from protonema to gametophore buds in P. patens.
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Affiliation(s)
- David Garcias-Morales
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
| | - V Miguel Palomar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave, Ann Arbor, MI, 48109-1085, USA
| | - Florence Charlot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, CP, 62210, Mexico
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2
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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3
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Koebke E, Stephan L, Stetter MG, Hülskamp M. Functional analysis of the BEige and Chediak-Higashi domain gene Mp SPIRRIG in Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2022; 13:915268. [PMID: 36212282 PMCID: PMC9537460 DOI: 10.3389/fpls.2022.915268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
BEige and Chediak-Higashi domain containing proteins (BDCPs) have been described to function in membrane-dependent processes in eukaryotes. This role was also observed for the BDCP SPIRRIG (SPI) in the model plant Arabidopsis thaliana in the context of cell morphogenesis. Additionally, AtSPI was found to control salt stress resistance by mediating mRNA stability and salt stress-dependent processing body formation. In this work, we utilize an evolutionarily comparative approach to unravel conserved, basal BDCP functions in the liverwort Marchantia polymorpha. Our phenotypic and physiological analyses show that MpSPI is involved in cell morphogenesis and salt resistance regulation, indicating that both functions are evolutionarily conserved between the two species. Co-localization was found with endosomal and P-body markers, suggesting links to membrane-dependent processes and mRNA metabolism. Finally, we present transcriptomics data showing that AtSPI and MpSPI regulate orthologous genes in A. thaliana and M. polymorpha.
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Affiliation(s)
| | | | | | - Martin Hülskamp
- Botanical Institute, University of Cologne, Cologne, Germany
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4
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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5
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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6
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Jia R, Li C, Wang Y, Qin X, Meng L, Sun X. Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. Int J Mol Sci 2022; 23:ijms23042089. [PMID: 35216201 PMCID: PMC8877895 DOI: 10.3390/ijms23042089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In this study, a genome-wide analysis of LBD genes was performed in D. catenatum and 24 LBD genes were identified. The genes were classified into two classes (I and II) based on phylogenetic relationships and motif structure. Subcellular localization analysis for DcaLBD6 and DcaLBD18 from class I and DcaLBD37 and DcaLBD41 from class II revealed that the proteins were localized in the nucleus. Transient expression analysis of DcaLBD6, DcaLBD18, DcaLBD37, and DcaLBD41 indicated that class I and class II members have opposite roles in regulating VASCULAR-RELATED NAC-DOMAIN 7 (VND7) expression. DcaLBD genes showed diverse expression patterns in response to different phytohormone treatments. Heat maps revealed diverse patterns of DcaLBD gene expression in different organs. These results lay the foundation for further detailed studies of the LBD gene family in D. catenatum.
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Affiliation(s)
- Ru Jia
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Cheng Li
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Wang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangshi Qin
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Lihua Meng
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
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7
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Medina-Jimenez K, Arteaga-Vazquez MA, Lorence A. An Automated High-Throughput Phenotyping System for Marchantia polymorpha. Methods Mol Biol 2022; 2539:11-17. [PMID: 35895191 DOI: 10.1007/978-1-0716-2537-8_2] [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] [Indexed: 06/15/2023]
Abstract
High-throughput phenotyping (HTP) allows automation of fast and precise acquisition and analysis of digital images for the detection of key traits in real time. HTP improves characterization of the growth and development of plants in controlled environments in a nondestructive fashion. Marchantia polymorpha has emerged as a very attractive model for studying the evolution of the physiological, cellular, molecular, and developmental adaptations that enabled plants to conquer their terrestrial environments. The availability of the M. polymorpha genome in combination with a full set of functional genomic tools including genetic transformation, homologous recombination, and genome editing has allowed the inspection of its genome through forward and reverse genetics approaches. The increasing number of mutants has made it possible to perform informative genome-wide analyses to study the phenotypic consequences of gene inactivation. Here we present an HTP protocol for M. polymorpha that will aid current efforts to quantify numerous morphological parameters that can potentially reveal genotype-to-phenotype relationships and relevant connections between individual traits.
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Affiliation(s)
| | - Mario A Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Mexico.
| | - Argelia Lorence
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA.
- Department of Chemistry and Physics, Arkansas State University, Jonesboro, AR, USA.
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8
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Petersen J, Rredhi A, Szyttenholm J, Oldemeyer S, Kottke T, Mittag M. The World of Algae Reveals a Broad Variety of Cryptochrome Properties and Functions. FRONTIERS IN PLANT SCIENCE 2021; 12:766509. [PMID: 34790217 PMCID: PMC8591175 DOI: 10.3389/fpls.2021.766509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 05/25/2023]
Abstract
Algae are photosynthetic eukaryotic (micro-)organisms, lacking roots, leaves, and other organs that are typical for land plants. They live in freshwater, marine, or terrestrial habitats. Together with the cyanobacteria they contribute to about half of global carbon fixation. As primary producers, they are at the basis of many food webs and they are involved in biogeochemical processes. Algae are evolutionarily distinct and are derived either by primary (e.g., green and red algae) or secondary endosymbiosis (e.g., diatoms, dinoflagellates, and brown algae). Light is a key abiotic factor needed to maintain the fitness of algae as it delivers energy for photosynthesis, regulates algal cell- and life cycles, and entrains their biological clocks. However, excess light can also be harmful, especially in the ultraviolet range. Among the variety of receptors perceiving light information, the cryptochromes originally evolved as UV-A and blue-light receptors and have been found in all studied algal genomes so far. Yet, the classification, biophysical properties, wavelength range of absorbance, and biological functions of cryptochromes are remarkably diverse among algal species, especially when compared to cryptochromes from land plants or animals.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Sabine Oldemeyer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
- Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
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9
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Hirayama T. PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation. Int J Mol Sci 2021; 22:ijms221910776. [PMID: 34639116 PMCID: PMC8509313 DOI: 10.3390/ijms221910776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 10/02/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.
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Affiliation(s)
- Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurahiki 710-0046, Okayama, Japan
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10
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Yan J, Chen Q, Cui X, Zhao P, Gao S, Yang B, Liu JX, Tong T, Deyholos MK, Jiang YQ. Ectopic overexpression of a membrane-tethered transcription factor gene NAC60 from oilseed rape positively modulates programmed cell death and age-triggered leaf senescence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:600-618. [PMID: 33119146 DOI: 10.1111/tpj.15057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Senescence is an integrative final stage of plant development that is governed by internal and external cues. The NAM, ATAF1/2, CUC2 (NAC) transcription factor (TF) family is specific to plants and membrane-tethered NAC TFs (MTTFs) constitute a unique and sophisticated mechanism in stress responses and development. However, the function of MTTFs in oilseed rape (Brassica napus L.) remains unknown. Here, we report that BnaNAC60 is an MTTF associated with the endoplasmic reticulum (ER) membrane. Expression of BnaNAC60 was induced during the progression of leaf senescence. Translocation of BnaNAC60 into nuclei was induced by ER stress and oxidative stress treatments. It binds to the NTLBS motif, rather than the canonical NAC recognition site. Overexpression of BnaNAC60 devoid of the transmembrane domain, but not the full-length BnaNAC60, induces significant reactive oxygen species (ROS) accumulation and hypersensitive response-like cell death in both tobacco (Nicotiana benthamiana) and oilseed rape protoplasts. Moreover, ectopic overexpression of BnaNAC60 devoid of the transmembrane domain, but not the full-length BnaNAC60, in Arabidopsis also induces precocious leaf senescence. Furthermore, screening and expression profiling identified an array of functional genes that are significantly induced by BnaNAC60 expression. Further it was found that BnaNAC60 can activate the promoter activities of BnaNYC1, BnaRbohD, BnaBFN1, BnaZAT12, and multiple BnaVPEs in a dual-luciferase reporter assay. Electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative PCR assays revealed that BnaNAC60 directly binds to the promoter regions of these downstream target genes. To summarize, our data show that BnaNAC60 is an MTTF that modulates cell death, ROS accumulation, and leaf senescence.
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Affiliation(s)
- Jingli Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Qinqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xing Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Peiyu Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Shidong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Bo Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Tiantian Tong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Yuan-Qing Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, 712100, China
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11
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Shimakawa G, Hanawa H, Wada S, Hanke GT, Matsuda Y, Miyake C. Physiological Roles of Flavodiiron Proteins and Photorespiration in the Liverwort Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2021; 12:668805. [PMID: 34489990 PMCID: PMC8418088 DOI: 10.3389/fpls.2021.668805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/30/2021] [Indexed: 05/19/2023]
Abstract
Against the potential risk in oxygenic photosynthesis, that is, the generation of reactive oxygen species, photosynthetic electron transport needs to be regulated in response to environmental fluctuations. One of the most important regulations is keeping the reaction center chlorophyll (P700) of photosystem I in its oxidized form in excess light conditions. The oxidation of P700 is supported by dissipating excess electrons safely to O2, and we previously found that the molecular mechanism of the alternative electron sink is changed from flavodiiron proteins (FLV) to photorespiration in the evolutionary history from cyanobacteria to plants. However, the overall picture of the regulation of photosynthetic electron transport is still not clear in bryophytes, the evolutionary intermediates. Here, we investigated the physiological roles of FLV and photorespiration for P700 oxidation in the liverwort Marchantia polymorpha by using the mutants deficient in FLV (flv1) at different O2 partial pressures. The effective quantum yield of photosystem II significantly decreased at 2kPa O2 in flv1, indicating that photorespiration functions as the electron sink. Nevertheless, it was clear from the phenotype of flv1 that FLV was dominant for P700 oxidation in M. polymorpha. These data suggested that photorespiration has yet not replaced FLV in functioning for P700 oxidation in the basal land plant probably because of the lower contribution to lumen acidification, compared with FLV, as reflected in the results of electrochromic shift analysis.
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Affiliation(s)
- Ginga Shimakawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Research Center for Solar Energy Chemistry, Osaka University, Suita, Japan
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Nishinomiya, Japan
- Core Research for Environmental Science and Technology, Japan Science and Technology Agency, Chiyoda, Japan
| | - Hitomi Hanawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinya Wada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Core Research for Environmental Science and Technology, Japan Science and Technology Agency, Chiyoda, Japan
| | - Guy T. Hanke
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom
| | - Yusuke Matsuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Nishinomiya, Japan
| | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Core Research for Environmental Science and Technology, Japan Science and Technology Agency, Chiyoda, Japan
- *Correspondence: Chikahiro Miyake,
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12
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Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants. Genomics 2020; 113:1096-1108. [PMID: 33171205 DOI: 10.1016/j.ygeno.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022]
Abstract
Polygalacturonase (PG) is a hydrolase that participates in pectin degradation, pod shattering and fruit softening. Here, we identified 2786 PG genes across 54 plants, which could be divided into three groups. Evolutionary analysis suggested that PG family originated from the charophyte green algae, and Subgroups A2-A4 evolved from the Subgroup A1 after the tracheophyte-angiosperm split. Whole-genome duplication was the major force leading to PG gene expansion. Interestingly, the PG genes continuously expanded in eudicots, whereas it contracted in monocots after the eudicot-monocot split. PG genes in Group A are expressed at high levels in floral organs, whereas genes in Groups B and C are expressed at high levels in various tissues. Moreover, three BnaPG15 members were found for their potential possibility in pod shattering in Brassica napus. Our results provide new insight into the evolutionary history of PG family, and their potentially functional role in plants.
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13
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Negrutiu I, Frohlich MW, Hamant O. Flowering Plants in the Anthropocene: A Political Agenda. TRENDS IN PLANT SCIENCE 2020; 25:349-368. [PMID: 31964603 DOI: 10.1016/j.tplants.2019.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/30/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Flowering plants are the foundation of human civilization, providing biomass for food, fuel, and materials to satisfy human needs, dependent on fertile soil, adequate water, and favorable weather. Conversely, failure of any of these inputs has caused catastrophes. Today, human appropriation of biomass is threatening planetary boundaries, inducing social and political unrest worldwide. Human societies are bound to rethink agriculture and forestry to restore and safeguard natural resources while improving the overall quality of life. Here, we explore why and how. Through an evolutionary and quantitative analysis of agriculture, and bridging plant and Earth sciences, we anticipate the advent of a research and policy framework, integrating plant science in all sectors: the economy, local and global governance, and geopolitics.
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Affiliation(s)
- Ioan Negrutiu
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
| | - Michael W Frohlich
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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14
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Kanazawa M, Ikeda Y, Nishihama R, Yamaoka S, Lee NH, Yamato KT, Kohchi T, Hirayama T. Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants. PLANT & CELL PHYSIOLOGY 2020; 61:470-480. [PMID: 31722408 DOI: 10.1093/pcp/pcz212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.
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Affiliation(s)
- Mai Kanazawa
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Yoko Ikeda
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Nam-Hee Lee
- Department of Life Sciences, Faculty of Science and Engineering, Sorbonne University, 4 Place Jussieu, Paris 75005, France
| | - Katsuyuki T Yamato
- Department of Biotechnological Science, Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takashi Hirayama
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
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15
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Luo W, Komatsu S, Abe T, Matsuura H, Takahashi K. Comparative Proteomic Analysis of Wild-Type Physcomitrella Patens and an OPDA-Deficient Physcomitrella Patens Mutant with Disrupted PpAOS1 and PpAOS2 Genes after Wounding. Int J Mol Sci 2020; 21:ijms21041417. [PMID: 32093080 PMCID: PMC7073133 DOI: 10.3390/ijms21041417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
Wounding is a serious environmental stress in plants. Oxylipins such as jasmonic acid play an important role in defense against wounding. Mechanisms to adapt to wounding have been investigated in vascular plants; however, those mechanisms in nonvascular plants remain elusive. To examine the response to wounding in Physcomitrella patens, a model moss, a proteomic analysis of wounded P. patens was conducted. Proteomic analysis showed that wounding increased the abundance of proteins related to protein synthesis, amino acid metabolism, protein folding, photosystem, glycolysis, and energy synthesis. 12-Oxo-phytodienoic acid (OPDA) was induced by wounding and inhibited growth. Therefore, OPDA is considered a signaling molecule in this plant. Proteomic analysis of a P. patens mutant in which the PpAOS1 and PpAOS2 genes, which are involved in OPDA biosynthesis, are disrupted showed accumulation of proteins involved in protein synthesis in response to wounding in a similar way to the wild-type plant. In contrast, the fold-changes of the proteins in the wild-type plant were significantly different from those in the aos mutant. This study suggests that PpAOS gene expression enhances photosynthesis and effective energy utilization in response to wounding in P. patens.
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Affiliation(s)
- Weifeng Luo
- Division of Fundamental Agroscience Research, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (W.L.); (T.A.); (H.M.)
| | - Setsuko Komatsu
- Department of Environmental and Food Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, 3-6-1 Gakuen, Fukui 910-8505, Japan;
| | - Tatsuya Abe
- Division of Fundamental Agroscience Research, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (W.L.); (T.A.); (H.M.)
| | - Hideyuki Matsuura
- Division of Fundamental Agroscience Research, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (W.L.); (T.A.); (H.M.)
| | - Kosaku Takahashi
- Division of Fundamental Agroscience Research, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (W.L.); (T.A.); (H.M.)
- Department of Nutritional Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 165-8502, Japan
- Correspondence:
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16
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E Z, Chen C, Yang J, Tong H, Li T, Wang L, Chen H. Genome-wide analysis of fatty acid desaturase genes in rice (Oryza sativa L.). Sci Rep 2019; 9:19445. [PMID: 31857634 PMCID: PMC6923433 DOI: 10.1038/s41598-019-55648-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/26/2019] [Indexed: 12/21/2022] Open
Abstract
Fatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns. The rice desaturase genes were distributed on ten of 12 chromosomes and phylogenetically classified into six subfamilies with the Arabidopsis counterparts, FAB2, FAD2, FAD3/7/8, FAD6, DES1 and SLD1. Among of them, 9 members were expanded via chromosomal tandem or segmental duplications. The gene structures and motif constituents were evolutionarily conserved in the same subfamilies. The majority of desaturase genes showed tissue-specific expression patterns and response to abiotic stresses and hormones based on microarray data and qRT-PCR analyses. This study will provide useful clues for functional validation of desaturase genes and contribute to produce nutritionally important fatty acids by genetic modification in rice.
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Affiliation(s)
- Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Chen Chen
- Key Laboratory of Plant Functional Genomics, Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Jinyu Yang
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hanhua Tong
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tingting Li
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lei Wang
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongqi Chen
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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17
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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18
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Abstract
Bryophytes, which comprise liverworts, mosses, and hornworts, are one of the earliest diverging lineages of extant land plants and a key plant group for understanding evolutionary aspects of land plant adaptation. Marchantia polymorpha, a liverwort, has recently been established as a model plant species having molecular genetic tractability. In M. polymorpha, phytochrome is encoded by a single-copy gene, MpPHY, with Mpphy regulating various physiological responses through PHYTOCHROME INTERACTING FACTOR (PIF)-mediated transcriptional regulation. The phytochrome signaling system of M. polymorpha, with its single Mpphy and single PIF (MpPIF), is relatively simple compared with other model plants carrying multiple phytochromes and PIFs. Consequently, investigation of phytochrome signaling using M. polymorpha may provide novel insights into fundamental mechanisms and roles of phytochrome during the course of land plant evolution. This chapter provides a number of basic procedures, along with some tips, for designing and performing experiments with M. polymorpha to study phytochrome signaling.
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19
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Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8683054. [PMID: 31396307 PMCID: PMC6668560 DOI: 10.1155/2019/8683054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/03/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022]
Abstract
The plant innate immune system has two major branches, the pathogen-triggered immunity and the effector-triggered immunity (ETI). The effectors are molecules released by plant attackers to evade host immunity. In addition to the foreign intruders, plants possess endogenous instigators produced in response to general cellular injury termed as damage-associated molecular patterns (DAMPs). In plants, DAMPs or alarmins are released by damaged, stressed, or dying cells following abiotic stress such as radiation, oxidative and drought stresses. In turn, a cascade of downstream signaling events is initiated leading to the upregulation of defense or response-related genes. In the present study, we have investigated more thoroughly the conservation status of the molecular mechanisms implicated in the danger signaling primarily in plants. Towards this direction, we have performed in silico phylogenetic and structural analyses of the associated biomolecules in taxonomically diverse plant species. On the basis of our results, the defense mechanisms appear to be largely conserved within the plant kingdom. Of note, the sequence and/or function of several components of these mechanisms was found to be conserved in animals, as well. At the same time, the molecules involved in plant defense were found to form a dense protein-protein interaction (PPi) network, suggesting a crosstalk between the various defense mechanisms to a variety of stresses, like oxidative stress.
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Affiliation(s)
- Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balcova, Izmir, Turkey
| | - Ezgi Karaca
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balcova, Izmir, Turkey
- Izmir Biomedicine and Genome Center, 35340 Balcova, Izmir, Turkey
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Athens, Greece
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20
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Roodt D, Li Z, Van de Peer Y, Mizrachi E. Loss of Wood Formation Genes in Monocot Genomes. Genome Biol Evol 2019; 11:1986-1996. [PMID: 31173081 PMCID: PMC6644875 DOI: 10.1093/gbe/evz115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2019] [Indexed: 12/23/2022] Open
Abstract
Woodiness (secondary xylem derived from vascular cambium) has been gained and lost multiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved in xylogenesis in fully sequenced angiosperm genomes, hypothesizing that monocots have lost some essential orthologs involved in this process. We analyzed the conservation of genes preferentially expressed in the developing secondary xylem of two eudicot trees in the sequenced genomes of 26 eudicot and seven monocot species, and the early diverging angiosperm Amborella trichopoda. We also reconstructed a regulatory model of early vascular cambial cell identity and differentiation and investigated the conservation of orthologs across the angiosperms. Additionally, we analyzed the genome of the aquatic seagrass Zostera marina for additional losses of genes otherwise essential to, especially, secondary cell wall formation. Despite almost complete conservation of orthology within the early cambial differentiation gene network, we show a clear pattern of loss of genes preferentially expressed in secondary xylem in the monocots that are highly conserved across eudicot species. Our study provides candidate genes that may have led to the loss of vascular cambium in the monocots, and, by comparing terrestrial angiosperms to an aquatic monocot, highlights genes essential to vasculature on land.
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Affiliation(s)
- Danielle Roodt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, South Africa
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Belgium
| | - Yves Van de Peer
- Genomics Research Institute, University of Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Belgium
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, South Africa
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21
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Walls RL, Cooper L, Elser J, Gandolfo MA, Mungall CJ, Smith B, Stevenson DW, Jaiswal P. The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. FRONTIERS IN PLANT SCIENCE 2019; 10:631. [PMID: 31214208 PMCID: PMC6558174 DOI: 10.3389/fpls.2019.00631] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
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Affiliation(s)
- Ramona L. Walls
- CyVerse, Bio5 Institute, The University of Arizona, Tucson, AZ, United States
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Maria Alejandra Gandolfo
- Liberty Hyde Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States
| | | | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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22
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He C, Si C, Teixeira da Silva JA, Li M, Duan J. Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid. BMC PLANT BIOLOGY 2019; 19:223. [PMID: 31138149 PMCID: PMC6540398 DOI: 10.1186/s12870-019-1836-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. RESULTS Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. CONCLUSIONS MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | | | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210014 China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
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23
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Komatsu A, Nishihama R, Kohchi T. Observation of Phototropic Responses in the Liverwort Marchantia polymorpha. Methods Mol Biol 2019; 1924:53-61. [PMID: 30694467 DOI: 10.1007/978-1-4939-9015-3_6] [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] [Indexed: 06/09/2023]
Abstract
The liverwort species, Marchantia polymorpha, shows environment-dependent morphological plasticity throughout its life cycle. Thalli, representing the predominant body form throughout most of this bryophyte's life cycle, grow with repeated dichotomous branching at the apex and develop horizontally under sufficient light intensity. Spores, after germination, produce a mass of cells, called sporelings, which then grow into thalli. Both thalli and sporelings, if grown under weak light conditions, form narrow shapes, and their apices grow toward the light source. These phototropic responses are specific to blue light and dependent on the blue-light receptor phototropin. This chapter provides several basic procedures, along with some tips, for designing and performing experiments with M. polymorpha to observe their phototropic responses, as well as methods for observing the localization of the phototropin "Mpphot" with a fluorescent protein tag.
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Affiliation(s)
- Aino Komatsu
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
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Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience 2018; 7:4924998. [PMID: 29697823 PMCID: PMC5915950 DOI: 10.1093/gigascience/giy020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition. Results We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the 3 Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of approximately 26% and approximately 38% of the homoeolog groups in B. hybridum changed toward nonadditive expression and nonancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggest that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum. Conclusions Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
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Affiliation(s)
- Kotaro Takahagi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Shimizu
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihiko Onda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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Yoshikawa M, Luo W, Tanaka G, Konishi Y, Matsuura H, Takahashi K. Wounding stress induces phenylalanine ammonia lyases, leading to the accumulation of phenylpropanoids in the model liverwort Marchantia polymorpha. PHYTOCHEMISTRY 2018; 155:30-36. [PMID: 30064058 DOI: 10.1016/j.phytochem.2018.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Wounding stress induces the biosynthesis of various specialized metabolites in plants. In this study, wounding induced the biosynthesis of luteolin, apigenin, and isoriccardin C, which are biosynthesized through the phenylpropanoid pathway, in the model liverwort Marchantia polymorpha L (Marchantiaceae). Recombinant M. polymorpha phenylalanine ammonia lyases (MpPALs) exhibited PAL activity in vitro and converted phenylalanine into trans-cinnamic acid. Based on semi-quantitative RT-PCR analysis, the expression levels of the MpPAL genes were up-regulated after wounding. α-Aminooxy-β-phenylpropionic acid, a PAL inhibitor, suppressed the production of wounding-induced phenolic compounds, luteolin, apigenin, and isoriccardin C, in M. polymorpha. Thus, PAL is a committed step in the biosynthesis of phenylpropanoids in response to wounding in M. polymorpha. This study suggests that wound-induced specialized metabolites such as phenylpropanoids comprise a conserved defense system in land plants.
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Affiliation(s)
- Mayu Yoshikawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Weifeng Luo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Genta Tanaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuka Konishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kosaku Takahashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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Metch JW, Burrows ND, Murphy CJ, Pruden A, Vikesland PJ. Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design. NATURE NANOTECHNOLOGY 2018; 13:253-259. [PMID: 29335567 DOI: 10.1038/s41565-017-0029-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/14/2017] [Indexed: 05/27/2023]
Abstract
Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.
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Affiliation(s)
- Jacob W Metch
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA
| | - Nathan D Burrows
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA.
| | - Peter J Vikesland
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA.
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Hussain T, Plunkett B, Ejaz M, Espley RV, Kayser O. Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata. FRONTIERS IN PLANT SCIENCE 2018; 9:537. [PMID: 29868043 PMCID: PMC5954354 DOI: 10.3389/fpls.2018.00537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/06/2018] [Indexed: 05/06/2023]
Abstract
The liverwort Radula marginata belongs to the bryophyte division of land plants and is a prospective alternate source of cannabinoid-like compounds. However, mechanistic insights into the molecular pathways directing the synthesis of these cannabinoid-like compounds have been hindered due to the lack of genetic information. This prompted us to do deep sequencing, de novo assembly and annotation of R. marginata transcriptome, which resulted in the identification and validation of the genes for cannabinoid biosynthetic pathway. In total, we have identified 11,421 putative genes encoding 1,554 enzymes from 145 biosynthetic pathways. Interestingly, we have identified all the upstream genes of the central precursor of cannabinoid biosynthesis, cannabigerolic acid (CBGA), including its two first intermediates, stilbene acid (SA) and geranyl diphosphate (GPP). Expression of all these genes was validated using quantitative real-time PCR. We have characterized the protein structure of stilbene synthase (STS), which is considered as a homolog of olivetolic acid in R. marginata. Moreover, the metabolomics approach enabled us to identify CBGA-analogous compounds using electrospray ionization mass spectrometry (ESI-MS/MS) and gas chromatography mass spectrometry (GC-MS). Transcriptomic analysis revealed 1085 transcription factors (TF) from 39 families. Comparative analysis showed that six TF families have been uniquely predicted in R. marginata. In addition, the bioinformatics analysis predicted a large number of simple sequence repeats (SSRs) and non-coding RNAs (ncRNAs). Our results collectively provide mechanistic insights into the putative precursor genes for the biosynthesis of cannabinoid-like compounds and a novel transcriptomic resource for R. marginata. The large-scale transcriptomic resource generated in this study would further serve as a reference transcriptome to explore the Radulaceae family.
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Affiliation(s)
- Tajammul Hussain
- Department of Technical Biochemistry, TU Dortmund University, Dortmund, Germany
- *Correspondence: Tajammul Hussain
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Mahwish Ejaz
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard V. Espley
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Oliver Kayser
- Department of Technical Biochemistry, TU Dortmund University, Dortmund, Germany
- Oliver Kayser
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Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer. Virus Res 2017; 244:36-52. [PMID: 29103997 PMCID: PMC5801114 DOI: 10.1016/j.virusres.2017.10.020] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/22/2022]
Abstract
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events.
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Kato H, Kouno M, Takeda M, Suzuki H, Ishizaki K, Nishihama R, Kohchi T. The Roles of the Sole Activator-Type Auxin Response Factor in Pattern Formation of Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2017; 58:1642-1651. [PMID: 29016901 DOI: 10.1093/pcp/pcx095] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/05/2017] [Indexed: 05/08/2023]
Abstract
Cell division patterning is important to determine body shape in plants. Nuclear auxin signaling mediated by AUXIN RESPONSE FACTOR (ARF) transcription factors affects plant growth and development through regulation of cell division, elongation and differentiation. The evolutionary origin of the ARF-mediated pathway dates back to at least the common ancestor of bryophytes and other land plants. The liverwort Marchantia polymorpha has three phylogenetically distinct ARFs: MpARF1, the sole 'activator' ARF; and MpARF2 and MpARF3, two 'repressor' ARFs. Genetic screens for auxin-resistant mutants revealed that loss of MpARF1 function conferred auxin insensitivity. Mparf1 mutants showed reduced auxin-inducible gene expression and various developmental defects, including thallus twisting and gemma malformation. We further investigated the role of MpARF1 in gemma development, which is traceable at the cellular level. In wild-type plants, a gemma initial first undergoes several transverse divisions to generate a single-celled stalk and a gemma proper, followed by rather synchronous longitudinal divisions in the latter. Mparf1 mutants often contained multicelled stalks and showed defects in the execution and timing of the longitudinal divisions. While wild-type gemmae finally generate two meristem notches, Mparf1 gemmae displayed various numbers of ectopic meristems. These results suggest that MpARF1 regulates formative cell divisions and axis formation through auxin responses. The mechanism for activator ARF regulation of pattern formation may be shared in land plants and therefore important for the general acquisition of three-dimensional body plans.
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Affiliation(s)
- Hirotaka Kato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masaru Kouno
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mayuko Takeda
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Yokota T, Ohnishi T, Shibata K, Asahina M, Nomura T, Fujita T, Ishizaki K, Kohchi T. Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern. PHYTOCHEMISTRY 2017; 136:46-55. [PMID: 28057327 DOI: 10.1016/j.phytochem.2016.12.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/01/2016] [Accepted: 12/23/2016] [Indexed: 05/05/2023]
Abstract
Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage.
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Affiliation(s)
- Takao Yokota
- Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan.
| | - Toshiyuki Ohnishi
- Graduate School of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kyomi Shibata
- Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan
| | - Masashi Asahina
- Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan
| | - Takahito Nomura
- Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takayuki Kohchi
- Laboratory of Plant Molecular Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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Ishizaki K. Evolution of land plants: insights from molecular studies on basal lineages. Biosci Biotechnol Biochem 2017; 81:73-80. [DOI: 10.1080/09168451.2016.1224641] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.
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Affiliation(s)
- Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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Mikulski P, Komarynets O, Fachinelli F, Weber AP, Schubert D. Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae. FRONTIERS IN PLANT SCIENCE 2017; 8:607. [PMID: 28484477 PMCID: PMC5405695 DOI: 10.3389/fpls.2017.00607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/04/2017] [Indexed: 05/03/2023]
Abstract
Polycomb Group (PcG) proteins mediate chromatin repression in plants and animals by catalyzing H3K27 methylation and H2AK118/119 mono-ubiquitination through the activity of the Polycomb repressive complex 2 (PRC2) and PRC1, respectively. PcG proteins were extensively studied in higher plants, but their function and target genes in unicellular branches of the green lineage remain largely unknown. To shed light on PcG function and modus operandi in a broad evolutionary context, we demonstrate phylogenetic relationship of core PRC1 and PRC2 proteins and H3K27me3 biochemical presence in several unicellular algae of different phylogenetic subclades. We focus then on one of the species, the model red alga Cyanidioschizon merolae, and show that H3K27me3 occupies both, genes and repetitive elements, and mediates the strength of repression depending on the differential occupancy over gene bodies. Furthermore, we report that H3K27me3 in C. merolae is enriched in telomeric and subtelomeric regions of the chromosomes and has unique preferential binding toward intein-containing genes involved in protein splicing. Thus, our study gives important insight for Polycomb-mediated repression in lower eukaryotes, uncovering a previously unknown link between H3K27me3 targets and protein splicing.
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Affiliation(s)
- Pawel Mikulski
- Institute of Biology, Free University of BerlinBerlin, Germany
- Institute of Genetics, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Olga Komarynets
- Institute of Genetics, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
- Faculty of Medicine, University of GenevaGeneva, Switzerland
| | - Fabio Fachinelli
- Institute of Plant Biochemistry, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Andreas P.M. Weber
- Institute of Plant Biochemistry, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Daniel Schubert
- Institute of Biology, Free University of BerlinBerlin, Germany
- Institute of Genetics, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
- *Correspondence: Daniel Schubert,
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Tanaka M, Esaki T, Kenmoku H, Koeduka T, Kiyoyama Y, Masujima T, Asakawa Y, Matsui K. Direct evidence of specific localization of sesquiterpenes and marchantin A in oil body cells of Marchantia polymorpha L. PHYTOCHEMISTRY 2016; 130:77-84. [PMID: 27406893 DOI: 10.1016/j.phytochem.2016.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/15/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Liverworts are a rich source of a diverse array of specialized metabolites, such as terpenoids and benzenoids, which are potentially useful for pharmaceutical or agrochemical applications, and also provide clues to elucidate the strategy by which liverworts adapt to the terrestrial environment. Liverworts, belonging to orders Marchantiales and Jungermanniales, possess oil bodies. In Marchantia polymorpha L., oil bodies are confined to scattered idioblastic oil body cells. It has been assumed that the specialized metabolites in M. polymorpha specifically accumulate in the oil bodies in oil body cells; however, no direct evidence was previously available for this specific accumulation. In this study, direct evidence was obtained using micromanipulation techniques coupled with MS analysis that demonstrated the specific accumulation of sesquiterpenoids and marchantin A in the oil body cells of M. polymorpha thalli. It was also observed that the number of oil body cells increased in thalli grown in low-mineral conditions. The amounts of sesquiterpenoids and marchantin A detected in crude extract prepared from the whole thallus were roughly proportional to the number of oil body cells found in a given volume of thallus, suggesting that oil body cell differentiation and sesquiterpenoid and marchantin A biosynthetic pathways are coordinated with each other.
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Affiliation(s)
- M Tanaka
- Department of Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - T Esaki
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - H Kenmoku
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - T Koeduka
- Department of Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Y Kiyoyama
- Department of Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - T Masujima
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - Y Asakawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - K Matsui
- Department of Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
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Rangan P, Furtado A, Henry RJ. New evidence for grain specific C4 photosynthesis in wheat. Sci Rep 2016; 6:31721. [PMID: 27530078 PMCID: PMC4987656 DOI: 10.1038/srep31721] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/22/2016] [Indexed: 11/30/2022] Open
Abstract
The C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi-110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
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37
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Abstract
Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.
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Affiliation(s)
- Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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Kobayashi Y, Otani T, Ishibashi K, Shikanai T, Nishimura Y. C-Terminal Region of Sulfite Reductase Is Important to Localize to Chloroplast Nucleoids in Land Plants. Genome Biol Evol 2016; 8:1459-66. [PMID: 27189994 PMCID: PMC4898807 DOI: 10.1093/gbe/evw093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chloroplast (cp) DNA is compacted into cpDNA-protein complexes, called cp nucleoids. An abundant and extensively studied component of cp nucleoids is the bifunctional protein sulfite reductase (SiR). The preconceived role of SiR as the core cp nucleoid protein, however, is becoming less likely because of the recent findings that SiRs do not associate with cp nucleoids in some plant species, such as Zea mays and Arabidopsis thaliana To address this discrepancy, we have performed a detailed phylogenetic analysis of SiRs, which shows that cp nucleoid-type SiRs share conserved C-terminally encoded peptides (CEPs). The CEPs are likely to form a bacterial ribbon-helix-helix DNA-binding motif, implying a potential role in attaching SiRs onto cp nucleoids. A proof-of-concept experiment was conducted by fusing the nonnucleoid-type SiR from A. thaliana (AtSiR) with the CEP from the cp nucleoid-type SiR of Phaseolus vulgaris The addition of the CEP drastically altered the intra-cp localization of AtSiR to cp nucleoids. Our analysis supports the possible functions of CEPs in determining the localization of SiRs to cp nucleoids and illuminates a possible evolutionary scenario for SiR as a cp nucleoid protein.
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Affiliation(s)
| | | | | | | | - Yoshiki Nishimura
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Japan
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Proost S, Mutwil M. Tools of the trade: studying molecular networks in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:143-150. [PMID: 26990519 DOI: 10.1016/j.pbi.2016.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Driven by recent technological improvements, genes can be now studied in a larger biological context. Genes and their protein products rarely operate as a single entity and large-scale mapping by protein-protein interactions can unveil the molecular complexes that form in the cell to carry out various functions. Expression analysis under multiple conditions, supplemented with protein-DNA binding data can highlight when genes are active and how they are regulated. Representing these data in networks and finding strongly connected sub-graphs has proven to be a powerful tool to predict the function of unknown genes. As such networks are gradually becoming available for various plant species, it becomes possible to study how networks evolve. This review summarizes currently available network data and related tools for plants. Furthermore we aim to provide an outlook of future analyses that can be done in plants based on work done in other fields.
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Affiliation(s)
- Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Cridge AG, Dearden PK, Brownfield LR. Convergent occurrence of the developmental hourglass in plant and animal embryogenesis? ANNALS OF BOTANY 2016; 117:833-843. [PMID: 27013176 PMCID: PMC4845807 DOI: 10.1093/aob/mcw024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The remarkable similarity of animal embryos at particular stages of development led to the proposal of a developmental hourglass. In this model, early events in development are less conserved across species but lead to a highly conserved 'phylotypic period'. Beyond this stage, the model suggests that development once again becomes less conserved, leading to the diversity of forms. Recent comparative studies of gene expression in animal groups have provided strong support for the hourglass model. How and why might such an hourglass pattern be generated? More importantly, how might early acting events in development evolve while still maintaining a later conserved stage? SCOPE The discovery that an hourglass pattern may also exist in the embryogenesis of plants provides comparative data that may help us explain this phenomenon. Whether the developmental hourglass occurs in plants, and what this means for our understanding of embryogenesis in plants and animals is discussed. Models by which conserved early-acting genes might change their functional role in the evolution of gene networks, how networks buffer these changes, and how that might constrain, or confer diversity, of the body plan are also discused. CONCLUSIONS Evidence of a morphological and molecular hourglass in plant and animal embryogenesis suggests convergent evolution. This convergence is likely due to developmental constraints imposed upon embryogenesis by the need to produce a viable embryo with an established body plan, controlled by the architecture of the underlying gene regulatory networks. As the body plan is largely laid down during the middle phases of embryo development in plants and animals, then it is perhaps not surprising this stage represents the narrow waist of the hourglass where the gene regulatory networks are the oldest and most robust and integrated, limiting species diversity and constraining morphological space.
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Affiliation(s)
- Andrew G Cridge
- Laboratory for Evolution and Development, Genetics Otago and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand and
| | - Peter K Dearden
- Laboratory for Evolution and Development, Genetics Otago and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand and
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Mao H, Yu L, Li Z, Liu H, Han R. Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L. Genetica 2016; 144:243-57. [PMID: 26979310 DOI: 10.1007/s10709-016-9896-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/13/2016] [Indexed: 01/18/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Lijuan Yu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Zhanjie Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Hui Liu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Ran Han
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
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Ishizaki K, Nishihama R, Yamato KT, Kohchi T. Molecular Genetic Tools and Techniques for Marchantia polymorpha Research. PLANT & CELL PHYSIOLOGY 2016; 57:262-70. [PMID: 26116421 DOI: 10.1093/pcp/pcv097] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/18/2015] [Indexed: 05/18/2023]
Abstract
Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants.
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Affiliation(s)
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Wakayama, 649-6493 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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43
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Tanaka D, Ishizaki K, Kohchi T, Yamato KT. Cryopreservation of Gemmae from the Liverwort Marchantia polymorpha L. PLANT & CELL PHYSIOLOGY 2016; 57:300-6. [PMID: 26561534 PMCID: PMC4788409 DOI: 10.1093/pcp/pcv173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 11/03/2015] [Indexed: 05/22/2023]
Abstract
The liverwort Marchantia polymorpha L. is one of the key model plants in evo-devo studies, and an increasing number of transgenic and mutant lines have been established. For reliable long-term preservation of M. polymorpha plants, spores have been used, but crossing is indispensable to obtain them. Gemmae, however, are vegetative clones and readily available in large numbers without crossing, thereby enabling the clonal preservation and rapid propagation of transgenic or mutant lines. Here, we report a simple cryopreservation protocol for in vitro grown M. polymorpha gemmae using aluminum cryoplates. Gemmae were pre-cultured on sucrose-containing medium, embedded in calcium alginate gel on the surface of a cryoplate, moderately dehydrated and stored in liquid nitrogen. After rapid thawing, the stored gemmae showed a 100% survival rate. Our protocol does not require plant growth regulators such as ABA, and takes only 1 h to complete except for 1 d of pre-culture. Furthermore, gemmae treated as described above but then air-dried for 2 h can be stored at -80°C for at least 1 year without a significant decrease in survival rate, which is convenient for most laboratories that have a -80°C freezer but not a liquid nitrogen container for long-term storage. These preservation techniques for M. polymorpha should increase their availability in the research community.
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Affiliation(s)
- Daisuke Tanaka
- IBBP Center, National Institute for Basic Biology, Okazaki, 444-8787 Japan Department of Basic Biology, the Graduate University for Advanced Studies, Okazaki, 444-8585 Japan Present address: Genetic Resources Conservation Research Unit, Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Kinokawa, 649-6493 Japan
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44
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Flores-Sandoval E, Dierschke T, Fisher TJ, Bowman JL. Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2016; 57:281-90. [PMID: 25971256 DOI: 10.1093/pcp/pcv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/07/2015] [Indexed: 05/07/2023]
Abstract
We describe the efficient use of artificial microRNAs (amiRs) in Marchantia polymorpha using both endogenous and heterologous primary microRNA (pri-miR) hairpin backbones. Targeting of two transcription factor genes, MpARF1 and MpRR-B, mediating different hormonal responses, demonstrated that amiRs can create specific and reproducible physiological and morphological defects, facilitating interpretation of gene function. A third amiR was designed to target a gene encoding a component of the Polycomb recessive complex 2, MpE(z), and constitutive expression of this amiR results in sporeling lethality. Adaptation of an estrogen-inducible system allowed analysis of the phenotypic effects of induction of this amiR during other stages of the life cycle. We discuss the advantages and challenges of the use of amiRs as a tool for reverse genetic analysis in M. polymorpha.
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Affiliation(s)
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, UC Davis, Davis, CA 95616, USA
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45
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Abstract
The genetic and molecular basis of the developmental programs underlying adaptive morphological changes is largely unknown. A new study reveals an ancient gene that has been instrumental for the generation of morphological diversity and adaptation in land plants.
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Affiliation(s)
- Mario A Arteaga-Vazquez
- University of Veracruz, Institute for Biotechnology and Applied Ecology (INBIOTECA), Avenida de las Culturas Veracruzanas 101, Colonia Emiliano Zapata, Xalapa, Veracruz, México.
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46
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Daku RM, Rabbi F, Buttigieg J, Coulson IM, Horne D, Martens G, Ashton NW, Suh DY. PpASCL, the Physcomitrella patens Anther-Specific Chalcone Synthase-Like Enzyme Implicated in Sporopollenin Biosynthesis, Is Needed for Integrity of the Moss Spore Wall and Spore Viability. PLoS One 2016; 11:e0146817. [PMID: 26752629 PMCID: PMC4709238 DOI: 10.1371/journal.pone.0146817] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022] Open
Abstract
Sporopollenin is the main constituent of the exine layer of spore and pollen walls. The anther-specific chalcone synthase-like (ASCL) enzyme of Physcomitrella patens, PpASCL, has previously been implicated in the biosynthesis of sporopollenin, the main constituent of exine and perine, the two outermost layers of the moss spore cell wall. We made targeted knockouts of the corresponding gene, PpASCL, and phenotypically characterized ascl sporophytes and spores at different developmental stages. Ascl plants developed normally until late in sporophytic development, when the spores produced were structurally aberrant and inviable. The development of the ascl spore cell wall appeared to be arrested early in microspore development, resulting in small, collapsed spores with altered surface morphology. The typical stratification of the spore cell wall was absent with only an abnormal perine recognisable above an amorphous layer possibly representing remnants of compromised intine and/or exine. Equivalent resistance of the spore walls of ascl mutants and the control strain to acetolysis suggests the presence of chemically inert, defective sporopollenin in the mutants. Anatomical abnormalities of late-stage ascl sporophytes include a persistent large columella and an air space incompletely filled with spores. Our results indicate that the evolutionarily conserved PpASCL gene is needed for proper construction of the spore wall and for normal maturation and viability of moss spores.
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Affiliation(s)
- Rhys M. Daku
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Fazle Rabbi
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Josef Buttigieg
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Ian M. Coulson
- Department of Geology, University of Regina, Regina, Saskatchewan, Canada
| | - Derrick Horne
- BioImaging Facility, University of British Colombia, Vancouver, British Columbia, Canada
| | - Garnet Martens
- BioImaging Facility, University of British Colombia, Vancouver, British Columbia, Canada
| | - Neil W. Ashton
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- * E-mail: (DYS); (NWA)
| | - Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
- * E-mail: (DYS); (NWA)
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47
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Suetsugu N, Wada M. Evolution of the Cp-Actin-based Motility System of Chloroplasts in Green Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:561. [PMID: 27200035 PMCID: PMC4853393 DOI: 10.3389/fpls.2016.00561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/11/2016] [Indexed: 05/10/2023]
Abstract
During the course of green plant evolution, numerous light responses have arisen that optimize their growth under fluctuating light conditions. The blue light receptor phototropin mediates several photomovement responses at the tissue, cellular and organelle levels. Chloroplast photorelocation movement is one such photomovement response, and is found not only in most green plants, but also in some red algae and photosynthetic stramenopiles. In general, chloroplasts move toward weak light to maximally capture photosynthetically active radiation (the chloroplast accumulation response), and they move away from strong light to avoid photodamage (the avoidance response). In land plants, chloroplast movement is dependent on specialized actin filaments, chloroplast-actin filaments (cp-actin filaments). Through molecular genetic analysis using Arabidopsis thaliana, many molecular factors that regulate chloroplast photorelocation were identified. In this Perspective, we discuss the evolutionary history of the molecular mechanism for chloroplast photorelocation movement in green plants in view of cp-actin filaments.
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Affiliation(s)
| | - Masamitsu Wada
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan UniversityTokyo, Japan
- *Correspondence: Masamitsu Wada,
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48
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Kobayashi Y, Takusagawa M, Harada N, Fukao Y, Yamaoka S, Kohchi T, Hori K, Ohta H, Shikanai T, Nishimura Y. Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution. Genome Biol Evol 2015; 8:1-16. [PMID: 26608058 PMCID: PMC4758235 DOI: 10.1093/gbe/evv233] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chloroplast (cp) DNA is thought to originate from the ancestral endosymbiont genome and is compacted to form nucleoprotein complexes, cp nucleoids. The structure of cp nucleoids is ubiquitously observed in diverse plants from unicellular algae to flowering plants and is believed to be a multifunctional platform for various processes, including cpDNA replication, repair/recombination, transcription, and inheritance. Despite its fundamental functions, the protein composition for cp nucleoids in flowering plants was suggested to be divergent from those of bacteria and algae, but the evolutionary process remains elusive. In this research, we aimed to reveal the evolutionary history of cp nucleoid organization by analyzing the key organisms representing the three evolutionary stages of eukaryotic phototrophs: the chlorophyte alga Chlamydomonas reinhardtii, the charophyte alga Klebsormidium flaccidum, and the most basal land plant Marchantia polymorpha. To clarify the core cp nucleoid proteins in C. reinhardtii, we performed an LC-MS/MS analysis using highly purified cp nucleoid fractions and identified a novel SAP domain-containing protein with a eukaryotic origin as a constitutive core component. Then, homologous genes for cp nucleoid proteins were searched for in C. reinhardtii, K. flaccidum, and M. polymorpha using the genome databases, and their intracellular localizations and DNA binding activities were investigated by cell biological/biochemical analyses. Based on these results, we propose a model that recurrent modification of cp nucleoid organization by eukaryotic factors originally related to chromatin organization might have been the driving force for the diversification of cp nucleoids since the early stage of green plant evolution.
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Affiliation(s)
- Yusuke Kobayashi
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Mari Takusagawa
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Naomi Harada
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Yoichiro Fukao
- Plant Global Educational Project, and Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan Department of Bioinformatics, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Koichi Hori
- Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan
| | - Hiroyuki Ohta
- Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan
| | - Toshiharu Shikanai
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Yoshiki Nishimura
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
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49
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Mukherjee A. Computational analysis of a cys-loop ligand gated ion channel from the green alga Chlamydomonas reinhardtii. Mol Biol 2015. [DOI: 10.1134/s002689331505012x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sagor GHM, Inoue M, Kim DW, Kojima S, Niitsu M, Berberich T, Kusano T. The polyamine oxidase from lycophyte Selaginella lepidophylla (SelPAO5), unlike that of angiosperms, back-converts thermospermine to norspermidine. FEBS Lett 2015; 589:3071-8. [PMID: 26348400 DOI: 10.1016/j.febslet.2015.08.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 12/29/2022]
Abstract
In the phylogeny of plant polyamine oxidases (PAOs), clade III members from angiosperms, such as Arabidopsis thaliana PAO5 and Oryza sativa PAO1, prefer spermine and thermospermine as substrates and back-convert both of these substrates to spermidine in vitro. A clade III representative of lycophytes, SelPAO5 from Selaginella lepidophylla, also prefers spermine and thermospermine but instead back-converts these substrates to spermidine and norspermidine, respectively. This finding indicates that the clade III PAOs of lycophytes and angiosperms oxidize thermospermine at different carbon positions. We discuss the physiological significance of this difference.
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Affiliation(s)
- G H M Sagor
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Masataka Inoue
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Dong Wook Kim
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Seiji Kojima
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan; Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki aza Aoba 6-3, Aoba, Sendai 980-8578, Japan
| | - Masaru Niitsu
- Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Thomas Berberich
- Biodiversity and Climate Research Center, Laboratory Center, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | - Tomonobu Kusano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan.
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