251
|
Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GKS, Melkonian M, Liu H, Liu X. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. NATURE PLANTS 2020; 6:95-106. [PMID: 31844283 PMCID: PMC7027972 DOI: 10.1038/s41477-019-0560-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/28/2019] [Indexed: 05/18/2023]
Abstract
Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.
Collapse
Affiliation(s)
- Sibo Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haoyuan Li
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongli Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wenfei Xian
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hongping Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zehra Çebi
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Tanja Reder
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Morten Peterson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Barbara Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB/UGent Center for Plant Systems Biology, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Shenzhen, China.
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany.
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| |
Collapse
|
252
|
The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty. Curr Biol 2020; 30:530-536.e2. [DOI: 10.1016/j.cub.2019.11.090] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022]
|
253
|
Evolution of Photorespiratory Glycolate Oxidase among Archaeplastida. PLANTS 2020; 9:plants9010106. [PMID: 31952152 PMCID: PMC7020209 DOI: 10.3390/plants9010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/17/2022]
Abstract
Photorespiration has been shown to be essential for all oxygenic phototrophs in the present-day oxygen-containing atmosphere. The strong similarity of the photorespiratory cycle in cyanobacteria and plants led to the hypothesis that oxygenic photosynthesis and photorespiration co-evolved in cyanobacteria, and then entered the eukaryotic algal lineages up to land plants via endosymbiosis. However, the evolutionary origin of the photorespiratory enzyme glycolate oxidase (GOX) is controversial, which challenges the common origin hypothesis. Here, we tested this hypothesis using phylogenetic and biochemical approaches with broad taxon sampling. Phylogenetic analysis supported the view that a cyanobacterial GOX-like protein of the 2-hydroxy-acid oxidase family most likely served as an ancestor for GOX in all eukaryotes. Furthermore, our results strongly indicate that GOX was recruited to the photorespiratory metabolism at the origin of Archaeplastida, because we verified that Glaucophyta, Rhodophyta, and Streptophyta all express GOX enzymes with preference for the substrate glycolate. Moreover, an “ancestral” protein synthetically derived from the node separating all prokaryotic from eukaryotic GOX-like proteins also preferred glycolate over l-lactate. These results support the notion that a cyanobacterial ancestral protein laid the foundation for the evolution of photorespiratory GOX enzymes in modern eukaryotic phototrophs.
Collapse
|
254
|
Tang RJ, Luan M, Wang C, Lhamo D, Yang Y, Zhao FG, Lan WZ, Fu AG, Luan S. Plant Membrane Transport Research in the Post-genomic Era. PLANT COMMUNICATIONS 2020; 1:100013. [PMID: 33404541 PMCID: PMC7747983 DOI: 10.1016/j.xplc.2019.100013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 05/17/2023]
Abstract
Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.
Collapse
Affiliation(s)
- Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Mingda Luan
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dhondup Lhamo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yang Yang
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Fu-Geng Zhao
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Wen-Zhi Lan
- Nanjing University–Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ai-Gen Fu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Corresponding author
| |
Collapse
|
255
|
Alova A, Erofeev A, Gorelkin P, Bibikova T, Korchev Y, Majouga A, Bulychev A. Prolonged oxygen depletion in microwounded cells of Chara corallina detected with novel oxygen nanosensors. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:386-398. [PMID: 31563950 DOI: 10.1093/jxb/erz433] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Primary physicochemical steps in microwounding of plants were investigated using electrochemical nano- and microprobes, with a focus on the role of oxygen in the wounding responses of individual plant cells. Electrochemical measurements of cell oxygen content were made with carbon-filled quartz micropipettes with platinum-coated tips (oxygen nanosensors). These novel platinum nanoelectrodes are useful for understanding cell oxygen metabolism and can be employed to study the redox biochemistry and biology of cells, tissues and organisms. We show here that microinjury of Chara corallina internodal cells with the tip of a glass micropipette is associated with a drastic decrease in oxygen concentration at the vicinity of the stimulation site. This decrease is reversible and lasts for up to 40 minutes. Membrane stretching, calcium influx, and cytoskeleton rearrangements were found to be essential for the localized oxygen depletion induced by cell wall microwounding. Inhibition of electron transport in chloroplasts or mitochondria did not affect the magnitude or timing of the observed response. In contrast, the inhibition of NADPH oxidase activity caused a significant reduction in the amplitude of the decrease in oxygen concentration. We suggest that the observed creation of localized anoxic conditions in response to cell wall puncture might be mediated by NADPH oxidase.
Collapse
Affiliation(s)
- Anna Alova
- Lomonosov Moscow State University, Leninskiye gory, Moscow, Russian Federation
| | - Alexander Erofeev
- Lomonosov Moscow State University, Leninskiye gory, Moscow, Russian Federation
- National University of Science and Technology 'MISIS', Moscow, Russian Federation
| | - Petr Gorelkin
- Medical Nanotechnology LLC, Skolkovo Innovation Center, Moscow, Russian Federation
| | - Tatyana Bibikova
- Lomonosov Moscow State University, Leninskiye gory, Moscow, Russian Federation
| | - Yury Korchev
- Department of Medicine, Imperial College, London, UK
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Alexander Majouga
- Lomonosov Moscow State University, Leninskiye gory, Moscow, Russian Federation
- Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya, Moscow, Russian Federation
| | - Alexander Bulychev
- Lomonosov Moscow State University, Leninskiye gory, Moscow, Russian Federation
| |
Collapse
|
256
|
Melo JP, Kalyna M, Duque P. Current Challenges in Studying Alternative Splicing in Plants: The Case of Physcomitrella patens SR Proteins. FRONTIERS IN PLANT SCIENCE 2020; 11:286. [PMID: 32265953 PMCID: PMC7105729 DOI: 10.3389/fpls.2020.00286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/26/2020] [Indexed: 05/04/2023]
Abstract
To colonize different terrestrial habitats, early land plants had to overcome the challenge of coping with harsh new environments. Alternative splicing - an RNA processing mechanism through which splice sites are differentially recognized, originating multiple transcripts and potentially different proteins from the same gene - can be key for plant stress tolerance. Serine/arginine-rich (SR) proteins constitute an evolutionarily conserved family of major alternative splicing regulators that in plants subdivides into six subfamilies. Despite being well studied in animals and a few plant species, such as the model angiosperm Arabidopsis thaliana and the crop Oryza sativa, little is known of these splicing factors in early land plants. Establishing the whole complement of SR proteins in different species is essential to understand the functional and evolutionary significance of alternative splicing. An in silico search for SR proteins in the extant moss Physcomitrella patens revealed inconsistencies both in the published data and available databases, likely arising from automatic annotation lacking adequate manual curation. These misannotations interfere with the description not only of the number and subfamily classification of Physcomitrella SR proteins but also of their domain architecture, potentially hindering the elucidation of their molecular functions. We therefore advise caution when looking into P. patens genomic resources. Our systematic survey nonetheless confidently identified 16 P. patens SR proteins that fall into the six described subfamilies and represent counterparts of well-established members in Arabidopsis and rice. Intensified research efforts should disclose whether SR proteins were already determining alternative splicing modulation and stress tolerance in early land plants.
Collapse
Affiliation(s)
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, BOKU – University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Maria Kalyna,
| | - Paula Duque
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
- Paula Duque,
| |
Collapse
|
257
|
Liang Z, Geng Y, Ji C, Du H, Wong CE, Zhang Q, Zhang Y, Zhang P, Riaz A, Chachar S, Ding Y, Wen J, Wu Y, Wang M, Zheng H, Wu Y, Demko V, Shen L, Han X, Zhang P, Gu X, Yu H. Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901850. [PMID: 31921561 PMCID: PMC6947507 DOI: 10.1002/advs.201901850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/10/2019] [Indexed: 05/02/2023]
Abstract
The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
Collapse
Affiliation(s)
- Zhe Liang
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Yuke Geng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Changmian Ji
- Biomarker TechnologiesBeijing101300China
- Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou571101China
| | - Hai Du
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Chui Eng Wong
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Qian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Ye Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Pingxian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Adeel Riaz
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Sadaruddin Chachar
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Yike Ding
- Department of EntomologyUniversity of California RiversideRiversideCA92521USA
| | - Jing Wen
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Yunwen Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | | | | | - Yanmin Wu
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Viktor Demko
- Department of Plant PhysiologyFaculty of Natural SciencesComenius University in BratislavaBratislava84215Slovakia
| | - Lisha Shen
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
| | - Xiao Han
- College of Biological Science and EngineeringFuzhou UniversityFuzhou350108China
| | - Pengpeng Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaofeng Gu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Hao Yu
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
| |
Collapse
|
258
|
Abstract
Two genomes of the closest algal sisters to land plants were sequenced, providing potential evidence that bacterial genes were key in adapting to terrestrial stresses.
Collapse
Affiliation(s)
- Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.
| |
Collapse
|
259
|
Chang X, Xie S, Wei L, Lu Z, Chen ZH, Chen F, Lai Z, Lin Z, Zhang L. Origins and Stepwise Expansion of R2R3-MYB Transcription Factors for the Terrestrial Adaptation of Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:575360. [PMID: 33424877 PMCID: PMC7785938 DOI: 10.3389/fpls.2020.575360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 05/14/2023]
Abstract
The R2R3-MYB transcription factors play critical roles in various processes in embryophytes (land plants). Here, we identified genes encoding R2R3-MYB proteins from rhodophytes, glaucophytes, Chromista, chlorophytes, charophytes, and embryophytes. We classified the R2R3-MYB genes into three subgroups (I, II, and III) based on their evolutionary history and gene structure. The subgroup I is the most ancient group that includes members from all plant lineages. The subgroup II was formed before the divergence of charophytes and embryophytes. The subgroup III genes form a monophyletic group and only comprise members from land plants with conserved exon-intron structure. Each subgroup was further divided into multiple clades. The subgroup I can be divided into I-A, I-B, I-C, and I-D. The I-A, I-B, and I-C are the most basal clades that have originated before the divergence of Archaeplastida. The I-D with the II and III subgroups form a monophyletic group, containing only green plants. The II and III subgroups form another monophyletic group with Streptophyta only. Once on land, the subgroup III genes have experienced two rounds of major expansions. The first round occurred before the origin of land plants, and the second round occurred after the divergence of land plants. Due to significant gene expansion, the subgroup III genes have become the predominant group of R2R3-MYBs in land plants. The highly unbalanced pattern of birth and death evolution of R2R3-MYB genes indicates their important roles in the successful adaptation and massive radiation of land plants to occupy a multitude of terrestrial environments.
Collapse
Affiliation(s)
- Xiaojun Chang
- College of Horticulture, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shupeng Xie
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Lanlan Wei
- College of Horticulture, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Fei Chen
- College of Horticulture, Faculty of Plant Science, Nanjing Agricultural University, Nanjing, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Zhongxiong Lai,
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, United States
- Zhenguo Lin,
| | - Liangsheng Zhang
- College of Horticulture, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Liangsheng Zhang, ;
| |
Collapse
|
260
|
Minamino N, Ueda T. RAB GTPases and their effectors in plant endosomal transport. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:61-68. [PMID: 31454706 DOI: 10.1016/j.pbi.2019.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The plant endomembrane system comprises distinctive membrane-bounded organelles connected with one another by the membrane trafficking system. The RAB GTPase is a key component of the membrane trafficking machinery that regulates the targeting and tethering of trafficking vesicles to target compartments by acting as a molecular switch cycling between active and inactive states. The functions of RAB GTPases are fulfilled through their interactions with several classes of interacting factors, including guanine nucleotide exchange factors (GEFs) and effector proteins. Effector proteins for plant RAB GTPases consist of evolutionarily conserved and plant-unique factors, which are involved in various membrane trafficking events in plant cells in ways unique to plants. In this review, we summarize recent findings on the functions of endosomal RAB GTPases that underwent unique diversification during plant evolution, with a special focus on RAB5/RABF and RAB11/RABA.
Collapse
Affiliation(s)
- Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, SOKENDAI (Graduate University of Advanced Studies), Okazaki, Aichi 444-8585, Japan.
| |
Collapse
|
261
|
Artz O, Dickopf S, Ranjan A, Kreiss M, Abraham ET, Boll V, Rensing SA, Hoecker U. Characterization of spa mutants in the moss Physcomitrella provides evidence for functional divergence of SPA genes during the evolution of land plants. THE NEW PHYTOLOGIST 2019; 224:1613-1626. [PMID: 31222750 DOI: 10.1111/nph.16004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.
Collapse
Affiliation(s)
- Oliver Artz
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stephen Dickopf
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Aashish Ranjan
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Melanie Kreiss
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Elena Theres Abraham
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Vanessa Boll
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| |
Collapse
|
262
|
Feng J, Chen L, Zuo J. Protein S-Nitrosylation in plants: Current progresses and challenges. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1206-1223. [PMID: 30663237 DOI: 10.1111/jipb.12780] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 01/14/2019] [Indexed: 05/21/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule regulating diverse biological processes in all living organisms. A major physiological function of NO is executed via protein S-nitrosylation, a redox-based posttranslational modification by covalently adding a NO molecule to a reactive cysteine thiol of a target protein. S-nitrosylation is an evolutionarily conserved mechanism modulating multiple aspects of cellular signaling. During the past decade, significant progress has been made in functional characterization of S-nitrosylated proteins in plants. Emerging evidence indicates that protein S-nitrosylation is ubiquitously involved in the regulation of plant development and stress responses. Here we review current understanding on the regulatory mechanisms of protein S-nitrosylation in various biological processes in plants and highlight key challenges in this field.
Collapse
Affiliation(s)
- Jian Feng
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Lichao Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
263
|
Busch A, Deckena M, Almeida-Trapp M, Kopischke S, Kock C, Schüssler E, Tsiantis M, Mithöfer A, Zachgo S. MpTCP1 controls cell proliferation and redox processes in Marchantia polymorpha. THE NEW PHYTOLOGIST 2019; 224:1627-1641. [PMID: 31433873 DOI: 10.1111/nph.16132] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/26/2019] [Indexed: 05/19/2023]
Abstract
TCP transcription factors are key regulators of angiosperm cell proliferation processes. It is unknown whether their regulatory growth capacities are conserved across land plants, which we examined in liverworts, one of the earliest diverging land plant lineages. We generated knockout mutants for MpTCP1, the single TCP-P clade gene in Marchantia polymorpha, and characterized its function by conducting cell proliferation and morphological analyses as well as messenger RNA expression, transcriptome, chemical, and DNA binding studies. Mptcp1ge lines show a reduced vegetative thallus growth and extra tissue formation in female reproductive structures. Additionally, mutant plants reveal increased hydrogen peroxide (H2 O2 ) levels and an enhanced pigmentation in the thallus caused by formation of secondary metabolites, such as aminochromes. MpTCP1 proteins interact redox dependently with DNA and regulate the expression of a comprehensive redox network, comprising enzymes involved in H2 O2 metabolism. MpTCP1 regulates Marchantia growth in a context-dependent manner. Redox sensitivity of the DNA binding capacity of MpTCP1 proteins provides a mechanism to respond to altered redox conditions. Our data suggest that MpTCP1 activity could thereby have contributed to diversification of land plant morphologies and to adaptations to abiotic and biotic challenges, as experienced by liverworts during early land plant colonization.
Collapse
Affiliation(s)
- Andrea Busch
- Botany, University of Osnabrück, Osnabrück, 49076, Germany
| | - Marek Deckena
- Botany, University of Osnabrück, Osnabrück, 49076, Germany
| | | | | | - Cilian Kock
- Botany, University of Osnabrück, Osnabrück, 49076, Germany
| | | | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Axel Mithöfer
- Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sabine Zachgo
- Botany, University of Osnabrück, Osnabrück, 49076, Germany
| |
Collapse
|
264
|
Yasui Y, Tsukamoto S, Sugaya T, Nishihama R, Wang Q, Kato H, Yamato KT, Fukaki H, Mimura T, Kubo H, Theres K, Kohchi T, Ishizaki K. GEMMA CUP-ASSOCIATED MYB1, an Ortholog of Axillary Meristem Regulators, Is Essential in Vegetative Reproduction in Marchantia polymorpha. Curr Biol 2019; 29:3987-3995.e5. [PMID: 31708390 DOI: 10.1016/j.cub.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/16/2019] [Accepted: 10/02/2019] [Indexed: 12/25/2022]
Abstract
A variety of plants in diverse taxa can reproduce asexually via vegetative propagation, in which clonal propagules with a new meristem(s) are generated directly from vegetative organs. A basal land plant, Marchantia polymorpha, develops clonal propagules, gemmae, on the gametophyte thallus from the basal epidermis of a specialized receptacle, the gemma cup. Here we report an R2R3-MYB transcription factor, designated GEMMA CUP-ASSOCIATED MYB1 (GCAM1), which is an essential regulator of gemma cup development in M. polymorpha. Targeted disruption of GCAM1 conferred a complete loss of gemma cup formation and gemma generation. Ectopic overexpression of GCAM1 resulted in formation of cell clumps, suggesting a function of GCAM1 in suppression of cell differentiation. Although gemma cups are a characteristic gametophyte organ for vegetative reproduction in a taxonomically restricted group of liverwort species, phylogenetic and interspecific complementation analyses support the orthologous relationship of GCAM1 to regulatory factors of axillary meristem formation, e.g., Arabidopsis REGULATOR OF AXILLARY MERISTEMS and tomato Blind, in angiosperm sporophytes. The present findings in M. polymorpha suggest an ancient acquisition of a transcriptional regulator for production of asexual propagules in the gametophyte and the use of the regulatory factor for diverse developmental programs, including axillary meristem formation, during land plant evolution.
Collapse
Affiliation(s)
- Yukiko Yasui
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Tomomi Sugaya
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Quan Wang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Hidehiro Fukaki
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Hiroyoshi Kubo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto 390-8621, Japan
| | - Klaus Theres
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | |
Collapse
|
265
|
Eremin A, Bulychev AA, Kluge C, Harbinson J, Foissner I. PH-dependent cell-cell interactions in the green alga Chara. PROTOPLASMA 2019; 256:1737-1751. [PMID: 31367920 PMCID: PMC6820879 DOI: 10.1007/s00709-019-01392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/29/2019] [Indexed: 06/10/2023]
Abstract
Characean internodal cells develop alternating patterns of acid and alkaline zones along their surface in order to facilitate uptake of carbon required for photosynthesis. In this study, we used a pH-indicating membrane dye, 4-heptadecylumbiliferone, to study the kinetics of alkaline band formation and decomposition. The differences in growth/decay kinetics suggested that growth occurred as an active, autocatalytic process, whereas decomposition was due to diffusion. We further investigated mutual interactions between internodal cells and found that their alignment parallel to each other induced matching of the pH banding patterns, which was mirrored by chloroplast activity. In non-aligned cells, the lowered photosynthetic activity was noted upon a rise of the external pH, suggesting that the matching of pH bands was due to a local elevation of membrane conductance by the high pH of the alkaline zones of neighboured cells. Finally, we show that the altered pH banding pattern caused the reorganization of the cortical cytoplasm. Complex plasma membrane elaborations (charasomes) were degraded via endocytosis, and mitochondria were moved away from the cortex when a previously acid region became alkaline and vice versa. Our data show that characean internodal cells react flexibly to environmental cues, including those originating from neighboured cells.
Collapse
Affiliation(s)
- Alexey Eremin
- Institute of Physics, Otto von Guericke University of Magdeburg, 39016, Magdeburg, Germany
| | - Alexander A Bulychev
- Department of Biophysics, Faculty of Biology, Moscow State University, Moscow, 119991, Russia
| | - Christopher Kluge
- Institute of Physics, Otto von Guericke University of Magdeburg, 39016, Magdeburg, Germany
| | - Jeremy Harbinson
- Department of Plant Sciences, University of Wageningen, 6708 PB, Wageningen, The Netherlands
| | - Ilse Foissner
- Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria.
| |
Collapse
|
266
|
Cheng S, Xian W, Fu Y, Marin B, Keller J, Wu T, Sun W, Li X, Xu Y, Zhang Y, Wittek S, Reder T, Günther G, Gontcharov A, Wang S, Li L, Liu X, Wang J, Yang H, Xu X, Delaux PM, Melkonian B, Wong GKS, Melkonian M. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution. Cell 2019; 179:1057-1067.e14. [DOI: 10.1016/j.cell.2019.10.019] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023]
|
267
|
Rippin M, Pichrtová M, Arc E, Kranner I, Becker B, Holzinger A. Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic). Environ Microbiol 2019; 21:4283-4299. [PMID: 31454446 PMCID: PMC6899726 DOI: 10.1111/1462-2920.14788] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/22/2019] [Indexed: 02/02/2023]
Abstract
Within streptophyte green algae Zygnematophyceae are the sister group to the land plants that inherited several traits conferring stress protection. Zygnema sp., a mat-forming alga thriving in extreme habitats, was collected from a field site in Svalbard, where the bottom layers are protected by the top layers. The two layers were investigated by a metatranscriptomic approach and GC-MS-based metabolite profiling. In the top layer, 6569 genes were significantly upregulated and 149 were downregulated. Upregulated genes coded for components of the photosynthetic apparatus, chlorophyll synthesis, early light-inducible proteins, cell wall and carbohydrate metabolism, including starch-degrading enzymes. An increase in maltose in the top layer and degraded starch grains at the ultrastructural levels corroborated these findings. Genes involved in amino acid, redox metabolism and DNA repair were upregulated. A total of 29 differentially accumulated metabolites (out of 173 identified ones) confirmed higher metabolic turnover in the top layer. For several of these metabolites, differential accumulation matched the transcriptional changes of enzymes involved in associated pathways. In summary, the findings support the hypothesis that in a Zygnema mat the top layer shields the bottom layers from abiotic stress factors such as excessive irradiation.
Collapse
Affiliation(s)
- Martin Rippin
- University of CologneBotanical InstituteCologneGermany
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - Erwann Arc
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - Ilse Kranner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | | |
Collapse
|
268
|
Allen JF, Thake B, Martin WF. Nitrogenase Inhibition Limited Oxygenation of Earth's Proterozoic Atmosphere. TRENDS IN PLANT SCIENCE 2019; 24:1022-1031. [PMID: 31447302 DOI: 10.1016/j.tplants.2019.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 05/24/2023]
Abstract
Cyanobacteria produced the oxygen that began to accumulate on Earth 2.5 billion years ago, at the dawn of the Proterozoic Eon. By 2.4 billion years ago, the Great Oxidation Event (GOE) marked the onset of an atmosphere containing oxygen. The oxygen content of the atmosphere then remained low for almost 2 billion years. Why? Nitrogenase, the sole nitrogen-fixing enzyme on Earth, controls the entry of molecular nitrogen into the biosphere. Nitrogenase is inhibited in air containing more than 2% oxygen: the concentration of oxygen in the Proterozoic atmosphere. We propose that oxygen inhibition of nitrogenase limited Proterozoic global primary production. Oxygen levels increased when upright terrestrial plants isolated nitrogen fixation in soil from photosynthetic oxygen production in shoots and leaves.
Collapse
Affiliation(s)
- John F Allen
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.
| | - Brenda Thake
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| |
Collapse
|
269
|
Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. PIN-driven auxin transport emerged early in streptophyte evolution. NATURE PLANTS 2019; 5:1114-1119. [PMID: 31712756 DOI: 10.1038/s41477-019-0542-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/07/2019] [Indexed: 05/27/2023]
Abstract
PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.
Collapse
Affiliation(s)
- Roman Skokan
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
- The Czech Academy of Sciences, Institute of Experimental Botany, Prague, Czech Republic
| | - Eva Medvecká
- CEITEC, Masaryk University, Mendel Centre for Genomics and Proteomics of Plants Systems, Brno, Czech Republic
| | - Tom Viaene
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stanislav Vosolsobě
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marta Zwiewka
- CEITEC, Masaryk University, Mendel Centre for Genomics and Proteomics of Plants Systems, Brno, Czech Republic
| | - Karel Müller
- The Czech Academy of Sciences, Institute of Experimental Botany, Prague, Czech Republic
| | - Petr Skůpa
- The Czech Academy of Sciences, Institute of Experimental Botany, Prague, Czech Republic
| | - Michal Karady
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | - Dorina P Janacek
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Ulrich Z Hammes
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tomasz Nodzyński
- CEITEC, Masaryk University, Mendel Centre for Genomics and Proteomics of Plants Systems, Brno, Czech Republic
| | - Jan Petrášek
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
- The Czech Academy of Sciences, Institute of Experimental Botany, Prague, Czech Republic
| | | |
Collapse
|
270
|
Hiwatashi T, Goh H, Yasui Y, Koh LQ, Takami H, Kajikawa M, Kirita H, Kanazawa T, Minamino N, Togawa T, Sato M, Wakazaki M, Yamaguchi K, Shigenobu S, Fukaki H, Mimura T, Toyooka K, Sawa S, Yamato KT, Ueda T, Urano D, Kohchi T, Ishizaki K. The RopGEF KARAPPO Is Essential for the Initiation of Vegetative Reproduction in Marchantia polymorpha. Curr Biol 2019; 29:3525-3531.e7. [PMID: 31607537 DOI: 10.1016/j.cub.2019.08.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/07/2018] [Accepted: 08/28/2019] [Indexed: 10/25/2022]
Abstract
Many plants can reproduce vegetatively, producing clonal progeny from vegetative cells; however, little is known about the molecular mechanisms underlying this process. Liverwort (Marchantia polymorpha), a basal land plant, propagates asexually via gemmae, which are clonal plantlets formed in gemma cups on the dorsal side of the vegetative thallus [1]. The initial stage of gemma development involves elongation and asymmetric divisions of a specific type of epidermal cell, called a gemma initial, which forms on the floor of the gemma cup [2, 3]. To investigate the regulatory mechanism underlying gemma development, we focused on two allelic mutants in which no gemma initial formed; these mutants were named karappo, meaning "empty." We used whole-genome sequencing of both mutants and molecular genetic analysis to identify the causal gene, KARAPPO (KAR), which encodes a ROP guanine nucleotide exchange factor (RopGEF) carrying a plant-specific ROP nucleotide exchanger (PRONE) catalytic domain. In vitro GEF assays showed that the full-length KAR protein and the PRONE domain have significant GEF activity toward MpROP, the only ROP GTPase in M. polymorpha. Moreover, genetic complementation experiments showed a significant role for the N- and C-terminal variable regions in gemma development. Our investigation demonstrates an essential role for KAR/RopGEF in the initiation of plantlet development from a differentiated cell, which may involve cell-polarity formation and subsequent asymmetric cell division via activation of ROP signaling, implying a similar developmental mechanism in vegetative reproduction of various land plants.
Collapse
Affiliation(s)
- Takuma Hiwatashi
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Honzhen Goh
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Yukiko Yasui
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Li Quan Koh
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Hideyuki Takami
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Masataka Kajikawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Hiroyuki Kirita
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan
| | - Taisuke Togawa
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan
| | - Hidehiro Fukaki
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | |
Collapse
|
271
|
Scutt CP. Flowering plants return to the sea…. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4591-4593. [PMID: 31552429 PMCID: PMC6760260 DOI: 10.1093/jxb/erz377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Charles P Scutt
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, F-69342 Lyon, France
| |
Collapse
|
272
|
Walker CH, Siu-Ting K, Taylor A, O'Connell MJ, Bennett T. Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation. BMC Biol 2019; 17:70. [PMID: 31488154 PMCID: PMC6728956 DOI: 10.1186/s12915-019-0689-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022] Open
Abstract
Background Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plants, SLs are synthesized by a core pathway of four enzymes and are perceived by the DWARF14 (D14) receptor, leading to degradation of SMAX1-LIKE7 (SMXL7) target proteins in a manner dependent on the SCFMAX2 ubiquitin ligase. The evolutionary history of SLs is poorly understood, and it is not clear whether SL synthesis and signalling are present in all land plant lineages, nor when these traits evolved. Results We have utilized recently-generated genomic and transcriptomic sequences from across the land plant clade to resolve the origin of each known component of SL synthesis and signalling. We show that all enzymes in the core SL synthesis pathway originated at or before the base of land plants, consistent with the previously observed distribution of SLs themselves in land plant lineages. We also show that the late-acting enzyme LATERAL BRANCHING OXIDOREDUCTASE (LBO) may be considerably more ancient than previously thought. We perform a detailed phylogenetic analysis of SMXL proteins and show that specific SL target proteins only arose in flowering plants. We also assess diversity and protein structure in the SMXL family, identifying several previously unknown clades. Conclusions Overall, our results suggest that SL synthesis is much more ancient than canonical SL signalling, consistent with the idea that SLs first evolved as rhizosphere signals and were only recruited much later as hormonal signals. Electronic supplementary material The online version of this article (10.1186/s12915-019-0689-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Catriona H Walker
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queens University, Belfast, BT7 1NN, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FD, UK
| | - Alysha Taylor
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Tom Bennett
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
273
|
Gould SB, Garg SG, Handrich M, Nelson-Sathi S, Gruenheit N, Tielens AGM, Martin WF. Adaptation to life on land at high O 2 via transition from ferredoxin-to NADH-dependent redox balance. Proc Biol Sci 2019; 286:20191491. [PMID: 31431166 PMCID: PMC6732389 DOI: 10.1098/rspb.2019.1491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.
Collapse
Affiliation(s)
- S B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - M Handrich
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S Nelson-Sathi
- Interdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - N Gruenheit
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - A G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
274
|
Zimorski V, Mentel M, Tielens AGM, Martin WF. Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation. Free Radic Biol Med 2019; 140:279-294. [PMID: 30935869 PMCID: PMC6856725 DOI: 10.1016/j.freeradbiomed.2019.03.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023]
Abstract
Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.
Collapse
Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 851 04, Bratislava, Slovakia.
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, The Netherlands; Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| |
Collapse
|
275
|
Hisanaga T, Yamaoka S, Kawashima T, Higo A, Nakajima K, Araki T, Kohchi T, Berger F. Building new insights in plant gametogenesis from an evolutionary perspective. NATURE PLANTS 2019; 5:663-669. [PMID: 31285561 DOI: 10.1038/s41477-019-0466-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/29/2019] [Indexed: 05/18/2023]
Abstract
Extant bryophytes are thought to preserve characteristics of ancestral land plants, with a life cycle dominated by the haploid gametophyte. The gametophyte produces gametes in specialized organs that differentiate after an extensive phase of vegetative development. During land plant evolution, these organs became extremely reduced. As a result, in flowers of angiosperms the haploid phase of the life cycle is reduced to few-celled gametophytes, namely the embryo sac (female) and pollen (male). Although many factors contributing to gametogenesis have been identified in flowering plants, the extreme reduction of the gametophytes has prevented a clear molecular dissection of key processes of gametogenesis. Recent studies in the model bryophyte Marchantia polymorpha have identified conserved transcription factors regulating the equivalent steps in the sexual reproduction of land plants. These include FEMALE GAMETOPHYTE MYB for female gametophyte development, BONOBO for gamete progenitor cell specification, DUO POLLEN1 for sperm differentiation and members of the RWP-RK domain family for female gamete formation. These studies demonstrate that M. polymorpha is a powerful model to untangle the core processes of gametogenesis in land plants. We anticipate that a deeper understanding of gametogenesis in bryophytes will circumscribe the origin of plant germ cells and define the differentiation programmes of sperm and eggs.
Collapse
Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
276
|
Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L. Neofunctionalisation of basic helix-loop-helix proteins occurred when embryophytes colonised the land. THE NEW PHYTOLOGIST 2019; 223:993-1008. [PMID: 30946484 DOI: 10.1111/nph.15829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes control the development of structures from single cells at the surface of embryophytes (land plants) such as rhizoids and root hairs. RSL proteins constitute a subclass (VIIIc) of the basic helix-loop-helix (bHLH) class VIII transcription factor family. The Charophyceae form the only class of streptophyte algae with tissue-like structures and rhizoids. To determine if the function of RSL genes in the control of cell differentiation in embryophytes was inherited from a streptophyte algal ancestor, we identified the single class VIII bHLH gene from the charophyceaen alga Chara braunii (CbbHLHVIII). CbbHLHVIII is sister to the RSL proteins; they constitute a monophyletic group. Expression of CbbHLHVIII does not compensate for loss of RSL functions in Marchantia polymorpha or Arabidopsis thaliana. In C. braunii CbbHLHVIII is expressed at sites of morphogenesis but not in rhizoids. This finding indicates that C. braunii class VIII protein is functionally different from land plant RSL proteins. This result suggests that the function of RSL proteins in cell differentiation at the plant surface evolved by neofunctionalisation in the land plants lineage after its divergence from its last common ancestor with C. braunii, at or before the colonisation of the land by embryophytes.
Collapse
Affiliation(s)
- Clémence Bonnot
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Clément Champion
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Holger Breuninger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| |
Collapse
|
277
|
Han X, Chang X, Zhang Z, Chen H, He H, Zhong B, Deng XW. Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization. MOLECULAR PLANT 2019; 12:847-862. [PMID: 31009752 DOI: 10.1016/j.molp.2019.04.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 05/22/2023]
Abstract
Light serves as the source of energy as well as an information signal for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signaling are still lacking. In this study, we took advantage of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domain to identify orthologous genes of core components involved in light perception and signaling and to reconstruct their evolutionary history. Our analyses suggested that acclimation to different distribution of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water and enabled plants to deal with ultraviolet B light (UV-B). After acquisition of UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize water surface where red light became the prominent light energy source. The seedling emergence pathway, which is mediated by a combination of light and phytohormone signals that orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of the plant and animal kingdoms, the coevolution and optimization of light perception and downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.
Collapse
Affiliation(s)
- Xue Han
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Haodong Chen
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| |
Collapse
|
278
|
Liu D, Shi S, Hao Z, Xiong W, Luo M. OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice. Int J Mol Sci 2019; 20:ijms20092360. [PMID: 31086007 PMCID: PMC6539606 DOI: 10.3390/ijms20092360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/15/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the most important food crops in the world. In plants, jasmonic acid (JA) plays essential roles in response to biotic and abiotic stresses. As one of the largest transcription factors (TFs), basic region/leucine zipper motif (bZIP) TFs play pivotal roles through the whole life of plant growth. However, the relationship between JA and bZIP TFs were rarely reported, especially in rice. In this study, we found two rice homologues of Arabidopsis VIP1 (VirE2-interacting protein 1), OsbZIP81, and OsbZIP84. OsbZIP81 has at least two alternative transcripts, OsbZIP81.1 and OsbZIP81.2. OsbZIP81.1 and OsbZIP84 are typical bZIP TFs, while OsbZIP81.2 is not. OsbZIP81.1 can directly bind OsPIOX and activate its expression. In OsbZIP81.1 overexpression transgenic rice plant, JA (Jasmonic Acid) and SA (Salicylic acid) were up-regulated, while ABA (Abscisic acid) was down-regulated. Moreover, Agrobacterium, Methyl Jasmonic Acid (MeJA), and PEG6000 can largely induce OsbZIP81. Based on ChIP-Seq and Random DNA Binding Selection Assay (RDSA), we identified a novel cis-element OVRE (Oryza VIP1 response element). Combining ChIP-Seq and RNA-Seq, we obtained 1332 targeted genes that were categorized in biotic and abiotic responses, including α-linolenic acid metabolism and fatty acid degradation. Together, these results suggest that OsbZIP81 may positively regulate JA levels by directly targeting the genes in JA signaling and metabolism pathway in rice.
Collapse
Affiliation(s)
- Defang Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shaopeng Shi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zhijun Hao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wentao Xiong
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
279
|
Abstract
Plant cells divide their cytoplasmic content by forming a new membrane compartment, the cell plate, via a rerouting of the secretory pathway toward the division plane aided by a dynamic cytoskeletal apparatus known as the phragmoplast. The phragmoplast expands centrifugally and directs the cell plate to the preselected division site at the plasma membrane to fuse with the parental wall. The division site is transiently decorated by the cytoskeletal preprophase band in preprophase and prophase, whereas a number of proteins discovered over the last decade reside continuously at the division site and provide a lasting spatial reference for phragmoplast guidance. Recent studies of membrane fusion at the cell plate have revealed the contribution of functionally conserved eukaryotic proteins to distinct stages of cell plate biogenesis and emphasize the coupling of cell plate formation with phragmoplast expansion. Together with novel findings concerning preprophase band function and the setup of the division site, cytokinesis and its spatial control remain an open-ended field with outstanding and challenging questions to resolve.
Collapse
Affiliation(s)
- Pantelis Livanos
- Department of Developmental Genetics, Center for Plant Molecular Biology, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany; ,
| | - Sabine Müller
- Department of Developmental Genetics, Center for Plant Molecular Biology, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany; ,
| |
Collapse
|
280
|
de Vries S, de Vries J, Rose LE. The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant⁻Microbe Interactions. Genes (Basel) 2019; 10:genes10040310. [PMID: 31010062 PMCID: PMC6523410 DOI: 10.3390/genes10040310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plants are exposed to diverse abiotic and biotic stimuli. These require fast and specific integrated responses. Such responses are coordinated at the protein and transcript levels and are incorporated into larger regulatory networks. Here, we focus on the evolution of transcriptional regulatory networks involved in plant–pathogen interactions. We discuss the evolution of regulatory networks and their role in fine-tuning plant defense responses. Based on the observation that many of the cornerstones of immune signaling in angiosperms are also present in streptophyte algae, it is likely that some regulatory components also predate the origin of land plants. The degree of functional conservation of many of these ancient components has not been elucidated. However, ongoing functional analyses in bryophytes show that some components are conserved. Hence, some of these regulatory components and how they are wired may also trace back to the last common ancestor of land plants or earlier. Of course, an understanding of the similarities and differences during the evolution of plant defense networks cannot ignore the lineage-specific coevolution between plants and their pathogens. In this review, we specifically focus on the small RNA regulatory networks involved in fine-tuning of the strength and timing of defense responses and highlight examples of pathogen exploitation of the host RNA silencing system. These examples illustrate well how pathogens frequently target gene regulation and thereby alter immune responses on a larger scale. That this is effective is demonstrated by the diversity of pathogens from distinct kingdoms capable of manipulating the same gene regulatory networks, such as the RNA silencing machinery.
Collapse
Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, 38106 Braunschweig, Germany.
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
- CEPLAS-Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany.
| |
Collapse
|
281
|
He J, Zhao H, Cheng Z, Ke Y, Liu J, Ma H. Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. Int J Mol Sci 2019; 20:E1945. [PMID: 31010036 PMCID: PMC6514703 DOI: 10.3390/ijms20081945] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/03/2023] Open
Abstract
The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.
Collapse
Affiliation(s)
- Jiadai He
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Hua Zhao
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Zhilu Cheng
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Yuwei Ke
- College of Life Sciences, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Jiaxi Liu
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Haoli Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| |
Collapse
|
282
|
Li ZK, Chen B, Li XX, Wang JP, Zhang Y, Wang XF, Yan YY, Ke HF, Yang J, Wu JH, Wang GN, Zhang GY, Wu LQ, Wang XY, Ma ZY. A newly identified cluster of glutathione S-transferase genes provides Verticillium wilt resistance in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:213-227. [PMID: 30561788 DOI: 10.1111/tpj.14206] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
As the largest cultivated fiber crop in the world, cotton (Gossypium hirsutum) is often exposed to various biotic stresses during its growth periods. Verticillium wilt caused by Verticillium dahliae is a severe disease in cotton, and the molecular mechanism of cotton resistance for Verticillium wilt needs to be further investigated. Here, we revealed that the cotton genome contains nine types of GST genes. An evolutionary analysis showed that a newly identified cluster (including Gh_A09G1508, Gh_A09G1509 and Gh_A09G1510) located on chromosome 09 of the A-subgenome was under positive selection pressure during the formation of an allotetraploid. Transcriptome analysis showed that this cluster participates in Verticillium wilt resistance. Because the Gh_A09G1509 gene showed the greatest differential expression in the resistant cultivar under V. dahliae stress, we overexpressed this gene in tobacco and found that its overexpression resulted in enhanced Verticillium wilt resistance. Suppression of the gene cluster via virus-induced gene silencing made cotton plants of the resistant cultivar Nongda601 significantly susceptible. These results demonstrated that the GST cluster played an important role in Verticillium wilt resistance. Further investigation showed that the encoded enzymes of the cluster were essential for the delicate equilibrium between the production and scavenging of H2 O2 during V. dahliae stress.
Collapse
Affiliation(s)
- Zhi-Kun Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Bin Chen
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xiu-Xin Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Peng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Yan Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xing-Fen Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan-Yuan Yan
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Hui-Feng Ke
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Hua Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Guo-Ning Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Gui-Yin Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Li-Qiang Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xi-Yin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhi-Ying Ma
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| |
Collapse
|
283
|
Han GZ. Origin and evolution of the plant immune system. THE NEW PHYTOLOGIST 2019; 222:70-83. [PMID: 30575972 DOI: 10.1111/nph.15596] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/02/2018] [Indexed: 05/11/2023]
Abstract
Contents Summary 70 I. Introduction 70 II. Ancient associations between plants and microbes 72 III. Evolutionary dynamics of plant-pathogen interactions 74 IV. Evolutionary signature of plant-pathogen interactions 74 V. Origin and evolution of RLK proteins 75 VI. Origin and evolution of NLR proteins 77 VII. Origin and evolution of SA signaling 78 VIII. Origin and evolution of RNA-based defense 79 IX. Perspectives 79 Acknowledgements 80 References 80 SUMMARY: Microbes have engaged in antagonistic associations with plants for hundreds of millions of years. Plants, in turn, have evolved diverse immune strategies to combat microbial pathogens. The conflicts between plants and pathogens result in everchanging coevolutionary cycles known as 'Red Queen' dynamics. These ancient and ongoing plant-pathogen interactions have shaped the evolution of both plant and pathogen genomes. With the recent explosion of plant genome-scale data, comparative analyses provide novel insights into the coevolutionary dynamics of plants and pathogens. Here, we discuss the ancient associations between plants and microbes as well as the evolutionary principles underlying plant-pathogen interactions. We synthesize and review the current knowledge on the origin and evolution of key components of the plant immune system. We also highlight the importance of studying algae and nonflowering land plants in understanding the evolution of the plant immune system.
Collapse
Affiliation(s)
- Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| |
Collapse
|
284
|
de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). THE NEW PHYTOLOGIST 2019; 222:565-575. [PMID: 30411803 DOI: 10.1111/nph.15587] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 05/05/2023]
Abstract
Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue. Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models. Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions. The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes.
Collapse
Affiliation(s)
- Filipe de Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | | | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Earth Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| |
Collapse
|
285
|
Sussmilch FC, Roelfsema MRG, Hedrich R. On the origins of osmotically driven stomatal movements. THE NEW PHYTOLOGIST 2019; 222:84-90. [PMID: 30444541 DOI: 10.1111/nph.15593] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
Contents Summary 84 I. Introduction 84 II. Stomatal form and biomechanics 85 III. Stomatal function 86 IV. Evolution of guard cell ion channels 87 V. Conclusions 88 Acknowledgements 88 Author contributions 88 References 88 SUMMARY: Stomatal pores with apertures that can be adjusted by changes in guard cell turgor have facilitated plant success in dry environments. We explore their evolutionary origins, considering recent findings from bryophytes. Unlike vascular plant stomata, which close to prevent water loss, bryophyte stomata become locked open to promote spore desiccation. We find that the families of ion channels, known to control stomatal movements in angiosperms, are ancient and represented across extant land plants. However, although angiosperm guard cells express specific ion channel genes, none appear specifically expressed in stomata-bearing moss tissues. Given the evolutionary shift in stomatal function from promotion to prevention of water loss, we postulate that ion channels adopted guard cell-specific functions after the divergence of bryophytes.
Collapse
Affiliation(s)
- Frances C Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
| | - M Rob G Roelfsema
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
| |
Collapse
|
286
|
Sussmilch FC, Schultz J, Hedrich R, Roelfsema MRG. Acquiring Control: The Evolution of Stomatal Signalling Pathways. TRENDS IN PLANT SCIENCE 2019; 24:342-351. [PMID: 30797685 DOI: 10.1016/j.tplants.2019.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 05/24/2023]
Abstract
In vascular plants, stomata balance two opposing functions: they open to facilitate CO2 uptake and close to prevent excessive water loss. Here, we discuss the evolution of three major signalling pathways that are known to control stomatal movements in angiosperms in response to light, CO2, and abscisic acid (ABA). We examine the evolutionary origins of key signalling genes involved in these pathways, and compare their expression patterns between an angiosperm and moss. We propose that variation in stomatal sensitivity to stimuli between plant groups are rooted in differences in: (i) gene presence/absence, (ii) specificity of gene spatial expression pattern, and (iii) protein characteristics and functional interactions.
Collapse
Affiliation(s)
- Frances C Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Jörg Schultz
- Center for Computational and Theoretical Biology, University of Würzburg, D-97218 Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - M Rob G Roelfsema
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany.
| |
Collapse
|
287
|
Nishitsuji K, Arimoto A, Higa Y, Mekaru M, Kawamitsu M, Satoh N, Shoguchi E. Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway. Sci Rep 2019; 9:4607. [PMID: 30872679 PMCID: PMC6418280 DOI: 10.1038/s41598-019-40955-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/22/2019] [Indexed: 01/21/2023] Open
Abstract
The brown alga, Nemacystus decipiens ("ito-mozuku" in Japanese), is one of the major edible seaweeds, cultivated principally in Okinawa, Japan. N. decipiens is also a significant source of fucoidan, which has various physiological activities. To facilitate brown algal studies, we decoded the ~154 Mbp draft genome of N. decipiens Onna-1 strain. The genome is estimated to contain 15,156 protein-coding genes, ~78% of which are substantiated by corresponding mRNAs. Mitochondrial genes analysis showed a close relationship between N. decipiens and Cladosiphon okamuranus. Comparisons with the C. okamuranus and Ectocarpus siliculosus genomes identified a set of N. decipiens-specific genes. Gene ontology annotation showed more than half of these are classified as molecular function, enzymatic activity, and/or biological process. Extracellular matrix analysis revealed domains shared among three brown algae. Characterization of genes that encode enzymes involved in the biosynthetic pathway for sulfated fucan showed two sets of genes fused in the genome. One is a fusion of L-fucokinase and GDP-fucose pyrophosphorylase genes, a feature shared with C. okamuranus. Another fusion is between an ST-domain-containing gene and an alpha/beta hydrolase gene. Although the function of fused genes should be examined in future, these results suggest that N. decipiens is another promising source of fucoidan.
Collapse
Affiliation(s)
- Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yoshimi Higa
- Onna Fisheries Cooperative, Onna, Okinawa, 904-0414, Japan
| | | | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| |
Collapse
|
288
|
Abstract
Epigenetic gene regulation ensures the mitotically or meiotically stable heritability (or both) of gene expression or protein activity states and maintains repetitive element repression and cellular identities. The repressive Polycomb-group (PcG) proteins consist of several large complexes that control cellular memory by acting on chromatin and are antagonized by the Trithorax-group proteins. Especially, Polycomb repressive complex 2 (PRC2) is highly conserved in plants and animals but its function in unicellular eukaryotes and during land plant evolution is less understood. Additional PcG complexes and associated proteins are only partially conserved and have evolved in a lineage-specific manner. In this review, I will focus on recent advances in the understanding of PcG function in the green lineage and its contribution to land plant evolution.
Collapse
Affiliation(s)
- Daniel Schubert
- Department of Biology, Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
289
|
Chara braunii genome: a new resource for plant electrophysiology. Biophys Rev 2019; 11:235-239. [PMID: 30830677 DOI: 10.1007/s12551-019-00512-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022] Open
Abstract
The large-celled green alga Chara provided early electrophysiological data, but this model organism lost popularity once the smaller cells of higher plants became accessible to electrophysiology and genetic manipulation. However, with the sequencing of the Chara braunii genome (Nishiyama et al. Cell 174: 448-464, 2018), the molecular identity of the underlaying ion transporters in Characeae can be found and placed in evolutionary context. As Characeae are close to ancestors of land plants, the wealth of electrophysiological data will provide insights into important aspects of plant physiology, such as salt tolerance and sensitivity, carbon concentrating mechanisms, pH banding and the action potential generation.
Collapse
|
290
|
Kisnieriene V, Lapeikaite I, Pupkis V, Beilby MJ. Modeling the Action Potential in Characeae Nitellopsis obtusa: Effect of Saline Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:82. [PMID: 30833949 PMCID: PMC6387969 DOI: 10.3389/fpls.2019.00082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/18/2019] [Indexed: 05/17/2023]
Abstract
Action potentials (AP) of characean cells were the first electrical transients identified in plants. APs provide information about plethora of environmental cues. Salinity stress is critical for plants and impacts on excitability. The AP of brackish Characeae Nitellopsis obtusa, obtained in artificial pond water (APW) and under osmotic stress of 90 or 180 mM sorbitol APW or saline stress of 50 or 100 mM NaCl APW, were simulated by the Thiel-Beilby model (Beilby and Al Khazaaly, 2016). The model is based on a paradigm from animal systems, featuring the second messenger inositol 1,4,5-triphosphate (IP3) mediating the opening of Ca2+ channels on internal stores. In plants the IP3 receptors have not been identified, so other second messengers might translate the threshold plasma membrane depolarization to Ca2+ release. The increased Ca2+ concentration in the cytoplasm activates Cl- channels, which lead to the depolarizing phase of the AP. The repolarization to normal resting potential difference (PD) results from the Ca2+ being re-sequestered by the Ca2+ pumps, the closure of the Cl- channels, efflux of K+ through the depolarization-activated outward rectifier channels and the continuing activity of the proton pump. The Nitellopsis AP form is longer in APW compared to that of Chara, with more gradual repolarization. The tonoplast component of the AP is larger than that in Chara australis. The plasma membrane AP is prolonged by the exposure to saline to a "rectangular" shape, similar to that in Chara. However, the changes are more gradual, allowing more insight into the mechanism of the process. It is possible that the cells recover the original AP form after prolonged exposure to brackish conditions. Some cells experience tonoplast APs only. As in Chara, the proton pump is transiently inhibited by the high cytoplasmic Ca2+ and gradually declines in saline media. However, if the cells are very hyperpolarized at the start of the experiment, the pump inhibition both by the AP and by the saline medium is mitigated. The model parameters and their changes with salinity are comparable to those in Chara.
Collapse
Affiliation(s)
- Vilma Kisnieriene
- Department of Neurobiology and Biophysics, Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Indre Lapeikaite
- Department of Neurobiology and Biophysics, Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Vilmantas Pupkis
- Department of Neurobiology and Biophysics, Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Mary Jane Beilby
- School of Physics, The University of NSW, Sydney, NSW, Australia
| |
Collapse
|
291
|
Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun 2019; 10:737. [PMID: 30760717 PMCID: PMC6374488 DOI: 10.1038/s41467-019-08703-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/23/2019] [Indexed: 01/19/2023] Open
Abstract
Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.
Collapse
Affiliation(s)
- Camilla Ferrari
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Sebastian Proost
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marcin Janowski
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Jörg Becker
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156, Oeiras, Portugal
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Dana Price
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Arren Bar-Even
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Alisdair Fernie
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Mark Stitt
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marek Mutwil
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
292
|
Bowman JL, Briginshaw LN, Fisher TJ, Flores-Sandoval E. Something ancient and something neofunctionalized-evolution of land plant hormone signaling pathways. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:64-72. [PMID: 30339930 DOI: 10.1016/j.pbi.2018.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/13/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
The evolution of land plants from a charophycean algal ancestor was accompanied by an increased diversity of regulatory networks, including signaling pathways mediating cellular communication within plants and between plants and the environment. Canonical land plant hormone signaling pathways were originally identified in angiosperms, and comparative studies in basal taxa show that they have been assembled from both ancient and newly evolved components, both before and during land plant evolution. In this review we present our current understanding, and highlight several uncertainties, of the evolution of hormone signaling pathways, focusing on the biosynthetic pathways generating putative ligands and the downstream perception and signaling pathways often leading to transcriptional responses.
Collapse
Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia.
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | | |
Collapse
|
293
|
Van Holle S, Van Damme EJM. Messages From the Past: New Insights in Plant Lectin Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:36. [PMID: 30761173 PMCID: PMC6362431 DOI: 10.3389/fpls.2019.00036] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/10/2019] [Indexed: 05/25/2023]
Abstract
Lectins are a large and diverse class of proteins, found in all kingdoms of life. Plants are known to express different types of carbohydrate-binding proteins, each containing at least one particular lectin domain which enables them to specifically recognize and bind carbohydrate structures. The group of plant lectins is heterogeneous in terms of structure, biological activity and function. Lectins control various aspects of plant development and defense. Some lectins facilitate recognition of exogenous danger signals or play a role in endogenous signaling pathways, while others are considered as storage proteins or involved in symbiotic relationships. In this study, we revisit the origin of the different plant lectin families in view of the recently reshaped tree of life. Due to new genomic sampling of previously unknown microbial lineages, the tree of life has expanded and was reshaped multiple times. In addition, more plant genomes especially from basal Phragmoplastophyta, bryophytes, and Salviniales (e.g., Chara braunii, Marchantia polymorpha, Physcomitrella patens, Azolla filiculoides, and Salvinia cucullata) have been analyzed, and annotated genome sequences have become accessible. We searched 38 plant genome sequences including core eudicots, monocots, gymnosperms, fern, lycophytes, bryophytes, charophytes, chlorophytes, glaucophytes, and rhodophytes for lectin motifs, performed an extensive comparative analysis of lectin domain architectures, and determined the phylogenetic and evolutionary history of lectins in the plant lineage. In conclusion, we describe the conservation of particular domains in plant lectin sequences obtained from algae to higher plants. The strong conservation of several lectin motifs highlights their significance for plants.
Collapse
|
294
|
Morozov SY, Solovyev AG. Emergence of Intronless Evolutionary Forms of Stress Response Genes: Possible Relation to Terrestrial Adaptation of Green Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:83. [PMID: 30792726 PMCID: PMC6374339 DOI: 10.3389/fpls.2019.00083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/21/2019] [Indexed: 05/18/2023]
Affiliation(s)
- Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
- *Correspondence: Sergey Y. Morozov
| | - Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
295
|
Corrigendum. THE NEW PHYTOLOGIST 2019; 221:1172. [PMID: 30569608 DOI: 10.1111/nph.15533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
|
296
|
Fitzek E, Orton L, Entwistle S, Grayburn WS, Ausland C, Duvall MR, Yin Y. Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. FRONTIERS IN PLANT SCIENCE 2019; 10:732. [PMID: 31231410 PMCID: PMC6566377 DOI: 10.3389/fpls.2019.00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the Cha+Emb group contains 4,174 OGCs found in both Cha and Emb but not Chl species, representing protein families that have evolved in the common ancestor of Cha and Emb. Different OGC groups were subjected to a Gene Ontology (GO) enrichment analysis with the Chl+Cha+Emb group (including 5,031 OGCs found in Chl and Cha and Emb) as the control. Interestingly, nine of the 20 top enriched GO terms in the Cha+Emb group are cell wall-related, such as biological processes involving celluloses, pectins, lignins, and xyloglucans. Furthermore, three glycosyltransferase families (GT2, 8, 43) were selected for in-depth phylogenetic analyses, which confirmed their presence in UTEX 1559. More importantly, of different CGA groups, only Zygnematophyceae has land plant cellulose synthase (CesA) orthologs, while other charophyte CesAs form a CGA-specific CesA-like (Csl) subfamily (likely also carries cellulose synthesis activity). Quantitative real-time-PCR experiments were performed on selected GT family genes in UTEX 1559. After osmotic stress treatment, significantly elevated expression was found for GT2 family genes ZcCesA, ZcCslC and ZcCslA-like (possibly mannan and xyloglucan synthases, respectively), as well as for GT8 family genes (possibly pectin synthases). All these suggest that the UTEX 1559 cell wall polysaccharide synthesis-related genes respond to osmotic stress in a manner that is similar to land plants.
Collapse
Affiliation(s)
- Elisabeth Fitzek
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld, Germany
| | - Lauren Orton
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Sarah Entwistle
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - W. Scott Grayburn
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Catherine Ausland
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Melvin R. Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska – Lincoln, Lincoln, NE, United States
- *Correspondence: Yanbin Yin, ;
| |
Collapse
|
297
|
Zhang S, Habets M, Breuninger H, Dolan L, Offringa R, van Duijn B. Evolutionary and Functional Analysis of a Chara Plasma Membrane H +-ATPase. FRONTIERS IN PLANT SCIENCE 2019; 10:1707. [PMID: 32038681 PMCID: PMC6985207 DOI: 10.3389/fpls.2019.01707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/04/2019] [Indexed: 05/12/2023]
Abstract
H+-ATPases are the main transporters in plant and fungal plasma membranes (PMs), comparable to the Na+/K+ ATPases in animal cells. At the molecular level, most studies on the PM H+-ATPases have been focused on land plants and fungi (yeast). The research of PM H+-ATPases in green algae falls far behind due to the lack of genetic information. Here we studied a potential PM H+-ATPase (CHA1) from Chara australis, a species of green algae belonging to the division Charophyta, members of which are considered to be one of the closest ancestors of land plants. The gene encodes a 107 kDa protein with all 6 P-type ATPase-specific motifs and a long, diverse C-terminal domain. A new amino acid sequence motif R*****Q in transmembrane segment 5 was identified among the known PM H+-ATPases from Charophyta and Chlorophyta algae, which is different from the typical PM H+-ATPases in yeast or land plants. Complementation analysis in yeast showed that CHA1 could successfully reach the PM, and that proton pump activity was obtained when the last 77 up to 87 amino acids of the C-terminal domain were deleted. PM localization was confirmed in Arabidopsis protoplasts; however, deletion of more than 55 amino acids at the N-terminus or more than 98 amino acids at the C-terminus resulted in failure of CHA1 to reach the PM in yeast. These results suggest that an auto-inhibition domain is located in the C-terminal domain, and that CHA1 is likely to have a different regulation mechanism compared to the yeast and land plant PM H+-ATPases.
Collapse
Affiliation(s)
- Suyun Zhang
- Plant Biodynamics Laboratory, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Myckel Habets
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Holger Breuninger
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Bert van Duijn
- Plant Biodynamics Laboratory, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Research Department, Fytagoras BV, Leiden, Netherlands
- *Correspondence: Bert van Duijn,
| |
Collapse
|
298
|
Herbst A, Schubert H. Age and site-specific pattern on encrustation of charophytes. BOTANICAL STUDIES 2018; 59:31. [PMID: 30569413 PMCID: PMC6300450 DOI: 10.1186/s40529-018-0247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
Encrustation and element content (Ca, Fe, K, Mg and P) of charophytes was studied along plant thalli to investigate the dependency of thallus age and site-specificity. Charophytes were collected from five sampling sites (Angersdorfer Teiche, Asche, Bruchwiesen, Krüselinsee and Lützlower See) which were distinct with respect to water chemistry. Furthermore, photosynthesis was measured to identify the physiological state of plants in habitat waters and with the addition of different ion concentrations (Ca2+, K+, Mg2+ and Na+). Age pattern on encrustation of charophytes was site-specific: carbonate content increased from the youngest to the oldest part (Angersdorfer Teiche), younger parts were less encrusted than older parts in Asche, Bruchwiesen and Krüselinsee, whereas encrustation in Lützlower See was the same along plants thallus. Charophytes showed species-specific encrustation in investigated sites. Encrustation of C. hispida in Angersdorfer Teiche was also as high as of individuals from hard-water lakes irrespective of 10.15 mS cm-1 (salinity of 6.3). For species growing in Angersdorfer Teiche, K/Na content and photosynthesis was lowest when compared to other sites. Photosynthesis of charophytes was enhanced after the addition of KCl and adversely affected by CaCl2, MgCl2 and NaCl. In summary, it was shown that encrustation of charophytes in water sites with strong ion anomalies could be as high as in hard-water lakes. It is assumed that ion composition, rather than ion concentration of Na+, Mg2+ and SO42-, impact on the encrustation of charophytes. The age pattern on encrustation in this study showed a strong site-specificity, whereas encrustation of charophytes was species-specific. Ion concentrations, either of habitats or actively added in laboratory measurements, impact on encrustation, element content and photosynthesis of charophytes.
Collapse
Affiliation(s)
- Anne Herbst
- University of Rostock, Biosciences, Albert-Einstein-Straße 3, 18059, Rostock, Germany.
| | - Hendrik Schubert
- University of Rostock, Biosciences, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| |
Collapse
|
299
|
Xu H, Ding A, Chen S, Marowa P, Wang D, Chen M, Hu R, Kong Y, O’Neill M, Chai G, Zhou G. Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes. FRONTIERS IN PLANT SCIENCE 2018; 9:1773. [PMID: 30619385 PMCID: PMC6302003 DOI: 10.3389/fpls.2018.01773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/15/2018] [Indexed: 05/13/2023]
Abstract
Sorghum (Sorghum bicolor) is an important bioenergy crop. Its biomass mainly consists of the cellulosic and non-cellulosic polysaccharides, both which can be converted to biofuels. The biosynthesis of non-cellulosic polysaccharides involves several glycosyltransferases (GT) families including GT47. However, there was no systemic study on GT47 family in sorghum to date. Here, we identified 39 sorghum GT47 family members and showed the functional divergences of MURUS3 (MUR3) homologs. Sorghum GT47 proteins were phylogenetically clustered into four distinct subfamilies. Within each subfamily, gene structure was relatively conserved between the members. Ten gene pairs were identified from the 39 GT47 genes, of which two pairs might be originated from tandem duplication. 25.6% (10/39) of sorghum GT47 genes were homologous to Arabidopsis MUR3, a xyloglucan biosynthesis gene in primary cell walls. SbGT47_2, SbGT47_7, and SbGT47_8, three most homologous genes of MUR3, exhibited different tissue expression patterns and were selected for complementation into Arabidopsis mur3-3. Physiological and cell wall analyses showed that SbGT47_2 and SbGT47_7 may be two functional xyloglucan galactosyltransferases in sorghum. Further studies found that MUR3-like genes are widely present in the seed plants but not in the chlorophytic alga Chlamydomonas reinhardtii. Our results provide novel information for evolutionary analysis and functional dissection of sorghum GT47 family members.
Collapse
Affiliation(s)
- Hua Xu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Anming Ding
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Sihui Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Prince Marowa
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dian Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Min Chen
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Ruibo Hu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingzhen Kong
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Malcolm O’Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Guohua Chai
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
300
|
Long-distance electrical signals as a link between the local action of stressors and the systemic physiological responses in higher plants. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:63-84. [PMID: 30508537 DOI: 10.1016/j.pbiomolbio.2018.11.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 12/27/2022]
Abstract
Our review is devoted to the analysis of the role of long-distance electrical signals in the development of the fast systemic physiological responses in higher plants. The characteristics and mechanisms of basic electrical signals (variation potential, action potential and system potential) are analyzed, and a potential schema of the generation and propagation of the system potential is proposed. The review summarizes the physiological changes induced by the variation potential, action potential and system potential in higher plants, including changes in gene expressions, the production of phytohormones, photosynthesis, phloem mass-flow, respiration, ATP content, transpiration and plant growth. Potential mechanisms of the changes are analyzed. Finally, a hypothetical schema, which describes a hierarchy of the variation potential, action potential and system potential, in the development of the fast systemic non-specific adaptation of plants to stressors, is proposed.
Collapse
|