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Hembach L, Niemeyer PW, Schmitt K, Zegers JMS, Scholz P, Brandt D, Dabisch JJ, Valerius O, Braus GH, Schwarzländer M, de Vries J, Rensing SA, Ischebeck T. Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1466-1486. [PMID: 38059656 DOI: 10.1111/tpj.16574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.
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Affiliation(s)
- Lea Hembach
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Philipp W Niemeyer
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Kerstin Schmitt
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Jaccoline M S Zegers
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Laboratoire Reproduction et Développement des Plantes (RDP), UCB Lyon 1, CNRS, INRAE, Université de Lyon, ENS de Lyon, Lyon, France
| | - Dennis Brandt
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Janis J Dabisch
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Oliver Valerius
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Gerhard H Braus
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Till Ischebeck
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
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Vollmeister E, Phokas A, Meyberg R, Böhm CV, Peter M, Kohnert E, Yuan J, Grosche C, Göttig M, Ullrich KK, Perroud PF, Hiltbrunner A, Kreutz C, Coates JC, Rensing SA. A DELAY OF GERMINATION 1 (DOG1)-like protein regulates spore germination in the moss Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:909-923. [PMID: 37953711 DOI: 10.1111/tpj.16537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain-containing genes in P. patens. Germination assays were performed to characterise a Ppdog1-like1 mutant, and replacement with AtDOG1 was carried out. Yeast two-hybrid assays were used to test the interaction of the PpDOG1-like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain-containing genes. The DOG1-like protein PpDOG1-L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1-l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1-LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination.
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Affiliation(s)
- Evelyn Vollmeister
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Alexandros Phokas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Clemens V Böhm
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Marlies Peter
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany
| | - Jinhong Yuan
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Christopher Grosche
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Marco Göttig
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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3
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A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis. Commun Biol 2023; 6:61. [PMID: 36650210 PMCID: PMC9845386 DOI: 10.1038/s42003-023-04428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.
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Leger MM, Stairs C. Eukaryotic evolution: Spatial proteomics sheds light on mitochondrial reduction. Curr Biol 2022; 32:R1308-R1311. [PMID: 36473440 DOI: 10.1016/j.cub.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-organelle spatial proteomics has revolutionized animal cell biology, but its use in protists has so far been limited. A new study delivers the first such proteome of a free-living protist, uncovering a previously overlooked function of highly reduced mitochondria.
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Affiliation(s)
- Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Courtney Stairs
- Microbiology Research Group, Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden.
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Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4291-4305. [PMID: 35148385 DOI: 10.1093/jxb/erac052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Sven B Gould
- Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
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Utsunomiya H, Saiki N, Kadoguchi H, Fukudome M, Hashimoto S, Ueda M, Takechi K, Takano H. Genes encoding lipid II flippase MurJ and peptidoglycan hydrolases are required for chloroplast division in the moss Physcomitrella patens. PLANT MOLECULAR BIOLOGY 2021; 107:405-415. [PMID: 33078277 DOI: 10.1007/s11103-020-01081-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Homologous genes for the peptidoglycan precursor flippase MurJ, and peptidoglycan hydrolases: lytic transglycosylase MltB, and DD-carboxypeptidase VanY are required for chloroplast division in the moss Physcomitrella patens. The moss Physcomitrella patens is used as a model plant to study plastid peptidoglycan biosynthesis. In bacteria, MurJ flippase transports peptidoglycan precursors from the cytoplasm to the periplasm. In this study, we identified a MurJ homolog (PpMurJ) in the P. patens genome. Bacteria employ peptidoglycan degradation and recycling pathways for cell division. We also searched the P. patens genome for genes homologous to bacterial peptidoglycan hydrolases and identified genes homologous for the lytic transglycosylase mltB, N-acetylglucosaminidase nagZ, and LD-carboxypeptidase ldcA in addition to a putative DD-carboxypeptidase vanY reported previously. Moreover, we found a ß-lactamase-like gene (Pplactamase). GFP fusion proteins with either PpMltB or PpVanY were detected in the chloroplasts, whereas fusion proteins with PpNagZ, PpLdcA, or Pplactamase localized in the cytoplasm. Experiments seeking PpMurJ-GFP fusion proteins failed. PpMurJ gene disruption in P. patens resulted in the appearance of macrochloroplasts in protonemal cells. Compared with the numbers of chloroplasts in wild-type plants (38.9 ± 4.9), PpMltB knockout and PpVanY knockout had lower numbers of chloroplasts (14.3 ± 6.7 and 28.1 ± 5.9, respectively). No differences in chloroplast numbers were observed after PpNagZ, PpLdcA, or Pplactamase single-knockout. Chloroplast numbers in PpMltB/PpVanY double-knockout cells were similar to those in PpMltB single-knockout cells. Zymogram analysis of the recombinant PpMltB protein revealed its peptidoglycan hydrolase activity. Our results imply that PpMurJ, PpMltB and PpVanY play a critical role in chloroplast division in the moss P. patens.
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Affiliation(s)
- Hanae Utsunomiya
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Nozomi Saiki
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Hayato Kadoguchi
- Faculty of Science, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Masaya Fukudome
- Faculty of Science, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Satomi Hashimoto
- Faculty of Science, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Mami Ueda
- Faculty of Science, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Katsuaki Takechi
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan.
| | - Hiroyoshi Takano
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan.
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Müller-Schüssele SJ, Bohle F, Rossi J, Trost P, Meyer AJ, Zaffagnini M. Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites. BMC PLANT BIOLOGY 2021; 21:322. [PMID: 34225654 PMCID: PMC8256493 DOI: 10.1186/s12870-021-03087-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Flexibility of plant metabolism is supported by redox regulation of enzymes via posttranslational modification of cysteine residues, especially in plastids. Here, the redox states of cysteine residues are partly coupled to the thioredoxin system and partly to the glutathione pool for reduction. Moreover, several plastid enzymes involved in reactive oxygen species (ROS) scavenging and damage repair draw electrons from glutathione. In addition, cysteine residues can be post-translationally modified by forming a mixed disulfide with glutathione (S-glutathionylation), which protects thiol groups from further oxidation and can influence protein activity. However, the evolution of the plastid glutathione-dependent redox network in land plants and the conservation of cysteine residues undergoing S-glutathionylation is largely unclear. RESULTS We analysed the genomes of nine representative model species from streptophyte algae to angiosperms and found that the antioxidant enzymes and redox proteins belonging to the plastid glutathione-dependent redox network are largely conserved, except for lambda- and the closely related iota-glutathione S-transferases. Focussing on glutathione-dependent redox modifications, we screened the literature for target thiols of S-glutathionylation, and found that 151 plastid proteins have been identified as glutathionylation targets, while the exact cysteine residue is only known for 17% (26 proteins), with one or multiple sites per protein, resulting in 37 known S-glutathionylation sites for plastids. However, 38% (14) of the known sites were completely conserved in model species from green algae to flowering plants, with 22% (8) on non-catalytic cysteines. Variable conservation of the remaining sites indicates independent gains and losses of cysteines at the same position during land plant evolution. CONCLUSIONS We conclude that the glutathione-dependent redox network in plastids is highly conserved in streptophytes with some variability in scavenging and damage repair enzymes. Our analysis of cysteine conservation suggests that S-glutathionylation in plastids plays an important and yet under-investigated role in redox regulation and stress response.
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Affiliation(s)
- Stefanie J Müller-Schüssele
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany.
- Present Address: Department of Biology, Technische Universität Kaiserslautern, 67663, Kaiserslautern, Germany.
| | - Finja Bohle
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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de Vries J, de Vries S, Curtis BA, Zhou H, Penny S, Feussner K, Pinto DM, Steinert M, Cohen AM, von Schwartzenberg K, Archibald JM. Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1025-1048. [PMID: 32333477 DOI: 10.1111/tpj.14782] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/28/2020] [Accepted: 04/08/2020] [Indexed: 05/20/2023]
Abstract
All land plants (embryophytes) share a common ancestor that likely evolved from a filamentous freshwater alga. Elucidating the transition from algae to embryophytes - and the eventual conquering of Earth's surface - is one of the most fundamental questions in plant evolutionary biology. Here, we investigated one of the organismal properties that might have enabled this transition: resistance to drastic temperature shifts. We explored the effect of heat stress in Mougeotia and Spirogyra, two representatives of Zygnematophyceae - the closest known algal sister lineage to land plants. Heat stress induced pronounced phenotypic alterations in their plastids, and high-performance liquid chromatography-tandem mass spectroscopy-based profiling of 565 transitions for the analysis of main central metabolites revealed significant shifts in 43 compounds. We also analyzed the global differential gene expression responses triggered by heat, generating 92.8 Gbp of sequence data and assembling a combined set of 8905 well-expressed genes. Each organism had its own distinct gene expression profile; less than one-half of their shared genes showed concordant gene expression trends. We nevertheless detected common signature responses to heat such as elevated transcript levels for molecular chaperones, thylakoid components, and - corroborating our metabolomic data - amino acid metabolism. We also uncovered the heat-stress responsiveness of genes for phosphorelay-based signal transduction that links environmental cues, calcium signatures and plastid biology. Our data allow us to infer the molecular heat stress response that the earliest land plants might have used when facing the rapidly shifting temperature conditions of the terrestrial habitat.
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Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37077, Goettingen, Germany
| | - Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitätsstr. 1, 40225, Duesseldorf, Germany
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
| | - Hong Zhou
- Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Institute of Plant Science and Microbiology, Universität Hamburg, 22609, Hamburg, Germany
| | - Susanne Penny
- National Research Council, Human Health Therapeutics, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), 37077, Goettingen, Germany
| | - Devanand M Pinto
- National Research Council, Human Health Therapeutics, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, NS, B3H 4R2, Canada
| | - Michael Steinert
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Alejandro M Cohen
- Biological Spectrometry Core Facility, Life Sciences Research Institute, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Klaus von Schwartzenberg
- Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Institute of Plant Science and Microbiology, Universität Hamburg, 22609, Hamburg, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Canadian Institute for Advanced Research, 661 University Ave, Suite 505, Toronto, ON, M5G 1M1, Canada
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Ruibal C, Castro A, Fleitas AL, Quezada J, Quero G, Vidal S. A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:845. [PMID: 32636864 PMCID: PMC7317016 DOI: 10.3389/fpls.2020.00845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.
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Affiliation(s)
- Cecilia Ruibal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrea L. Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jorge Quezada
- Unidad de Biotecnología Vegetal, Instituto de Biología Molecular y Biotecnología, Carrera de Biología – Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Teubner M, Lenzen B, Espenberger LB, Fuss J, Nickelsen J, Krause K, Ruwe H, Schmitz-Linneweber C. The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA. PLANTS 2020; 9:plants9030367. [PMID: 32192026 PMCID: PMC7154868 DOI: 10.3390/plants9030367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 01/25/2023]
Abstract
Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B's preference for psbA, suggesting that there are other determinants of specificity in vivo.
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Affiliation(s)
- Marlene Teubner
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Benjamin Lenzen
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Lucas Bernal Espenberger
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Janina Fuss
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway; (J.F.); (K.K.)
| | - Jörg Nickelsen
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, 82152 Planegg-Martinsried, Germany;
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway; (J.F.); (K.K.)
| | - Hannes Ruwe
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
| | - Christian Schmitz-Linneweber
- Institute of Biology, Department of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; (M.T.); (B.L.); (L.B.E.); (H.R.)
- Correspondence: ; Tel.: ++49-30-2093-49700
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11
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Bodensohn US, Simm S, Fischer K, Jäschke M, Groß LE, Kramer K, Ehmann C, Rensing SA, Ladig R, Schleiff E. The intracellular distribution of the components of the GET system in vascular plants. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1650-1662. [PMID: 31233800 DOI: 10.1016/j.bbamcr.2019.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022]
Abstract
The guided entry of tail-anchored proteins (GET) pathway facilitates targeting and insertion of tail-anchored proteins into membranes. In plants, such a protein insertion machinery for the endoplasmic reticulum as well as constituents within mitochondrial and chloroplasts were discovered. Previous phylogenetic analysis revealed that Get3 sequences of Embryophyta form two clades representing cytosolic ("a") and organellar ("bc") GET3 homologs, respectively. Cellular fractionation of Arabidopsis thaliana seedlings and usage of the self-assembly GFP system in protoplasts verified the cytosolic (ATGet3a), plastidic (ATGet3b) and mitochondrial (ATGet3c) localization of the different homologs. The identified plant homologs of Get1 and Get4 in A. thaliana are localized in ER and cytosol, respectively, implicating a degree of conservation of the GET pathway in A. thaliana. Transient expression of Get3 homologs of Solanum lycopersicum, Medicago × varia or Physcomitrella patens with the self-assembly GFP technique in homologous and heterologous systems verified that multiple Get3 homologs with differing subcellular localizations are common in plants. Chloroplast localized Get3 homologs were detected in all tested plant systems. In contrast, mitochondrial localized Get3 homologs were not identified in S. lycopersicum, or P. patens, while we confirmed on the example of A. thaliana proteins that mitochondrial localized Get3 proteins are properly targeted in S. lycopersicum as well.
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Affiliation(s)
- Uwe S Bodensohn
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Simm
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany; Frankfurt Institute of Advanced Studies, Ruth-Moufang-Straße 1, D-60438 Frankfurt, Germany
| | - Ken Fischer
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Michelle Jäschke
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Lucia E Groß
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Katharina Kramer
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Christian Ehmann
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan A Rensing
- Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Roman Ladig
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany; Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 15, D-60438 Frankfurt, Germany; Frankfurt Institute of Advanced Studies, Ruth-Moufang-Straße 1, D-60438 Frankfurt, Germany.
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12
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Sharma M, Bennewitz B, Klösgen RB. Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts. PHOTOSYNTHESIS RESEARCH 2018; 138:335-343. [PMID: 29946965 DOI: 10.1007/s11120-018-0543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/20/2018] [Indexed: 05/11/2023]
Abstract
Dual targeting of a nuclearly encoded protein into two different cell organelles is an exceptional event in eukaryotic cells. Yet, the frequency of such dual targeting is remarkably high in case of mitochondria and chloroplasts, the two endosymbiotic organelles of plant cells. In most instances, it is mediated by "ambiguous" transit peptides, which recognize both organelles as the target. A number of different approaches including in silico, in organello as well as both transient and stable in vivo assays are established to determine the targeting specificity of such transit peptides. In this review, we will describe and compare these approaches and discuss the potential role of this unusual targeting process. Furthermore, we will present a hypothetical scenario how dual targeting might have arisen during evolution.
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Affiliation(s)
- Mayank Sharma
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle/Saale, Germany
| | - Bationa Bennewitz
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle/Saale, Germany
| | - Ralf Bernd Klösgen
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle/Saale, Germany.
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13
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Abstract
The evolution of land plants from algae is an age-old question in biology. The entire terrestrial flora stems from a grade of algae, the streptophyte algae. Recent phylogenomic studies have pinpointed the Zygnematophyceae as the modern-day streptophyte algal lineage that is most closely related to the algal land plant ancestor. Here, we provide insight into the biology of this ancestor that might have aided in its conquest of land. Specifically, we uncover the existence of stress-signaling pathways and the potential for intimate plastid-nucleus communication. Plastids act as environmental sensors in land plants; our data suggest that this feature was present in a common ancestor they shared with streptophyte algae. Streptophytes are unique among photosynthetic eukaryotes in having conquered land. As the ancestors of land plants, streptophyte algae are hypothesized to have possessed exaptations to the environmental stressors encountered during the transition to terrestrial life. Many of these stressors, including high irradiance and drought, are linked to plastid biology. We have investigated global gene expression patterns across all six major streptophyte algal lineages, analyzing a total of around 46,000 genes assembled from a little more than 1.64 billion sequence reads from six organisms under three growth conditions. Our results show that streptophyte algae respond to cold and high light stress via expression of hallmark genes used by land plants (embryophytes) during stress–response signaling and downstream responses. Among the strongest differentially regulated genes were those associated with plastid biology. We observed that among streptophyte algae, those most closely related to land plants, especially Zygnema, invest the largest fraction of their transcriptional budget in plastid-targeted proteins and possess an array of land plant-type plastid-nucleus communication genes. Streptophyte algae more closely related to land plants also appear most similar to land plants in their capacity to respond to plastid stressors. Support for this notion comes from the detection of a canonical abscisic acid receptor of the PYRABACTIN RESISTANCE (PYR/PYL/RCAR) family in Zygnema, the first found outside the land plant lineage. We conclude that a fine-tuned response toward terrestrial plastid stressors was among the exaptations that allowed streptophytes to colonize the terrestrial habitat on a global scale.
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Sharma M, Bennewitz B, Klösgen RB. Dual or Not Dual?-Comparative Analysis of Fluorescence Microscopy-Based Approaches to Study Organelle Targeting Specificity of Nuclear-Encoded Plant Proteins. FRONTIERS IN PLANT SCIENCE 2018; 9:1350. [PMID: 30298079 PMCID: PMC6160753 DOI: 10.3389/fpls.2018.01350] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/27/2018] [Indexed: 05/20/2023]
Abstract
Plant cells are unique as they carry two organelles of endosymbiotic origin, namely mitochondria and chloroplasts (plastids) which have specific but partially overlapping functions, e. g., in energy and redox metabolism. Despite housing residual genomes of limited coding capacity, most of their proteins are encoded in the nucleus, synthesized by cytosolic ribosomes and need to be transported "back" into the respective target organelle. While transport is in most instances strictly monospecific, a group of proteins carries "ambiguous" transit peptides mediating transport into both, mitochondria and plastids. However, such dual targeting is often disputed due to variability in the results obtained from different experimental approaches. We have therefore compared and evaluated the most common methods established to study protein targeting into organelles within intact plant cells. All methods are based on fluorescent protein technology and live cell imaging. For our studies, we have selected four candidate proteins with proven dual targeting properties and analyzed their subcellular localization in vivo utilizing four different methods (particle bombardment, protoplast transformation, Agrobacterium infiltration, and transgenic plants). Though using identical expression constructs in all instances, a given candidate protein does not always show the same targeting specificity in all approaches, demonstrating that the choice of method is important, and depends very much on the question to be addressed.
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15
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Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora. Curr Biol 2017; 27:2763-2773.e5. [DOI: 10.1016/j.cub.2017.08.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/12/2017] [Accepted: 08/03/2017] [Indexed: 01/03/2023]
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Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 2017; 6. [PMID: 28498102 PMCID: PMC5462543 DOI: 10.7554/elife.23717] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history. DOI:http://dx.doi.org/10.7554/eLife.23717.001 The cells of most plants and algae contain compartments called chloroplasts that enable them to capture energy from sunlight in a process known as photosynthesis. Chloroplasts are the remnants of photosynthetic bacteria that used to live freely in the environment until they were consumed by a larger cell. “Complex” chloroplasts can form if a cell that already has a chloroplast is swallowed by another cell. The most abundant algae in the oceans are known as diatoms. These algae belong to a group called the stramenopiles, which also includes giant seaweeds such as kelp. The stramenopiles have a complex chloroplast that they acquired from a red alga (a relative of the seaweed used in sushi). However, some of the proteins in their chloroplasts are from other sources, such as the green algal relatives of plants, and it was not clear how these chloroplast proteins have contributed to the evolution of this group. Many of the proteins that chloroplasts need to work properly are produced by the host cell and are then transported into the chloroplasts. Dorrell et al. studied the genetic material of many stramenopile species and identified 770 chloroplast-targeted proteins that are predicted to underpin the origins of this group. Experiments in a diatom called Phaeodactylum confirmed these predictions and show that many of these chloroplast-targeted proteins have been recruited from green algae, bacteria, and other compartments within the host cell to support the chloroplast. Further experiments suggest that another major group of algae called the haptophytes once had a stramenopile chloroplast. The current haptophyte chloroplast does not come from the stramenopiles so the haptophytes appear to have replaced their chloroplasts at least once in their evolutionary history. The findings show that algal chloroplasts are mosaics, supported by proteins from many different species. This helps us understand why certain species succeed in the wild and how they may respond to environmental changes in the oceans. In the future, these findings may help researchers to engineer new species of algae and plants for food and fuel production. DOI:http://dx.doi.org/10.7554/eLife.23717.002
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Affiliation(s)
- Richard G Dorrell
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gillian Gile
- School of Life Sciences, Arizona State University, Tempe, United States
| | - Giselle McCallum
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Raphaël Méheust
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | - Eric P Bapteste
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | | | | | | | - Daniel J Richter
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS UMR 7144.,Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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17
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Teubner M, Fuß J, Kühn K, Krause K, Schmitz-Linneweber C. The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:472-485. [PMID: 27743418 DOI: 10.1111/tpj.13396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/29/2016] [Accepted: 10/07/2016] [Indexed: 06/06/2023]
Abstract
Chloroplast RNA metabolism depends on a multitude of nuclear-encoded RNA-binding proteins (RBPs). Most known chloroplast RBPs address specific RNA targets and RNA-processing functions. However, members of the small chloroplast ribonucleoprotein family (cpRNPs) play a global role in processing and stabilizing chloroplast RNAs. Here, we show that the cpRNP CP33A localizes to a distinct sub-chloroplastic domain and is essential for chloroplast development. The loss of CP33A yields albino seedlings that exhibit aberrant leaf development and can only survive in the presence of an external carbon source. Genome-wide RNA association studies demonstrate that CP33A associates with all chloroplast mRNAs. For a given transcript, quantification of CP33A-bound versus free RNAs demonstrates that CP33A associates with the majority of most mRNAs analyzed. Our results further show that CP33A is required for the accumulation of a number of tested mRNAs, and is particularly relevant for unspliced and unprocessed precursor mRNAs. Finally, CP33A fails to associate with polysomes or to strongly co-precipitate with ribosomal RNA, suggesting that it defines a ribodomain that is separate from the chloroplast translation machinery. Collectively, these findings suggest that CP33A contributes to globally essential RNA processes in the chloroplasts of higher plants.
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Affiliation(s)
- Marlene Teubner
- Humboldt-Universität Berlin, Institut für Biologie, Chausseestrasse 117, 10115, Berlin, Germany
| | - Janina Fuß
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Dramsvegen 201, 9037, Tromsø, Norway
| | - Kristina Kühn
- Humboldt-Universität Berlin, Institut für Biologie, Chausseestrasse 117, 10115, Berlin, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Dramsvegen 201, 9037, Tromsø, Norway
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18
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Khan AA, Khan Z, Kalam MA, Khan AA. Inter-kingdom prediction certainty evaluation of protein subcellular localization tools: microbial pathogenesis approach for deciphering host microbe interaction. Brief Bioinform 2016; 19:12-22. [DOI: 10.1093/bib/bbw093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/19/2022] Open
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19
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Wang Y, Lyu W, Berkowitz O, Radomiljac JD, Law SR, Murcha MW, Carrie C, Teixeira PF, Kmiec B, Duncan O, Van Aken O, Narsai R, Glaser E, Huang S, Roessner U, Millar AH, Whelan J. Inactivation of Mitochondrial Complex I Induces the Expression of a Twin Cysteine Protein that Targets and Affects Cytosolic, Chloroplastidic and Mitochondrial Function. MOLECULAR PLANT 2016; 9:696-710. [PMID: 26829715 DOI: 10.1016/j.molp.2016.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 12/09/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
At12Cys-1 (At5g64400) and At12Cys-2 (At5g09570) are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutants with disrupted mitochondrial proteins, but an increase in At12Cys protein is only detected in mutants with reduced mitochondrial complex I abundance. Induction of At12Cys protein in mutants that lack mitochondrial complex I is accompanied by At12Cys protein located in mitochondria, chloroplasts, and the cytosol. Biochemical analyses revealed that even single gene deletions, i.e., At12cys-1 or At12cys-2, have an effect on mitochondrial and chloroplast functions. However, only double mutants, i.e., At12cys-1:At12cys-2, affect the abundance of protein and mRNA transcripts encoding translation elongation factors as well as rRNA abundance. Blue native PAGE showed that At12Cys co-migrated with mitochondrial supercomplex I + III. Likewise, deletion of both At12cys-1 and At12cys-2 genes, but not single gene deletions, results in enhanced tolerance to drought and light stress and increased anti-oxidant capacity. The induction and multiple localization of At12Cys upon a reduction in complex I abundance provides a mechanism to specifically signal mitochondrial dysfunction to the cytosol and then beyond to other organelles in the cell.
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Affiliation(s)
- Yan Wang
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Wenhui Lyu
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jordan D Radomiljac
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Simon R Law
- Umeå Plant Science Centre (UPSC), Faculty of Science and Technology, Umeå University, Umeå, Sweden
| | - Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Chris Carrie
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, 10691 Stockholm, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, 10691 Stockholm, Sweden
| | - Owen Duncan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Olivier Van Aken
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, 10691 Stockholm, Sweden
| | - Shaobai Huang
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia.
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Turowski VR, Aknin C, Maliandi MV, Buchensky C, Leaden L, Peralta DA, Busi MV, Araya A, Gomez-Casati DF. Frataxin Is Localized to Both the Chloroplast and Mitochondrion and Is Involved in Chloroplast Fe-S Protein Function in Arabidopsis. PLoS One 2015; 10:e0141443. [PMID: 26517126 PMCID: PMC4636843 DOI: 10.1371/journal.pone.0141443] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/07/2015] [Indexed: 11/19/2022] Open
Abstract
Frataxin plays a key role in eukaryotic cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (Fe-S) cluster biosynthesis. However, its precise role has yet to be elucidated. In this work, we studied the subcellular localization of Arabidopsis frataxin, AtFH, using confocal microscopy, and found a novel dual localization for this protein. We demonstrate that plant frataxin is targeted to both the mitochondria and the chloroplast, where it may play a role in Fe-S cluster metabolism as suggested by functional studies on nitrite reductase (NIR) and ferredoxin (Fd), two Fe-S containing chloroplast proteins, in AtFH deficient plants. Our results indicate that frataxin deficiency alters the normal functioning of chloroplasts by affecting the levels of Fe, chlorophyll, and the photosynthetic electron transport chain in this organelle.
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Affiliation(s)
- Valeria R. Turowski
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Cindy Aknin
- UMR5234 Microbiologie Fondamentale et Pathogénicité, Centre National de la Recherche Scientifique and Université Bordeaux-Segalen, 146 rue Léo Saignat, 33076, Bordeaux cedex, France
| | - Maria V. Maliandi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH) CONICET/UNSAM, Camino de Circunvaación Km 6, 7130, Chascomús, Argentina
| | - Celeste Buchensky
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Laura Leaden
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Diego A. Peralta
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Maria V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Alejandro Araya
- Centre National de la Recherche Scientifique & UMR 1332 –Biologie du Fruit et Pathologie, Institute National de la Recherche Agronomique (INRA) Bordeaux Aquitaine, 71 avenue Edouard Bourlaux, 33882, Villenave D’Ornon, France
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
- * E-mail:
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21
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Mani J, Meisinger C, Schneider A. Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes. Mol Biol Evol 2015; 33:337-51. [PMID: 26474847 DOI: 10.1093/molbev/msv219] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are essential for eukaryotic life and more than 95% of their proteins are imported as precursors from the cytosol. The targeting signals for this posttranslational import are conserved in all eukaryotes. However, this conservation does not hold true for the protein translocase of the mitochondrial outer membrane that serves as entry gate for essentially all precursor proteins. Only two of its subunits, Tom40 and Tom22, are conserved and thus likely were present in the last eukaryotic common ancestor. Tom7 is found in representatives of all supergroups except the Excavates. This suggests that it was added to the core of the translocase after the Excavates segregated from all other eukaryotes. A comparative analysis of the biochemically and functionally characterized outer membrane translocases of yeast, plants, and trypanosomes, which represent three eukaryotic supergroups, shows that the receptors that recognize the conserved import signals differ strongly between the different systems. They present a remarkable example of convergent evolution at the molecular level. The structural diversity of the functionally conserved import receptors therefore provides insight into the early evolutionary history of mitochondria.
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Affiliation(s)
- Jan Mani
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Chris Meisinger
- Institut für Biochemie und Molekularbiologie, ZBMZ and BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM. Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes. Genome Biol Evol 2015; 7:1728-42. [PMID: 25994931 PMCID: PMC4494062 DOI: 10.1093/gbe/evv095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The internal compartmentation of eukaryotic cells not only allows separation of biochemical processes but it also creates the requirement for systems that can selectively transport proteins across the membrane boundaries. Although most proteins function in a single subcellular compartment, many are able to enter two or more compartments, a phenomenon known as dual or multiple targeting. The aminoacyl-tRNA synthetases (aaRSs), which catalyze the ligation of tRNAs to their cognate amino acids, are particularly prone to functioning in multiple subcellular compartments. They are essential for translation, so they are required in every compartment where translation takes place. In diatoms, there are three such compartments, the plastid, the mitochondrion, and the cytosol. In cryptophytes, translation also takes place in the periplastid compartment (PPC), which is the reduced cytoplasm of the plastid’s red algal ancestor and which retains a reduced red algal nucleus. We searched the organelle and nuclear genomes of the cryptophyte Guillardia theta and the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana for aaRS genes and found an insufficient number of genes to provide each compartment with a complete set of aaRSs. We therefore inferred, with support from localization predictions, that many aaRSs are dual targeted. We tested four of the predicted dual targeted aaRSs with green fluorescent protein fusion localizations in P. tricornutum and found evidence for dual targeting to the mitochondrion and plastid in P. tricornutum and G. theta, and indications for dual targeting to the PPC and cytosol in G. theta. This is the first report of dual targeting in diatoms or cryptophytes.
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Affiliation(s)
- Gillian H Gile
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Moog
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Uwe-G Maier
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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