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Hirata R, Mogi Y, Takahashi K, Nozaki H, Higashiyama T, Yoshida Y. Simple prerequisite of presequence for mitochondrial protein import in the unicellular red alga Cyanidioschyzon merolae. J Cell Sci 2024; 137:jcs262042. [PMID: 38940185 PMCID: PMC11298712 DOI: 10.1242/jcs.262042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024] Open
Abstract
Mitochondrial biogenesis relies on hundreds of proteins that are derived from genes encoded in the nucleus. According to the characteristic properties of N-terminal targeting peptides (TPs) and multi-step authentication by the protein translocase called the TOM complex, nascent polypeptides satisfying the requirements are imported into mitochondria. However, it is unknown whether eukaryotic cells with a single mitochondrion per cell have a similar complexity of presequence requirements for mitochondrial protein import compared to other eukaryotes with multiple mitochondria. Based on putative mitochondrial TP sequences in the unicellular red alga Cyanidioschyzon merolae, we designed synthetic TPs and showed that functional TPs must have at least one basic residue and a specific amino acid composition, although their physicochemical properties are not strictly determined. Combined with the simple composition of the TOM complex in C. merolae, our results suggest that a regional positive charge in TPs is verified solely by TOM22 for mitochondrial protein import in C. merolae. The simple authentication mechanism indicates that the monomitochondrial C. merolae does not need to increase the cryptographic complexity of the lock-and-key mechanism for mitochondrial protein import.
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Affiliation(s)
- Riko Hirata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuko Mogi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kohei Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki 305-8506, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yamato Yoshida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Japan Science and Technology Agency (JST), PRESTO, Tokyo 113-0033, Japan
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2
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Seger M, Mammadova F, Villegas-Valencia M, Bastos de Freitas B, Chang C, Isachsen I, Hemstreet H, Abualsaud F, Boring M, Lammers PJ, Lauersen KJ. Engineered ketocarotenoid biosynthesis in the polyextremophilic red microalga Cyanidioschyzon merolae 10D. Metab Eng Commun 2023; 17:e00226. [PMID: 37449053 PMCID: PMC10336515 DOI: 10.1016/j.mec.2023.e00226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The polyextremophilic Cyanidiophyceae are eukaryotic red microalgae with promising biotechnological properties arising from their low pH and elevated temperature requirements which can minimize culture contamination at scale. Cyanidioschyzon merolae 10D is a cell wall deficient species with a fully sequenced genome that is amenable to nuclear transgene integration by targeted homologous recombination. C. merolae maintains a minimal carotenoid profile and here, we sought to determine its capacity for ketocarotenoid accumulation mediated by heterologous expression of a green algal β-carotene ketolase (BKT) and hydroxylase (CHYB). To achieve this, a synthetic transgene expression cassette system was built to integrate and express Chlamydomonas reinhardtii (Cr) sourced enzymes by fusing native C. merolae transcription, translation and chloroplast targeting signals to codon-optimized coding sequences. Chloramphenicol resistance was used to select for the integration of synthetic linear DNAs into a neutral site within the host genome. CrBKT expression caused accumulation of canthaxanthin and adonirubin as major carotenoids while co-expression of CrBKT with CrCHYB generated astaxanthin as the major carotenoid in C. merolae. Unlike green algae and plants, ketocarotenoid accumulation in C. merolae did not reduce total carotenoid contents, but chlorophyll a reduction was observed. Light intensity affected global ratios of all pigments but not individual pigment compositions and phycocyanin contents were not markedly different between parental strain and transformants. Continuous illumination was found to encourage biomass accumulation and all strains could be cultivated in simulated summer conditions from two different extreme desert environments. Our findings present the first example of carotenoid metabolic engineering in a red eukaryotic microalga and open the possibility for use of C. merolae 10D for simultaneous production of phycocyanin and ketocarotenoid pigments.
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Affiliation(s)
- Mark Seger
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Fakhriyya Mammadova
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Melany Villegas-Valencia
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Bárbara Bastos de Freitas
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Clarissa Chang
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Iona Isachsen
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Haley Hemstreet
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Fatimah Abualsaud
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Malia Boring
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Peter J. Lammers
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Kyle J. Lauersen
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
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3
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Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella. iScience 2022; 25:104974. [PMID: 36093053 PMCID: PMC9450145 DOI: 10.1016/j.isci.2022.104974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 01/12/2023] Open
Abstract
The primary plastid endosymbiosis (∼124 Mya) that occurred in the heterotrophic amoeba lineage, Paulinella, is at an earlier stage of evolution than in Archaeplastida, and provides an excellent model for studying organelle integration. Using genomic data from photosynthetic Paulinella, we identified a plausible mechanism for the evolution of host control of endosymbiont (termed the chromatophore) biosynthetic pathways and functions. Specifically, random gene loss from the chromatophore and compensation by nuclear-encoded gene copies enables host control of key pathways through a minimal number of evolutionary innovations. These gene losses impact critical enzymatic steps in nucleotide biosynthesis and the more peripheral components of multi-protein DNA replication complexes. Gene retention in the chromatophore likely reflects the need to maintain a specific stoichiometric balance of the encoded products (e.g., involved in DNA replication) rather than redox state, as in the highly reduced plastid genomes of algae and plants. Endosymbiont DNA replication cannot be completed without several key host proteins Endosymbiont nucleotide biosynthesis is completed by import of host proteins Limited gene loss allowed the host to gain control of endosymbiont division Paulinella regulates chromatophore function using the stringent response pathway
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4
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Sato N. Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae? Genes (Basel) 2021; 12:genes12060823. [PMID: 34071987 PMCID: PMC8227023 DOI: 10.3390/genes12060823] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/08/2021] [Accepted: 05/25/2021] [Indexed: 12/04/2022] Open
Abstract
Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the notion that chloroplasts originated from cyanobacterial endosymbiosis. However, studies in the post-genomic era revealed that various substances (glycolipids, peptidoglycan, etc.) shared by cyanobacteria and chloroplasts are synthesized by different pathways or phylogenetically unrelated enzymes. Membranes and genomes are essential components of a cell (or an organelle), but the origins of these turned out to be different. Besides, phylogenetic trees of chloroplast-encoded genes suggest an alternative possibility that chloroplast genes could be acquired from at least three different lineages of cyanobacteria. We have to seriously examine that the chloroplast genome might be chimeric due to various independent gene flows from cyanobacteria. Chloroplast formation could be more complex than a single event of cyanobacterial endosymbiosis. I present the “host-directed chloroplast formation” hypothesis, in which the eukaryotic host cell that had acquired glycolipid synthesis genes as an adaptation to phosphate limitation facilitated chloroplast formation by providing glycolipid-based membranes (pre-adaptation). The origins of the membranes and the genome could be different, and the origin of the genome could be complex.
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Affiliation(s)
- Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
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5
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Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa. Pathogens 2020; 9:pathogens9040257. [PMID: 32244644 PMCID: PMC7238167 DOI: 10.3390/pathogens9040257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 11/17/2022] Open
Abstract
The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, “plant and protist organellar DNA polymerase (POP)” in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa—Kinetoplastea, Diplonemea, and Euglenida—to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.
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6
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García-Medel PL, Baruch-Torres N, Peralta-Castro A, Trasviña-Arenas CH, Torres-Larios A, Brieba LG. Plant organellar DNA polymerases repair double-stranded breaks by microhomology-mediated end-joining. Nucleic Acids Res 2019; 47:3028-3044. [PMID: 30698803 PMCID: PMC6451138 DOI: 10.1093/nar/gkz039] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 12/23/2018] [Accepted: 01/15/2019] [Indexed: 12/27/2022] Open
Abstract
Double-stranded breaks (DSBs) in plant organelles are repaired via genomic rearrangements characterized by microhomologous repeats. These microhomologous signatures predict the existence of an unidentified enzymatic machinery capable of repairing of DSBs via microhomology-mediated end-joining (MMEJ) in plant organelles. Here, we show that organellar DNA polymerases from Arabidopsis thaliana (AtPolIA and AtPolIB) perform MMEJ using microhomologous sequences as short as six nucleotides. AtPolIs execute MMEJ by virtue of two specialized amino acid insertions located in their thumb subdomains. Single-stranded binding proteins (SSBs) unique to plants, AtWhirly2 and organellar single-stranded binding proteins (AtOSBs), hinder MMEJ, whereas canonical mitochondrial SSBs (AtmtSSB1 and AtmtSSB2) do not interfere with MMEJ. Our data predict that organellar DNA rearrangements by MMEJ are a consequence of a competition for the 3'-OH of a DSBs. If AtWhirlies or AtOSBs gain access to the single-stranded DNA (ssDNA) region of a DSB, the reaction will shift towards high-fidelity routes like homologous recombination. Conversely MMEJ would be favored if AtPolIs or AtmtSSBs interact with the DSB. AtPolIs are not phylogenetically related to metazoan mitochondrial DNA polymerases, and the ability of AtPolIs to execute MMEJ may explain the abundance of DNA rearrangements in plant organelles in comparison to animal mitochondria.
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Affiliation(s)
- Paola L García-Medel
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Antolín Peralta-Castro
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
| | - Alfredo Torres-Larios
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado postal 70-243, Mexico City 04510, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México
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7
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Grisdale CJ, Smith DR, Archibald JM. Relative Mutation Rates in Nucleomorph-Bearing Algae. Genome Biol Evol 2019; 11:1045-1053. [PMID: 30859201 PMCID: PMC6456004 DOI: 10.1093/gbe/evz056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2019] [Indexed: 12/23/2022] Open
Abstract
Chlorarachniophyte and cryptophyte algae are unique among plastid-containing species in that they have a nucleomorph genome: a compact, highly reduced nuclear genome from a photosynthetic eukaryotic endosymbiont. Despite their independent origins, the nucleomorph genomes of these two lineages have similar genomic architectures, but little is known about the evolutionary pressures impacting nucleomorph DNA, particularly how their rates of evolution compare to those of the neighboring genetic compartments (the mitochondrion, plastid, and nucleus). Here, we use synonymous substitution rates to estimate relative mutation rates in the four genomes of nucleomorph-bearing algae. We show that the relative mutation rates of the host versus endosymbiont nuclear genomes are similar in both chlorarachniophytes and cryptophytes, despite the fact that nucleomorph gene sequences are notoriously highly divergent. There is some evidence, however, for slightly elevated mutation rates in the nucleomorph DNA of chlorarachniophytes-a feature not observed in that of cryptophytes. For both lineages, relative mutation rates in the plastid appear to be lower than those in the nucleus and nucleomorph (and, in one case, the mitochondrion), which is consistent with studies of other plastid-bearing protists. Given the divergent nature of nucleomorph genes, our finding of relatively low evolutionary rates in these genomes suggests that for both lineages a burst of evolutionary change and/or decreased selection pressures likely occurred early in the integration of the secondary endosymbiont.
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Affiliation(s)
- Cameron J Grisdale
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David R Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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8
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Organellar DNA Polymerases in Complex Plastid-Bearing Algae. Biomolecules 2019; 9:biom9040140. [PMID: 30959949 PMCID: PMC6523293 DOI: 10.3390/biom9040140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 01/16/2023] Open
Abstract
DNA replication in plastids and mitochondria is generally regulated by nucleus-encoded proteins. In plants and red algae, a nucleus-encoded enzyme called POP (plant and protist organellar DNA polymerase) is involved in DNA replication in both organelles by virtue of its dual localization. POPs are family A DNA polymerases, which include bacterial DNA polymerase I (PolI). POP homologs have been found in a wide range of eukaryotes, including plants, algae, and non-photosynthetic protists. However, the phylogeny and subcellular localizations of POPs remain unclear in many algae, especially in secondary and tertiary plastid-bearing groups. In this study, we report that chlorarachniophytes possess two evolutionarily distinct POPs, and fluorescent protein-tagging experiments demonstrate that they are targeted to the secondary plastids and mitochondria, respectively. The timing of DNA replication is different between the two organelles in the chlorarachniophyte Bigelowiella natans, and this seems to be correlated to the transcription of respective POP genes. Dinoflagellates also carry two distinct POP genes, possibly for their plastids and mitochondria, whereas haptophytes and ochrophytes have only one. Therefore, unlike plants, some algal groups are likely to have evolved multiple DNA polymerases for various organelles. This study provides a new insight into the evolution of organellar DNA replication in complex plastid-bearing organisms.
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9
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Mori N, Moriyama T, Sato N. Uncommon properties of lipid biosynthesis of isolated plastids in the unicellular red alga Cyanidioschyzon merolae. FEBS Open Bio 2018; 9:114-128. [PMID: 30652079 PMCID: PMC6325583 DOI: 10.1002/2211-5463.12551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/22/2022] Open
Abstract
Red algae are a large group of photosynthetic eukaryotes that diverged from green algae over one billion years ago, and have various traits distinct from those of both green algae and land plants. Although most red algae are marine species (both unicellular and macrophytic), the Cyanidiales class of red algae includes unicellular species which live in hot springs, such as Cyanidioschyzon merolae, which is a model species for biochemical and molecular biological studies. Lipid metabolism in red algae has previously been studied in intact cells. Here, we present the results of radiolabeling and stable isotope labeling experiments in intact plastids isolated from the unicellular red alga C. merolae. We focused on two uncommon features: First, the galactose moiety of monogalactosyldiacylglycerol was efficiently labeled with bicarbonate, indicating that an unknown pathway for providing UDP-galactose exists within the plastid. Second, saturated fatty acids, namely, palmitic and stearic acids, were the sole products of fatty acid synthesis in the plastid, and they were efficiently exported. This finding suggests that the endoplasmic reticulum is the sole site of desaturation. We present a general principle of red algal lipid biosynthesis, namely, 'indigenous C18 fatty acids are neither desaturated nor directly utilized within the plastid'. We believe that this is valid in both C. merolae lacking polyunsaturated fatty acids and marine red algae with a high content of arachidonic and eicosapentaenoic acids.
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Affiliation(s)
- Natsumi Mori
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
| | - Takashi Moriyama
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
| | - Naoki Sato
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
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10
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Sakamoto W, Takami T. Chloroplast DNA Dynamics: Copy Number, Quality Control and Degradation. PLANT & CELL PHYSIOLOGY 2018; 59:1120-1127. [PMID: 29860378 DOI: 10.1093/pcp/pcy084] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/01/2018] [Indexed: 05/16/2023]
Abstract
Endosymbiotically originated chloroplast DNA (cpDNA) encodes part of the genetic information needed to fulfill chloroplast function, including fundamental processes such as photosynthesis. In the last two decades, advances in genome analysis led to the identification of a considerable number of cpDNA sequences from various species. While these data provided the consensus features of cpDNA organization and chloroplast evolution in plants, how cpDNA is maintained through development and is inherited remains to be fully understood. In particular, the fact that cpDNA exists as multiple copies despite its limited genetic capacity raises the important question of how copy number is maintained or whether cpDNA is subjected to quantitative fluctuation or even developmental degradation. For example, cpDNA is abundant in leaves, where it forms punctate structures called nucleoids, which seemingly alter their morphologies and numbers depending on the developmental status of the chloroplast. In this review, we summarize our current understanding of 'cpDNA dynamics', focusing on the changes in DNA abundance. A special focus is given to the cpDNA degradation mechanism, which appears to be mediated by Defective in Pollen organelle DNA degradation 1 (DPD1), a recently discovered organelle exonuclease. The physiological significance of cpDNA degradation in flowering plants is also discussed.
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Affiliation(s)
- Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
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11
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Lipid metabolism and potentials of biofuel and high added-value oil production in red algae. World J Microbiol Biotechnol 2017; 33:74. [DOI: 10.1007/s11274-017-2236-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/01/2017] [Indexed: 10/20/2022]
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12
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Mori N, Moriyama T, Toyoshima M, Sato N. Construction of Global Acyl Lipid Metabolic Map by Comparative Genomics and Subcellular Localization Analysis in the Red Alga Cyanidioschyzon merolae. FRONTIERS IN PLANT SCIENCE 2016; 7:958. [PMID: 28066454 PMCID: PMC4928187 DOI: 10.3389/fpls.2016.00958] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/15/2016] [Indexed: 05/03/2023]
Abstract
Pathways of lipid metabolism have been established in land plants, such as Arabidopsis thaliana, but the information on exact pathways is still under study in microalgae. In contrast with Chlamydomonas reinhardtii, which is currently studied extensively, the pathway information in red algae is still in the state in which enzymes and pathways are estimated by analogy with the knowledge in plants. Here we attempt to construct the entire acyl lipid metabolic pathways in a model red alga, Cyanidioschyzon merolae, as an initial basis for future genetic and biochemical studies, by exploiting comparative genomics and localization analysis. First, the data of whole genome clustering by Gclust were used to identify 121 acyl lipid-related enzymes. Then, the localization of 113 of these enzymes was analyzed by GFP-based techniques. We found that most of the predictions on the subcellular localization by existing tools gave erroneous results, probably because these tools had been tuned for plants or green algae. The experimental data in the present study as well as the data reported before in our laboratory will constitute a good training set for tuning these tools. The lipid metabolic map thus constructed show that the lipid metabolic pathways in the red alga are essentially similar to those in A. thaliana, except that the number of enzymes catalyzing individual reactions is quite limited. The absence of fatty acid desaturation to produce oleic and linoleic acids within the plastid, however, highlights the central importance of desaturation and acyl editing in the endoplasmic reticulum, for the synthesis of plastid lipids as well as other cellular lipids. Additionally, some notable characteristics of lipid metabolism in C. merolae were found. For example, phosphatidylcholine is synthesized by the methylation of phosphatidylethanolamine as in yeasts. It is possible that a single 3-ketoacyl-acyl carrier protein synthase is involved in the condensation reactions of fatty acid synthesis in the plastid. We will also discuss on the redundant β-oxidation enzymes, which are characteristic to red algae.
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Affiliation(s)
- Natsumi Mori
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyTokyo, Japan
| | - Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyTokyo, Japan
| | - Masakazu Toyoshima
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyTokyo, Japan
| | - Naoki Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologyTokyo, Japan
- *Correspondence: Naoki Sato
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13
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Diversification of DnaA dependency for DNA replication in cyanobacterial evolution. ISME JOURNAL 2015; 10:1113-21. [PMID: 26517699 DOI: 10.1038/ismej.2015.194] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/01/2015] [Accepted: 09/27/2015] [Indexed: 11/08/2022]
Abstract
Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.
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Moriyama T, Mori N, Sato N. Activation of oxidative carbon metabolism by nutritional enrichment by photosynthesis and exogenous organic compounds in the red alga Cyanidioschyzon merolae: evidence for heterotrophic growth. SPRINGERPLUS 2015; 4:559. [PMID: 26435905 PMCID: PMC4586181 DOI: 10.1186/s40064-015-1365-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/21/2015] [Indexed: 11/30/2022]
Abstract
Respiration is an important process in photosynthetic organisms, as it is in other organisms, for the supply of ATP and metabolites required for biosynthesis. Furthermore, individual enzymatic activity is subject to regulation by metabolic intermediates in glycolysis and the citric acid cycle. However, little is known about how glycolysis or catabolism are related to photosynthetic activity or accumulation of photosynthetic products. We previously developed a flat-plate culture apparatus assembled from materials commonly used for gel electrophoresis, which enables high-density culture of the unicellular red alga Cyanidioschyzon merolae. In this study, a stationary dense culture of C. merolae, when re-activated in this culture apparatus, exhibited an accumulation of photosynthetically produced starch. We demonstrated that respiratory activity increased during the culture period, while photosynthetic activity remained constant. Gene expression analysis revealed that the genes involved in cytosolic glycolysis and the citric acid cycle were selectively activated, compared to the genes for the oxidative pentose phosphate pathway and the Calvin–Benson cycle. Measurements of the respiratory rate after addition of various organic substances showed that C. merolae can utilize almost any exogenous organic compound as a respiratory substrate, although the effectiveness of each compound was dependent on the culture time in the flat-plate culture, suggesting that glycolysis was rate-limiting to respiration, and its activity depended on the level of photosynthetic products within the cells. We also demonstrated that organic substances increased the rate of cell growth under dim light and, interestingly, C. merolae could grow heterotrophically in the presence of glycerol. Obligate photoautotrophy should be considered an ecological, rather than physiological, characteristic of C. merolae.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902 Japan ; JST, CREST, K's Gobancho 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
| | - Natsumi Mori
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902 Japan ; JST, CREST, K's Gobancho 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
| | - Naoki Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902 Japan ; JST, CREST, K's Gobancho 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
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Moriyama T, Sakurai K, Sekine K, Sato N. Subcellular distribution of central carbohydrate metabolism pathways in the red alga Cyanidioschyzon merolae. PLANTA 2014; 240:585-98. [PMID: 25009310 DOI: 10.1007/s00425-014-2108-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/10/2014] [Indexed: 05/19/2023]
Abstract
Comprehensive subcellular localization analysis revealed that the subcellular distribution of carbohydrate metabolic pathways in the red alga Cyanidioschyzon is essentially identical with that in Arabidopsis , except the lack of transaldolase. In plants, the glycolysis and oxidative pentose phosphate pathways (oxPPP) are located in both cytosol and plastids. However, in algae, particularly red algae, the subcellular localization of enzymes involved in carbon metabolism is unclear. Here, we identified and examined the localization of enzymes related to glycolysis, oxPPP, and tricarboxylic acid (TCA) and Calvin-Benson cycles in the red alga Cyanidioschyzon merolae. A gene encoding transaldolase of the oxPPP was not found in the C. merolae genome, and no transaldolase activity was detected in cellular extracts. The subcellular localization of 65 carbon metabolic enzymes tagged with green fluorescent protein or hemagglutinin was examined in C. merolae cells. As expected, TCA and Calvin-Benson cycle enzymes were localized to mitochondria and plastids, respectively. The analyses also revealed that the cytosol contains the entire glycolytic pathway and partial oxPPP, whereas the plastid contains a partial glycolytic pathway and complete oxPPP, with the exception of transaldolase. Together, these results suggest that the subcellular distribution of carbohydrate metabolic pathways in C. merolae is essentially identical with that reported in the photosynthetic tissue of Arabidopsis thaliana; however, it appears that substrates typically utilized by transaldolase are consumed by glycolytic enzymes in the plastidic oxPPP of C. merolae.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan,
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Moriyama T, Sato N. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes. FRONTIERS IN PLANT SCIENCE 2014; 5:480. [PMID: 25278952 PMCID: PMC4166229 DOI: 10.3389/fpls.2014.00480] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/30/2014] [Indexed: 05/18/2023]
Abstract
Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- Japan Science and Technology Agency – Core Research for Evolutional Science and TechnologyTokyo, Japan
| | - Naoki Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- Japan Science and Technology Agency – Core Research for Evolutional Science and TechnologyTokyo, Japan
- *Correspondence: Naoki Sato, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan e-mail:
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Krupinska K, Oetke S, Desel C, Mulisch M, Schäfer A, Hollmann J, Kumlehn J, Hensel G. WHIRLY1 is a major organizer of chloroplast nucleoids. FRONTIERS IN PLANT SCIENCE 2014; 5:432. [PMID: 25237316 PMCID: PMC4154442 DOI: 10.3389/fpls.2014.00432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/13/2014] [Indexed: 05/20/2023]
Abstract
WHIRLY1 is an abundant protein of chloroplast nucleoids, which has also been named pTAC-1 with regard to its detection in the proteome of transcriptionally active chromosomes (TAC). In barley primary foliage leaves, expression of the WHIRLY1 gene is highest at the base whereas protein accumulation is highest in the middle of the leaf where young developing chloroplasts are found. In order to elucidate the function of WHIRLY1 in chloroplast nucleoids, transgenic barley plants with an RNAi-mediated knock-down of the HvWHIRLY1 gene (RNAi-W1) were generated. The homozygous RNAi-W1-7 plants, barely containing traces of the WHIRLY1 protein, were chosen for detailed analyses of nucleoids. Nucleic acid specific-staining with YO-PRO®-1 revealed that in comparison to wild type chloroplasts, which have multiple small nucleoids attached to thylakoids, chloroplasts of the transgenic plants contain large irregularly formed patches of DNA besides nucleoids that are similar in size and shape to those of wild type chloroplasts. In large electron lucent areas, filamentous structures were detected by conventional transmission electron microscopy. Analyses of ptDNA levels by both DNA dot-blot hybridization and quantitative PCR showed that leaves of the transgenic plants have a two- to three-fold higher level of ptDNA than the wild type. The higher ptDNA level in RNAi-W1 plants coincided with an enhanced expression of the gene encoding a putative organelle targeted DNA polymerase in the mid part of primary foliage leaves. Furthermore, overexpression of the barley WHIRLY1 gene in E. coli cells revealed a higher compaction of bacterial nucleoids. These results suggest that WHIRLY1 belongs to the group of plastid nucleoid associated proteins (ptNAP) having a function in compacting a subpopulation of chloroplast nucleoids thereby affecting DNA replication.
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Affiliation(s)
- Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
- *Correspondence: Karin Krupinska, Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany e-mail:
| | - Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Christine Desel
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Maria Mulisch
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
- Central Microscopy of the Center of Biology, Christian-Albrechts-University of KielKiel, Germany
| | - Anke Schäfer
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland/OT Gatersleben, Germany
| | - Götz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland/OT Gatersleben, Germany
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