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Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
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Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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2
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He Y, Ma S, Yang Q, Lai H, Zhang J. Characterization of the mitochondrial genome of Chlorolobion braunii ITBB-AG6, an azolla-associated green alga isolated from sanitary sewage. Mitochondrial DNA B Resour 2023; 8:826-830. [PMID: 37545555 PMCID: PMC10402853 DOI: 10.1080/23802359.2023.2241573] [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: 01/05/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023] Open
Abstract
Sphaeropleales have the characteristics of rapid growth, high oil content, and efficient removal rates of nitrogen and phosphorus in sewage waters, and is potentially valuable in biodiesel production and environmental remediation. In this study, we isolated a strain of Sphaeropleales, Chlorolobion braunii strain ITBB-AG6 from an azolla community in a sewage pond. Its mitochondrial genome contains 110,124 bp and harbors at least 40 genes, including 15 protein-coding genes, 20 tRNA genes, and three rRNA genes. The protein-coding genes include two for ATP synthases, seven for NAD(P)H-quinone oxidoreductases (nad), three for cytochrome c oxidase subunits (coxs), and one for cytochrome b (cob). Transfer RNA genes for 18 amino acids were identified, in which the tRNA genes for leucine and serine are doubled, but the tRNA genes for threonine and valine are not annotated. Phylogenetic analysis using the mitochondrial genomes of seven families of Sphaeropleales indicated that ITBB-AG6 is closely related to Monoraphidium neglectum, and falls in the family Selenastraceae with 100% bootstrap support. Two species in the family Neochloridaceae are separated by a species in Hydrodictyaceae, indicating a polyphyletic nature. These findings revealed the complicated phylogenetic relationships of the Sphaeropleales and the necessity of genome sequences in the taxonomy of microalgae.
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Affiliation(s)
- Yiliang He
- College of Agriculture, Hainan University, Haikou, China
| | - Shuai Ma
- Institute of Tropical Bioscience and Biotechnology, Hainan Key Laboratory of Microbiological Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qiaoqiao Yang
- College of Agriculture, Hainan University, Haikou, China
| | - Huanggui Lai
- College of Agriculture, Hainan University, Haikou, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, Hainan Key Laboratory of Microbiological Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria). mBio 2023; 14:e0030223. [PMID: 36939357 PMCID: PMC10127745 DOI: 10.1128/mbio.00302-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria-the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.
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Tanaka Y, Iida R, Takada S, Kubota T, Yamanaka M, Sugiyama N, Abdelnour Y, Ogra Y. Quantitative Elemental Analysis of a Single Cell by Using Inductively Coupled Plasma‐Mass Spectrometry in Fast Time‐Resolved Analysis Mode. Chembiochem 2020; 21:3266-3272. [DOI: 10.1002/cbic.202000358] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/13/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Yu‐ki Tanaka
- Graduate School of Pharmaceutical Sciences Chiba University 1-8-1 Inohana Chuo Chiba 260-8675 Japan
| | - Risako Iida
- Graduate School of Pharmaceutical Sciences Chiba University 1-8-1 Inohana Chuo Chiba 260-8675 Japan
| | - Shohei Takada
- Graduate School of Pharmaceutical Sciences Chiba University 1-8-1 Inohana Chuo Chiba 260-8675 Japan
| | - Tetsuo Kubota
- Agilent Technologies International Japan, Ltd. 9-1 Takakura-machi Hachioji Tokyo 192-0033 Japan
| | - Michiko Yamanaka
- Agilent Technologies International Japan, Ltd. 9-1 Takakura-machi Hachioji Tokyo 192-0033 Japan
| | - Naoki Sugiyama
- Agilent Technologies International Japan, Ltd. 9-1 Takakura-machi Hachioji Tokyo 192-0033 Japan
| | - Yolande Abdelnour
- Agilent Technologies, France Parc Technopolis, Bâtiment Olympe 3 avenue du Canada 91940 Les Ulis France
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences Chiba University 1-8-1 Inohana Chuo Chiba 260-8675 Japan
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Li YB, Zhang YZ, Jin Y, Zeng H, Duan JY, Liu LX, Liu YG, Sui ZH. The complete mitochondrial genome of a microalgae Chlamydomonas moewusii strain XJCH-01 from Tarim Basin of Xinjiang, China. Mitochondrial DNA B Resour 2020; 5:1204-1205. [PMID: 33366913 PMCID: PMC7510814 DOI: 10.1080/23802359.2020.1731371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 11/24/2022] Open
Abstract
Chlamydomonas moewusii is a microalga isolated from the Tarim Basin of Xinjiang, China. The complete mitochondrial genome sequence of C. moewusii strain XJCH-01 was determined in this study (Accession number MT015649). The mitogenome (22,887 bp, 34.58% G + C) consists of 7 protein-coding genes (PCG), discontinuous large and small subunit ribosomal RNA (rRNA), and 4 transfer RNA (tRNA) genes. The complete mitochondrial genome sequence of the C. moewusii strain XJCH-01 enriches data resources for further study in genetic and functional evolution.
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Affiliation(s)
- Yan-Bin Li
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer, China
| | - Yan-Zhen Zhang
- College of Life Sciences and Technology, Xinjiang University, Urumqi, China
- College of Life Sciences, Linyi University, Linyi, China
| | - Ying Jin
- Qingdao Customs District P.R.China, Qingdao, China
| | - Hong Zeng
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer, China
| | - Jia-Yu Duan
- College of Life Sciences, Linyi University, Linyi, China
| | - Ling-Xiao Liu
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Yun-Guo Liu
- College of Life Sciences, Linyi University, Linyi, China
| | - Zhi-Hai Sui
- College of Life Sciences, Linyi University, Linyi, China
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Cecchin M, Marcolungo L, Rossato M, Girolomoni L, Cosentino E, Cuine S, Li‐Beisson Y, Delledonne M, Ballottari M. Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1289-1305. [PMID: 31437318 PMCID: PMC6972661 DOI: 10.1111/tpj.14508] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/05/2023]
Abstract
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Luca Marcolungo
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Marzia Rossato
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Laura Girolomoni
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Emanuela Cosentino
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Stephan Cuine
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Yonghua Li‐Beisson
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Massimo Delledonne
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Matteo Ballottari
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
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Noutahi E, Calderon V, Blanchette M, El-Mabrouk N, Lang BF. Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes. Mol Biol Evol 2019; 36:766-783. [PMID: 30698742 PMCID: PMC6551751 DOI: 10.1093/molbev/msz016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Genetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes). Besides confirming known stop-to-sense reassignments, our study documents the first cases of sense-to-sense codon reassignments in Chlorophyta mtDNAs. In several Sphaeropleales, we report the decoding of AGG codons (normally arginine) as alanine, by tRNA(CCU) of various origins that carry the recognition signature for alanine tRNA synthetase. In Chromochloris, we identify tRNA variants decoding AGG as methionine and the synonymous codon CGG as leucine. Finally, we find strong evidence supporting the decoding of AUA codons (normally isoleucine) as methionine in Pycnococcus. Our results rely on a recently developed conceptual framework (CoreTracker) that predicts codon reassignments based on the disparity between DNA sequence (codons) and the derived protein sequence. These predictions are then validated by an evaluation of tRNA phylogeny, to identify the evolution of new tRNAs via gene duplication and loss, and structural modifications that lead to the assignment of new tRNA identities and a change in the genetic code.
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Affiliation(s)
- Emmanuel Noutahi
- Département d'Informatique et de Recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
| | - Virginie Calderon
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Montréal, QC H3A 0E9, Canada
- McGill Centre for Bioinformatics, McGill University, Montréal, QC, Canada
| | - Nadia El-Mabrouk
- Département d'Informatique et de Recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
| | - Bernd Franz Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada
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8
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Cox2A/Cox2B subunit interaction in Polytomella sp. cytochrome c oxidase: role of the Cox2B subunit extension. J Bioenerg Biomembr 2017; 49:453-461. [PMID: 29043530 DOI: 10.1007/s10863-017-9728-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
Subunit II of cytochrome c oxidase (Cox2) is usually encoded in the mitochondrial genome, synthesized in the organelle, inserted co-translationally into the inner mitochondrial membrane, and assembled into the respiratory complex. In chlorophycean algae however, the cox2 gene was split into the cox2a and cox2b genes, and in some algal species like Chlamydomonas reinhardtii and Polytomella sp. both fragmented genes migrated to the nucleus. The corresponding Cox2A and Cox2B subunits are imported into mitochondria forming a heterodimeric Cox2 subunit. When comparing the sequences of chlorophycean Cox2A and Cox2B proteins with orthodox Cox2 subunits, a C-terminal extension in Cox2A and an N-terminal extension in Cox2B were identified. It was proposed that these extensions favor the Cox2A/Cox2B interaction. In vitro studies carried out in this work suggest that the removal of the Cox2B extension only partially affects binding of Cox2B to Cox2A. We conclude that this extension is dispensable, but when present it weakly reinforces the Cox2A/Cox2B interaction.
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Zhou L, Wang L, Zhang J, Cai C, He P. Complete mitochondrial genome of Ulva prolifera, the dominant species of green macroalgal blooms in Yellow Sea, China. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:76-78. [PMID: 33473415 PMCID: PMC7799800 DOI: 10.1080/23802359.2015.1137831] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.
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Affiliation(s)
- Lingjie Zhou
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Lingke Wang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Jianheng Zhang
- College of Marine Sciences, Shanghai Ocean University, Shanghai, P. R. China
| | - Chuner Cai
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P. R. China
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Zhou L, Wang L, Zhang J, Cai C, He P. Complete mitochondrial genome of Ulva linza, one of the causal species of green macroalgal blooms in Yellow Sea, China. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:31-33. [PMID: 33473396 PMCID: PMC7799859 DOI: 10.1080/23802359.2015.1137806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ulva linza, a green macroalgae, is one of the causal species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U.linza (GenBank accession no. KU189740). The genome consists of circular chromosomes of 70 858 bp and encodes a total of 28 protein-coding genes including eight rps genes, three rpl genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. linza clustered into Ulvophyceae clade and had close genetic relationship with algae Ulva prolifera.
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Affiliation(s)
- Lingjie Zhou
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Lingke Wang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Jianheng Zhang
- College of Marine Sciences, Shanghai Ocean University, Shanghai, PR China
| | - Chuner Cai
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
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Jackson CJ, Reyes-Prieto A. The mitochondrial genomes of the glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multilocus phylogenetics suggests a monophyletic archaeplastida. Genome Biol Evol 2014; 6:2774-85. [PMID: 25281844 PMCID: PMC4224345 DOI: 10.1093/gbe/evu218] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2014] [Indexed: 12/16/2022] Open
Abstract
A significant limitation when testing the putative single origin of primary plastids and the monophyly of the Archaeplastida supergroup, comprised of the red algae, viridiplants, and glaucophytes, is the scarce nuclear and organellar genome data available from the latter lineage. The Glaucophyta are a key algal group when investigating the origin and early diversification of photosynthetic eukaryotes. However, so far only the plastid and mitochondrial genomes of the glaucophytes Cyanophora paradoxa (strain CCMP 329) and Glaucocystis nostochinearum (strain UTEX 64) have been completely sequenced. Here, we present the complete mitochondrial genomes of Gloeochaete wittrockiana SAG 46.84 (36.05 kb; 33 protein-coding genes, 6 unidentified open reading frames [ORFs], and 28 transfer RNAs [tRNAs]) and Cyanoptyche gloeocystis SAG 4.97 (33.24 kb; 33 protein-coding genes, 6 unidentified ORFs, and 26 tRNAs), which represent two genera distantly related to the "well-known" Cyanophora and Glaucocystis. The mitochondrial gene repertoire of the four glaucophyte species is highly conserved, whereas the gene order shows considerable variation. Phylogenetic analyses of 14 mitochondrial genes from representative taxa from the major eukaryotic supergroups, here including novel sequences from the glaucophytes Cyanophora tetracyanea (strain NIES-764) and Cyanophora biloba (strain UTEX LB 2766), recover a clade uniting the three Archaeplastida lineages; this recovery is dependent on our novel glaucophyte data, demonstrating the importance of greater taxon sampling within the glaucophytes.
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Affiliation(s)
- Christopher J Jackson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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12
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Fučíková K, Lewis PO, González-Halphen D, Lewis LA. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta). Genome Biol Evol 2014; 6:2170-80. [PMID: 25106621 PMCID: PMC4159012 DOI: 10.1093/gbe/evu172] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available—that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mitochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25–53 kb and variation in intron content (0–11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis. In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae.
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Affiliation(s)
- Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut
| | - Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Departamento de Genética Molecular Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut
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13
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Vázquez-Acevedo M, Rubalcava-Gracia D, González-Halphen D. In vitro import and assembly of the nucleus-encoded mitochondrial subunit III of cytochrome c oxidase (Cox3). Mitochondrion 2014; 19 Pt B:314-22. [PMID: 24561572 DOI: 10.1016/j.mito.2014.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/24/2014] [Accepted: 02/12/2014] [Indexed: 11/17/2022]
Abstract
The cox3 gene, encoding subunit III of cytochrome c oxidase (Cox3) is in mitochondrial genomes except in chlorophycean algae, where it is localized in the nucleus. Therefore, algae like Chlamydomonas reinhardtii, Polytomella sp. and Volvox carteri, synthesize the Cox3 polypeptide in the cytosol, import it into mitochondria, and integrate it into the cytochrome c oxidase complex. In this work, we followed the in vitro internalization of the Cox3 precursor by isolated, import-competent mitochondria of Polytomella sp. In this colorless alga, the precursor Cox3 protein is synthesized with a long, cleavable, N-terminal mitochondrial targeting sequence (MTS) of 98 residues. In an import time course, a transient Cox3 intermediate was identified, suggesting that the long MTS is processed more than once. The first processing step is sensitive to the metalo-protease inhibitor 1,10-ortophenantroline, suggesting that it is probably carried out by the matrix-located Mitochondrial Processing Protease. Cox3 is readily imported through an energy-dependent import pathway and integrated into the inner mitochondrial membrane, becoming resistant to carbonate extraction. Furthermore, the imported Cox3 protein was assembled into cytochrome c oxidase, as judged by the presence of a labeled band co-migrating with complex IV in Blue Native Electrophoresis. A model for the biogenesis of Cox3 in chlorophycean algae is proposed. This is the first time that the in vitro mitochondrial import of a cytosol-synthesized Cox3 subunit is described.
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Affiliation(s)
- Miriam Vázquez-Acevedo
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, México 04510, D.F., Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, México 04510, D.F., Mexico
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, México 04510, D.F., Mexico.
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Yang S, Guarnieri MT, Smolinski S, Ghirardi M, Pienkos PT. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:118. [PMID: 23971877 PMCID: PMC3846465 DOI: 10.1186/1754-6834-6-118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism. RESULTS In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites. CONCLUSIONS Herein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.
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Affiliation(s)
| | | | - Sharon Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Maria Ghirardi
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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15
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Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta). Mol Phylogenet Evol 2012; 64:166-76. [PMID: 22724135 DOI: 10.1016/j.ympev.2012.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In most eukaryotes the subunit 2 of cytochrome c oxidase (COX2) is encoded in intact mitochondrial genes. Some green algae, however, exhibit split cox2 genes (cox2a and cox2b) encoding two polypeptides (COX2A and COX2B) that form a heterodimeric COX2 subunit. Here, we analyzed the distribution of intact and split cox2 gene sequences in 39 phylogenetically diverse green algae in phylum Chlorophyta obtained from databases (28 sequences from 22 taxa) and from new cox2 data generated in this work (23 sequences from 18 taxa). Our results support previous observations based on a smaller number of taxa, indicating that algae in classes Prasinophyceae, Ulvophyceae, and Trebouxiophyceae contain orthodox, intact mitochondrial cox2 genes. In contrast, all of the algae in Chlorophyceae that we examined exhibited split cox2 genes, and could be separated into two groups: one that has a mitochondrion-localized cox2a gene and a nucleus-localized cox2b gene ("Scenedesmus-like"), and another that has both cox2a and cox2b genes in the nucleus ("Chlamydomonas-like"). The location of the split cox2a and cox2b genes was inferred using five different criteria: differences in amino acid sequences, codon usage (mitochondrial vs. nuclear), codon preference (third position frequencies), presence of nucleotide sequences encoding mitochondrial targeting sequences and presence of spliceosomal introns. Distinct green algae could be grouped according to the form of cox2 gene they contain: intact or fragmented, mitochondrion- or nucleus-localized, and intron-containing or intron-less. We present a model describing the events that led to mitochondrial cox2 gene fragmentation and the independent and sequential migration of cox2a and cox2b genes to the nucleus in chlorophycean green algae. We also suggest that the distribution of the different forms of the cox2 gene provides important insights into the phylogenetic relationships among major groups of Chlorophyceae.
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In Polytomella sp. mitochondria, biogenesis of the heterodimeric COX2 subunit of cytochrome c oxidase requires two different import pathways. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:819-27. [DOI: 10.1016/j.bbabio.2012.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/22/2022]
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18
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Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD, Lavrov DV. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. MITOCHONDRIAL DNA 2011; 22:130-42. [PMID: 21985407 PMCID: PMC3313829 DOI: 10.3109/19401736.2011.624611] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum--Ctenophora--has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies.
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Affiliation(s)
- Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Joseph F. Ryan
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Pang
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, HI 96813, USA
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Q. Martindale
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, HI 96813, USA
| | - Andreas D. Baxevanis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dennis V. Lavrov
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50010, USA
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19
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Li W, Ruf S, Bock R. Chloramphenicol acetyltransferase as selectable marker for plastid transformation. PLANT MOLECULAR BIOLOGY 2011; 76:443-51. [PMID: 20721602 DOI: 10.1007/s11103-010-9678-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 08/06/2010] [Indexed: 05/07/2023]
Abstract
Chloroplast transformation remains a demanding technique and is still restricted to relatively few plant species. The limited availability of selectable marker genes and the lack of selection markers that would be universally applicable to all plant species represent some of the most serious technical problems involved in extending the species range of plastid transformation. Here we report the development of the chloramphenicol acetyltransferase gene cat as a new selectable marker for plastid transformation. We show that, by selecting for chloramphenicol resistance, tobacco chloroplast transformants are readily obtained. Transplastomic lines quickly reach the homoplasmic state (typically in one additional regeneration round), accumulate the chloramphenicol acetyltransferase enzyme to high levels and transmit their plastid transgenes maternally into the next generation. No spontaneous antibiotic resistance mutants appear upon chloramphenicol selection. Several lines of evidence support the assumption that plant mitochondria are also sensitive to chloramphenicol suggesting that the chloramphenicol acetyltransferase may be a good candidate selectable marker for plant mitochondrial transformation.
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Affiliation(s)
- Weimin Li
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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20
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Hancock L, Goff L, Lane C. Red algae lose key mitochondrial genes in response to becoming parasitic. Genome Biol Evol 2010; 2:897-910. [PMID: 21081313 PMCID: PMC3014286 DOI: 10.1093/gbe/evq075] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Red algal parasites are unusual because the vast majority of them parasitize species with which they share a recent common ancestor. This strategy has earned them the name “adelphoparasites,” from the Greek, adelpho, meaning “kin.” Intracellular adelphoparasites are very rare in nature, yet have independently evolved hundreds of times among the floridiophyte red algae. Much is known about the life history and infection cycle of these parasites but nearly nothing in known about their genomes. We sequenced the mitochondrial genomes of the free-living Gracilariopsis andersonii and its closely related parasite Gracilariophila oryzoides to determine what effect a parasitic lifestyle has on the genomes of red algal parasites. Whereas the parasite genome is similar to the host in many ways, the genes encoding essential proteins ATP8 and SDHC are pseudogenes in the parasite. The mitochondrial genome of parasite from a different class of red algae, Plocamiocolax puvinata, has lost the atp8 gene entirely, indicating that this gene is no longer critical in red algal parasite mitochondria.
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Affiliation(s)
- Lillian Hancock
- Department of Biological Sciences, University of Rhode Island, RI, USA
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21
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Smith DR, Hua J, Lee RW. Evolution of linear mitochondrial DNA in three known lineages of Polytomella. Curr Genet 2010; 56:427-38. [PMID: 20574726 DOI: 10.1007/s00294-010-0311-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/02/2010] [Accepted: 06/04/2010] [Indexed: 11/30/2022]
Abstract
Although DNA sequences of linear mitochondrial genomes are available for a wide variety of species, sequence and conformational data from the extreme ends of these molecules (i.e., the telomeres) are limited. Data on the telomeres is important because it can provide insights into how linear genomes overcome the end-replication problem. This study explores the evolution of linear mitochondrial DNAs (mtDNAs) in the green-algal genus Polytomella (Chlorophyceae, Chlorophyta), the members of which are non-photosynthetic. Earlier works analyzed the linear and linear-fragmented mitochondrial genomes of Polytomella capuana and Polytomella parva. Here we present the mtDNA sequence for Polytomella strain SAG 63-10 [also known as Polytomella piriformis (Pringsheim 1963)], which is the only known representative of a mostly unexplored Polytomella lineage. We show that the P. piriformis mtDNA is made up of two linear fragments of 13 and 3 kb. The telomeric sequences of the large and small fragments are terminally inverted, and appear to end in vitro with either closed (hairpin-loop) or open (nicked-loop) structures as also shown here for P. parva and shown earlier for P. capuana. The structure of the P. piriformis mtDNA is more similar to that of P. parva, which is also fragmented, than to that of P. capuana, which is contained in a single chromosome. Phylogenetic analyses reveal high substitution rates in the mtDNA of all three Polytomella species relative to other chlamydomonadalean algae. These elevated rates could be the result of a greater number of vegetative cell divisions and/or small population sizes in Polytomella species as compared with other chlamydomonadalean algae.
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Affiliation(s)
- David Roy Smith
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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22
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Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC PLANT BIOLOGY 2010; 10:83. [PMID: 20459666 PMCID: PMC3017802 DOI: 10.1186/1471-2229-10-83] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 05/07/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of beta-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. RESULTS The D. salina organelle genomes are large, circular-mapping molecules with approximately 60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: approximately 1.5 and approximately 0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. CONCLUSIONS These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming D. salina nuclear genome sequence, placing D. salina in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.
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Affiliation(s)
- David Roy Smith
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
| | - Robert W Lee
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS200, 311B Fleischmann Agriculture, University of Nevada, Reno, NV 89557-0014, USA
| | - Jon K Magnuson
- Chemical and Biological Process Development, Energy and Environment Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Duc Tran
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Ave, 200 NE, Brooklyn, NY 11210, USA
| | - Jürgen EW Polle
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Ave, 200 NE, Brooklyn, NY 11210, USA
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Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ. Organization and expression of organellar genomes. Philos Trans R Soc Lond B Biol Sci 2010; 365:785-97. [PMID: 20124345 DOI: 10.1098/rstb.2009.0250] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana. In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a 'viral-type' RNA polymerase, although a 'bacterial-type' enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.
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Affiliation(s)
- Adrian C Barbrook
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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24
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A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii. J Mol Evol 2010; 70:203-14. [PMID: 20135105 DOI: 10.1007/s00239-010-9322-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
Reduction in size of flagellated chlorophytes occurred multiple times during evolution, providing the opportunity to study the consequences of cell reduction on genome architecture. Recent investigations on the chloroplast genomes of the tiny prasinophyceans Ostreococcus tauri (Mamiellales), Micromonas sp. RCC299 (Mamiellales), and Pycnococcus provasolii (Pseudocourfieldiales) highlighted their extreme compaction and reduced gene repertoires. Genome compaction is also exemplified by the Ostreococcus and Micromonas mitochondrial DNAs (mtDNAs) although they have retained almost all of the about 65 genes presumably present in the mitochondria of ancestral prasinophyceans. In this study, the mitochondrial genome of Pycnococcus was sequenced and compared to those of previously examined chlorophytes. Our results document the first case where cellular reduction of a free-living alga was accompanied by marked reduction in gene content of both the mitochondrial and chloroplast genomes. At 24,321 bp, the intronless Pycnococcus mitochondrial genome falls within the lower size range displayed by green algal mtDNAs. The 36 conserved genes, specifying two rRNAs with conventional structures, 16 tRNAs and 18 proteins, are all encoded on the same DNA strand and represent 88% of the genome. Besides a pronounced codon bias, the protein-coding genes feature a variant genetic code characterized by the use of TGA (normally a stop codon) to code for tryptophan, and the unprecedented use of TTA and TTG (normally leucine codons) as stop codons. We conclude that substantial reduction of the mitochondrial genome occurred in at least three independent chlorophyte lineages and that this process entailed a number of convergent changes in these lineages.
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Le P, Fisher PR, Barth C. Transcription of the Dictyostelium discoideum mitochondrial genome occurs from a single initiation site. RNA (NEW YORK, N.Y.) 2009; 15:2321-2330. [PMID: 19861424 PMCID: PMC2779680 DOI: 10.1261/rna.1710309] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 09/18/2009] [Indexed: 05/28/2023]
Abstract
Transcription of the mitochondrial genome in Dictyostelium discoideum gives rise to eight major polycistronic RNA species that can be detected by Northern hybridization. In order to determine whether these transcripts could possibly derive from processing of even larger transcripts, reverse transcriptase polymerase chain reactions (RT-PCRs) were performed in an attempt to amplify the intervening regions between the eight major transcripts. All but one intervening region were successfully reverse transcribed and amplified, indicating that even larger transcripts existed and that the eight major transcripts detected previously may be the products of transcript processing. Southern hybridization analyses of DNA fragments representing the sequences between the eight major transcripts with in vitro capped mitochondrial RNA identified the 5' end of only one of the eight major transcripts as a genuine transcription start site. The ability to initiate transcription from DNA sequences upstream of the identified transcription initiation site was demonstrated in bacterial cells expressing the Dictyostelium mitochondrial RNA polymerase. We conclude that transcription of the Dictyostelium mitochondrial genome is initiated at a single site, generating a large polycistronic transcript that is very efficiently, probably cotranscriptionally processed into mature RNA species. This is the first report on a protist mitochondrial DNA that is, although much larger in size than its metazoan counterparts, transcribed from a single transcription initiation site.
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Affiliation(s)
- Phuong Le
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia
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26
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The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol 2009; 68:665-78. [PMID: 19475442 DOI: 10.1007/s00239-009-9240-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 04/03/2009] [Accepted: 04/15/2009] [Indexed: 10/20/2022]
Abstract
Land plants possess some of the most unusual mitochondrial genomes among eukaryotes. However, in early land plants these genomes resemble those of green and red algae or early eukaryotes. The question of when during land plant evolution the dramatic change in mtDNAs occurred remains unanswered. Here we report the first completely sequenced mitochondrial genome of the hornwort, Megaceros aenigmaticus, a member of the sister group of vascular plants. It is a circular molecule of 184,908 base pairs, with 32 protein genes, 3 rRNA genes, 17 tRNA genes, and 30 group II introns. The genome contains many genes arranged in the same order as in those of a liverwort, a moss, several green and red algae, and Reclinomonas americana, an early-branching eukaryote with the most ancestral form of mtDNA. In particular, the gene order between mtDNAs of the hornwort and Physcomitrella patens (moss) differs by only 8 inversions and translocations. However, the hornwort mtDNA possesses 4 derived features relative to green alga mtDNAs--increased genome size, RNA editing, intron gains, and gene losses--which were all likely acquired during the origin and early evolution of land plants. Overall, this genome and those of other 2 bryophytes show that mitochondrial genomes in early land plants, unlike their seed plant counterparts, exhibit a mixed mode of conservative yet dynamic evolution.
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27
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Abstract
In Chlamydomonas reinhardtii several nucleus-encoded proteins that participate in the mitochondrial oxidative phosphorylation are targeted to the organelle by unusually long mitochondrial targeting sequences. Here, we explored the components of the mitochondrial import machinery of the green alga. We mined the algal genome, searching for yeast and plant homologs, and reconstructed the mitochondrial import machinery. All the main translocation components were identified in Chlamydomonas as well as in Arabidopsis thaliana and in the recently sequenced moss Physcomitrella patens. Some of these components appear to be duplicated, as is the case of Tim22. In contrast, several yeast components that have relatively large hydrophilic regions exposed to the cytosol or to the intermembrane space seem to be absent in land plants and green algae. If present at all, these components of plants and algae may differ significantly from their yeast counterparts. We propose that long mitochondrial targeting sequences in some Chlamydomonas mitochondrial protein precursors are involved in preventing the aggregation of the hydrophobic proteins they carry.
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Abstract
The human cell is a symbiosis of two life forms, the nucleus-cytosol and the mitochondrion. The nucleus-cytosol emphasizes structure and its genes are Mendelian, whereas the mitochondrion specializes in energy and its mitochondrial DNA (mtDNA) genes are maternal. Mitochondria oxidize calories via oxidative phosphorylation (OXPHOS) to generate a mitochondrial inner membrane proton gradient (DeltaP). DeltaP then acts as a source of potential energy to produce ATP, generate heat, regulate reactive oxygen species (ROS), and control apoptosis, etc. Interspecific comparisons of mtDNAs have revealed that the mtDNA retains a core set of electron and proton carrier genes for the proton-translocating OXPHOS complexes I, III, IV, and V. Human mtDNA analysis has revealed these genes frequently contain region-specific adaptive polymorphisms. Therefore, the mtDNA with its energy controlling genes may have been retained to permit rapid adaptation to new environments.
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Affiliation(s)
- Douglas C Wallace
- Center for Molecular and Mitochondrial Medicine and Genetics, Department of Biological Chemistry, University of California, Irvine, California 92697-3940, USA.
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Gachon CMM, Day JG, Campbell CN, Pröschold T, Saxon RJ, Küpper FC. The Culture Collection of Algae and Protozoa (CCAP): a biological resource for protistan genomics. Gene 2007; 406:51-7. [PMID: 17614217 DOI: 10.1016/j.gene.2007.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 03/16/2007] [Accepted: 05/24/2007] [Indexed: 11/25/2022]
Abstract
CCAP, the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland (http://www.ccap.ac.uk). The Collection comprises more than 2700 strains in the public domain, of which 1050 are marine algae, 1300 freshwater algae, and 350 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. It also has a support and advisory function on all aspects of protistan science. In addition, it is involved in the training of students and researchers in algal identification and culture techniques. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. At present, the Collection holds several hundred strains of genomic model taxa including: Acanthamoeba, Cafeteria, Cercomonas, Chlamydomonas, Chlorella, Cyanophora, Dictyostelium, Dunaliella, Ectocarpus, Emiliania, Euglena, Micromonas, Naegleria, Nephroselmis, Paramecium, Pavlova, Phaeodactylum, Porphyra, Pseudendoclonium, Pylaiella, Rhodomonas, Scenedesmus, Staurastrum, Tetrahymena, Thalassiosira, Volvox and Zygnema. These strains provide a defined representation of natural variation within model organisms, an increasingly useful resource for post-genomics approaches. Our aim over the next 2-5 years is to add value to the Collection by increasing the number of genome model species, and by offering an integrated, up-to-date, easy-to-use resource that would provide curated information on our strain holdings. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their associated bioinformatics data.
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Affiliation(s)
- Claire M M Gachon
- Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Dunbeg by Oban, Argyll, PA37 1QA, Scotland, UK.
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Turmel M, Otis C, Lemieux C. An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus. BMC Genomics 2007; 8:137. [PMID: 17537252 PMCID: PMC1894977 DOI: 10.1186/1471-2164-8-137] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/30/2007] [Indexed: 11/29/2022] Open
Abstract
Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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Affiliation(s)
- Monique Turmel
- Département de biochimie et de microbiologie, Université Laval, Québec, QC, G1K 7P4, Canada
| | - Christian Otis
- Département de biochimie et de microbiologie, Université Laval, Québec, QC, G1K 7P4, Canada
| | - Claude Lemieux
- Département de biochimie et de microbiologie, Université Laval, Québec, QC, G1K 7P4, Canada
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Sengupta S, Yang X, Higgs PG. The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol 2007; 64:662-88. [PMID: 17541678 PMCID: PMC1894752 DOI: 10.1007/s00239-006-0284-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Accepted: 03/07/2007] [Indexed: 11/26/2022]
Abstract
Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The “gain” represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The “loss” represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.
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Affiliation(s)
- Supratim Sengupta
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1 Canada
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 Canada
| | - Xiaoguang Yang
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1 Canada
| | - Paul G. Higgs
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1 Canada
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Massey SE, Garey JR. A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs. J Mol Evol 2007; 64:399-410. [PMID: 17390094 DOI: 10.1007/s00239-005-0260-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.
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Affiliation(s)
- Steven E Massey
- Department of Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
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Abstract
The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.
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Affiliation(s)
- Cristina E Popescu
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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Pombert JF, Beauchamp P, Otis C, Lemieux C, Turmel M. The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae. Curr Genet 2006; 50:137-47. [PMID: 16721603 DOI: 10.1007/s00294-006-0076-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 04/11/2006] [Accepted: 04/13/2006] [Indexed: 10/24/2022]
Abstract
The mitochondrial genome displays a highly plastic architecture in the green algal division comprising the classes Prasinophyceae, Trebouxiophyceae, Ulvophyceae, and Chlorophyceae (Chlorophyta). The compact mitochondrial DNAs (mtDNAs) of Nephroselmis (Prasinophyceae) and Prototheca (Trebouxiophyceae) encode about 60 genes and have been ascribed an 'ancestral' pattern of evolution, whereas those of chlorophycean green algae are much more reduced in gene content and size. Although the mtDNA of the early-diverging ulvophyte Pseudendoclonium contains 57 conserved genes, it differs from 'ancestral' chlorophyte mtDNAs by its unusually large size (96 kb) and long intergenic spacers. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we have determined the complete mtDNA sequence of Oltmannsiellopsis viridis, an ulvophyte belonging to a distinct, early-diverging lineage. This 56,761 bp genome harbours 54 conserved genes, numerous repeated sequences, and only three introns. From our comparative analyses with Pseudendoclonium mtDNA, we infer that the mitochondrial genome of the last common ancestor of the two ulvophytes closely resembled that of the trebouxiophyte Prototheca in terms of gene content and gene density. Our results also provide strong evidence for the intracellular, interorganellar transfer of a group I intron and for two distinct events of intercellular, horizontal DNA transfer.
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Affiliation(s)
- Jean-François Pombert
- Département de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval, Québec, Canada
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Dombrovska O, Qiu YL. Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Mol Phylogenet Evol 2005; 32:246-63. [PMID: 15186811 DOI: 10.1016/j.ympev.2003.12.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Revised: 12/17/2003] [Indexed: 10/26/2022]
Abstract
Forty-six species of diverse land plants were investigated by sequencing for their intron content in the mitochondrial gene nad1. A total of seven introns, all belonging to group II, were found, and two were newly discovered in this study. All 13 liverworts examined contain no intron, the same condition as in green algae. Mosses and hornworts, however, share one intron by themselves and another one with vascular plants. These intron distribution patterns are consistent with the hypothesis that liverworts represent the basal-most land plants and that the two introns were gained in the common ancestor of mosses-hornworts-vascular plants after liverworts had diverged. Hornworts also possess a unique intron of their own. A fourth intron was found only in Equisetum L., Marattiaceae, Ophioglossum L., Osmunda L., Asplenium L., and Adiantum L., and was likely acquired in their common ancestor, which supports the monophyly of moniliformopses. Three introns that were previously characterized in angiosperms and a few pteridophytes are now all extended to lycopods, and were likely gained in the common ancestor of vascular plants. Phylogenetic analyses of the intron sequences recovered topologies mirroring those of the plants, suggesting that the introns have all been vertically inherited. All seven nad1 group II introns show broad phylogenetic distribution patterns, with the narrowest being in moniliformopses and hornworts, lineages that date back to at least the Devonian (345 million years ago) and Silurian (435 million years ago), respectively. Hence, these introns must have invaded the genes via ancient transpositional events during the early stage of land plant evolution. Potentially heavy RNA editing was observed in nad1 of Haplomitrium Dedecek, Takakia Hatt. & Inoue, hornworts, Isoetes L., Ophioglossum, and Asplenium. A new nomenclature is proposed for group II introns.
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Affiliation(s)
- Olena Dombrovska
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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Abstract
Over the past several decades, our knowledge of the origin and evolution of mitochondria has been greatly advanced by determination of complete mitochondrial genome sequences. Among the most informative mitochondrial genomes have been those of protists (primarily unicellular eukaryotes), some of which harbor the most gene-rich and most eubacteria-like mitochondrial DNAs (mtDNAs) known. Comparison of mtDNA sequence data has provided insights into the radically diverse trends in mitochondrial genome evolution exhibited by different phylogenetically coherent groupings of eukaryotes, and has allowed us to pinpoint specific protist relatives of the multicellular eukaryotic lineages (animals, plants, and fungi). This comparative genomics approach has also revealed unique and fascinating aspects of mitochondrial gene expression, highlighting the mitochondrion as an evolutionary playground par excellence.
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Affiliation(s)
- Michael W Gray
- Robert Cedergren Center, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Canada.
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Lewis LA, McCourt RM. Green algae and the origin of land plants. AMERICAN JOURNAL OF BOTANY 2004; 91:1535-56. [PMID: 21652308 DOI: 10.3732/ajb.91.10.1535] [Citation(s) in RCA: 384] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastructural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classification at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly flagellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least five monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. The reorganization of taxa stimulated by molecular analyses is expected to continue as more data accumulate and new taxa and habitats are sampled.
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Affiliation(s)
- Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 USA
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González-Halphen D, Funes S, Pérez-Martínez X, Reyes-Prieto A, Claros MG, Davidson E, King MP. Genetic Correction of Mitochondrial Diseases: Using the Natural Migration of Mitochondrial Genes to the Nucleus in Chlorophyte Algae as a Model System. Ann N Y Acad Sci 2004; 1019:232-9. [PMID: 15247021 DOI: 10.1196/annals.1297.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mitochondrial diseases display great diversity in clinical symptoms and biochemical characteristics. Although mtDNA mutations have been identified in many patients, there are currently no effective treatments. A number of human diseases result from mutations in mtDNA-encoded proteins, a group of proteins that are hydrophobic and have multiple membrane-spanning regions. One method that has great potential for overcoming the pathogenic consequences of these mutations is to place a wild-type copy of the affected gene in the nucleus, and target the expressed protein to the mitochondrion to function in place of the defective protein. Several respiratory chain subunit genes, which are typically mtDNA encoded, are nucleus encoded in the chlorophyte algae Chlamydomonas reinhardtii and Polytomella sp. Analysis of these genes has revealed adaptations that facilitated their expression from the nucleus. The nucleus-encoded proteins exhibited diminished physical constraints for import as compared to their mtDNA-encoded homologues. The hydrophobicity of the nucleus-encoded proteins is diminished in those regions that are not involved in subunit-subunit interactions or that contain amino acids critical for enzymatic reactions of the proteins. In addition, these proteins have unusually large mitochondrial targeting sequences. Information derived from these studies should be applicable toward the development of genetic therapies for human diseases resulting from mutations in mtDNA-encoded polypeptides.
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Affiliation(s)
- Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico D.F., Mexico
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Fan J, Schnare MN, Lee RW. Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva. Nucleic Acids Res 2003; 31:769-78. [PMID: 12527787 PMCID: PMC140509 DOI: 10.1093/nar/gkg144] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have identified previously in mitochondrial DNA of the colorless, chlorophycean, green algal taxon, Polytomella parva, potential coding regions for four small subunit (SSU) and eight large subunit (LSU) rRNA fragments. In this study with P.parva, we isolated RNA from a mitochondrial-enriched preparation, characterized the 12 mitochondrial rRNA transcripts by either northern blot analysis or chemical sequencing and performed secondary structure modeling of the SSU and LSU rRNA sequences. The results show the following features about the mitochondrial SSU and LSU rRNAs of P.parva: (i) they are considerably shorter than their homologs from other green algae, although the main domains typical of conventional rRNAs are conserved; (ii) the rRNA fragmentation pattern is most similar to that of Chlamydomonas reinhardtii among green algae that have been characterized; (iii) three nucleotides are missing from the normally highly conserved GTPase center of the LSU rRNA; and (iv) post-transcriptional modification of the 3'-terminal region of the SSU rRNA is unusual in that it has the 'eubacterial' 3-methyluridine (corresponding to m(3)U at Escherichia coli 16S rRNA position 1498) but lacks the more highly conserved modifications at two adjacent A residues (corresponding to N(6),N(6)-dimethyladenosine at E.coli 16S rRNA positions 1518 and 1519). This is the first report of the characterization by direct sequencing of fragmented mitochondrial rRNAs from a green alga.
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Affiliation(s)
- Jinshui Fan
- Biology Department, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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Ojaimi J, Pan J, Santra S, Snell WJ, Schon EA. An algal nucleus-encoded subunit of mitochondrial ATP synthase rescues a defect in the analogous human mitochondrial-encoded subunit. Mol Biol Cell 2002; 13:3836-44. [PMID: 12429828 PMCID: PMC133596 DOI: 10.1091/mbc.e02-05-0306] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Unlike most organisms, the mitochondrial DNA (mtDNA) of Chlamydomonas reinhardtii, a green alga, does not encode subunit 6 of F(0)F(1)-ATP synthase. We hypothesized that C. reinhardtii ATPase 6 is nucleus encoded and identified cDNAs and a single-copy nuclear gene specifying this subunit (CrATP6, with eight exons, four of which encode a mitochondrial targeting signal). Although the algal and human ATP6 genes are in different subcellular compartments and the encoded polypeptides are highly diverged, their secondary structures are remarkably similar. When CrATP6 was expressed in human cells, a significant amount of the precursor polypeptide was targeted to mitochondria, the mitochondrial targeting signal was cleaved within the organelle, and the mature polypeptide was assembled into human ATP synthase. In spite of the evolutionary distance between algae and mammals, C. reinhardtii ATPase 6 functioned in human cells, because deficiencies in both cell viability and ATP synthesis in transmitochondrial cell lines harboring a pathogenic mutation in the human mtDNA-encoded ATP6 gene were overcome by expression of CrATP6. The ability to express a nucleus-encoded version of a mammalian mtDNA-encoded protein may provide a way to import other highly hydrophobic proteins into mitochondria and could serve as the basis for a gene therapy approach to treat human mitochondrial diseases.
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Affiliation(s)
- Joseline Ojaimi
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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Fan J, Lee RW. Mitochondrial genome of the colorless green alga Polytomella parva: two linear DNA molecules with homologous inverted repeat Termini. Mol Biol Evol 2002; 19:999-1007. [PMID: 12082120 DOI: 10.1093/oxfordjournals.molbev.a004180] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. agilis), a colorless, naturally wall-less relative of C. reinhardtii, we have detected two linear mitochondrial DNA (mtDNA) components with sizes of 13.5 and 3.5 kb. Sequences spanning 97% and 86% of the 13.5- and 3.5-kb mtDNAs, respectively, reveal that these molecules contain long, at least 1.3 kb, homologous inverted repeat sequences at their termini. The 3.5-kb mtDNA has only one coding region (nad6), the functionality of which is supported by both the relative rate at which it has accumulated nonsynonymous nucleotide substitutions and its absence from the 13.5-kb mtDNA which encodes nine genes (i.e., large and small subunit rRNA [LSU and SSU rRNA] genes, one tRNA gene, and six protein-coding genes). On the basis of DNA sequence data, we propose that a variant start codon, GTG, is utilized by the P. parva 13.5-kb mtDNA-encoded gene, nad5. Using the relative rate test with Chlamydomonas moewusii (=C. eugametos) as the outgroup, we conclude that the nonsynonymous nucleotide substitution rate in the mitochondrial protein-coding genes of P. parva is on an average about 3.3 times that of the C. reinhardtii counterparts.
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Affiliation(s)
- Jinshui Fan
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Funes S, Davidson E, Claros MG, van Lis R, Pérez-Martínez X, Vázquez-Acevedo M, King MP, González-Halphen D. The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii. J Biol Chem 2002; 277:6051-8. [PMID: 11744727 DOI: 10.1074/jbc.m109993200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The atp6 gene, encoding the ATP6 subunit of F(1)F(0)-ATP synthase, has thus far been found only as an mtDNA-encoded gene. However, atp6 is absent from mtDNAs of some species, including that of Chlamydomonas reinhardtii. Analysis of C. reinhardtii expressed sequence tags revealed three overlapping sequences that encoded a protein with similarity to ATP6 proteins. PCR and 5'- and 3'-RACE were used to obtain the complete cDNA and genomic sequences of C. reinhardtii atp6. The atp6 gene exhibited characteristics of a nucleus-encoded gene: Southern hybridization signals consistent with nuclear localization, the presence of introns, and a codon usage and a polyadenylation signal typical of nuclear genes. The corresponding ATP6 protein was confirmed as a subunit of the mitochondrial F(1)F(0)-ATP synthase from C. reinhardtii by N-terminal sequencing. The predicted ATP6 polypeptide has a 107-amino acid cleavable mitochondrial targeting sequence. The mean hydrophobicity of the protein is decreased in those transmembrane regions that are predicted not to participate directly in proton translocation or in intersubunit contacts with the multimeric ring of c subunits. This is the first example of a mitochondrial protein with more than two transmembrane stretches, directly involved in proton translocation, that is nucleus-encoded.
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Affiliation(s)
- Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510 México D.F., Mexico
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Chevalier BS, Stoddard BL. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 2001; 29:3757-74. [PMID: 11557808 PMCID: PMC55915 DOI: 10.1093/nar/29.18.3757] [Citation(s) in RCA: 334] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Homing endonucleases confer mobility to their host intervening sequence, either an intron or intein, by catalyzing a highly specific double-strand break in a cognate allele lacking the intervening sequence. These proteins are characterized by their ability to bind long DNA target sites (14-40 bp) and their tolerance of minor sequence changes in these sites. A wealth of biochemical and structural data has been generated for these enzymes over the past few years. Herein we review our current understanding of homing endonucleases, including their diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them to bind novel DNA substrates.
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Affiliation(s)
- B S Chevalier
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue North A3-023, Seattle, WA 98109, USA
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Pérez-Martínez X, Antaramian A, Vazquez-Acevedo M, Funes S, Tolkunova E, d'Alayer J, Claros MG, Davidson E, King MP, González-Halphen D. Subunit II of cytochrome c oxidase in Chlamydomonad algae is a heterodimer encoded by two independent nuclear genes. J Biol Chem 2001; 276:11302-9. [PMID: 11094061 DOI: 10.1074/jbc.m010244200] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial genomes of Chlamydomonad algae lack the cox2 gene that encodes the essential subunit COX II of cytochrome c oxidase. COX II is normally a single polypeptide encoded by a single mitochondrial gene. In this work we cloned two nuclear genes encoding COX II from both Chlamydomonas reinhardtii and Polytomella sp. The cox2a gene encodes a protein, COX IIA, corresponding to the N-terminal portion of subunit II of cytochrome c oxidase, and the cox2b gene encodes COX IIB, corresponding to the C-terminal region. The cox2a and cox2b genes are located in the nucleus and are independently transcribed into mRNAs that are translated into separate polypeptides. These two proteins assemble with other cytochrome c oxidase subunits in the inner mitochondrial membrane to form the mature multi-subunit complex. We propose that during the evolution of the Chlorophyte algae, the cox2 gene was divided into two mitochondrial genes that were subsequently transferred to the nucleus. This event was evolutionarily distinct from the transfer of an intact cox2 gene to the nucleus in some members the Leguminosae plant family.
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Affiliation(s)
- X Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, México 04510, D.F. Mexico
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45
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Imaizumi M, Hamada J. Inhibition of cytoplasmic DNA synthesis may be an initial signal for the induction of sexual reproduction in Closterium ehrenbergii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 160:57-66. [PMID: 11164577 DOI: 10.1016/s0168-9452(00)00361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We investigated the effect that inhibitors of cytoplasmic DNA (cytDNA) and/or nuclear DNA (nDNA) synthesis have on the frequency of zygote formation in Closterium ehrenbergii and whether these inhibitors correlate with arrest of pyrenoid production and enlargement of pyrenoidal size accompanying pregametogenesis in the alga. CytDNA inhibitors, ethidium bromide (EB), acridine orange and novobiocin (NB), enhanced zygote formation in the presence of nitrate, and these chemicals correlated with both a decrease in pyrenoid production and an increase in pyrenoidal size. By contrast, a nDNA inhibitor, aphidicolin (APC), enhanced zygote formation in the presence and absence of nitrate, and correlated with only an increase in pyrenoidal size. Meanwhile, inhibitors of both nDNA and cytDNA synthesis, mitomycin C (MC), hydroxyurea (HU) and arabinosyl cytosine (Ara-C), enhanced zygote formation in the presence and/or absence of nitrate. In addition, MC and HU correlated with only an increase in pyrenoidal size and Ara-C only a decrease in pyrenoid production. This result seemed to indicate that MC and HU functioned as selective inhibitors of nDNA synthesis, and Ara-C as a selective inhibitor of cytDNA synthesis. It is suggested that differentiation into pregametes correlates with the inhibition of both nDNA and cytDNA synthesis, levels of which are probably low, the inhibition of cytDNA synthesis being the initial signal for pregametogenesis.
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Affiliation(s)
- M Imaizumi
- Department of Biology, Shiga University of Medical Science, 520-2192, Ohtsu, Japan
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Pérez-Martínez X, Vazquez-Acevedo M, Tolkunova E, Funes S, Claros MG, Davidson E, King MP, González-Halphen D. Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae. J Biol Chem 2000; 275:30144-52. [PMID: 10899162 DOI: 10.1074/jbc.m003940200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The algae of the family Chlamydomonadaceae lack the gene cox3 that encodes subunit III of cytochrome c oxidase in their mitochondrial genomes. This observation has raised the question of whether this subunit is present in cytochrome c oxidase or whether the corresponding gene is located in the nucleus. Cytochrome c oxidase was isolated from the colorless chlamydomonad Polytomella spp., and the existence of subunit III was established by immunoblotting analysis with an antibody directed against Saccharomyces cerevisiae subunit III. Based partly upon the N-terminal sequence of this subunit, oligodeoxynucleotides were designed and used for polymerase chain reaction amplification, and the resulting product was used to screen a cDNA library of Chlamydomonas reinhardtii. The complete sequences of the cox3 cDNAs from Polytomella spp. and C. reinhardtii are reported. Evidence is provided that the genes for cox3 are encoded by nuclear DNA, and the predicted polypeptides exhibit diminished physical constraints for import as compared with mitochondrial-DNA encoded homologs. This indicates that transfer of this gene to the nucleus occurred before Polytomella diverged from the photosynthetic Chlamydomonas lineage and that this transfer may have occurred in all chlamydomonad algae.
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Affiliation(s)
- X Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, 04510
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Nedelcu AM, Lee RW, Lemieux C, Gray MW, Burger G. The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res 2000; 10:819-31. [PMID: 10854413 PMCID: PMC310893 DOI: 10.1101/gr.10.6.819] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/1999] [Accepted: 03/29/2000] [Indexed: 11/24/2022]
Abstract
Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced-derived, Chlamydomonas-like type and an ancestral, Prototheca-like type. To determine if this unexpected dichotomy is real or is due to insufficient or biased sampling and to define trends in the evolution of the green algal mitochondrial genome, we sequenced and analyzed the mitochondrial DNA (mtDNA) of Scenedesmus obliquus. This genome is 42,919 bp in size and encodes 42 conserved genes (i.e., large and small subunit rRNA genes, 27 tRNA and 13 respiratory protein-coding genes), four additional free-standing open reading frames with no known homologs, and an intronic reading frame with endonuclease/maturase similarity. No 5S rRNA or ribosomal protein-coding genes have been identified in Scenedesmus mtDNA. The standard protein-coding genes feature a deviant genetic code characterized by the use of UAG (normally a stop codon) to specify leucine, and the unprecedented use of UCA (normally a serine codon) as a signal for termination of translation. The mitochondrial genome of Scenedesmus combines features of both green algal mitochondrial genome types: the presence of a more complex set of protein-coding and tRNA genes is shared with the ancestral type, whereas the lack of 5S rRNA and ribosomal protein-coding genes as well as the presence of fragmented and scrambled rRNA genes are shared with the reduced-derived type of mitochondrial genome organization. Furthermore, the gene content and the fragmentation pattern of the rRNA genes suggest that this genome represents an intermediate stage in the evolutionary process of mitochondrial genome streamlining in green algae.
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Affiliation(s)
- A M Nedelcu
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada.
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Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-52. [PMID: 10742046 DOI: 10.1093/oxfordjournals.molbev.a026334] [Citation(s) in RCA: 6837] [Impact Index Per Article: 284.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
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Affiliation(s)
- J Castresana
- European Molecular Biology Laboratory, Heidelberg, Germany.
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Saguez C, Lecellier G, Koll F. Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility. Nucleic Acids Res 2000; 28:1299-306. [PMID: 10684923 PMCID: PMC111034 DOI: 10.1093/nar/28.6.1299] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements which, during evolution, have colonized pre-existing introns converting them into invasive elements. This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities which recognize and cut the insertion site of the optional sequence. This constitutes the first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss the role that such a mobile sequence could have played during evolution.
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Affiliation(s)
- C Saguez
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif Sur Yvette Cedex, France
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