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Li S, Wang Z, Jing Y, Duan W, Yang X. Graph-based mitochondrial genomes of three foundation species in the Saccharum genus. PLANT CELL REPORTS 2024; 43:191. [PMID: 38977492 DOI: 10.1007/s00299-024-03277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.
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Affiliation(s)
- Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Zhen Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yanfen Jing
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, 650221, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences /Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China.
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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Guo H, Liu Q, Chen Y, Niu H, Zhao Q, Song H, Pang R, Huang X, Zhang J, Zhao Z, Liu D, Zhu J. Comprehensive assembly and comparative examination of the full mitochondrial genome in Castanea mollissima Blume. Genomics 2023; 115:110740. [PMID: 37923179 DOI: 10.1016/j.ygeno.2023.110740] [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: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The Chinese chestnut, Castanea mollissima Blume, a nut-bearing tree native to China and North Korea, belongs to the Fagaceae family. As an important genetic resource, C. mollissima is vital in enhancing edible chestnut varieties and offers significant insights into the origin and evolution of chestnut species. While the chloroplast genome of C. mollissima has been sequenced, its mitochondrial genome (mitogenome) remains largely uncharted. In this study, we have characterized the C. mollissima mitogenome, assembling it utilizing reads from both BGI and Nanopore sequencing platforms, and conducted a comparative analysis with the mitochondrial genomes of closely related species. The mitogenome of C. mollissima manifests a polycyclic structure consisting of two circular molecules measuring 363,232 bp and 24,806 bp, respectively. This genome encompasses 35 unique protein-coding genes, 19 tRNA genes, and three rRNA genes. A total of 139 SSRs were identified throughout the entire C. mollissima mitogenome. Furthermore, the combined length of homologous fragments between the chloroplast and mitochondrial genomes was 5766 bp, constituting 1.49% of the mitogenome. We also predicted 484 RNA editing sites in C. mollissima, demonstrating C-to-U RNA editing. Phylogenetic analysis of related species' mitogenomes showed that C. mollissima was closely related to Lithocarpus litseifolius (Hance) Chun and Quercus acutissima Carruth. Interestingly, the mitogenome sequences of C. mollissima, L. litseifolius, Q. acutissima, Fagus sylvatica L., and Juglans mandshurica Maxim did not show conservation in their alignments, indicating frequent genome reorganization. This report marks the inaugural study of the C. mollissima mitogenome, serving as a benchmark genome for economically significant plants within the Castanea genus. Moreover, it supplies invaluable information that can guide future molecular breeding efforts and contribute to the broader understanding of chestnut genomics.
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Affiliation(s)
- Haili Guo
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Qiong Liu
- Shandong Refining and Chemical Energy Group Co., Ltd., Jinan 250199, China
| | - Ying Chen
- Shandong Provincial Forestry Protection and Development Service Center, Jinan 250109, China
| | - Hongyun Niu
- Shandong Provincial Center of Aviation Emergency and Rescue, Jinan 250014, China
| | | | - Hui Song
- Shandong Institute of Land Spatial Data and Remote Sensing Technology, Jinan 250002, China
| | - Ruidong Pang
- Shandong Provincial Archives of Natural Resources, Jinan 250013, China
| | - Xiaolu Huang
- Guangxi Forestry Research Institute, Nanning 530002, China
| | - Jingzheng Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Zhiheng Zhao
- Guangxi Forestry Research Institute, Nanning 530002, China; Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China.
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China.
| | - Jingle Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China.
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Lee HJ, Lee Y, Lee SC, Kim CK, Kang JN, Kwon SJ, Kang SH. Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica. FRONTIERS IN PLANT SCIENCE 2023; 14:1183406. [PMID: 37469771 PMCID: PMC10352487 DOI: 10.3389/fpls.2023.1183406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023]
Abstract
The family Schisandraceae is a basal angiosperm plant group distributed in East and Southeast Asia and includes many medicinal plant species such as Schisandra chinensis. In this study, mitochondrial genomes (mitogenomes) of two species, Schisandra repanda and Kadsura japonica, in the family were characterized through de novo assembly using sequencing data obtained with Oxford Nanopore and Illumina sequencing technologies. The mitogenomes of S. repanda were assembled into one circular contig (571,107 bp) and four linear contigs (10,898-607,430 bp), with a total of 60 genes: 38 protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The mitogenomes of K. japonica were assembled into five circular contigs (211,474-973,503 bp) and three linear contigs (8,010-72,712 bp), with a total of 66 genes: 44 PCGs, 19 tRNA genes, and 3 rRNA genes. The mitogenomes of the two species had complex structural features with high repeat numbers and chloroplast-derived sequences, as observed in other plant mitogenomes. Phylogenetic analysis based on PCGs revealed the taxonomical relationships of S. repanda and K. japonica with other species from Schisandraceae. Finally, molecular markers were developed to distinguish between S. repanda, K. japonica, and S. chinensis on the basis of InDel polymorphisms present in the mitogenomes. The mitogenomes of S. repanda and K. japonica will be valuable resources for molecular and taxonomic studies of plant species that belong to the family Schisandraceae.
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Affiliation(s)
- Hyo Ju Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
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Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops. Gene 2022; 823:146342. [PMID: 35219813 DOI: 10.1016/j.gene.2022.146342] [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: 10/07/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/20/2022]
Abstract
The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.
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Fang B, Li J, Zhao Q, Liang Y, Yu J. Assembly of the Complete Mitochondrial Genome of Chinese Plum ( Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes (Basel) 2021; 12:genes12121970. [PMID: 34946920 PMCID: PMC8701122 DOI: 10.3390/genes12121970] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.
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Affiliation(s)
- Bo Fang
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
| | - Qian Zhao
- Fruit Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (B.F.); (Q.Z.)
| | - Yuping Liang
- College of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China;
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China;
- Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, Chongqing 400716, China
- Correspondence:
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Fertet A, Graindorge S, Koechler S, de Boer GJ, Guilloteau-Fonteny E, Gualberto JM. Sequence of the Mitochondrial Genome of Lactuca virosa Suggests an Unexpected Role in Lactuca sativa's Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:697136. [PMID: 34381482 PMCID: PMC8350775 DOI: 10.3389/fpls.2021.697136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The involvement of the different Lactuca species in the domestication and diversification of cultivated lettuce is not totally understood. Lactuca serriola is considered as the direct ancestor and the closest relative to Lactuca sativa, while the other wild species that can be crossed with L. sativa, Lactuca virosa, and Lactuca saligna, would have just contributed to the latter diversification of cultivated typologies. To contribute to the study of Lactuca evolution, we assembled the mtDNA genomes of nine Lactuca spp. accessions, among them three from L. virosa, whose mtDNA had not been studied so far. Our results unveiled little to no intraspecies variation among Lactuca species, with the exception of L. serriola where the accessions we sequenced diverge significantly from the mtDNA of a L. serriola accession already reported. Furthermore, we found a remarkable phylogenetic closeness between the mtDNA of L. sativa and the mtDNA of L. virosa, contrasting to the L. serriola origin of the nuclear and plastidial genomes. These results suggest that a cross between L. virosa and the ancestor of cultivated lettuce is at the origin of the actual mitochondrial genome of L. sativa.
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Affiliation(s)
- Arnaud Fertet
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stéfanie Graindorge
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Gert-Jan de Boer
- Enza Zaden Research and Development B.V., Enkhuizen, Netherlands
| | | | - José M. Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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Varré JS, D'Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, Scotti N. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int J Mol Sci 2019; 20:E4788. [PMID: 31561566 PMCID: PMC6801519 DOI: 10.3390/ijms20194788] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.
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Affiliation(s)
- Jean-Stéphane Varré
- Univ. Lille, CNRS, Centrale Lille, UMR 9189-CRIStAL-Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - José Manuel Gualberto
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
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The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes. Mol Phylogenet Evol 2019; 137:274-284. [PMID: 31112782 DOI: 10.1016/j.ympev.2019.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/14/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022]
Abstract
Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.
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Dong S, Zhao C, Chen F, Liu Y, Zhang S, Wu H, Zhang L, Liu Y. The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination. BMC Genomics 2018; 19:614. [PMID: 30107780 PMCID: PMC6092842 DOI: 10.1186/s12864-018-4991-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms. RESULTS Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome. CONCLUSIONS The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.
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Affiliation(s)
- Shanshan Dong
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chaoxian Zhao
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shouzhou Zhang
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, 518083 China
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Bonavita S, Regina TMR. The evolutionary conservation of rps3 introns and rps19-rps3-rpl16 gene cluster in Adiantum capillus-veneris mitochondria. Curr Genet 2015; 62:173-84. [PMID: 26281979 DOI: 10.1007/s00294-015-0512-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 11/26/2022]
Abstract
Ferns are a large and evolutionarily critical group of vascular land plants for which quite limited mitochondrial gene content and genome organization data are, currently, available. This study reports that the gene for the ribosomal protein S3 (rps3) is preserved and physically clustered to an upstream rps19 and a downstream overlapping rpl16 locus in the mitochondrial DNA of the true fern Adiantum capillus-veneris L. Sequence analysis also revealed that the rps3 gene is interrupted by two cis-splicing group II introns, like the counterpart in lycopod and gymnosperm representatives. A preliminary polymerase chain reaction (PCR) survey confirmed a scattered distribution pattern of both the rps3 introns also in other fern lineages. Northern blot and reverse transcription (RT)-PCR analyses demonstrated that the three ribosomal protein genes are co-transcribed as a polycistronic mRNA and modified by RNA editing. Particularly, the U-to-C type editing amends numerous genomic stop codons in the A. capillus-veneris rps19, rps3 and rpl16 sequences, thus, assuring the synthesis of complete and functional polypeptides. Collectively, the findings from this study further expand our knowledge of the mitochondrial rps3 architecture and evolution, also, bridging the significant molecular data gaps across the so far underrepresented ferns and all land plants.
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Affiliation(s)
- Savino Bonavita
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy
| | - Teresa Maria Rosaria Regina
- Dipartimento di Biologia, Ecologia e Scienze della Terra (DiBEST), Università della Calabria, via Ponte P. Bucci, 87036, Arcavacata di Rende, Cosenza, Italy.
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11
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Atluri S, Rampersad SN, Bonen L. Retention of functional genes for S19 ribosomal protein in both the mitochondrion and nucleus for over 60 million years. Mol Genet Genomics 2015; 290:2325-33. [DOI: 10.1007/s00438-015-1087-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
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Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD. The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol 2013. [PMID: 23587068 DOI: 10.1186/2f1741-7007-11-29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. RESULTS We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. CONCLUSIONS Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution.
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13
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Richardson AO, Rice DW, Young GJ, Alverson AJ, Palmer JD. The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol 2013; 11:29. [PMID: 23587068 PMCID: PMC3646698 DOI: 10.1186/1741-7007-11-29] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. RESULTS We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. CONCLUSIONS Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution.
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14
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Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. THE PLANT CELL 2011; 23:2499-513. [PMID: 21742987 PMCID: PMC3226218 DOI: 10.1105/tpc.111.087189] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 05/18/2023]
Abstract
Members of the flowering plant family Cucurbitaceae harbor the largest known mitochondrial genomes. Here, we report the 1685-kb mitochondrial genome of cucumber (Cucumis sativus). We help solve a 30-year mystery about the origins of its large size by showing that it mainly reflects the proliferation of dispersed repeats, expansions of existing introns, and the acquisition of sequences from diverse sources, including the cucumber nuclear and chloroplast genomes, viruses, and bacteria. The cucumber genome has a novel structure for plant mitochondria, mapping as three entirely or largely autonomous circular chromosomes (lengths 1556, 84, and 45 kb) that vary in relative abundance over a twofold range. These properties suggest that the three chromosomes replicate independently of one another. The two smaller chromosomes are devoid of known functional genes but nonetheless contain diagnostic mitochondrial features. Paired-end sequencing conflicts reveal differences in recombination dynamics among chromosomes, for which an explanatory model is developed, as well as a large pool of low-frequency genome conformations, many of which may result from asymmetric recombination across intermediate-sized and sometimes highly divergent repeats. These findings highlight the promise of genome sequencing for elucidating the recombinational dynamics of plant mitochondrial genomes.
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MESH Headings
- Base Sequence
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Chromosomes, Plant/ultrastructure
- Cucumis sativus/genetics
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- Gene Transfer, Horizontal
- Genes, Plant
- Genome, Mitochondrial
- Genome, Plant
- Introns/genetics
- Molecular Sequence Data
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
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Affiliation(s)
- Andrew J Alverson
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Danny W Rice
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | | | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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15
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Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 2010; 27:1436-48. [PMID: 20118192 DOI: 10.1093/molbev/msq029] [Citation(s) in RCA: 330] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.
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16
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Kubo N, Arimura SI. Discovery of the rpl10 gene in diverse plant mitochondrial genomes and its probable replacement by the nuclear gene for chloroplast RPL10 in two lineages of angiosperms. DNA Res 2009; 17:1-9. [PMID: 19934175 PMCID: PMC2818186 DOI: 10.1093/dnares/dsp024] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial genomes of plants are much larger than those of mammals and often contain conserved open reading frames (ORFs) of unknown function. Here, we show that one of these conserved ORFs is actually the gene for ribosomal protein L10 (rpl10) in plant. No rpl10 gene has heretofore been reported in any mitochondrial genome other than the exceptionally gene-rich genome of the protist Reclinomonas americana. Conserved ORFs corresponding to rpl10 are present in a wide diversity of land plant and green algal mitochondrial genomes. The mitochondrial rpl10 genes are transcribed in all nine land plants examined, with five seed plant genes subject to RNA editing. In addition, mitochondrial-rpl10-like cDNAs were identified in EST libraries from numerous land plants. In three lineages of angiosperms, rpl10 is either lost from the mitochondrial genome or a pseudogene. In two of them (Brassicaceae and monocots), no nuclear copy of mitochondrial rpl10 is identifiably present, and instead a second copy of nuclear-encoded chloroplast rpl10 is present. Transient assays using green fluorescent protein indicate that this duplicate gene is dual targeted to mitochondria and chloroplasts. We infer that mitochondrial rpl10 has been functionally replaced by duplicated chloroplast counterparts in Brassicaceae and monocots.
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Affiliation(s)
- Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Seika, Kyoto, Japan.
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17
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Subramanian S, Bonen L. Rapid evolution in sequence and length of the nuclear-located gene for mitochondrial L2 ribosomal protein in cereals. Genome 2006; 49:275-81. [PMID: 16604111 DOI: 10.1139/g05-098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The L2 ribosomal protein is typically one of the most conserved proteins in the ribosome and is universally present in bacterial, archaeal, and eukaryotic cytosolic and organellar ribosomes. It is usually 260–270 amino acids long and its binding to the large-subunit ribosomal RNA near the peptidyl transferase center is mediated by a β-barrel RNA-binding domain with 10 β strands. In the diverse land plants Marchantia polymorpha (liverwort) and Oryza sativa (rice), the mitochondrial-encoded L2 ribosomal protein is about 500 amino acids long owing to a centrally located expansion containing the β3–β4 strand region. We have determined that, in wheat, the functional rpl2 gene has been trans ferred to the nucleus and much of the plant-specific internal insert has been deleted. Its mRNA is only 1.2 kb, and two expressed copies in wheat encode proteins of 318 and 319 amino acids, so they are considerably shorter than the maize nuclear-located rpl2 gene of 448 codons. Comparative sequence analysis of cereal mitochondrial L2 ribosomal proteins indicates that the mid region has undergone unexpectedly rapid evolution during the last 60 million years.Key words: mitochondria, ribosomal protein, plants, evolutionary gene transfer.
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MESH Headings
- Amino Acid Sequence
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Edible Grain/genetics
- Evolution, Molecular
- Genes, Plant
- Histidine/chemistry
- Introns
- Molecular Sequence Data
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- Selvi Subramanian
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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18
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Bonen L, Calixte S. Comparative analysis of bacterial-origin genes for plant mitochondrial ribosomal proteins. Mol Biol Evol 2005; 23:701-12. [PMID: 16368778 DOI: 10.1093/molbev/msj080] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial ribosomes contain bacterial-type proteins reflecting their endosymbiotic heritage, and a subset of these genes is retained within the mitochondrion in land plants. Variation in gene location is observed, however, because migration to the nucleus is still an ongoing evolutionary process in plants. To gain insights into adaptation events related to successful gene transfer, we have compiled data for bacterial-origin mitochondrial-type ribosomal protein genes from the completely sequenced Arabidopsis and rice genomes. Approximately 75% of such nuclear-located genes encode amino-terminal extensions relative to their Escherichia coli counterparts, and of that set, only about 30% have introns at (or near) the junction in support of an exon shuffling-type recruitment of upstream expression/targeting signals. We find that genes that were transferred to the nucleus early in eukaryotic evolution have, on average, about twofold higher density of introns within the core ribosomal protein sequences than do those that moved to the nucleus more recently. About 20% of such introns are at positions identical to those in human orthologs, consistent with their ancestral presence. Plant mitochondrial-type ribosomal protein genes have dispersed chromosomal locations in the nucleus, and about 20% of them are present in multiple unlinked copies. This study provides new insights into the evolutionary history of endosymbiotic bacterial-type genes that have been transferred from the mitochondrion to the nucleus.
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Affiliation(s)
- Linda Bonen
- Biology Department, University of Ottawa, Ottawa, Canada.
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19
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Fallahi M, Crosthwait J, Calixte S, Bonen L. Fate of mitochondrially located S19 ribosomal protein genes after transfer of a functional copy to the nucleus in cereals. Mol Genet Genomics 2005; 273:76-83. [PMID: 15711972 DOI: 10.1007/s00438-004-1102-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 12/06/2004] [Indexed: 11/30/2022]
Abstract
Mitochondrial genes for ribosomal proteins undergo relatively frequent transfer to the nucleus during plant evolution, and when migration is successful the mitochondrial copy becomes redundant and can be lost. We have examined the status of the mitochondrial rps19 gene for ribosomal protein S19 in closely related cereals. In oat, the mitochondrial rps19 reading frame is blocked by a premature termination codon and lacks abundant transcripts, whereas in the mitochondria of wheat and rye rps19 is a 5'-truncated pseudogene which is co-transcribed with the downstream nad4L gene. In barley and maize, rps19 sequences are completely absent from the mitochondrion. All five of these cereals differ from rice, in which an intact, transcriptionally active mitochondrial rps19 gene is found, and this is preceded by rpl2 in an organization reminiscent of that seen in bacteria. Based on EST sequence data for maize, barley and wheat, it can be inferred that a functional rps19 gene was transferred to the nucleus prior to the divergence of the maize and rice lineages (approximately 50 million years ago), and the present-day nuclear copies encode an N-terminal sequence related to the mitochondrial targeting signal of Hsp70 (heat shock protein) in cereals. Subsequent evolutionary events have included independent losses of the mitochondrial copies in the barley and maize lineages. In the rice lineage, on the other hand, the nuclear copy was lost. This is reflected in the persistence of the mitochondrial rps19 after a period during which rps19 genes coexisted in both compartments. These observations illustrate the dynamic nature of the location and structure of genes for mitochondrial ribosomal proteins in flowering plants.
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Affiliation(s)
- Magid Fallahi
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, Canada, K1N 6N5
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20
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Handa H. The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res 2004; 31:5907-16. [PMID: 14530439 PMCID: PMC219474 DOI: 10.1093/nar/gkg795] [Citation(s) in RCA: 262] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The entire mitochondrial genome of rapeseed (Brassica napus L.) was sequenced and compared with that of Arabidopsis thaliana. The 221 853 bp genome contains 34 protein-coding genes, three rRNA genes and 17 tRNA genes. This gene content is almost identical to that of Arabidopsis: However the rps14 gene, which is a pseudo-gene in Arabidopsis, is intact in rapeseed. On the other hand, five tRNA genes are missing in rapeseed compared to Arabidopsis, although the set of mitochondrially encoded tRNA species is identical in the two Cruciferae. RNA editing events were systematically investigated on the basis of the sequence of the rapeseed mitochondrial genome. A total of 427 C to U conversions were identified in ORFs, which is nearly identical to the number in Arabidopsis (441 sites). The gene sequences and intron structures are mostly conserved (more than 99% similarity for protein-coding regions); however, only 358 editing sites (83% of total editings) are shared by rapeseed and Arabidopsis: Non-coding regions are mostly divergent between the two plants. One-third (about 78.7 kb) and two-thirds (about 223.8 kb) of the rapeseed and Arabidopsis mitochondrial genomes, respectively, cannot be aligned with each other and most of these regions do not show any homology to sequences registered in the DNA databases. The results of the comparative analysis between the rapeseed and Arabidopsis mitochondrial genomes suggest that higher plant mitochondria are extremely conservative with respect to coding sequences and somewhat conservative with respect to RNA editing, but that non-coding parts of plant mitochondrial DNA are extraordinarily dynamic with respect to structural changes, sequence acquisition and/or sequence loss.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Bacterial Proteins
- Beta vulgaris/genetics
- Binding Sites/genetics
- Brassica rapa/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Genome, Plant
- Introns/genetics
- Membrane Proteins/genetics
- Mitochondrial Proteins/genetics
- Molecular Sequence Data
- Oryza/genetics
- Plant Proteins/genetics
- RNA/genetics
- RNA/metabolism
- RNA Editing
- RNA, Mitochondrial
- RNA, Ribosomal/genetics
- RNA, Transfer/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Ribosomal Proteins/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- Hirokazu Handa
- Laboratory of Plant Genecology, National Agricultural Research Center for Hokkaido Region, Sapporo 062-8555, Japan.
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21
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22
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Sandoval P, León G, Gómez I, Carmona R, Figueroa P, Holuigue L, Araya A, Jordana X. Transfer of RPS14 and RPL5 from the mitochondrion to the nucleus in grasses. Gene 2004; 324:139-47. [PMID: 14693379 DOI: 10.1016/j.gene.2003.09.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Gene transfer from the mitochondrion to the nucleus, a process of outstanding importance to the evolution of the eukaryotic cell, is an on-going phenomenon in higher plants. After transfer, the mitochondrial gene has to be adapted to the nuclear context by acquiring a new promoter and targeting information to direct the protein back to the organelle. To better understand the strategies developed by higher plants to transfer organellar genes during evolution, we investigated the fate of the mitochondrial RPL5-RPS14 locus in grasses. While maize mitochondrial genome does not contain RPS14 and RPL5 genes, wheat mitochondrial DNA contains an intact RPL5 gene and a nonfunctional RPS14 pseudogene. RPL5 and PsiRPS14 are co-transcribed and their transcripts are edited. In wheat, the functional RPS14 gene is located in the nucleus, within the intron of the respiratory complex II iron-sulfur subunit gene (SDH2). Its organization and expression mechanisms are similar to those previously described in maize and rice, allowing us to conclude that RPS14 transfer and nuclear activation occurred before divergence of these grasses. Unexpectedly, we found evidence for a more recent RPL5 transfer to the nucleus in wheat. This nuclear wheat RPL5 acquired its targeting information by duplication of an existing targeting presequence for another mitochondrial protein, ribosomal protein L4. Thus, mitochondrial and nuclear functional RPL5 genes appear to be maintained in wheat, supporting the hypothesis that in an intermediate stage of the transfer process, both nuclear and mitochondrial functional genes coexist. Finally, we show that RPL5 has been independently transferred to the nucleus in the maize lineage and has acquired regulatory elements for its expression and a mitochondrial targeting peptide from an unknown source.
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Affiliation(s)
- Pamela Sandoval
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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23
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Adams KL, Daley DO, Whelan J, Palmer JD. Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts. THE PLANT CELL 2002; 14:931-43. [PMID: 11971146 PMCID: PMC150693 DOI: 10.1105/tpc.010483] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2001] [Accepted: 01/21/2002] [Indexed: 05/18/2023]
Abstract
Often during flowering plant evolution, ribosomal protein genes have been lost from the mitochondrion and transferred to the nucleus. Here, we show that substitution by a duplicated, divergent gene originally encoding the chloroplast or cytosolic ribosomal protein counterpart accounts for two missing mitochondrial genes in diverse angiosperms. The rps13 gene is missing from the mitochondrial genome of many rosids, and a transferred copy of this gene is not evident in the nucleus of Arabidopsis, soybean, or cotton. Instead, these rosids contain a divergent nuclear copy of an rps13 gene of chloroplast origin. The product of this gene from all three rosids was shown to be imported into isolated mitochondria but not into chloroplasts. The rps8 gene is missing from the mitochondrion and nucleus of all angiosperms examined. A divergent copy of the gene encoding its cytosolic counterpart (rps15A) was identified in the nucleus of four angiosperms and one gymnosperm. The product of this gene from Arabidopsis and tomato was imported successfully into mitochondria. We infer that rps13 was lost from the mitochondrial genome and substituted by a duplicated nuclear gene of chloroplast origin early in rosid evolution, whereas rps8 loss and substitution by a gene of nuclear/cytosolic origin occurred much earlier, in a common ancestor of angiosperms and gymnosperms.
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Affiliation(s)
- Keith L Adams
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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24
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Regina TMR, Lopez L, Picardi E, Quagliariello C. Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria. Gene 2002; 286:33-41. [PMID: 11943458 DOI: 10.1016/s0378-1119(01)00802-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ribosomal protein S4 gene (rps4) has been identified as a single copy sequence in the mitochondrial genomes of two distant higher plants, Magnolia and Helianthus. Sequence analysis revealed that the rps4 genes present in the magnolia and sunflower mitochondrial genomes encode S4 polypeptides of 352 and 331 amino acids, respectively, longer than their counterparts in liverwort and bacteria. Expression of the rps4 genes in the investigated higher plant mitochondria was confirmed by Western blot analysis. In Helianthus, one of two short nucleotide insertions at the 3'-end introduces in the coding region a premature termination codon. Northern hybridizations and reverse transcription-polymerase chain reaction analysis demonstrated that the monocistronic RNA transcripts generated from the rps4 locus in Magnolia and Helianthus mitochondria are modified by RNA editing at 28 and 13 positions, respectively. Although evolutionarily conserved, RNA editing requirements of the rps4 appear more extensive in Magnolia than in Helianthus and in the other higher plants so far investigated. Furthermore, our analysis also suggests that selection of editing sites is RNA sequence-specific in a duplicated sequence context.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Southern
- Blotting, Western
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Helianthus/genetics
- Magnoliopsida/genetics
- Molecular Sequence Data
- RNA Editing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Teresa M R Regina
- Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, 87030 Arcavacata di Rende, Italy
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25
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Regina TM, Lopez L, Bruno R, Quagliariello C. RNA editing of the ribosomal protein S13 transcripts in magnolia and sunflower mitochondria. PLANT & CELL PHYSIOLOGY 2001; 42:768-74. [PMID: 11479385 DOI: 10.1093/pcp/pce088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To obtain information on ribosomal protein gene content and RNA editing in plant mitochondria, we investigated the conservation of the gene for ribosomal protein S13 (rps13) in the mitochondrial genomes of Magnolia spp. and Helianthus annuus. A complete rps13 open reading frame was identified in the mitochondrial genome of Magnolia and Helianthus. Comparison of genomic and cDNA sequences revealed that transcripts from the mitochondrial rps13 locus in both Magnolia and Helianthus undergo RNA editing suggesting the functionality of the related gene. Six and four editing events in the rps13 transcript population of Magnolia and Helianthus mitochondria, respectively, cause critical changes of codons and, consequently, induce 5 and 3.4% amino acid modifications in the respective genomically-encoded S13 polypeptides. Both editing pattern and efficiency of RNA editing differ in the reverse transcription (RT)-PCR-derived cDNA populations from the rps13 locus from the analyzed plant species with only the Magnolia rps13 being fully edited.
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Affiliation(s)
- T M Regina
- Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, 87030 Arcavacata di Rende, Italy
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26
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Zhuo D, Nguyen-Lowe HT, Subramanian S, Bonen L. The S7 ribosomal protein gene is truncated and overlaps a cytochrome c biogenesis gene in pea mitochondria. PLANT MOLECULAR BIOLOGY 1999; 40:91-7. [PMID: 10394948 DOI: 10.1023/a:1026499906338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The pea mitochondrial genome contains a truncated rps7 gene lacking ca. 40 codons at its 5' terminus. This single-copy sequence is immediately downstream of and slightly overlapping an actively transcribed and edited reading frame of 744 bp (designated ccb248) homologous to the bacterial helC gene which encodes a subunit of the ABC-type heme transporter involved in cytochrome c biogenesis. This region of mitochondrial DNA appears recombinogenic, and the carboxy-termini of helC-type proteins are predicted to vary in sequence and length among plants. Sequences corresponding to the 5' coding region of rps7 were not detected elsewhere in the pea mitochondrial genome using wheat rps7 probes, and only a very short internal rps7 segment was observed in soybean mitochondrial DNA. The presence of rps7-homologous sequences in the nuclear genomes of pea and soybean is consistent with the recent transfer of a functional mitochondrial rps7 gene to the nucleus in certain plant lineages.
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Affiliation(s)
- D Zhuo
- Biology Department, University of Ottawa, Canada
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27
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Kadowaki K, Kubo N, Ozawa K, Hirai A. Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals. EMBO J 1996; 15:6652-61. [PMID: 8978691 PMCID: PMC452489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have cloned a gene for mitochondrial ribosomal protein S11 (RPS11), which is encoded in lower plants by the mitochondrial genome, in higher plants by the nuclear genome, demonstrating genetic information transfer from the mitochondrial genome to the nucleus during flowering plant evolution. The sequence s11-1 encodes an N-terminal extension as well as an organelle-derived RPS11 region. Surprisingly, the N-terminal region has high amino acid sequence similarity with the presequence of the beta-subunit of ATP synthase from plant mitochondria, suggesting a common lineage of the presequences. The deduced N-terminal region of s11-2, a second nuclear-encoded homolog of rps11, shows high sequence similarity with the putative presequence of cytochrome oxidase subunit Vb. The sharing of the N-terminal region together with its 5' flanking untranslated nucleotide sequence in different proteins strongly suggests an involvement of duplication/recombination for targeting signal acquisition after gene migration. A remnant of ancestral rps11 sequence, transcribed and subjected to RNA editing, is found in the mitochondrial genome, indicating that inactivation of mitochondrial rps11 gene expression was initiated at the translational level prior to termination of transcription.
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Affiliation(s)
- K Kadowaki
- National Institute of Agrobiological Resources, Department of Molecular Biology, Tsukuba, Ibaraki, Japan
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28
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Kubo N, Ozawa K, Hino T, Kadowaki K. A ribosomal protein L2 gene is transcribed, spliced, and edited at one site in rice mitochondria. PLANT MOLECULAR BIOLOGY 1996; 31:853-62. [PMID: 8806415 DOI: 10.1007/bf00019472] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The mitochondrial ribosomal protein L2 gene (rpl2) is coded by two exons of 840 and 669 bp separated by an intron sequence of 1481 bp in the rice mitochondrial genome. The rpl2 gene is located three nucleotides upstream of the ribosomal protein S19 gene (rps19) and both genes are co-transcribed. cDNA sequence analysis identified splicing of the intron sequence from the rpl2 mRNA as well as RNA editing events. The deduced secondary structure of the rpl2 intron sequence shows the characteristic features of a group-II intron. A single RNA editing site is identified in rpl2 and six editing sites in rps19 transcripts. In addition, one editing site is observed in the 3 nucleotide intergenic region. Analysis of individual cDNA clones showed a different extent of RNA editing. The rice rpl2 intron is located at a different site and shows no significant nucleotide sequence similarity with the rpl2 intron of liverwort. However, 60% nucleotide sequence identity is observed between the rice rpl2 intron and the Oenothera nad5 intron in a 234 nucleotide region. The mitochondrial rpl2 sequence is absent from the pea mitochondrial genome and we consequently propose that the mitochondrial RPL2 protein is encoded by a nuclear gene in pea.
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Affiliation(s)
- N Kubo
- Department of Molecular Biology, National Institute of Agrobiological Resources, Ibaraki, Japan
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29
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Quiñones V, Zanlungo S, Moenne A, Gómez I, Holuigue L, Litvak S, Jordana X. The rpl5-rps14-cob gene arrangement in Solanum tuberosum: rps14 is a transcribed and unedited pseudogene. PLANT MOLECULAR BIOLOGY 1996; 31:937-43. [PMID: 8806426 DOI: 10.1007/bf00019483] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The L5 ribosomal protein gene (rpl5) and a S14 ribosomal protein pseudogene were identified by sequence analysis in the potato mitochondrial genome. The two genes are separated by one nucleotide and are found upstream of the apocytochrome b gene (cob), an arrangement conserved also in Arabidopsis and Brassica. The rpl5 gene has an intact open reading frame while the rps14 locus is disrupted by a five nucleotide duplication that introduces a frameshift in the reading frame. Editing of rpl5 and pseudorps14 cotranscripts has been studied by cDNA sequence analysis. Eight C residues are edited into U in the rpl5 coding region, resulting in eight amino acid changes that increase the homology between potato and other RPL5 polypeptides. Interestingly, the rps14 pseudogene sequence is not edited at any nucleotide position.
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Affiliation(s)
- V Quiñones
- Departmento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago, Chile
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30
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Perrotta G, Regina TM, Ceci LR, Quagliariello C. Conservation of the organization of the mitochondrial nad3 and rps12 genes in evolutionarily distant angiosperms. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:326-37. [PMID: 8676875 DOI: 10.1007/bf02172523] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The organization of the genes nad3 and rps12 has been investigated in the mitochondrial genome of two dicotyledonous plants - Helianthus and Magnolia - and one monocotyledonous plant (Allium). These plants all contain a complete rps12 gene downstream of the nad3 gene. This arrangement is thus highly conserved within angiosperms. The two genes are co-transcribed and the transcript is modified at several positions by RNA editing of the C to U-type, thus confirming that both genes encode functional proteins. Some 26, 35 and 27 editing events have been identified in the PCR-derived nad3-rps12 cDNA population from sunflower, Magnolia and onion, respectively. Editing of the nad3-rps12 transcript is thus more extensive in Magnolia than in the other angiosperms so far investigated and radically changes the genomically encoded polypeptide sequence. A novel species-specific codon modification was observed in Magnolia. Several homologous sites show differences in editing pattern among plant species. A C-to-U alteration is also found in the non-coding region separating the nad3 and rps12 genes in sunflower. The PCR-derived cDNA populations from the nad3-rps12 loci analysed were found to be differently edited. In addition the plant species show marked variations in the completeness of RNA editing, with only the Magnolia nad3 mRNA being edited fully.
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Affiliation(s)
- G Perrotta
- Dipartimento di Biologia Cellulare, Università della Calabria, Arcavacata di Rende, Italy
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31
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Sánchez H, Fester T, Kloska S, Schröder W, Schuster W. Transfer of rps19 to the nucleus involves the gain of an RNP-binding motif which may functionally replace RPS13 in Arabidopsis mitochondria. EMBO J 1996; 15:2138-49. [PMID: 8641279 PMCID: PMC450136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The discovery of disrupted rps19 genes in Arabidopsis mitochondria prompted speculation about the transfer to the nuclear compartment. We here describe the functional gene transfer of rps19 into the nucleus of Arabidopsis. Molecular cloning and sequence analysis of rps19 show that the nuclear gene encodes a long N-terminal extension. Import studies of the precursor protein indicate that only a small part of this extension is cleaved off during import. The larger part of the extension, which shows high similarity to conserved RNA-binding domains of the RNP-CS type, became part of the S19 protein. In the Escherichia coli ribosome S19 forms an RNA-binding complex as heterodimer with S13. By using immuno-analysis and import studies we show that a eubacterial-like S13 protein is absent from Arabidopsis mitochondria, and is not substituted by either a chloroplastic or a cytosolic homologue of this ribosomal protein. We therefore propose that either a highly diverged or missing RPS13 has been functionally replaced by an RNP domain that most likely derived from a glycine-rich RNA-binding protein. These results represent the first case of a functional replacement of a ribosomal protein by a common RNA-binding domain and offer a new view on the flexibility of biological systems in using well-adapted functional domains for different jobs.
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Affiliation(s)
- H Sánchez
- Institut für Genbiologische Forschung Berlin GmbH, Germany
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32
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Lippok B, Brennicke A, Unseld M. The rps4-gene is encoded upstream of the nad2-gene in Arabidopsis mitochondria. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1996; 377:251-7. [PMID: 8737990 DOI: 10.1515/bchm3.1996.377.4.251] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In Arabidopsis mitochondria the nad2-gene consists of five exons (a-e) which are separated by three cis-splicing introns and one trans-splicing intron. Sequence analysis of the region upstream of exons a and b reveals an open reading frame encoding ribosomal protein S4 (rps4). In the second nad2 coding region (exons c-e) a pseudo tRNA(Tyr) sequence and a fragment of the plastid psbA gene are located upstream of the trans-spliced exon c. Primer extension analysis identifies RNA 5'-termini within the pseudo-tRNA(Tyr) confirming this sequence to be non-functional. Northern blot analysis suggests the rps4-gene to be cotranscribed with at least the first part of the nad2-gene. The rps4 and nad2 coding sequences as well as the first cis-intron and the trans-intron sequences of the nad2 gene are altered by RNA editing. RNA editing in the open reading frames improves in most instances conservation of the specified amino acids.
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Affiliation(s)
- B Lippok
- Institut für Genbiologische Forschung, Berlin, Germany
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33
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Wischmann C, Schuster W. Transfer of rps10 from the mitochondrion to the nucleus in Arabidopsis thaliana: evidence for RNA-mediated transfer and exon shuffling at the integration site. FEBS Lett 1995; 374:152-6. [PMID: 7589523 DOI: 10.1016/0014-5793(95)01100-s] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Rps10, a gene coding for ribosomal protein S10 of Arabidopsis mitochondria has been transferred to the nuclear compartment, while in pea and potato the active rps10 is mitochondrially located. The nuclear rps10 gene contains an intron at the junction of the target signal sequence and the mitochondrial-derived sequence, indicating that exon shuffling may have been involved in the addition of the transit peptide signal. Sequence comparison of Arabidopsis rps10 to the plant mitochondrial counterparts shows that the edited version is present in the nucleus of Arabidopsis. This finding corroborates RNA as an intermediate of a functional gene transfer between mitochondria and the nucleus. In vitro-translated RPS10 protein is efficiently imported into potato mitochondria and a presequence of about 7 kDa is removed resulting in a mature protein that is larger compared to organellar and bacterial RPS10 proteins.
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Affiliation(s)
- C Wischmann
- Institut für Genbiologische Forschung Berlin GmbH, Germany
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34
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Chow LP, Fukaya N, Miyatake N, Horimoto K, Sugiura Y, Tabuchi K, Ueno Y, Tsugita A. Resolution of Fusarium sporotrichioides Proteins by Two-Dimensional Polyacrylamide Gel Electrophoresis and Identification by Sequence Homology Comparison in Protein Data Base. J Biomed Sci 1995; 2:343-352. [PMID: 11725071 DOI: 10.1007/bf02255221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Proteins from Fusarium sporotrichioides M-1-1, a T2-toxin-producing strain, were separated by two-dimensional polyacrylamide gel electrophoresis. One thousand two hundred and forty-four protein spots were resolved and 103 protein spots were subjected to N-terminal sequencing. Fifty-eight protein spots were sequenced and 48 proteins were observed to have blocked N termini. Forty out of 58 sequenced proteins were identified by homology search against the PIR protein sequence data base and protein superfamily data base, while the residual 18 sequences were not identified. Twenty-seven of the N-terminal-blocked proteins were subjected to mild anhydrous hydrazine vapor deblocking. Twenty-four spots were not deblocked indicating the presence of acyl groups at the N termini, while 3 proteins were deblocked showing the blocked group to be pyrroglutamyl carboxylic acid residues. The results can provide a more global view of cellular genetic expression than any other technique. The created data may offer a unique opportunity to link information with DNA sequence data. Copyright 1995 S. Karger AG, Basel
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Affiliation(s)
- L.-P. Chow
- Research Institute for Biosciences, Science University of Tokyo, Noda, Japan
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35
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Pan C, Mason TL. Identification of the yeast nuclear gene for the mitochondrial homologue of bacterial ribosomal protein L16. Nucleic Acids Res 1995; 23:3673-7. [PMID: 7478995 PMCID: PMC307264 DOI: 10.1093/nar/23.18.3673] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An open reading frame encoding a member of the L16 family of ribosomal proteins is adjacent to the URA7 gene on the left arm of chromosome II in Saccharomyces cerevisiae. The predicted L16-like polypeptide is basic (pl 11.12), contains 232 amino acids (26.52 kDa) and has 36% amino acid sequence identity to E. coli L16. Immunoblot analysis with polyclonal antibodies to the L16-like polypeptide showed specific cross-reaction with a 22,000 Mr mitochondrial polypeptide that co-sediments with the large subunit of the mitochondrial ribosome in sucrose density gradients. The levels of the L16 mRNA and protein varied in response to carbon source. In [rho degree] cells lacking mitochondrial rRNA, the L16 mRNA accumulated at normal levels, but the protein was barely detectable, indicating RNA-dependent accumulation of the L16 protein. Gene disruption experiments demonstrated that the yeast mitochondrial L16 is an essential ribosomal protein in vivo.
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Affiliation(s)
- C Pan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
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36
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Kumar R, Drouaud J, Raynal M, Small I. Characterization of the nuclear gene encoding chloroplast ribosomal protein S13 from Arabidopsis thaliana. Curr Genet 1995; 28:346-52. [PMID: 8590480 DOI: 10.1007/bf00326432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have characterised a cDNA clone and a nuclear gene encoding the chloroplast 30 s ribosomal protein S13 from Arabidopsis thaliana. The identification is based on the high similarity of the predicted amino-acid sequence with eubacterial S13 protein sequences, and immunodetection of a 14.5-kDa chloroplast ribosomal polypeptide using antibodies raised against the polypeptide produced from part of the cDNA expressed in bacteria. The predicted amino-acid sequence contains an N-terminal extension which has several features characteristic of chloroplast transit peptides. Experiments suggest there is a single copy of this gene in A. thaliana and multiple copies in Brassica species. The origin of the mitochondrial S13 polypeptide in crucifers is also discussed.
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Affiliation(s)
- R Kumar
- Station de Génétique et d'Amélioration des Plantes, INRA, Versailles, France
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37
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Knoop V, Ehrhardt T, Lättig K, Brennicke A. The gene for ribosomal protein S10 is present in mitochondria of pea and potato but absent from those of Arabidopsis and Oenothera. Curr Genet 1995; 27:559-64. [PMID: 7553942 DOI: 10.1007/bf00314448] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A novel group II intron has been identified in the pea (Pisum sativum) mitochondrial genome. The gene harbouring this intron is identified as rps10 (encoding protein S10 of the small ribosomal subunit) by similarity to its known homologues in bacteria and in the mitochondrion of the liverwort Marchantia polymorpha. The rps10 gene is transcribed in pea, the intron is removed, and RNA editing in the rps10 reading frame increases similarity to its homologue in the M. polymorpha mitochondrion. Contrary to the situation in bacteria and Marchantia, rps10 is not part of a ribosomal-protein gene cluster in pea. It is flanked upstream by the genes trnF and trnP, encoding phenylalanine- and proline-accepting tRNAs, and downstream by cox1, encoding subunit 1 of the cytochrome-c-oxidase. Southern hybridization shows that sequences homologous to rps10 exist in potato mitochondria but not in mitochondria of Oenothera berteriana and Arabidopsis thaliana. The pea rps10 intron is homologous to introns in rrn26 and cox3 in the Marchantia mitochondrial genome, while the Marchantia rps10 gene lacks an intron.
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Affiliation(s)
- V Knoop
- Institut für Genbiologische Forschung GmbH, Berlin, Germany
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38
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Zanlungo S, Quiñones V, Moenne A, Holuigue L, Jordana X. Splicing and editing of rps10 transcripts in potato mitochondria. Curr Genet 1995; 27:565-71. [PMID: 7553943 DOI: 10.1007/bf00314449] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The structure and expression of the potato mitochondrial gene rps10, encoding ribosomal protein S10, has been characterized. The RPS10 polypeptide of 129 amino acids is encoded by two exons of 307 bp and 80 bp respectively, which are separated by a 774-bp class-II intron. Editing of the complete rps10 coding region was studied by sequence analysis of spliced cDNAs. Four C residues are edited into U, resulting in the creation of a putative translational initiation codon, a new stop codon which eliminated ten carboxy-terminal residues, and two additional amino-acid alterations. All these changes increase the similarity between the potato and liverwort polypeptides. One additional C-to-U RNA editing event, observed in the intron sequence of unspliced cDNAs, improves the stability of the secondary structure in stem I (i) of domain I and may thus be required for the splicing reaction. All spliced cDNAs, and most unspliced cDNAs, were completely edited, suggesting that editing is an early step of rps10 mRNA processing and precedes splicing. Earlier work on potato rps10 (Zanlungo et al. 1994) is now known to comprise only a partial analysis of the gene, since the short downstream exon was not identified.
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Affiliation(s)
- S Zanlungo
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago
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39
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40
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Nakazono M, Itadani H, Wakasugi T, Tsutsumi N, Sugiura M, Hirai A. The rps3-rpl16-nad3-rps12 gene cluster in rice mitochondrial DNA is transcribed from alternative promoters. Curr Genet 1995; 27:184-9. [PMID: 7788722 DOI: 10.1007/bf00313433] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The two gene clusters rps3-rpl16 and nad3-rps12 are separated from each other in the mitochondrial genome and are expressed as the individual transcription units in many plants. In rice mitochondrial DNA (mtDNA), the four genes rps3, rpl16, nad3 and rps12 are located within a region of 6 kbp. Northern-blot analysis revealed that a large transcript (6.6 kb) hybridized to both the rps3-rpl16 and the nad3-rps12 gene clusters. Using RT-PCR, we amplified a fragment of anticipated size (790 bp) from two primers that corresponded to sequences in the coding regions of rpl16 and nad3, demonstrating that at least two of the four genes, namely rpl16 and nad3, were co-transcribed. These results together indicated that all four genes, namely, rps3, rpl16, nad3 and rps12, were co-transcribed in rice mitochondria. Transcription initiation sites were determined by an in vitro capping/ribonuclease protection assay and primer extension analysis. Two initiation sites were identified in the rps3-rpl16-nad3-rps12 gene cluster: one was located upstream of rps3 and the other was located between rpl16 and nad3. This evidence indicates that the rps3-rpl16-nad3-rps12 gene cluster is transcribed from two alternative promoters.
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Affiliation(s)
- M Nakazono
- Laboratory of Radiation Genetics, Faculty of Agriculture, University of Tokyo, Japan
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42
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Abstract
Consistent with their postulated origin from endosymbiotic cyanobacteria, chloroplasts of plants and algae have ribosomes whose component RNAs and proteins are strikingly similar to those of eubacteria. Comparison of the secondary structures of 16S rRNAs of chloroplasts and bacteria has been particularly useful in identifying highly conserved regions likely to have essential functions. Comparative analysis of ribosomal protein sequences may likewise prove valuable in determining their roles in protein synthesis. This review is concerned primarily with the RNAs and proteins that constitute the chloroplast ribosome, the genes that encode these components, and their expression. It begins with an overview of chloroplast genome structure in land plants and algae and then presents a brief comparison of chloroplast and prokaryotic protein-synthesizing systems and a more detailed analysis of chloroplast rRNAs and ribosomal proteins. A description of the synthesis and assembly of chloroplast ribosomes follows. The review concludes with discussion of whether chloroplast protein synthesis is essential for cell survival.
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Affiliation(s)
- E H Harris
- DCMB Group, Department of Botany, Duke University, Durham, North Carolina 27708-1000
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43
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Zanlungo S, Quiñones V, Moenne A, Holuigue L, Jordana X. A ribosomal protein S10 gene is found in the mitochondrial genome in Solanum tuberosum. PLANT MOLECULAR BIOLOGY 1994; 25:743-749. [PMID: 8061325 DOI: 10.1007/bf00029612] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The S10 ribosomal protein gene (rps10), which has not been previously reported in any angiosperm mitochondrial genome, was identified by sequence analysis in the potato mitochondrial DNA. This gene is found downstream of a truncated non-functional apocytochrome b (cob) pseudogene, and is expressed as multiple transcripts ranging in size from 0.8 to 5.0 kb. Southern hybridization analysis indicates that rps10-homologous sequences are not present in the wheat mitochondrial genome. Sequence analysis of a single-copy region of the pea mitochondrial genome located upstream of cox1 [11] shows that a non-functional rps10 pseudogene is present in this species. These results suggest that the functional genes coding for wheat and pea mitochondrial RPS10 polypeptides have been translocated to the nucleus.
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Affiliation(s)
- S Zanlungo
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago
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Dequard-Chablat M, Sellem C. The S12 ribosomal protein of Podospora anserina belongs to the S19 bacterial family and controls the mitochondrial genome integrity through cytoplasmic translation. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36558-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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45
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Bock H, Brennicke A, Schuster W. Rps3 and rpl16 genes do not overlap in Oenothera mitochondria: GTG as a potential translation initiation codon in plant mitochondria? PLANT MOLECULAR BIOLOGY 1994; 24:811-818. [PMID: 8193306 DOI: 10.1007/bf00029863] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Characterization of the Oenothera mitochondrial ribosomal gene cluster rps19-rps3-rpl16 shows the two genes rps3 and rpl16 to be separated by 9 nucleotides. The first codon of rpl16 is a GTG codon for valine and the only potential translational start. This GTG codon is conserved at the same position in maize, Petunia and Marchantia mitochondria, while sequences diverge upstream. These observations suggest that GTG at least at this position may act as translation initiation codon in plant mitochondria. Analysis of RNA editing suggests both genes to code for functional ribosomal proteins in Oenothera mitochondria. A duplication/recombination event at a decanucleotide in the intron of rps3 created a pseudogene missing part of the intron and the 3' exon.
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Affiliation(s)
- H Bock
- Institut für Genbiologische Forschung, Berlin, FRG
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46
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Abstract
Molecular data (particularly sequence analyses) have established that two eukaryotic organelles, the mitochondrion and the plastid, are the descendants of endosymbiotic (eu)bacteria whose closest living relatives are the alpha-Proteobacteria (mitochondrion) and Cyanobacteria (plastid). This review describes recent data that favor the view that each organelle arose via this primary endosymbiotic pathway only once (monophyletic origin), such as the discovery of group I introns that appear to be structurally homologous and have identical insertion sites in metaphyte, chlorophyte and fungal mitochondrial genomes. However, it is also evident that the plastids in certain algal groups were acquired secondarily through a eukaryotic rather than a prokaryotic endosymbiont.
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Affiliation(s)
- M W Gray
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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47
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Brandt P, Unseld M, Eckert-Ossenkopp U, Brennicke A. An rps14 pseudogene is transcribed and edited in Arabidopsis mitochondria. Curr Genet 1993; 24:330-6. [PMID: 7916674 DOI: 10.1007/bf00336785] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sequence analysis of the region upstream of the apocytochrome b (cob) gene in the Arabidopsis mitochondrial genome identifies an open reading frame with homology to ribosomal protein L5, (rpl5), and a pseudogene with similarity to ribosomal protein S14 (rps14) genes. Both cob and rpl5 genes have intact reading frames, but the rps14 homology is disrupted by a stop codon and a deleted nucleotide. The rpl5 gene, the rps14 pseudogene, and the cob gene are separated by one nucleotide and a 1604-nucleotide-long spacer respectively. A plastid-like tRNA(Ser) is encoded downstream from the cob gene. The entire region is transcribed into a 5-kb transcript, containing the rps14 pseudogene and the cob gene. Cob and rpl5 mRNAs are edited in several positions with different frequencies. The rps14 pseudogene is transcribed and edited in one position in common with other plants. Since no intact rps14 gene is found in the mitochondrial genome of Arabidopsis, the functional gene is presumably encoded in the nucleus.
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Affiliation(s)
- P Brandt
- Institut für Genbiologische Forschung, Berlin, Germany
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48
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Ye F, Bernhardt J, Abel WO. Genes for ribosomal proteins S3, L16, L5 and S14 are clustered in the mitochondrial genome of Brassica napus L. Curr Genet 1993; 24:323-9. [PMID: 8252643 DOI: 10.1007/bf00336784] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have cloned and sequenced an 8.9-kb mitochondrial-DNA fragment from rapeseed (Brassica napus L.). The nucleotide sequence indicates a gene cluster that encodes four ribosomal proteins (S3, L16, L5, S14), two tRNA genes (trnD, trnK), and the 5' region of the cob gene. The arrangement of these seven genes is trnD-trnK-rps3-rpl16-rpl5-rps14-cob. The rps3 and rpl16 frames overlap by 131 bp. The rpl5 and rps14 genes are separated by a 4-bp spacer. A 1474-basepair intron is located in the rps3 gene. The tRNA(Asp) gene (trnD) is very similar to the corresponding gene from chloroplasts (cp-like-tRNA(Asp)). Gene-specific probes for each ribosomal protein gene, and for the cp-like-trnD, trnK and cob genes, hybridized to a common pre-mRNA of an estimated size of 10 kilobases, indicating that these seven genes may be expressed as a single transcription unit. The rps3-rpl16-rpl5-rps14 region of B. napus mtDNA may function as a ribosomal operon, similar to the S10 and SPC operons of Escherichia coli and to the ribosomal protein operon of the chloroplast genome from Euglena gracilis.
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Affiliation(s)
- F Ye
- Arbeitsbereich Genetik, Institut für Allgemeine Botanik, Universität Hamburg, Germany
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Gonzalez DH, Bonnard G, Grienenberger JM. A gene involved in the biogenesis of c-type cytochromes is co-transcribed with a ribosomal protein gene in wheat mitochondria [corrected]. Curr Genet 1993; 24:248-55. [PMID: 8221934 DOI: 10.1007/bf00351799] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Sequence analysis of a transcribed region of the wheat mitochondrial (mt) genome revealed two open reading frames (orfs) coding for proteins of 589 and 174 amino acids. Both genes are co-transcribed in a 2.6-kb RNA. The largest orf codes for a hydrophobic protein which bears similarity to a bacterial protein involved in the biogenesis of c-type cytochromes. Its corresponding RNA sequence is fully edited at 34 positions. The second orf encodes a protein homologous to the amino-terminal third of E. coli ribosomal protein S1, corresponding to the ribosome-binding domain of this protein. Its RNA sequence is edited at four positions, one of the edits creating a stop codon. The presence of both proteins in wheat mitochondria was demonstrated using specific antibodies raised against fusion proteins obtained in E. coli from the corresponding cDNAs.
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Affiliation(s)
- D H Gonzalez
- Institute de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, Strasbourg, France
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Abstract
Chloroplasts contain a complete translational apparatus which, in land plants, synthesizes the 80 or so polypeptides encoded by the organelle's own small genome. Recent molecular genetic studies have revealed much about the chloroplast ribosomal proteins (RPs). Some of these proteins are encoded by the chloroplast genome and others by the nuclear genome. Many of these genes have now been cloned and characterized, including some that have no prokaryotic homologues.
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Affiliation(s)
- A R Subramanian
- Max-Planck-Institute for Molecular Genetics, Berlin-Dahlem, Germany
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