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Butenko A, Lukeš J, Speijer D, Wideman JG. Mitochondrial genomes revisited: why do different lineages retain different genes? BMC Biol 2024; 22:15. [PMID: 38273274 PMCID: PMC10809612 DOI: 10.1186/s12915-024-01824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA.
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2
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Tum S, Toda K, Matsui T, Kikuchi R, Kong S, Meas P, Ear U, Ohtomo Y, Otake T, Sato T. Seasonal effects of natural attenuation on drainage contamination from artisanal gold mining, Cambodia: Implication for passive treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150398. [PMID: 34563902 DOI: 10.1016/j.scitotenv.2021.150398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
In Mondulkiri province, Cambodia, artisanal gold miners dump tailings and wastewater from gold processing into a tributary of the Prek Te River. In the rainy season, heavy metal concentrations in the tributary decrease below the WHO drinking water standard levels through natural attenuation; however, this does not occur in the dry season. To further understand the natural attenuation mechanism, detailed analyses of the wastewater from tailing and tributary water, tributary sediments, waste rock, and ore minerals were undertaken in both seasons. The high concentration of dissolved Fe in the contaminated tributary plays a significant role in As removal during the rainy season, whereas other elements such as Ni, Se, and Cu concentration decrease due to dilution. Schwertmannite formation, controlled by iron-oxidizing bacteria, was only found at the bottom of the tributary during the rainy season. In the dry season, As, Ni, Se, and Cu concentrations remained at their original levels because there was no formation of schwertmannite or dilution by rainwater. The existing schwertmannite also starts to dissolve as the pH decreases. Seasonal dynamics cause the failure of natural attenuation; thus, methods for maintaining its effectiveness in the dry season are needed. In addition, geochemical modeling was conducted to determine the significant roles of schwertmannite formation and dilution of rainwater in the tributary. Schwertmannite is a potential adsorbent for As removal from drainage. However, dilution provided indirect and direct impacts on the tributary, such as increasing the pH and diluting the concentration of toxic elements.
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Affiliation(s)
- Sereyroith Tum
- Graduate School of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan.
| | - Kanako Toda
- Nuclear Professional School, School of Engineering, University of Tokyo, 2-22 Shirakata, Tokai, Ibaraki 319-1188, Japan
| | - Tatsuya Matsui
- Graduate School of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan
| | - Ryosuke Kikuchi
- Faculty of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan
| | - Sitha Kong
- Geology Department, Ministry of Mine and Energy, Pasteur Street 51, Phnom Penh 12210, Cambodia
| | - Panha Meas
- Geology Department, Ministry of Mine and Energy, Pasteur Street 51, Phnom Penh 12210, Cambodia
| | - Unsovath Ear
- Geology Department, Ministry of Mine and Energy, Pasteur Street 51, Phnom Penh 12210, Cambodia
| | - Yoko Ohtomo
- Faculty of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan
| | - Tsubasa Otake
- Faculty of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan
| | - Tsutomu Sato
- Faculty of Engineering, Hokkaido University, N13W8, Kita-Ku, Sapporo 060-8628, Japan
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Hall ND, Zhang H, Mower JP, McElroy JS, Goertzen LR. The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content within Poaceae. Genome Biol Evol 2020; 12:3684-3697. [PMID: 31665327 PMCID: PMC7145533 DOI: 10.1093/gbe/evz229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Plant mitochondrial (mt) genome assembly provides baseline data on size, structure, and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The mt genome for Eleusine indica (Poaceae: goosegrass) is comprehensibly analyzed here, providing key reference data for an economically significant invasive species that is also the maternal parent of the allotetraploid crop Finger millet (Eleusine coracana). The assembled E. indica genome contains 33 protein coding genes, 6 rRNA subunits, 24 tRNA, 8 large repetitive regions 15 kb of transposable elements across a total of 520,691 bp. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4, and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of publicly available data. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade.
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Affiliation(s)
- Nathan D Hall
- Department of Biological Sciences, Auburn University
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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Kan SL, Shen TT, Gong P, Ran JH, Wang XQ. The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome. BMC Evol Biol 2020; 20:10. [PMID: 31959109 PMCID: PMC6971862 DOI: 10.1186/s12862-020-1582-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/13/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.
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Affiliation(s)
- Sheng-Long Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ping Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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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: 31] [Impact Index Per Article: 6.2] [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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Liu JL, Yao J, Wang F, Min N, Gu JH, Li ZF, Sunahara G, Duran R, Solevic-Knudsen T, Hudson-Edwards KA, Alakangas L. Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:98-107. [PMID: 30669085 DOI: 10.1016/j.envpol.2018.12.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/08/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.
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Affiliation(s)
- Jian-Li Liu
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Fei Wang
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ning Min
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Ji-Hai Gu
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China
| | - Zi-Fu Li
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resource and Environment Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Tatjana Solevic-Knudsen
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoseva 12, PO Box 473, 11001, Belgrade, Serbia
| | - Karen A Hudson-Edwards
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, UK
| | - Lena Alakangas
- Department of Chemical Engineering and Geosciences, Luleå University of Technology, SE-97187 Luleå, Sweden
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Zhu Y, Vaughn JC. Experimental Verification and Evolutionary Origin of 5'-UTR Polyadenylation Sites in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:969. [PMID: 30026753 PMCID: PMC6041940 DOI: 10.3389/fpls.2018.00969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Messenger RNA (mRNA) polyadenylation is an indispensable step during post-transcriptional pre-mRNA processing for most genes in eukaryotes. The usage of one poly(A) site over another is known as alternative polyadenylation (APA). APA has been implicated in gene expression regulation through its role of selecting the ends of a transcript. Recent studies of polyadenylation profiles in the Arabidopsis database unexpectedly predicted that a portion of the poly(A) sites are located in the 5'-UTR, which remains to be experimentally verified. We selected 16 genes from a dataset of 744, based on criteria designed to minimize problems in interpretation. Here, we experimentally verify 5'-UTR-APA in Arabidopsis for 10 of the 16 selected genes, and show for the first time existence of independent polyadenylated 5'-UTR transcripts, arising due to alternative polyadenylation. We used 3'-RACE and sequencing to validate poly(A) sites and northern blot to show that the observed short upstream transcripts do not arise from the 3'-end of a previously unrecognized convergent gene. Evidence is reported showing that two of the independent upstream open reading frame (uORF) transcripts studied, one containing a complex dual uORF, very likely arose by exon shuffling following duplication of the 5'-end from the downstream major open reading frame (mORF). Finally, results are presented to show that the uORF in this gene may encode two short functional proteins, based on observation of amino acid sequence conservation encoded by the dual uORFs.
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Szafranski P. Intercompartmental Piecewise Gene Transfer. Genes (Basel) 2017; 8:genes8100260. [PMID: 28984842 PMCID: PMC5664110 DOI: 10.3390/genes8100260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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9
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Wu Z, Sloan DB, Brown CW, Rosenblueth M, Palmer JD, Ong HC. Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses. Mol Biol Evol 2017; 34:2340-2354. [PMID: 28541477 PMCID: PMC5850859 DOI: 10.1093/molbev/msx170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Colin W. Brown
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
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10
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Restovic F, Espinoza-Corral R, Gómez I, Vicente-Carbajosa J, Jordana X. An active Mitochondrial Complex II Present in Mature Seeds Contains an Embryo-Specific Iron-Sulfur Subunit Regulated by ABA and bZIP53 and Is Involved in Germination and Seedling Establishment. FRONTIERS IN PLANT SCIENCE 2017; 8:277. [PMID: 28293251 PMCID: PMC5329045 DOI: 10.3389/fpls.2017.00277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/14/2017] [Indexed: 05/20/2023]
Abstract
Complex II (succinate dehydrogenase) is an essential mitochondrial enzyme involved in both the tricarboxylic acid cycle and the respiratory chain. In Arabidopsis thaliana, its iron-sulfur subunit (SDH2) is encoded by three genes, one of them (SDH2.3) being specifically expressed during seed maturation in the embryo. Here we show that seed SDH2.3 expression is regulated by abscisic acid (ABA) and we define the promoter region (-114 to +49) possessing all the cis-elements necessary and sufficient for high expression in seeds. This region includes between -114 and -32 three ABRE (ABA-responsive) elements and one RY-enhancer like element, and we demonstrate that these elements, although necessary, are not sufficient for seed expression, our results supporting a role for the region encoding the 5' untranslated region (+1 to +49). The SDH2.3 promoter is activated in leaf protoplasts by heterodimers between the basic leucine zipper transcription factors bZIP53 (group S1) and bZIP10 (group C) acting through the ABRE elements, and by the B3 domain transcription factor ABA insensitive 3 (ABI3). The in vivo role of bZIP53 is further supported by decreased SDH2.3 expression in a knockdown bzip53 mutant. By using the protein synthesis inhibitor cycloheximide and sdh2 mutants we have been able to conclusively show that complex II is already present in mature embryos before imbibition, and contains mainly SDH2.3 as iron-sulfur subunit. This complex plays a role during seed germination sensu-stricto since we have previously shown that seeds lacking SDH2.3 show retarded germination and now we demonstrate that low concentrations of thenoyltrifluoroacetone, a complex II inhibitor, also delay germination. Furthermore, complex II inhibitors completely block hypocotyl elongation in the dark and seedling establishment in the light, highlighting an essential role of complex II in the acquisition of photosynthetic competence and the transition from heterotrophy to autotrophy.
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Affiliation(s)
- Franko Restovic
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Roberto Espinoza-Corral
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Isabel Gómez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas – UPM-INIA, Campus de Montegancedo, Universidad Politécnica de MadridMadrid, Spain
| | - Xavier Jordana
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
- *Correspondence: Xavier Jordana,
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11
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Jacoby RP, Millar AH, Taylor NL. Opportunities for wheat proteomics to discover the biomarkers for respiration-dependent biomass production, stress tolerance and cytoplasmic male sterility. J Proteomics 2016; 143:36-44. [DOI: 10.1016/j.jprot.2016.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/10/2016] [Accepted: 02/17/2016] [Indexed: 01/23/2023]
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12
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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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13
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Park S, Ruhlman TA, Sabir JSM, Mutwakil MHZ, Baeshen MN, Sabir MJ, Baeshen NA, Jansen RK. Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. BMC Genomics 2014; 15:405. [PMID: 24884625 PMCID: PMC4045975 DOI: 10.1186/1471-2164-15-405] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/15/2014] [Indexed: 11/17/2022] Open
Abstract
Background Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. Results The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Conclusions Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-405) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
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14
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Rousseau-Gueutin M, Huang X, Higginson E, Ayliffe M, Day A, Timmis JN. Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages. PLANT PHYSIOLOGY 2013; 161:1918-29. [PMID: 23435694 PMCID: PMC3613465 DOI: 10.1104/pp.113.214528] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic acetyl-CoA carboxylase subunit (accD) gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to green fluorescent protein was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified, and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.
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Affiliation(s)
- Mathieu Rousseau-Gueutin
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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15
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Sloan DB, Müller K, McCauley DE, Taylor DR, Štorchová H. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility. THE NEW PHYTOLOGIST 2012; 196:1228-1239. [PMID: 23009072 DOI: 10.1111/j.1469-8137.2012.04340.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/17/2012] [Indexed: 05/04/2023]
Abstract
In angiosperms, mitochondrial-encoded genes can cause cytoplasmic male sterility (CMS), resulting in the coexistence of female and hermaphroditic individuals (gynodioecy). We compared four complete mitochondrial genomes from the gynodioecious species Silene vulgaris and found unprecedented amounts of intraspecific diversity for plant mitochondrial DNA (mtDNA). Remarkably, only about half of overall sequence content is shared between any pair of genomes. The four mtDNAs range in size from 361 to 429 kb and differ in gene complement, with rpl5 and rps13 being intact in some genomes but absent or pseudogenized in others. The genomes exhibit essentially no conservation of synteny and are highly repetitive, with evidence of reciprocal recombination occurring even across short repeats (< 250 bp). Some mitochondrial genes exhibit atypically high degrees of nucleotide polymorphism, while others are invariant. The genomes also contain a variable number of small autonomously mapping chromosomes, which have only recently been identified in angiosperm mtDNA. Southern blot analysis of one of these chromosomes indicated a complex in vivo structure consisting of both monomeric circles and multimeric forms. We conclude that S. vulgaris harbors an unusually large degree of variation in mtDNA sequence and structure and discuss the extent to which this variation might be related to CMS.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Karel Müller
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Lysolaje, 16502, Czech Republic
| | - David E McCauley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Helena Štorchová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Lysolaje, 16502, Czech Republic
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16
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Triant DA, Hayes LD. Molecular approaches in behavioural research: a cautionary note regarding mitochondrial transfers to the nucleus (numts). Anim Behav 2011. [DOI: 10.1016/j.anbehav.2011.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura SI, Tsutsumi N, Kadowaki KI. Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol Biol Evol 2008; 25:1566-75. [PMID: 18453549 DOI: 10.1093/molbev/msn102] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. Even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. Gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. Gene loss is an ongoing process in the mitochondria and chloroplasts of higher plants. The gene for ribosomal protein S16 (rps16) is encoded in the chloroplast genome of most higher plants but not in Medicago truncatula and Populus alba. Here, we show that these 2 species have compensated for loss of the rps16 from the chloroplast genome by having a mitochondrial rps16 that can target the chloroplasts as well as mitochondria. Furthermore, in Arabidopsis thaliana, Lycopersicon esculentum, and Oryza sativa, whose chloroplast genomes encode the rps16, we show that the product of the mitochondrial rps16 has dual targeting ability. These results suggest that the dual targeting of RPS16 to the mitochondria and chloroplasts emerged before the divergence of monocots and dicots (140-150 MYA). The gene substitution of the chloroplast rps16 by the nuclear-encoded rps16 in higher plants is the first report about ongoing gene substitution by dual targeting and provides evidence for an intermediate stage in the formation of this heterogeneous organelle.
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Affiliation(s)
- Minoru Ueda
- Genetic Diversity Department, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki, Japan
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18
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Mizuno N, Sugie A, Kobayashi F, Takumi S. Mitochondrial alternative pathway is associated with development of freezing tolerance in common wheat. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:462-7. [PMID: 17766003 DOI: 10.1016/j.jplph.2007.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 04/29/2007] [Accepted: 04/30/2007] [Indexed: 05/17/2023]
Abstract
Cold acclimation is an adaptive process for acquiring cold/freezing tolerance in wheat. To clarify the cultivar difference of freezing tolerance, we compared mitochondrial respiration activity and the expression profile of alternative oxidase (AOX) genes under low-temperature conditions using two common wheat cultivars differing in freezing tolerance. During cold acclimation, the respiration capacity of the alternative pathway significantly increased in a freezing-tolerant cultivar compared with a freezing-sensitive cultivar. More abundant accumulation of the AOX and uncoupling protein gene transcripts was also observed under the low-temperature conditions in the tolerant cultivar than in the sensitive cultivar. These results suggest that the mitochondrial alternative pathway might be partly associated with the cold acclimation and freezing tolerance in wheat.
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Affiliation(s)
- Nobuyuki Mizuno
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan
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19
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Liu SL, Adams K. Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evol Biol 2008; 8:25. [PMID: 18221556 PMCID: PMC2258280 DOI: 10.1186/1471-2148-8-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 01/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene duplication has been a fundamental process in the evolution of eukaryotic genomes. After duplication one copy (or both) can undergo divergence in sequence, expression pattern, and function. Two divergent copies of the ribosomal protein S13 gene (rps13) of chloroplast origin are found in the nucleus of the rosids Arabidopsis, Gossypium, and Glycine. One encodes chloroplast-imported RPS13 (nucp rps13), while the other encodes mitochondria-imported RPS13 (numit rps13). The rps13 gene has been lost from mitochondrial DNA (mt rps13) of many rosids. RESULTS We studied sequence evolution of numit rps13 in comparison with nucp rps13 in seven rosid genera. Ka/Ks analysis and likelihood ratio tests showed considerably higher Ka values and Ka/Ks ratios in numit rps13 than in nucp rps13, indicating increased amino acid sequence divergence in numit rps13. Two positively selected codons were detected in numit RPS13 in regions that are inferred to interact with the 16S rRNA. Several amino acids in numit RPS13 have changed from the one present in nucp RPS13 to the one present in mt RPS13, showing that numit rps13 is becoming more like mt rps13. Comparison of expression patterns and levels of numit rps13 and nucp rps13 in Arabidopsis using microarray data indicated divergence in gene expression. We discovered that in addition to numit rps13, Malus (apple) contains a transcribed mt rps13 gene. To determine if partitioning of expression takes place between numit rps13 and mt rps13, expression of both copies and RNA editing of mt rps13 were examined by RT-PCR, qRT-PCR, and sequencing from 14 different organ types plus seedlings subjected to five different abiotic stresses. Co-expression of numit rps13 and mt rps13 was observed in all the organs and various stress treatments. We determined that purifying selection is acting on both numit rps13 and mt rps13 in Malus. CONCLUSION Our data provide evidence that numit rps13 genes in rosids have experienced adaptive sequence evolution and convergent evolution with mt rps13. Co-expression of numit rps13 and mt rps13 and purifying selection on both genes in Malus suggest that both are functional. The three organellar rps13 genes in rosids provide a distinctive case of gene duplication involving the co-evolution of the nuclear and cytoplasmic genomes.
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Affiliation(s)
- Shao-Lun Liu
- UBC Botanical Garden & Centre for Plant Research and Botany Department, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
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20
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Sugie A, Murai K, Takumi S. Alteration of respiration capacity and transcript accumulation level of alternative oxidase genes in necrosis lines of common wheat. Genes Genet Syst 2007; 82:231-9. [PMID: 17660693 DOI: 10.1266/ggs.82.231] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial alternative oxidase (AOX) is the terminal oxidase responsible for cyanide-insensitive and salicylhydroxamic acid-sensitive respiration in plants. AOX is a key enzyme of the alternative respiration pathway. To study the effects of necrotic cell death on the mitochondrial function, production of reactive oxygen species (ROS), respiration capacities and accumulation patterns of mitochondria-targeted protein-encoding gene transcripts were compared between wild-type, lesion-mimic mutant and hybrid necrosis wheat plants. Around cells with the necrosis symptom, ROS accumulated abundantly in the intercellular spaces. The ratio of the alternative pathway to the cytochrome pathway was markedly enhanced in the necrotic leaves. Transcripts of a wheat AOX gene, Waox1a, were more abundant in a novel lesion-mimic mutant of common wheat than in the wild-type plants. An increased level of the Waox1a transcripts was also observed in hybrid plants containing Ne1 and Ne2 genes. These results indicated that an increase of the wheat AOX transcript level resulted in enhancement of respiration capacity of the alternative pathway in the necrotic cells.
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Affiliation(s)
- Atsushi Sugie
- Laboratory of Plant Genetics, Faculty of Agriculture, and Graduate School of Science and Technology, Kobe University, Nada-ku, Kobe, Japan
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21
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Mower JP, Palmer JD. Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics 2006; 276:285-93. [PMID: 16862402 DOI: 10.1007/s00438-006-0139-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 05/23/2006] [Indexed: 11/27/2022]
Abstract
RNA editing is a process that modifies the information in transcripts of almost all angiosperm mitochondrial protein-coding genes. In order to determine the frequency and distribution of mitochondrial RNA editing in Beta vulgaris, cDNAs were sequenced and compared to the published genome sequence. 357 C to U conversions were identified across the 31 known protein genes and pseudogenes in Beta, the fewest so far for a plant mitochondrial genome. Editing patterns in the putative gene orf518 indicate that it is most likely a functional ccmC homolog, indicating that patterns of editing can be a useful determinant of gene functionality. orf518 also contains a triplicated repeat region whose members are nearly identical yet differentially edited, most likely due to differences in the sequence context of the editing sites. In addition, we show that partial editing in Beta is common at silent editing sites but rare at nonsilent editing sites, extending previous observations to a complete plant mitochondrial genome. Finally, the degree of partial editing observed for certain genes was dependent on the choice of primers used, demonstrating that care must be taken when designing primers for use in editing studies.
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Affiliation(s)
- Jeffrey P Mower
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. [corrected]
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22
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Ong HC, Palmer JD. Pervasive survival of expressed mitochondrial rps14 pseudogenes in grasses and their relatives for 80 million years following three functional transfers to the nucleus. BMC Evol Biol 2006; 6:55. [PMID: 16842621 PMCID: PMC1543663 DOI: 10.1186/1471-2148-6-55] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Accepted: 07/14/2006] [Indexed: 01/10/2023] Open
Abstract
Background Many mitochondrial genes, especially ribosomal protein genes, have been frequently transferred as functional entities to the nucleus during plant evolution, often by an RNA-mediated process. A notable case of transfer involves the rps14 gene of three grasses (rice, maize, and wheat), which has been relocated to the intron of the nuclear sdh2 gene and which is expressed and targeted to the mitochondrion via alternative splicing and usage of the sdh2 targeting peptide. Although this transfer occurred at least 50 million years ago, i.e., in a common ancestor of these three grasses, it is striking that expressed, nearly intact pseudogenes of rps14 are retained in the mitochondrial genomes of both rice and wheat. To determine how ancient this transfer is, the extent to which mitochondrial rps14 has been retained and is expressed in grasses, and whether other transfers of rps14 have occurred in grasses and their relatives, we investigated the structure, expression, and phylogeny of mitochondrial and nuclear rps14 genes from 32 additional genera of grasses and from 9 other members of the Poales. Results Filter hybridization experiments showed that rps14 sequences are present in the mitochondrial genomes of all examined Poales except for members of the grass subfamily Panicoideae (to which maize belongs). However, PCR amplification and sequencing revealed that the mitochondrial rps14 genes of all examined grasses (Poaceae), Cyperaceae, and Joinvilleaceae are pseudogenes, with all those from the Poaceae sharing two 4-NT frameshift deletions and all those from the Cyperaceae sharing a 5-NT insertion (only one member of the Joinvilleaceae was examined). cDNA analysis showed that all mitochondrial pseudogenes examined (from all three families) are transcribed, that most are RNA edited, and that surprisingly many of the edits are reverse (U→C) edits. Putatively nuclear copies of rps14 were isolated from one to several members of each of these three Poales families. Multiple lines of evidence indicate that the nuclear genes are probably the products of three independent transfers. Conclusion The rps14 gene has, most likely, been functionally transferred from the mitochondrion to the nucleus at least three times during the evolution of the Poales. The transfers in Cyperaceae and Poaceae are relatively ancient, occurring in the common ancestor of each family, roughly 80 million years ago, whereas the putative Joinvilleaceae transfer may be the most recent case of functional organelle-to-nucleus transfer yet described in any organism. Remarkably, nearly intact and expressed pseudogenes of rps14 have persisted in the mitochondrial genomes of most lineages of Poaceae and Cyperaceae despite the antiquity of the transfers and of the frameshift and RNA editing mutations that mark the mitochondrial genes as pseudogenes. Such long-term, nearly pervasive survival of expressed, apparent pseudogenes is to our knowledge unparalleled in any genome. Such survival probably reflects a combination of factors, including the short length of rps14, its location immediately downstream of rpl5 in most plants, and low rates of nucleotide substitutions and indels in plant mitochondrial DNAs. Their survival also raises the possibility that these rps14 sequences may not actually be pseudogenes despite their appearance as such. Overall, these findings indicate that intracellular gene transfer may occur even more frequently in angiosperms than already recognized and that pseudogenes in plant mitochondrial genomes can be surprisingly resistant to forces that lead to gene loss and inactivation.
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Affiliation(s)
- Han Chuan Ong
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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23
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Affiliation(s)
- Linda Bonen
- Biology Department, University of Ottawa, Ottawa, Canada K1N 6N5.
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24
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Choi C, Liu Z, Adams KL. Evolutionary transfers of mitochondrial genes to the nucleus in the Populus lineage and coexpression of nuclear and mitochondrial Sdh4 genes. THE NEW PHYTOLOGIST 2006; 172:429-39. [PMID: 17083674 DOI: 10.1111/j.1469-8137.2006.01821.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The transfer of mitochondrial genes to the nucleus is an ongoing evolutionary process in flowering plants. Evolutionarily recent gene transfers provide insights into the evolutionary dynamics of the process and the way in which transferred genes become functional in the nucleus. Genes that are present in the mitochondrion of some angiosperms but have been transferred to the nucleus in the Populus lineage were identified by searches of Populus sequence databases. Sequence analyses and expression experiments were used to characterize the transferred genes. Two succinate dehydrogenase genes and six mitochondrial ribosomal protein genes have been transferred to the nucleus in the Populus lineage and have become expressed. Three transferred genes have gained an N-terminal mitochondrial targeting presequence from other pre-existing genes and two of the transferred genes do not contain an N-terminal targeting presequence. Intact copies of the succinate dehydrogenase gene Sdh4 are present in both the mitochondrion and the nucleus. Both copies of Sdh4 are expressed in multiple organs of two Populus species and RNA editing occurs in the mitochondrial copy. These results provide a genome-wide perspective on mitochondrial genes that were transferred to the nucleus and became expressed, functional genes during the evolutionary history of Populus.
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Affiliation(s)
- Catherine Choi
- UBC Botanical Garden & Centre for Plant Research, and Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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25
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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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26
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Regina TMR, Picardi E, Lopez L, Pesole G, Quagliariello C. A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms. J Mol Evol 2005; 60:196-206. [PMID: 15785848 DOI: 10.1007/s00239-004-0098-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 09/09/2004] [Indexed: 10/25/2022]
Abstract
Comparative analysis of the ribosomal protein S3 gene (rps3) in the mitochondrial genome of Cycas with newly sequenced counterparts from Magnolia and Helianthus and available sequences from higher plants revealed that the positional clustering with the genes for ribosomal protein S19 (rps19) and L16 (rpl16) is preserved in gymnosperms. However, in contrast to the other land plant species, the rps3 gene in Cycas mitochondria is unique in possessing a second intron: rps3i2. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the transcripts generated from the rps19-rps3-rpl16 cluster in Cycas mitochondria demonstrated that the genes are cotranscribed and extensively modified by RNA editing and that both introns are efficiently spliced. Despite remarkable size heterogeneity, the Cycas rps3i1 can be shown to be homologous to the group IIA introns present within the rps3 gene of algae and land plants, including Magnolia and Helianthus. Conversely, sequences similar to the rps3i2 have not been reported previously. On the basis of conserved primary and secondary structure the second intervening sequence interrupting the Cycas rps3 gene has been classified as a group II intron. The close relationship of the rps3i2 to a group of different plant mitochondrial introns is intriguing and suggestive of a mitochondrial derivation for this novel intervening sequence. Interestingly, the rps3i2 appears to be conserved at the same gene location in other gymnosperms. Furthermore, the pattern of the rps3i2 distribution among algae and land plants provides evidence for the evolutionary acquisition of this novel intron in gymnosperms via intragenomic transposition or retrotransposition.
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MESH Headings
- Base Sequence
- Cycas/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Genes, Plant
- Genome, Plant
- Helianthus/genetics
- Introns
- Magnolia/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plant Proteins/genetics
- RNA Editing
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribosomal Proteins/genetics
- Species Specificity
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Affiliation(s)
- Teresa M R Regina
- Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, 87036 Arcavacata di Rende, Italy
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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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28
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Mizumoto K, Murai K, Nakamura C, Takumi S. Preferential expression of a HLP homolog encoding a mitochondrial L14 ribosomal protein in stamens of common wheat. Gene 2004; 343:281-9. [PMID: 15588583 DOI: 10.1016/j.gene.2004.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 08/15/2004] [Accepted: 09/10/2004] [Indexed: 11/23/2022]
Abstract
Interaction between nucleus and cytoplasm has essential roles in plant development, including that of floral organs. We isolated a wheat homolog Whlp of Arabidopsis HUELLENLOS PARALOG (HLP) gene encoding a mitochondrial (mt) ribosomal protein L14. Transient expression analysis using the green fluorescent protein (GFP) fusion protein showed that 50 amino residues located on the N-terminal of the wheat HLP homolog (WHLP) protein acted as a mt-targeting signal (MTS). Expression patterns of the Whlp gene were compared among floral organs of alloplasmic lines of wheat, in which intrinsic cytoplasms were replaced by the cytoplasm of a wild relative Aegilops crassa. In these alloplasmic lines, pistillody (homeotic transformation of stamens into pistil-like organs) is induced by the alien cytoplasm in the absence of nuclear restorer genes. The Whlp transcripts preferentially accumulated in stamens compared with pistils, leaves, and roots. The expression level of Whlp in the pistillate stamens of the alloplasmic lines was similar to that in genuine pistils of both euplasmic lines and fertile alloplasmic lines. The result suggested that the elevated expression of the Whlp gene plays a role in aiding the development of male reproductive organ but not in the determination of its whorl identity. A comparable expression pattern was observed in another nuclear-encoded mt ribosomal protein gene but not in a mt-encoded gene. The different expression patterns of different mt ribosomal protein genes suggest that the abundance of mt ribosomal proteins is differentially regulated in the organ/tissue development in wheat.
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Affiliation(s)
- Kota Mizumoto
- Laboratory of Plant Genetics, Department of Biological and Environmental Science, Faculty of Agriculture, and Division of Life Science, Graduate School of Science and Technology, Kobe University, Nada-ku, Kobe 657-8501, Japan
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Knoop V. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 2004; 46:123-39. [PMID: 15300404 DOI: 10.1007/s00294-004-0522-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2004] [Revised: 07/06/2004] [Accepted: 07/07/2004] [Indexed: 11/25/2022]
Abstract
Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.
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Affiliation(s)
- Volker Knoop
- IZMB--Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, Bonn, Germany.
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