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He X, Zhang X, Deng Y, Yang R, Yu LX, Jia S, Zhang T. Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species. Int J Mol Sci 2023; 24:17334. [PMID: 38139163 PMCID: PMC10743518 DOI: 10.3390/ijms242417334] [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: 10/12/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Plant mitochondria are crucial for species evolution, phylogenetics, classification, and identification as maternal genetic material. However, the presence of numerous repetitive sequences, complex structures, and a low number of genes in the mitochondrial genome has hindered its complete assembly and related research endeavors. In this study, we assembled two mitochondrial genomes of alfalfa varieties of Zhongmu No.1 (299,123 bp) and Zhongmu No.4 (306,983 bp), based on a combination of PacBio, Illumina, and Hi-C sequences. The comparison of genome assemblies revealed that the same number of mitochondrial genes, including thirty-three protein-coding genes, sixteen tRNA genes, and three rRNA genes existed in the two varieties. Additionally, large fragments of repetitive sequences were found underlying frequent mitochondrial recombination events. We observed extensive transfer of mitochondrial fragments into the nuclear genome of Zhongmu No.4. Analysis of the cox1 and rrn18s genes in 35 Medicago accessions revealed the presence of population-level deletions and substitutions in the rrn18s gene. We propose that mitochondrial structural reorganizations may contribute to alfalfa evolution.
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Affiliation(s)
- Xiaofan He
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Xiaopeng Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Yantian Deng
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Rui Yang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA;
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (X.H.); (X.Z.); (Y.D.); (R.Y.)
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Lung B, Zemann A, Madej MJ, Schuelke M, Techritz S, Ruf S, Bock R, Hüttenhofer A. Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res 2006; 34:3842-52. [PMID: 16899451 PMCID: PMC1557801 DOI: 10.1093/nar/gkl448] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 06/12/2006] [Accepted: 06/12/2006] [Indexed: 12/31/2022] Open
Abstract
Small non-protein-coding RNAs (ncRNAs) have been identified in a wide spectrum of organisms ranging from bacteria to humans. In eukarya, systematic searches for ncRNAs have so far been restricted to the nuclear or cytosolic compartments of cells. Whether or not small stable non-coding RNA species also exist in cell organelles, in addition to tRNAs or ribosomal RNAs, is unknown. We have thus generated cDNA libraries from size-selected mammalian mitochondrial RNA and plant chloroplast RNA and searched for small ncRNA species in these two types of DNA-containing cell organelles. In total, we have identified 18 novel candidates for organellar ncRNAs in these two cellular compartments and confirmed expression of six of them by northern blot analysis or RNase A protection assays. Most candidate ncRNA genes map to intergenic regions of the organellar genomes. As found previously in bacteria, the presumptive ancestors of present-day chloroplasts and mitochondria, we also observed examples of antisense ncRNAs that potentially could target organelle-encoded mRNAs. The structural features of the identified ncRNAs as well as their possible cellular functions are discussed. The absence from our libraries of abundant small RNA species that are not encoded by the organellar genomes suggests that the import of RNAs into cell organelles is of very limited significance or does not occur at all.
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Affiliation(s)
- Birgit Lung
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical UniversityFritz-Pregl-Strasse 3, 6020 Innsbruck, Austria
- Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität MünsterVon-Esmarch Strasse 56, 48149 Münster, Germany
- Department of Neuropediatrics, Charité University HospitalAugustenburger Platz 1, D-13353 Berlin, Germany
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1D-14476, Potsdam-Golm, Germany
| | - Anja Zemann
- Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität MünsterVon-Esmarch Strasse 56, 48149 Münster, Germany
| | - Monika J. Madej
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical UniversityFritz-Pregl-Strasse 3, 6020 Innsbruck, Austria
- Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität MünsterVon-Esmarch Strasse 56, 48149 Münster, Germany
- Department of Neuropediatrics, Charité University HospitalAugustenburger Platz 1, D-13353 Berlin, Germany
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1D-14476, Potsdam-Golm, Germany
| | - Markus Schuelke
- Department of Neuropediatrics, Charité University HospitalAugustenburger Platz 1, D-13353 Berlin, Germany
| | - Sandra Techritz
- Department of Neuropediatrics, Charité University HospitalAugustenburger Platz 1, D-13353 Berlin, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1D-14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1D-14476, Potsdam-Golm, Germany
| | - Alexander Hüttenhofer
- To whom correspondence should be addressed. Tel: +43 512 9003 70250; Fax: +43 512 9003 73100;
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Rasmusson AG, Heiser V, Zabaleta E, Brennicke A, Grohmann L. Physiological, biochemical and molecular aspects of mitochondrial complex I in plants. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1364:101-11. [PMID: 9593845 DOI: 10.1016/s0005-2728(98)00021-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory complex I of plant mitochondria has to date been investigated with respect to physiological function, biochemical properties and molecular structure. In the respiratory chain complex I is the major entry gate for low potential electrons from matrix NADH, reducing ubiquinone and utilizing the released energy to pump protons across the inner membrane. Plant complex I is active against a background of several other NAD(P)H dehydrogenases, which do not contribute in proton pumping, but permit and establish several different routes of shuttling electrons from NAD(P)H to ubiquinone. Identification of the corresponding molecular structures, that is the proteins and genes of the different NADH dehydrogenases, will allow more detailed studies of this interactive regulatory network in plant mitochondria. Present knowledge of the structure of complex I and the respective mitochondrial and nuclear genes encoding various subunits of this complex in plants is summarized here. Copyright 1998 Elsevier Science B.V.
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Affiliation(s)
- AG Rasmusson
- Allgemeine Botanik, Universitat Ulm, Albert-Einstein-Allee 11, D-89069 Ulm, Germany
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Howad W, Kempken F. Cell type-specific loss of atp6 RNA editing in cytoplasmic male sterile Sorghum bicolor. Proc Natl Acad Sci U S A 1997; 94:11090-5. [PMID: 9380764 PMCID: PMC23623 DOI: 10.1073/pnas.94.20.11090] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA editing and cytoplasmic male sterility are two important phenomena in higher plant mitochondria. To determine whether correlations might exist between the two, RNA editing in different tissues of Sorghum bicolor was compared employing reverse transcription-PCR and subsequent sequence analysis. In etiolated shoots, RNA editing of transcripts of plant mitochondrial atp6, atp9, nad3, nad4, and rps12 genes was identical among fertile or cytoplasmic male sterile plants. We then established a protocol for mitochondrial RNA isolation from plant anthers and pollen to include in these studies. Whereas RNA editing of atp9, nad3, nad4, and rps12 transcripts in anthers was similar to etiolated shoots, mitochondrial atp6 RNA editing was strongly reduced in anthers of the A3Tx398 male sterile line of S. bicolor. atp6 transcripts of wheat and selected plastid transcripts in S. bicolor showed normal RNA editing, indicating that loss of atp6 RNA editing is specific for cytoplasmic male sterility S. bicolor mitochondria. Restoration of fertility in F1 and F2 lines correlated with an increase in RNA editing of atp6 transcripts. Our data suggest that loss of atp6 RNA editing contributes to or causes cytoplasmic male sterility in S. bicolor. Further analysis of the mechanism of cell type-specific loss of atp6 RNA editing activity may advance our understanding of the mechanism of RNA editing.
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Affiliation(s)
- W Howad
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Freyer R, Kiefer-Meyer MC, Kössel H. Occurrence of plastid RNA editing in all major lineages of land plants. Proc Natl Acad Sci U S A 1997; 94:6285-90. [PMID: 9177209 PMCID: PMC21041 DOI: 10.1073/pnas.94.12.6285] [Citation(s) in RCA: 156] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
RNA editing changes posttranscriptionally single nucleotides in chloroplast-encoded transcripts. Although much work has been done on mechanistic and functional aspects of plastid editing, little is known about evolutionary aspects of this RNA processing step. To gain a better understanding of the evolution of RNA editing in plastids, we have investigated the editing patterns in ndhB and rbcL transcripts from various species comprising all major groups of land plants. Our results indicate that RNA editing occurs in plastids of bryophytes, fern allies, true ferns, gymnosperms, and angiosperms. Both editing frequencies and editing patterns show a remarkable degree of interspecies variation. Furthermore, we have found that neither plastid editing frequencies nor the editing pattern of a specific transcript correlate with the phylogenetic tree of the plant kingdom. The poor evolutionary conservation of editing sites among closely related species as well as the occurrence of single species-specific editing sites suggest that the differences in the editing patterns and editing frequencies are probably due both to independent loss and to gain of editing sites. In addition, our results indicate that RNA editing is a relatively ancient process that probably predates the evolution of land plants. This supposition is in good agreement with the phylogenetic data obtained for plant mitochondrial RNA editing, thus providing additional evidence for common evolutionary roots of the two plant organellar editing systems.
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Affiliation(s)
- R Freyer
- Institut für Biologie III, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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