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Sanchez-Puerta MV, Zubko MK, Palmer JD. Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant. THE NEW PHYTOLOGIST 2015; 206:381-396. [PMID: 25441621 PMCID: PMC4342287 DOI: 10.1111/nph.13188] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/14/2014] [Indexed: 05/10/2023]
Abstract
The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants. We conducted the first study in which the organellar genomes of a cybrid - between Nicotiana tabacum and Hyoscyamus niger - were sequenced and compared to those of its parents. This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes. Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double-strand break repair and/or break-induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene - and genome - transfer in angiosperm mitochondrial DNAs.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- Facultad de Ciencias Exactas y Naturales and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo & IBAM-CONICET, Chacras de Coria, 5500, Mendoza, Argentina
| | - Mikhajlo K Zubko
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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2
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Stoddard BL. Homing endonucleases from mobile group I introns: discovery to genome engineering. Mob DNA 2014; 5:7. [PMID: 24589358 PMCID: PMC3943268 DOI: 10.1186/1759-8753-5-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/13/2014] [Indexed: 12/20/2022] Open
Abstract
Homing endonucleases are highly specific DNA cleaving enzymes that are encoded within genomes of all forms of microbial life including phage and eukaryotic organelles. These proteins drive the mobility and persistence of their own reading frames. The genes that encode homing endonucleases are often embedded within self-splicing elements such as group I introns, group II introns and inteins. This combination of molecular functions is mutually advantageous: the endonuclease activity allows surrounding introns and inteins to act as invasive DNA elements, while the splicing activity allows the endonuclease gene to invade a coding sequence without disrupting its product. Crystallographic analyses of representatives from all known homing endonuclease families have illustrated both their mechanisms of action and their evolutionary relationships to a wide range of host proteins. Several homing endonucleases have been completely redesigned and used for a variety of genome engineering applications. Recent efforts to augment homing endonucleases with auxiliary DNA recognition elements and/or nucleic acid processing factors has further accelerated their use for applications that demand exceptionally high specificity and activity.
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Affiliation(s)
- Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N, A3-025, Seattle, WA 98109, USA.
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3
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Mitochondrial and nuclear mitoribosomal suppressors that enable misreading of ochre codons in yeast mitochondria : I. Isolation, localization and allelism of suppressors. Curr Genet 2013; 9:1-10. [PMID: 24173504 DOI: 10.1007/bf00396198] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/1984] [Indexed: 10/26/2022]
Abstract
A systematic search for suppressors of mutations which cause a deficiency in the splicing of mitochondrial RNA has been undertaken. These splicing mutations were localized in the mRNA-maturase coding sequence of the second intron of the cob-boxgene, i.e. in the box3locus. A total of 953 revertants (mostly spontaneous in origin) were isolated and their genetic nature (nuclear vs. mitochondrial) and phenotype characterized.Most revertants were mitochondrially determined and displayed a wild-type phenotype. A mitochondrial suppressor unlinked with the box3 (-)target mutation was uncovered among the revertants displaying a pseudo-wild phenotype: out of 26 revertants analyzed, derived from 7 different box3(-) mutants only one such suppressor mutation mim3-1 was found. It was localized by rho(-) deletion mapping in the region between the oxi2 and oxi3 gene, within (or in the vicinity) the gene specifying the 15S ribosomal RNA.Nuclear suppressors were isolated from seven different box3 (-)mutants. All were recessive and had a pseudo-wild phenotype. Three such suppressors nam3-1, nam3-2 and nam3-3 were investigated more extensively. Tetrad analysis has shown that they are alleles of the same nuclear locus NAM3 and mitotic analysis has shown that they do not segregate mitotically.
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4
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Spreitzer RJ, Chastain CJ, Ogren WL. Chloroplast gene suppression of defective ribulosebisphosphate carboxylase/oxygenase in Chlamydomonas reinhardii: evidence for stable heteroplasmic genes. Curr Genet 2013; 9:83-9. [PMID: 24173514 DOI: 10.1007/bf00396208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/1984] [Indexed: 11/28/2022]
Abstract
The rcl-u-1-18-5B chloroplast mutation results in the absence of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) holoenzyme in the green alga Chlamydomonas reinhardii. The 18-5B mutant strain lacks photosynthesis and displays alight-sensitive, acetate-requiring phenotype. In the present investigations, revertants of 18-5B were recovered that regained photosynthetic competence. These revertants have decreased levels of Rubisco holoenzyme relative to wild type and display heteroplasmicity, segregating wild-type (revertant) and acetate-requiring phenotypes during vegetative growth or through meiosis. One of these revertants, R10-I, was studied further. The heteroplasmicity associated with photoautotrophically-grown R10-I was found to be stable through subcloning and heritable through several crosses. During growth in acetate medium in the dark, where photosynthesis provides no selective advantage, the wild-type phenotype was lost. Acetate-requiring segregants became homoplasmic but wild-type segregants did not. Organellar intergenic-suppression is discussed in light of the observed stable heteroplasmicity.
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Affiliation(s)
- R J Spreitzer
- Department of Agronomy, University of Illinois, US Department of Agriculture, Agricultural Research Service, 61801, Urbana, Illinois, USA
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5
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Doetsch M, Gstrein T, Schroeder R, Fürtig B. Mechanisms of StpA-mediated RNA remodeling. RNA Biol 2010; 7:735-43. [PMID: 21057189 DOI: 10.4161/rna.7.6.13882] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In bacteria, transcription, translation and gene regulation are highly coupled processes. The achievement of a certain functional structure at a distinct temporal and spatial position is therefore essential for RNA molecules. Proteins that facilitate this proper folding of RNA molecules are called RNA chaperones. Here a prominent example from E. coli is reviewed: the nucleoid associated protein StpA. Based on its various RNA remodeling functions, we propose a mechanistic model that explains how StpA promotes RNA folding. Through transient interactions via the RNA backbone, thereby shielding repelling charges in RNA, it pre-positions the RNA molecules for the successful formation of transition states from encounter complexes.
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6
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Szczepanek T, Gora M, Monteilhet C, Wysocka M, Lazowska J, Golik P. In vivo analysis of the relationships between the splicing and homing activities of a group I intron-encoded I-ScaI/bi2-maturase of Saccharomyces capensis produced in the yeast cytoplasm. FEMS Yeast Res 2006; 6:823-35. [PMID: 16879432 DOI: 10.1111/j.1567-1364.2006.00064.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The I-ScaI/bi2-maturase of Saccharomyces capensis acts as a specific homing endonuclease promoting intron homing, and as a maturase promoting intron splicing. Using the universal code equivalent of the mitochondrial gene encoding the I-ScaI/bi2-maturase, a number of truncated forms of the synthetic gene were constructed, shortened on either side, as were several mutated alleles of the protein. The shortest translation product that fully retains both activities in vivo corresponds to 228 codons of the C-terminal region of the bi2 intron-encoded protein, whereas proteins resulting from more extensive deletions either at the N-terminus or at the C-terminus (up to 73 and four residues, respectively) were able to complement wholly the lack of endogenous maturase, but all lost the endonuclease activity. Similarly, all introduced mutations completely abolished the I-ScaI activity while some mutant proteins retained substantial splicing function. Immunodetection experiments demonstrated that different cytoplasmically translated forms of the I-ScaI/bi2-maturase protein were imported into mitochondria and correctly processed. They appeared to be tightly associated with mitochondrial membranes. Homology modelling of the I-ScaI/bi2-maturase protein allowed us to relate both enzymatic activities to elements of enzyme structure.
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7
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Downing ME, Brady KL, Caprara MG. A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing. RNA (NEW YORK, N.Y.) 2005; 11:437-446. [PMID: 15769873 PMCID: PMC1370733 DOI: 10.1261/rna.7225205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Accepted: 01/06/2005] [Indexed: 05/24/2023]
Abstract
Group I introns often encode proteins that catalyze site-specific DNA hydrolysis. Some of these proteins have acquired the ability to promote splicing of their cognate intron, but whether these two activities reside in different regions of the protein remains obscure. A crystal structure of I-AniI, a dual function intron-encoded protein, has shown that the protein has two pseudo-symmetric domains of equal size. Each domain contacts its DNA substrate on either side of two cleavage sites. As a first step to identify the RNA binding surface, the N- and C-terminal domains of I-AniI were separately expressed and tested for promoting the splicing of the mitochondrial (mt) COB pre-RNA. The N-terminal protein showed no splicing activation or RNA binding, suggesting that this domain plays a minimal role in activity or is improperly folded. Remarkably, the 16-kDa C-terminal half facilitates intron splicing with a rate similar to that of the full-length protein. Both the C-terminal fragment and full-length proteins bind tightly to the COB intron. RNase footprinting shows that the C-terminal and full-length proteins bind to the same regions and induce the same conformational changes in the COB intron. Together, these results show that the C-terminal fragment of I-AniI is necessary and sufficient for maturase activity and suggests that I-AniI acquired splicing function by utilizing a relatively small protein surface that likely represents a novel RNA binding motif. This fragment of I-AniI represents the smallest group I intron splicing cofactor described to date.
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Affiliation(s)
- Maureen E Downing
- Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106-4960, USA
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8
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Maciaszczyk E, Ulaszewski S, Lazowska J. Intragenic suppressors that restore the activity of the maturase encoded by the second intron of the Saccharomyces cerevisiae cyt b gene. Curr Genet 2004; 46:67-71. [PMID: 15168075 DOI: 10.1007/s00294-004-0509-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Revised: 04/19/2004] [Accepted: 04/23/2004] [Indexed: 11/25/2022]
Abstract
The protein encoded by the second intron (bi2) of the mitochondrial cyt b gene from Saccharomyces cerevisiae functions as a maturase promoting intron splicing. This protein belongs to a large family characterized by the presence of two conserved motifs: LAGLIDADG (or P1 and P2). We have isolated and characterized spontaneous revertants from two mis-sense mutations, G85D and H92P (localized in the P1 motif of the bi2-maturase), that have a detrimental effect on intron splicing. All analyzed revertants are intragenic and resulted from monosubstitutions in the mutated codons. Only true back-mutations that restor the initial glycine 85 and a pseudoreversion that replaces the deleterious aspartic acid 85 by alanine were found in revertants of the mutant G85D. In contrast, all possible monosubstitutions in the mutated codon H92P were identified among the revertants of this mutant. The maturase activity of all novel forms of the protein is similar to the wild-type protein.
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Affiliation(s)
- Ewa Maciaszczyk
- Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette, France
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9
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Langkjaer RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J. Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts. Nucleic Acids Res 2003; 31:3081-91. [PMID: 12799436 PMCID: PMC162263 DOI: 10.1093/nar/gkg423] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2003] [Revised: 04/11/2003] [Accepted: 04/11/2003] [Indexed: 11/13/2022] Open
Abstract
The complete sequences of mitochondrial DNA (mtDNA) from the two budding yeasts Saccharomyces castellii and Saccharomyces servazzii, consisting of 25 753 and 30 782 bp, respectively, were analysed and compared to Saccharomyces cerevisiae mtDNA. While some of the traits are very similar among Saccharomyces yeasts, others have highly diverged. The two mtDNAs are much more compact than that of S.cerevisiae and contain fewer introns and intergenic sequences, although they have almost the same coding potential. A few genes contain group I introns, but group II introns, otherwise found in S.cerevisiae mtDNA, are not present. Surprisingly, four genes (ATP6, COX2, COX3 and COB) in the mtDNA of S.servazzii contain, in total, five +1 frameshifts. mtDNAs of S.castellii, S.servazzii and S.cerevisiae contain all genes on the same strand, except for one tRNA gene. On the other hand, the gene order is very different. Several gene rearrangements have taken place upon separation of the Saccharomyces lineages, and even a part of the transcription units have not been preserved. It seems that the mechanism(s) involved in the generation of the rearrangements has had to ensure that all genes stayed encoded by the same DNA strand.
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MESH Headings
- Base Sequence
- DNA, Intergenic
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Endodeoxyribonucleases/metabolism
- Endoribonucleases/genetics
- Gene Order
- Genes, rRNA
- Introns
- Mitochondrial Proteins/genetics
- Molecular Sequence Data
- Open Reading Frames
- RNA/chemistry
- RNA/metabolism
- RNA, Catalytic/genetics
- RNA, Mitochondrial
- RNA, Transfer/genetics
- Repetitive Sequences, Nucleic Acid
- Ribonuclease P
- Saccharomyces/genetics
- Saccharomyces cerevisiae/genetics
- Sequence Analysis, DNA
- Species Specificity
- Transcription Initiation Site
- Transcription, Genetic
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Affiliation(s)
- R B Langkjaer
- BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Kgl. Lyngby, Denmark
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10
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Chatterjee P, Brady KL, Solem A, Ho Y, Caprara MG. Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease. J Mol Biol 2003; 329:239-51. [PMID: 12758073 DOI: 10.1016/s0022-2836(03)00426-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A large number of group I introns encode a family of homologous proteins that either promote intron splicing (maturases) or are site-specific DNA endonucleases that function in intron mobility (a process called "homing"). Genetic studies have shown that some of these proteins have both activities, yet how a single protein carries out both functions remains obscure. The similarity between respective DNA-binding sites and the RNA structure near the 5' and 3' splice sites has fueled speculation that such proteins may use analogous interactions to perform both functions. The Aspergillus nidulans mitochondrial COB group I intron encodes a bi-functional protein, I-AniI, that has both RNA maturase and site-specific DNA endonuclease activities in vitro. Here, we show that I-AniI shows distinctive features of the endonuclease family to which it belongs, including highly specific, tight binding and sequential DNA strand cleavage. Competition experiments demonstrate that I-AniI binds the COB intron RNA even in saturating concentrations of its DNA target site substrate, suggesting that the protein has a separate binding site for RNA. In addition, we provide evidence that two different DNA-binding site mutants of I-AniI have little effect on the protein's RNA maturation activity. Since RNA splicing is likely a secondary adaptation of the protein, these observations support a model in which homing endonucleases may have developed maturase function by utilizing a hitherto "non-functional" protein surface.
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Affiliation(s)
- Piyali Chatterjee
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4960, USA
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11
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Geese WJ, Kwon YK, Wen X, Waring RB. In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1543-54. [PMID: 12654010 DOI: 10.1046/j.1432-1033.2003.03518.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The AnCOB group I intron from Aspergillus nidulans encodes a homing DNA endonuclease called I-AniI which also functions as a maturase, assisting in AnCOB intron RNA splicing. In this investigation we biochemically characterized the endonuclease activity of I-AniI in vitro and utilized competition assays to probe the relationship between the RNA- and DNA-binding sites. Despite functioning as an RNA maturase, I-AniI still retains several characteristic properties of homing endonucleases including relaxed substrate specificity, DNA cleavage product retention and instability in the reaction buffer, which suggest that the protein has not undergone dramatic structural adaptations to function as an RNA-binding protein. Nitrocellulose filter binding and kinetic burst assays showed that both nucleic acids bind I-AniI with the same 1 : 1 stoichiometry. Furthermore, in vitro competition activity assays revealed that the RNA substrate, when prebound to I-AniI, stoichiometrically inhibits DNA cleavage activity, yet in reciprocal experiments, saturating amounts of prebound DNA substrate fails to inhibit RNA splicing activity. The data suggest therefore that both nucleic acids do not bind the same single binding site, rather that I-AniI appears to contain two binding sites.
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Affiliation(s)
- William J Geese
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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12
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Chevalier BS, Stoddard BL. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 2001; 29:3757-74. [PMID: 11557808 PMCID: PMC55915 DOI: 10.1093/nar/29.18.3757] [Citation(s) in RCA: 334] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Homing endonucleases confer mobility to their host intervening sequence, either an intron or intein, by catalyzing a highly specific double-strand break in a cognate allele lacking the intervening sequence. These proteins are characterized by their ability to bind long DNA target sites (14-40 bp) and their tolerance of minor sequence changes in these sites. A wealth of biochemical and structural data has been generated for these enzymes over the past few years. Herein we review our current understanding of homing endonucleases, including their diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them to bind novel DNA substrates.
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Affiliation(s)
- B S Chevalier
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue North A3-023, Seattle, WA 98109, USA
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13
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Abstract
Persistence of a mobile DNA element in a population reflects a balance between the ability of the host to eliminate the element and the ability of the element to survive and to disseminate to other individuals. In each of the three biological kingdoms, several families of a mobile DNA element have been identified which encode a single protein that acts on nucleic acids. Collectively termed homing endonuclease genes (HEGs), these elements employ varied strategies to ensure their survival. Some members of the HEG families have a minimal impact on host fitness because they associate with genes having self-splicing introns or inteins that remove the HEGs at the RNA or protein level. The HEG and the intron/intein gene spread throughout the population by a gene conversion process initiated by the HEG-encoded endonuclease called 'homing' in which the HEG and intron/intein genes are copied to cognate alleles that lack them. The endonuclease activity also contributes to a high frequency of lateral transmission of HEGs between species as has been documented in plants and other systems. Other HEGs have positive selection value because the proteins have evolved activities that benefit their host organisms. The success of HEGs in colonizing diverse genetic niches results from the flexibility of the encoded endonucleases in adopting new specificities.
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Affiliation(s)
- F S Gimble
- Center for Genome Research, Institute of Biosciences and Technology, The Texas A and M University System Health Science Center, 2121 W. Holcombe Blvd., Texas A and M University, Houston, TX, USA.
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14
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Monteilhet C, Dziadkowiec D, Szczepanek T, Lazowska J. Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli. Nucleic Acids Res 2000; 28:1245-51. [PMID: 10666469 PMCID: PMC102596 DOI: 10.1093/nar/28.5.1245] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The second intron in the mitochondrial cytb gene of Saccharomyces capensis, belonging to group I, encodes a 280 amino acid protein containing two LAGLIDADG motifs. Genetic and molecular studies have previously shown that this protein has a dual function in the wild-type strain. It acts as a specific homing endonuclease I- Sca I promoting intron mobility and as a maturase promoting intron splicing. Here we describe the synthesis of a universal code equivalent to the mitochondrial sequence coding for this protein and the in vitro characterization of I- Sca I endonuclease activity, using a truncated mutant form of the protein p28bi2 produced in Escherichia coli. We have also determined the cleavage pattern as well as the recognition site of p28bi2. It was found that p28bi2 generates a double-strand cleavage downstream from the intron insertion site with 4 nt long 3'-overhangs. Mutational analysis of the DNA target site shows that p28bi2 recognizes a 16-19 bp sequence from positions -11 to +8 with respect to the intron insertion site.
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Affiliation(s)
- C Monteilhet
- Centre de Génétique Moléculaire CNRS, 91198 Gif-sur Yvette Cedex, France.
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15
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Ho Y, Kim SJ, Waring RB. A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease. Proc Natl Acad Sci U S A 1997; 94:8994-9. [PMID: 9256423 PMCID: PMC22997 DOI: 10.1073/pnas.94.17.8994] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Some group I introns self-splice in vitro, but almost all are thought to be assisted by proteins in vivo. Mutational analysis has shown that the splicing of certain group I introns depends upon a maturase protein encoded by the intron itself. However the effect of a protein on splicing can be indirect. We now provide evidence that a mitochondrial intron-encoded protein from Aspergillus nidulans directly facilitates splicing in vitro. This demonstrates that a maturase is an RNA splicing protein. The protein-assisted reaction is as fast as that of any other known group I intron. Interestingly the protein is also a DNA endonuclease, an activity required for intron mobilization. Mobile elements frequently encode proteins that promote their propagation. Intron-encoded proteins that also assist RNA splicing would facilitate both the transposition and horizontal transmission of introns.
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Affiliation(s)
- Y Ho
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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16
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Ogawa S, Naito K, Angata K, Morio T, Urushihara H, Tanaka Y. A site-specific DNA endonuclease specified by one of two ORFs encoded by a group I intron in Dictyostelium discoideum mitochondrial DNA. Gene 1997; 191:115-21. [PMID: 9210597 DOI: 10.1016/s0378-1119(97)00050-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The second intron (DdOX1/2.2) of Dictyostelium discoideum cytochrome oxidase subunit 1/2 fused gene has two free-standing ORF genes (Dd ai2a and Dd ai2b) in a loop, which have similar amino acid sequences and are homologous to aI4 DNA endonuclease (I-SceII) of Saccharomyces cerevisiae. To elucidate the functions of these ORFs, we cloned the ORFs into an expression vector and introduced the composite vectors into E. coli. The expression of Dd ai2a in E. coli caused growth inhibition and degradation of the E. coli genomic DNA. To determine whether Dd ai2a protein is a homing type DNA endonuclease, the ability to cleave the homing site of its intron in vivo was examined. Dd ai2a cleaved only one strand of intronless DNA sequence at the site which coincides with the I-SceII cleavage recognition site. We suppose that Dd ai2a functions actually as a homing type DNA endonuclease in D. discoideum mitochondria by virtue of other factors. To obtain further information about the relationship between the existence of introns and the mating system, we carried out in vitro self-splicing assay and polymerase chain reaction analysis using 13 strains of the cellular slime mold.
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Affiliation(s)
- S Ogawa
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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17
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Mercure S, Cousineau L, Montplaisir S, Belhumeur P, Lemay G. Expression of a reporter gene interrupted by the Candida albicans group I intron is inhibited by base analogs. Nucleic Acids Res 1997; 25:431-7. [PMID: 9016575 PMCID: PMC146449 DOI: 10.1093/nar/25.2.431] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We previously reported the identification of an intron (CaLSU) in the 25S ribosomal RNA of some Candida albicans yeast strains. CaLSU was shown to self-splice and has the potential to adopt a secondary structure typical of group I introns. The presence of CaLSU inC. albicans strains correlates with a high degree of susceptibility to base analog antifungal agents, 5-fluorocytosine (5-FC) or 5-fluorouracil (5-FU). Cell death, resulting from addition of base analogs to growing cultures, precluded demonstration of a causal relationship between CaLSU presence and susceptibility to base analogs. In the present study, CaLSU was inserted in a non-essential lacZ reporter gene and expression was examined in Saccharomyces cerevisiae. Different mutations affecting in vitro self-splicing also had similar effects on reporter gene expression in vivo. This indicates that in vivo removal of CaLSU from the reporter gene occurs through the typical self-splicing mechanism of group I introns. Base analogs inhibited expression of the reporter gene product in a concentration-dependent manner upon their addition to the cultures. This supports a model in which disruption of intron secondary structure, consecutive to the incorporation of nucleotide analogs, is a major factor determining the susceptibility of C.albicans cells to base analogs.
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Affiliation(s)
- S Mercure
- Département de Microbiologie et Immunologie, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Québec H3C 3J7, Canada
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18
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Li GY, Bécam AM, Slonimski PP, Herbert CJ. In vitro mutagenesis of the mitochondrial leucyl tRNA synthetase of Saccharomyces cerevisiae shows that the suppressor activity of the mutant proteins is related to the splicing function of the wild-type protein. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:667-75. [PMID: 8917309 DOI: 10.1007/bf02173972] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The NAM2 gene of Saccharomyces cerevisiae encodes the mitochondrial leucyl tRNA synthetase (mLRS), which is necessary for the excision of the fourth intron of the mitochondrial cytb gene (bI4) and the fourth intron of the mitochondrial coxI gene (aI4), as well as for mitochondrial protein synthesis. Some dominant mutant alleles of the gene are able to suppress mutations that inactivate the bI4 maturase, which is essential for the excision of the introns aI4 and bI4. Here we report mutagenesis studies which focus on the splicing and suppressor functions of the protein. Small deletions in the C-terminal region of the protein preferentially reduce the splicing, but not the synthetase activity; and all the C-terminal deletions tested abolish the suppressor activity. Mutations which increase the volume of the residue at position 240 in the wild-type mLRS without introducing a charge, lead to a suppressor activity. The mutant 238C, which is located in the suppressor region, has a reduced synthetase activity and no detectable splicing activity. These data show that the splicing and suppressor functions are linked and that the suppressor activity of the mutant alleles results from a modification of the wild-type splicing activity.
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Affiliation(s)
- G Y Li
- Centre de Génétique Moléculaire, Laboratoire propre du CNRS associé á I'Université Pierre et Marie Curie, Gif-sur-Yvette, France
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19
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Claros MG, Perea J, Jacq C. Allotopic expression of yeast mitochondrial maturase to study mitochondrial import of hydrophobic proteins. Methods Enzymol 1996; 264:389-403. [PMID: 8965712 DOI: 10.1016/s0076-6879(96)64036-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- M G Claros
- Ecole Normale Superieure Laboratoire de Génétique Moléculaire, CNRS URA 1302, Paris, France
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20
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Guo WW, Moran JV, Hoffman PW, Henke RM, Butow RA, Perlman PS. The mobile group I intron 3 alpha of the yeast mitochondrial COXI gene encodes a 35-kDa processed protein that is an endonuclease but not a maturase. J Biol Chem 1995; 270:15563-70. [PMID: 7797552 DOI: 10.1074/jbc.270.26.15563] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Three mitochondrial mutants were characterized that block the splicing of aI3 alpha, a mobile group I intron of the COXI gene of yeast mtDNA. Mutant C1085 alters helical structures known to be important for splicing of group I introns. M44 and C1072 are point mutants in exon 3 that block correct splicing but allow some splicing at cryptic 5'-splice sites. M44 alters the P1 helix needed for 5'-splice site definition, while the mutation in C1072 is a new kind of mutation because it is located upstream of the exon sequence involved in the P1 helix. All three mutants accumulate novel proteins of 35 and 44 kDa (p35 and p44, respectively) detected both by labeling of mitochondrial translation products and by Western blotting. Partial protease digestions indicate that p44 and p35 are closely related, probably as precursor and processed protein. The level of the intron-encoded endonuclease activity, I-SceIII, is elevated approximately 10-fold in the mutants. Partial purification of I-SceIII from the mutants showed that most, if not all, of the activity is associated with p35. Finally, because aI3 alpha splices accurately in a petite mutant, we conclude that aI3 alpha splicing does not depend on a mtDNA-encoded maturase.
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Affiliation(s)
- W W Guo
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA
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21
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Abu-Amero SN, Charter NW, Buck KW, Brasier CM. Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene. Curr Genet 1995; 28:54-9. [PMID: 8536313 DOI: 10.1007/bf00311881] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The nucleotide sequence of a mitochondrial plasmid (2234 bp) in a diseased isolate of Ophiostoma novo-ulmi, and sequences of the mitochondrial DNA that overlap and flank the plasmid end-points, have been determined. The plasmid was shown to be derived from the O. novo-ulmi mitochondrial large subunit ribosomal RNA gene and contained most of intron 1, the whole of exon 2, and probably the first part of intron 2. Within intron 1 there is an open reading frame with the potential to encode a 323 amino-acid polypeptide which contained dodecapeptide sequences typical of RNA maturases and DNA endonucleases. The endpoints of the plasmid in the mtDNA were located within two 90-bp direct imperfect repeat sequences, one of which comprised the last 7 bp of exon 1 and the first 83 bp of intron 1 whilst the other comprised the last 7 bp of exon 2 and the first 83 bp of intron 2. It is proposed that the Ld plasmid was generated by intramolecular recombination between these two repeats with the crossover point probably within the last 15 bp.
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Affiliation(s)
- S N Abu-Amero
- Department of Biology, Imperial College of Science, Technology and Medicine, London, UK
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22
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Netter P, Robineau S, Lemaire C. Mutations in the mitochondrial split gene COXI are preferentially located in exons: a mapping study of 170 mutants. MOLECULAR & GENERAL GENETICS : MGG 1995; 246:445-54. [PMID: 7891658 DOI: 10.1007/bf00290448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have analysed the precise location of a large number (170) of mutations affecting the structural gene for subunit I of the cytochrome c oxidase complex. This gene, COXI, is 12.9 kb long and the major part of the sequence (i.e. 11.3 kb) is composed of introns. Several conclusions can be drawn from this study: (1) A significant proportion (84/170) of the mutations cannot be assigned to a single position within the gene by deletion mapping, in spite of clearly being located in it. These mutations are probably large deletions or multiple mutations. (2) Four mutants carry distant double mutations, which have been individually localized. (3) Eighty-two mutants have lesions that are restricted to very short regions of the gene and we therefore conclude that they are most probably due to single hits; amongst these single mutations, 41 are unambiguously located in exons and 28 in introns. This result implies that, at least in this particular split gene, the probability of selection of a mutant phenotype in an exon is, on the average, 13.3 times greater than in an intron, in spite of the existence, within most of these introns, of open reading frames specifying intronic proteins. The evolutionary significance and biological implications of these results are discussed.
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Affiliation(s)
- P Netter
- Centre de Génétique Moléculaire du CNRS, Laboratoire associé à l'Université Pierre et Marie Curie, Gif-sur-Yvette, France
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23
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Abstract
All proteins encoded by mitochondrial DNA (mtDNA) are dependent on proteins encoded by nuclear genes for their synthesis and function. Recent developments in the identification of these genes and the elucidation of the roles their products play at various stages of mitochondrial gene expression are covered in this review, which focuses mainly on work with the yeast Saccharomyces cerevisiae. The high degree of evolutionary conservation of many cellular processes between this yeast and higher eukaryotes, the ease with which mitochondrial biogenesis can be manipulated both genetically and physiologically, and the fact that it will be the first organism for which a complete genomic sequence will be available within the next 2 to 3 years makes it the organism of choice for drawing up an inventory of all nuclear genes involved in mitochondrial biogenesis and for the identification of their counterparts in other organisms.
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Affiliation(s)
- L A Grivell
- Department of Molecular Cell Biology, University of Amsterdam, Netherlands
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24
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Schäfer B, Wilde B, Massardo DR, Manna F, Del Giudice L, Wolf K. A mitochondrial group-I intron in fission yeast encodes a maturase and is mobile in crosses. Curr Genet 1994; 25:336-41. [PMID: 8082176 DOI: 10.1007/bf00351487] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The open reading frame in the first intron of the mitochondrial gene encoding subunit I of cytochrome c oxidase encodes a maturase and stimulates homologous recombination in Escherichia coli. In this paper, we demonstrate that this intron is mobile in crosses, indicating that it also encodes an endonuclease. This is the first report on an intron which possesses mobility and acts as a maturase.
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Affiliation(s)
- B Schäfer
- Institut für Biologie IV (Mikrobiologie), Rheinisch-Westfälische Technische Hochschule, Aachen, Germany
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25
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Szczepanek T, Macadre C, Meunier B, Lazowska J. Two homologous introns from related Saccharomyces species differ in their mobility. Gene 1994; 139:1-7. [PMID: 8112577 DOI: 10.1016/0378-1119(94)90516-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have studied gene conversion initiated by the ai3 intron of the Saccharomyces cerevisiae mitochondrial (mt) COXI gene and its homologous intron (S.cap.ai1) from Saccharomyces capensis. The approach used involved the measurement of intron transmission amongst the progeny of crosses between constructed recipient and donor strains. We found that the S. cerevisiae ai3 intron is extremely active as a donor in gene conversion, whereas its homologous S. capensis intron is not. We have established the sequence of S.cap.ai1 and compared its open reading frame (ORF) with that of I-SceIII encoded by the homologous S. cerevisiae intron. The two protein-coding intron sequences are almost identical, except that the S. capensis ORF contains an in-frame stop codon. This finding provides a strong indication that the 3' part of the S. cerevisiae intron ORF encoding I-SceIII (which should not be translated in the S. capensis intron) must be critical for function of mtDNA endonucleases to mediate intron mobility.
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Affiliation(s)
- T Szczepanek
- Centre de Génétique Moléculaire du C.N.R.S., Laboratoire Propre Associé à L'Université Pierre et Marie Curie, Gif-sur-Yvette, France
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26
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Dieckmann CL, Staples RR. Regulation of mitochondrial gene expression in Saccharomyces cerevisiae. INTERNATIONAL REVIEW OF CYTOLOGY 1994; 152:145-81. [PMID: 8206703 DOI: 10.1016/s0074-7696(08)62556-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- C L Dieckmann
- Department of Biochemistry, University of Arizona, Tucson 85721
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27
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Gimble F, Thorner J. Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80618-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Affiliation(s)
- H J Pel
- Department of Molecular Cell Biology, University of Amsterdam, The Netherlands
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29
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Pietrokovski S, Trifonov EN. Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics. Gene 1992; 122:129-37. [PMID: 1452019 DOI: 10.1016/0378-1119(92)90040-v] [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: 12/27/2022]
Abstract
In addition to universally appearing mitochondrial (mt) genes, origins of replication and transcription start regions typical of all mt genome variants of the yeast Saccharomyces cerevisiae, the mt genomes of some of the strains contain variable sequences. These sequences are apparently largely dispensable. They are mainly composed of group-I and -II introns and intergenic open reading frames (ORFs). Many of the introns contain ORFs, some of which were shown by genetic and biochemical means to be involved in splicing and transposition of the mt introns. Some of the optional sequences are hypothesized to be mobile genetic elements. Nucleotide (nt) sequences of the mt genome of S. cerevisiae were examined by analyzing occurrences of oligodeoxyribonucleotide (oligo) 'words'. This linguistic technique had been found to be sensitive to both function and origin of the sequence [Pietrokovski et al., J. Biomol. Struct. Dyn. 7 (1990) 1251-1268]. A clear difference is found between the oligo vocabularies of the optional and basic yeast mt sequences. The difference is mainly located in protein coding segments of the optional sequences which contain conserved amino acid motifs, characteristic of intronic and intergenic ORFs. The use of nt linguistics to detect the sequence dissimilarity and its causes in yeast mitochondria provides fast and straightforward results, identifying the intronic and intergenic ORFs as DNA sequences of foreign, non-mt origin.
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Affiliation(s)
- S Pietrokovski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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30
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Moran JV, Wernette CM, Mecklenburg KL, Butow RA, Perlman PS. Intron 5 alpha of the COXI gene of yeast mitochondrial DNA is a mobile group I intron. Nucleic Acids Res 1992; 20:4069-76. [PMID: 1324475 PMCID: PMC334089 DOI: 10.1093/nar/20.15.4069] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have found that intron 5 alpha of the COXI gene (al5 alpha) of yeast mtDNA is a mobile group I intron in crosses between strains having or lacking the intron. We have demonstrated the following hallmarks of that process: 1) co-conversion of flanking optional intron markers; 2) mutations that truncate the intron open reading frame block intron mobility; and 3) the intron open reading frame encodes an endonuclease activity that is required for intron movement. The endonuclease activity, termed I-Sce IV, cleaves the COXI allele lacking al5 alpha near the site of intron insertion, making a four-base staggered cut with 3' OH overhangs. Three cloned DNAs derived from different forms of the COXI gene, which differ in primary sequence at up to seven nucleotides around the cleavage site, are all good substrates for in vitro I-Sce IV cleavage activity. Two of the strains from which these substrates were derived were tested in crosses and are comparably efficient as al5 alpha recipients. When compared with omega mobility occurring simultaneously in one cross, al5 alpha is less efficient as a mobile element.
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Affiliation(s)
- J V Moran
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9038
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31
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Bolotin-Fukuhara M, Grivell LA. Genetic approaches to the study of mitochondrial biogenesis in yeast. Antonie Van Leeuwenhoek 1992; 62:131-53. [PMID: 1444332 DOI: 10.1007/bf00584467] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In contrast to most other organisms, the yeast Saccharomyces cerevisiae can survive without functional mitochondria. This ability has been exploited in genetic approaches to the study of mitochondrial biogenesis. In the last two decades, mitochondrial genetics have made major contributions to the identification of genes on the mitochondrial genome, the mapping of these genes and the establishment of structure-function relationships in the products they encode. In parallel, more than 200 complementation groups, corresponding to as many nuclear genes necessary for mitochondrial function or biogenesis have been described. Many of the latter are required for post-transcriptional events in mitochondrial gene expression, including the processing of mitochondrial pre-RNAs, the translation of mitochondrial mRNAs, or the assembly of mitochondrial translation products into the membrane. The aim of this review is to describe the genetic approaches used to unravel the intricacies of mitochondrial biogenesis and to summarize recent insights gained from their application.
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Affiliation(s)
- M Bolotin-Fukuhara
- Laboratoire de Génétique Moléculaire, Université Paris-Sud, Orsay, France
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32
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Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments. Mol Cell Biol 1992. [PMID: 1310149 DOI: 10.1128/mcb.12.2.696] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intron-encoded proteins bI4 RNA maturase and aI4 DNA endonuclease can be faithfully expressed in yeast cytoplasm from engineered forms of their mitochondrial coding sequences. In this work we studied the relationships between these two activities associated with two homologous intron-encoded proteins: the bI4 RNA maturase encoded in the fourth intron of the cytochrome b gene and the aI4 DNA endonuclease (I-SceII) encoded in the fourth intron of the gene coding for the subunit I of cytochrome oxidase. Taking advantage of both the high recombinogenic properties of yeast and the similarities between the two genes, we constructed in vivo a family of hybrid genes carrying parts of both RNA maturase and DNA endonuclease coding sequences. The presence of a sequence coding for a mitochondrial targeting peptide upstream from these hybrid genes allowed us to study the properties of their translation products within the mitochondria in vivo. We thus could analyze the ability of the recombinant proteins to complement RNA maturase deficiencies in different strains. Many combinations of the two parental intronic sequences were found in the recombinants. Their structural and functional analysis revealed the following features. (i) The N-terminal half of the bI4 RNA maturase could be replaced in total by its equivalent from the aI4 DNA endonuclease without affecting the RNA maturase activity. In contrast, replacing the C-terminal half of the bI4 RNA maturase with its equivalent from the aI4 DNA endonuclease led to a very weak RNA maturase activity, indicating that this region is more differentiated and linked to the maturase activity. (ii) None of the hybrid proteins carrying an RNA maturase activity kept the DNA endonuclease activity, suggesting that the latter requires the integrity of the aI4 protein. These observations are interesting because the aI4 DNA endonuclease is known to promote the propagation, at the DNA level, of the aI4 intron, whereas the bI4 RNA maturase, which is required for the splicing of its coding intron, also controls the splicing process of the aI4 intron. We propose a scenario for the evolution of these intronic proteins that relies on a switch from DNA endonuclease to RNA maturase activity.
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33
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Pel HJ, Tzagoloff A, Grivell LA. The identification of 18 nuclear genes required for the expression of the yeast mitochondrial gene encoding cytochrome c oxidase subunit 1. Curr Genet 1992; 21:139-46. [PMID: 1314704 DOI: 10.1007/bf00318473] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Eighteen nuclear mutants of the yeast Saccharomyces cerevisae, each disturbed in the biosynthesis of the mitochondrially encoded cytochrome c oxidase subunit 1 (cox1) and each representing a distinct complementation group, have been examined to identify the level at which COX1 expression is affected. RNA blotting revealed that most have a defect in the processing of COX1 precursor-mRNA; only a few are defective in COX1 transcription and/or pre-mRNA stability. In most RNA-processing mutants, the absence of the COX1 messenger results from a defect in the splicing of one or more COX1 introns. In turn, this defect can be ascribed to a mutation in a nuclear gene which is either directly involved in splicing or else acts indirectly by impairing COX1 translation.
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Affiliation(s)
- H J Pel
- Department of Molecular Cell Biology, University of Amsterdam, The Netherlands
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34
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Goguel V, Delahodde A, Jacq C. Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments. Mol Cell Biol 1992; 12:696-705. [PMID: 1310149 PMCID: PMC364267 DOI: 10.1128/mcb.12.2.696-705.1992] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The intron-encoded proteins bI4 RNA maturase and aI4 DNA endonuclease can be faithfully expressed in yeast cytoplasm from engineered forms of their mitochondrial coding sequences. In this work we studied the relationships between these two activities associated with two homologous intron-encoded proteins: the bI4 RNA maturase encoded in the fourth intron of the cytochrome b gene and the aI4 DNA endonuclease (I-SceII) encoded in the fourth intron of the gene coding for the subunit I of cytochrome oxidase. Taking advantage of both the high recombinogenic properties of yeast and the similarities between the two genes, we constructed in vivo a family of hybrid genes carrying parts of both RNA maturase and DNA endonuclease coding sequences. The presence of a sequence coding for a mitochondrial targeting peptide upstream from these hybrid genes allowed us to study the properties of their translation products within the mitochondria in vivo. We thus could analyze the ability of the recombinant proteins to complement RNA maturase deficiencies in different strains. Many combinations of the two parental intronic sequences were found in the recombinants. Their structural and functional analysis revealed the following features. (i) The N-terminal half of the bI4 RNA maturase could be replaced in total by its equivalent from the aI4 DNA endonuclease without affecting the RNA maturase activity. In contrast, replacing the C-terminal half of the bI4 RNA maturase with its equivalent from the aI4 DNA endonuclease led to a very weak RNA maturase activity, indicating that this region is more differentiated and linked to the maturase activity. (ii) None of the hybrid proteins carrying an RNA maturase activity kept the DNA endonuclease activity, suggesting that the latter requires the integrity of the aI4 protein. These observations are interesting because the aI4 DNA endonuclease is known to promote the propagation, at the DNA level, of the aI4 intron, whereas the bI4 RNA maturase, which is required for the splicing of its coding intron, also controls the splicing process of the aI4 intron. We propose a scenario for the evolution of these intronic proteins that relies on a switch from DNA endonuclease to RNA maturase activity.
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Affiliation(s)
- V Goguel
- Laboratoire de Génétique Moléculaire, CNRS URA 1302, Ecole Normale Supérieure, Paris, France
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35
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Zagorski W, Castaing B, Herbert CJ, Labouesse M, Martin R, Slonimski PP. Purification and characterization of the Saccharomyces cerevisiae mitochondrial leucyl-tRNA synthetase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52278-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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36
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Skelly PJ, Maleszka R. Distribution of mitochondrial intron sequences among 21 yeast species. Curr Genet 1991; 19:89-94. [PMID: 2065366 DOI: 10.1007/bf00326288] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mitochondrial and nuclear genomes of 21 yeast species belonging to 12 genera have been tested for the presence of sequences similar to seven S. cerevisiae mitochondrial introns (Se cox1.1,2,3,4,5c, Sc cob.4 and Sc LSU.1) and one K. lactis mitochondrial intron (K1 cox1.2). Some introns, (Sc cox1.4, Sc cob.4, Sc LSU.1 and Kl cox1.2-all group I type), are widely distributed and are found in species with either basidiomycete or ascomycete affinities. This distribution is suggestive of recent sequence transfer between species. The remaining S. cerevisiae introns cross react with an additional species but with no set pattern. Pulsed field gel electrophoretic studies confirm that none of the tested mitochondrial introns cross react with nuclear DNA. These introns are, therefore, mitochondria-specific. Seven strains of K. lactis exhibit striking variability in intron content. In contrast to all mitochondrial introns tested, two introns of nuclear genes (the K. lactis actin gene and the S. cerevisiae RP29B gene) are not detected beyond their source species.
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Affiliation(s)
- P J Skelly
- Research School of Biological Sciences, Australian National University, Canberra
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37
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Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)30611-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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38
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Sargueil B, Hatat D, Delahodde A, Jacq C. In vivo and in vitro analyses of an intron-encoded DNA endonuclease from yeast mitochondria. Recognition site by site-directed mutagenesis. Nucleic Acids Res 1990; 18:5659-65. [PMID: 2216759 PMCID: PMC332297 DOI: 10.1093/nar/18.19.5659] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The pal 4 nuclease (termed I-Sce II) is encoded in the group I al 4 intron of the COX I gene of Saccharomyces cerevisiae. It introduces a specific double-strand break at the junction of the two exons A4-A5 and thus mediates the insertion of the intron into an intronless strain. To define the sequence recognized by pal 4 we introduced 35 single mutations in its target sequence and examined their cleavage properties either in vivo in E. coli (when different forms of the pal 4 proteins were artificially produced) or in vitro with mitochondrial extracts of a mutant yeast strain blocked in the splicing of the al 4 intron. We also detected the pal 4 DNA endonuclease activity in extracts of the wild type strain. The results suggest that 6 to 9 noncontiguous bases in the 17 base-pair region examined are necessary for pal 4 nuclease to bind and cleave its recognition site. We observed that the pal 4 nuclease specificity can be significantly different with the different forms of the protein thus explaining why only some forms are highly toxic in E. coli. This study shows that pal 4 recognition site is a complex phenomenon and this might have evolutionary implications on the transfer properties of the intron.
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Affiliation(s)
- B Sargueil
- Laboratoire de Génétique Moléculaire, CNRS UA 1302, Ecole Normale Supérieure, Paris, France
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39
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Dandekar T, Sibbald PR. Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates. Nucleic Acids Res 1990; 18:4719-25. [PMID: 2395638 PMCID: PMC331928 DOI: 10.1093/nar/18.16.4719] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Several known trans-splicing RNA structures were used to define a canonical trans-splicing structure which was then used to perform a computer search of the EMBL nucleotide database. In addition to most known trans-splicing structures, many putative new trans-splicing sites were detected. These were found in a broad range of organisms including the vertebrates. Control experiments indicate that the search predicts known false positives at a rate of only 20%. Trans-splicing may therefore be a very wide-spread phenomenon.
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Affiliation(s)
- T Dandekar
- European Molecular Biology Laboratory, Heidelberg, FRG
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40
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Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum. Mol Cell Biol 1990. [PMID: 2355911 DOI: 10.1128/mcb.10.7.3386] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel and only recently recognized class of enzymes is composed of the site-specific endonucleases encoded by some group I introns. We have characterized several aspects of I-Ppo, the endonuclease that mediates the mobility of intron 3 in the ribosomal DNA of Physarum polycephalum. This intron is unique among mobile group I introns in that it is located in nuclear DNA. We found that I-Ppo is encoded by an open reading frame in the 5' half of intron 3, upstream of the sequences required for self-splicing of group I introns. Either of two AUG initiation codons could start this reading frame, one near the beginning of the intron and the other in the upstream exon, leading to predicted polypeptides of 138 and 160 amino acid residues. The longer polypeptide was the major form translated in vitro in a reticulocyte extract. From nuclease assays of proteins synthesized in vitro with partially deleted DNAs, we conclude that both polypeptides possess endonuclease activity. We also have expressed I-Ppo in Escherichia coli, using a bacteriophage T7 RNA polymerase expression system. The longer polypeptide also was the predominant form made in this system. It showed enzymatic activity in bacteria in vivo, as demonstrated by the cleavage of a plasmid carrying the target site. Like several other intron-encoded endonucleases, I-Ppo makes a four-base staggered cut in its ribosomal DNA target sequence, very near the site where intron 3 becomes integrated in crosses of intron 3-containing and intron 3-lacking Physarum strains.
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Muscarella DE, Ellison EL, Ruoff BM, Vogt VM. Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum. Mol Cell Biol 1990; 10:3386-96. [PMID: 2355911 PMCID: PMC360768 DOI: 10.1128/mcb.10.7.3386-3396.1990] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel and only recently recognized class of enzymes is composed of the site-specific endonucleases encoded by some group I introns. We have characterized several aspects of I-Ppo, the endonuclease that mediates the mobility of intron 3 in the ribosomal DNA of Physarum polycephalum. This intron is unique among mobile group I introns in that it is located in nuclear DNA. We found that I-Ppo is encoded by an open reading frame in the 5' half of intron 3, upstream of the sequences required for self-splicing of group I introns. Either of two AUG initiation codons could start this reading frame, one near the beginning of the intron and the other in the upstream exon, leading to predicted polypeptides of 138 and 160 amino acid residues. The longer polypeptide was the major form translated in vitro in a reticulocyte extract. From nuclease assays of proteins synthesized in vitro with partially deleted DNAs, we conclude that both polypeptides possess endonuclease activity. We also have expressed I-Ppo in Escherichia coli, using a bacteriophage T7 RNA polymerase expression system. The longer polypeptide also was the predominant form made in this system. It showed enzymatic activity in bacteria in vivo, as demonstrated by the cleavage of a plasmid carrying the target site. Like several other intron-encoded endonucleases, I-Ppo makes a four-base staggered cut in its ribosomal DNA target sequence, very near the site where intron 3 becomes integrated in crosses of intron 3-containing and intron 3-lacking Physarum strains.
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Affiliation(s)
- D E Muscarella
- Section of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, New York 14853
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Anziano PQ, Moran JV, Gerber D, Perlman PS. Novel hybrid maturases in unstable pseudorevertants of maturaseless mutants of yeast mitochondrial DNA. Nucleic Acids Res 1990; 18:3233-9. [PMID: 1972561 PMCID: PMC330928 DOI: 10.1093/nar/18.11.3233] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Unstable pseudorevertants of mitochondrial mutants of Saccharomyces cerevisiae lacking the maturase function encoded by the fourth intron of the cytochrome b gene (bI4) were isolated. They were found to be heteroplasmic cells owing their regained ability to respire (and grow on glycerol medium) to the presence of a rearranged (rho-) mtDNA that contains an in-frame fusion of the reading frames of the group I introns bI4 and intron 4 alpha of the coxl gene encoding subunit I of cytochrome c oxidase (aI4 alpha). The products of those gene fusions suppress the bI4 maturase deficiency still present in those heteroplasmic cells. Similar heteroplasmic pseudorevertants of a group II maturaseless mutant of the first intron of the coxI gene were characterized; they result from partial deletion of the coxI gene that fuses the reading frames of introns 1 and 2. These heteroplasms provide independent support for the existence of RNA maturases encoded by group I and group II introns. Also, since the petite/mit- heteroplasms arise spontaneously at very high frequencies they provide a system that can be used to obtain mutants unable to form or maintain heteroplasmic cells.
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Affiliation(s)
- P Q Anziano
- Molecular Cellular and Developmental Biology Program, Ohio State University, Columbus 43210-1292
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Mitochondrial Aminoacyl-?RNA Synthetases. ACTA ACUST UNITED AC 1990. [PMID: 2247606 DOI: 10.1016/s0079-6603(08)60625-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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Affiliation(s)
- P S Perlman
- Department of Molecular Genetics, Ohio State University, Columbus 43210
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Netter P, Robineau S. The differential overamplification of short sequences in the mitochondrial DNA of rho- petites in Saccharomyces cerevisiae stimulates recombination. Gene 1989; 83:25-38. [PMID: 2556330 DOI: 10.1016/0378-1119(89)90400-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
It is well known that the yeast Saccharomyces cerevisiae can be affected by mutations, called 'petite colonie', which correspond to the loss of the major part of the mitochondrial DNA and the concomitant amplification of the remaining sequence, the basic repeat unit (BRU). We describe here a new phenomenon, the internal overamplification (IOA), due to the differential amplification (up to 20-fold) of short sequences within the BRU. These IOAs are very stable and stimulate the recombination. We discuss here the possible mechanisms giving rise to the appearance and maintenance of the IOAs within the BRU and their effect on the recombination process.
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Affiliation(s)
- P Netter
- Laboratoire Propre Associé à l'Université Pierre et Marie Curie, Centre de Génétique Moléculaire du C.N.R.S., Gif-sur-Yvette, France
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Abstract
Group I introns form a structural and functional group of introns with widespread but irregular distribution among very diverse organisms and genetic systems. Evidence is now accumulating that several group I introns are mobile genetic elements with properties similar to those originally described for the omega system of Saccharomyces cerevisiae: mobile group I introns encode sequence-specific double-strand (ds) endoDNases, which recognize and cleave intronless genes to insert a copy of the intron by a ds-break repair mechanism. This mechanism results in: the efficient propagation of group I introns into their cognate sites; their maintenance at the site against spontaneous loss; and, perhaps, their transposition to different sites. The spontaneous loss of group I introns occurs with low frequency by an RNA-mediated mechanism. This mechanism eliminates introns defective for mobility and/or for RNA splicing. Mechanisms of intron acquisition and intron loss must create an equilibrium, which explains the irregular distribution of group I introns in various genetic systems. Furthermore, the observed distribution also predicts that horizontal transfer of intron sequences must occur between unrelated species, using vectors yet to be discovered.
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Affiliation(s)
- B Dujon
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, Paris, France
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Involvement of tyrosyl-tRNA synthetase in splicing of group I introns in Neurospora crassa mitochondria: biochemical and immunochemical analyses of splicing activity. Mol Cell Biol 1989. [PMID: 2526294 DOI: 10.1128/mcb.9.5.2089] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We reported previously that mitochondrial tyrosyl-tRNA synthetase, which is encoded by the nuclear gene cyt-18 in Neurospora crassa, functions in splicing several group I introns in N. crassa mitochondria (R. A. Akins and A. M. Lambowitz, Cell 50:331-345, 1987). Two mutants in the cyt-18 gene (cyt-18-1 and cyt-18-2) are defective in both mitochondrial protein synthesis and splicing, and an activity that splices the mitochondrial large rRNA intron copurifies with a component of mitochondrial tyrosyl-tRNA synthetase. Here, we used antibodies against different trpE-cyt-18 fusion proteins to identify the cyt-18 gene product as a basic protein having an apparent molecular mass of 67 kilodaltons (kDa). Both the cyt-18-1 and cyt-18-2 mutants contain relatively high amounts of inactive cyt-18 protein detected immunochemically. Biochemical experiments show that the 67-kDa cyt-18 protein copurifies with splicing and synthetase activity through a number of different column chromatographic procedures. Some fractions having splicing activity contain only one or two prominent polypeptide bands, and the cyt-18 protein is among the few, if not only, major bands in common between the different fractions that have splicing activity. Phosphocellulose columns resolve three different forms or complexes of the cyt-18 protein that have splicing or synthetase activity or both. Gel filtration experiments show that splicing activity has a relatively small molecular mass (peak at 150 kDa with activity trailing to lower molecular masses) and could correspond simply to dimers or monomers, or both, of the cyt-18 protein. Finally, antibodies against different segments of the cyt-18 protein inhibit splicing of the large rRNA intron in vitro. Our results indicate that both splicing and tyrosyl-tRNA synthetase activity are associated with the same 67-kDa protein encoded by the cyt-18 gene. This protein is a key constituent of splicing activity; it functions directly in splicing, and few, if any, additional components are required for splicing the large rRNA intron.
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Majumder AL, Akins RA, Wilkinson JG, Kelley RL, Snook AJ, Lambowitz AM. Involvement of tyrosyl-tRNA synthetase in splicing of group I introns in Neurospora crassa mitochondria: biochemical and immunochemical analyses of splicing activity. Mol Cell Biol 1989; 9:2089-104. [PMID: 2526294 PMCID: PMC363003 DOI: 10.1128/mcb.9.5.2089-2104.1989] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We reported previously that mitochondrial tyrosyl-tRNA synthetase, which is encoded by the nuclear gene cyt-18 in Neurospora crassa, functions in splicing several group I introns in N. crassa mitochondria (R. A. Akins and A. M. Lambowitz, Cell 50:331-345, 1987). Two mutants in the cyt-18 gene (cyt-18-1 and cyt-18-2) are defective in both mitochondrial protein synthesis and splicing, and an activity that splices the mitochondrial large rRNA intron copurifies with a component of mitochondrial tyrosyl-tRNA synthetase. Here, we used antibodies against different trpE-cyt-18 fusion proteins to identify the cyt-18 gene product as a basic protein having an apparent molecular mass of 67 kilodaltons (kDa). Both the cyt-18-1 and cyt-18-2 mutants contain relatively high amounts of inactive cyt-18 protein detected immunochemically. Biochemical experiments show that the 67-kDa cyt-18 protein copurifies with splicing and synthetase activity through a number of different column chromatographic procedures. Some fractions having splicing activity contain only one or two prominent polypeptide bands, and the cyt-18 protein is among the few, if not only, major bands in common between the different fractions that have splicing activity. Phosphocellulose columns resolve three different forms or complexes of the cyt-18 protein that have splicing or synthetase activity or both. Gel filtration experiments show that splicing activity has a relatively small molecular mass (peak at 150 kDa with activity trailing to lower molecular masses) and could correspond simply to dimers or monomers, or both, of the cyt-18 protein. Finally, antibodies against different segments of the cyt-18 protein inhibit splicing of the large rRNA intron in vitro. Our results indicate that both splicing and tyrosyl-tRNA synthetase activity are associated with the same 67-kDa protein encoded by the cyt-18 gene. This protein is a key constituent of splicing activity; it functions directly in splicing, and few, if any, additional components are required for splicing the large rRNA intron.
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Affiliation(s)
- A L Majumder
- Department of Molecular Genetics, Ohio State University, Columbus 43210
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