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Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA. Curr Genet 2023; 69:55-65. [PMID: 36447017 PMCID: PMC9925561 DOI: 10.1007/s00294-022-01259-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 12/05/2022]
Abstract
Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Shneider M, Ignatov A, Miroshnikov K. Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics. Curr Issues Mol Biol 2022; 44:889-927. [PMID: 35723345 PMCID: PMC8929003 DOI: 10.3390/cimb44020060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str., 49, 127434 Moscow, Russia;
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Moscow Institute of Physics and Technology, Federal University, Institutskiy per., 9, 141701 Dolgoprudny, Moscow Oblast, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia;
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Correspondence: (P.E.); (K.M.)
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Tallei TE. Putative DNA-dependent RNA polymerase in Mitochondrial Plasmid of Paramecium caudatum Stock GT704. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.1016/j.hjb.2016.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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4
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Monteiro-Vitorello CB, Hausner G, Searles DB, Gibb EA, Fulbright DW, Bertrand H. The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases. Fungal Genet Biol 2009; 46:837-48. [PMID: 19607930 DOI: 10.1016/j.fgb.2009.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 06/24/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
Abstract
The mt-rns gene of Cryphonectria parasitica is 9872bp long and includes two group I and two group II introns. An analysis of intronic protein-encoding sequences revealed that LAGLIDADG ORFs, which usually are associated with group I introns, were transferred at least twice into group II introns. A plasmid-like mitochondrial element (plME) that appears in high amounts in previously mutagen-induced mit1 and mit2 hypovirulent mutants of the Ep155 standard virulent strain of C. parasitica was found to be derived from a short region of the mt-rns gene, including the exon 1 and most of the first intron. The plME is a 4.2-kb circular, multimeric DNA and an autonomously-replicating mtDNA fragment. Although sexual transmission experiments indicate that the plME does not directly cause hypovirulence, its emergence is one manifestation of the many complex molecular and genetic events that appear to underlie this phenotype.
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Didek-brumec M, Gaberc-porekar V, Alačević M. Relationship between theClavicepsLife Cycle and Productivity of Ergot Alkaloids. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388559609147423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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6
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McDermott P, Connolly V, Kavanagh TA. The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:459-470. [PMID: 18504541 DOI: 10.1007/s00122-008-0790-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 05/02/2008] [Indexed: 05/26/2023]
Abstract
The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) was shown to contain a 9.6 kb element, LpCMSi, that is absent in the mitochondrial genome of fertile lines. LpCMSi contains the previously described chimeric gene orfC9, and three additional open reading frames (orfs) encoding a unique 45 kDa predicted protein of unknown function, a family B-like DNA polymerase (LpDpo), and a phage-type single subunit RNA polymerase (LpRpo). The latter two proteins shared significant similarity with DNA and RNA polymerases encoded by extrachromosomal linear mitochondrial plasmids of plants and fungi, and also to integrated plasmid-like sequences found in various plant and fungal mitochondrial genomes. Transcripts for both LpDpo and LpRpo were detected by RT-PCR in mitochondria of the CMS line. PCR-based investigations further revealed the presence of LpCMSi-like sequences in fertile L. perenne lines that are likely maintained as low-copy number extrachromosomal replicons. The absence of integrated forms of LpCMSi in the mitochondrial genome of fertile lines suggests that LpCMSi integration adjacent to the atp9 gene may be responsible, directly or indirectly, for the sterility phenotype of the CMS line.
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Affiliation(s)
- Paul McDermott
- Plant Molecular Genetics Laboratory, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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7
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Abstract
Plant mitochondria contain small extrachromosomal DNAs in addition to a large and complex main mitochondrial genome. These molecules can be regarded as extrachromosomal replicons or plasmids, of which there are two forms, circular and linear. Linear mitochondrial plasmids are present in many fungi and in some plants, but they seem to be absent from most animal cells. They usually have a common structural feature, called an invertron, that is characterized by the presence of terminal inverted repeats and proteins covalently attached to their 5 termini. Linear mitochondrial plasmids possess one to six ORFs that can encode unknown proteins but often code for the DNA and RNA polymerases. Although the functions of most linear plasmids in plant mitochondria are unknown, some plasmids may be associated with mitochondrial genome rearrangements and may have phenotypic effects due to their integration into mitochondrial genome. The Brassica 11.6-kb plasmid, one of the linear mitochondrial plasmids in plants, shows a non-maternal inheritance, in contrast to mitochondrial genomes. The origin of these plasmids is still a mystery, but indirect evidence indicates the possibility of horizontal transfer from fungal mitochondria. In this review, the main features of these unique DNAs present in plant mitochondria are described.
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Láday M, Stubnya V, Hamari Z, Hornok L. Characterization of a new mitochondrial plasmid from Fusarium proliferatum. Plasmid 2008; 59:127-33. [DOI: 10.1016/j.plasmid.2007.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 11/08/2007] [Accepted: 11/18/2007] [Indexed: 11/25/2022]
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9
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Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Lin GN, Meyer L, Sun H, Kim K, Wang C, Du F, Xu D, Gibson M, Cifrese J, Clifton SW, Newton KJ. Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 2007; 177:1173-92. [PMID: 17660568 PMCID: PMC2034622 DOI: 10.1534/genetics.107.073312] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,825 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5-120 kb) account for most of the size increases. Plastid DNA accounts for 2.3-4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65-7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding "native" mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.
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Affiliation(s)
- James O Allen
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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Mouhamadou B, Barroso G, Labarère J. Molecular evolution of a mitochondrial polB gene, encoding a family B DNA polymerase, towards the elimination from Agrocybe mitochondrial genomes. Mol Genet Genomics 2004; 272:257-63. [PMID: 15365817 DOI: 10.1007/s00438-004-1050-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Two genes (Ac-polB O1and Ac-polB O2), each encoding a family B DNA polymerase, were characterized from the mitochondrial genome of the basidiomycete Agrocybe chaxingu. These two polB genes constitute orthologs of the potentially functional Aa-polB gene and its disrupted paralog Aa-polB P1, previously described in the closely related species A. aegerita. Unlike the case in Aa-polB, both gene copies in A. chaxingu are constituted by large but disrupted ORFs, which very probably encode nonfunctional enzymes: Ac-polB O1 has a deletion of 126 bp between the segments encoding the Exo II and Pol I domains and a 78-bp insertion between the Exo II and Exo III domains, whereas Ac-polB O2 has a large deletion of 1208 bp between the Exo II and Pol III domains and a deletion of 54-bp involving the 3' end of the gene. Hence, rearrangements in the Ac-polB ORFs appear to have led to their functional erosion in the mitochondrial genome in this species. Phylogenetic analysis has shown a close relationship between the mitochondrial polB genes and homologous genes carried by fungal linear plasmids, suggesting that they may have been acquired by the integration of linear plasmids into the mitochondrial genome.
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Affiliation(s)
- B Mouhamadou
- Laboratoire de Génétique Moléculaire et d'Amélioration des Champignons Cultivés, INRA UMR 1090 (Génomique, Développement et Pouvoir Pathogène), Université Victor Segalen Bordeaux 2, CRA de Bordeaux, BP 81, 33883 Villenave d'Ornon, France
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11
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TSUKII Y, ENDOH H, YAZAKI K. Distribution and genetic variabilities of mitochondrial plasmid-like DNAs in Paramecium. Genes Genet Syst 2004. [DOI: 10.1266/ggs.69.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Giese H, Lyngkjaer MF, Stummann BM, Grell MN, Christiansen SK. Analysis of the structure and inheritance of a linear plasmid from the obligate biotrophic fungus Blumeria graminis f. sp. hordei. Mol Genet Genomics 2003; 269:699-705. [PMID: 12838413 DOI: 10.1007/s00438-003-0876-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Accepted: 05/30/2003] [Indexed: 10/26/2022]
Abstract
A linear plasmid is widespread among isolates of the obligate biotrophic fungus Blumeria graminis f.sp. hordei (synonym Erysiphe graminis) (Bgh), the organism that causes the disease powdery mildew on barley. We cloned and sequenced the entire plasmid of 7965 bp. The plasmid contains two identical terminal inverted repeats (TIR) of 610 bp. Two ORFs are present on opposite strands, one encoding a phage-type DNA polymerase and the other a phage-type RNA polymerase. Two large transcripts of approximately 4.2 and 5.6 kb were identified in conidia, germinating conidia and Bgh -infected barley leaves, indicating that the polymerases are transcribed at most stages of the lifecycle. The transcription start sites were localised within the TIR regions, where a putative 11-bp ARS consensus sequence was also identified. To follow the sexual transmission of the plasmid we screened 27 Bgh isolates for mitochondrial polymorphisms. One polymorphism allowed us to carry out a cross between two isolates that differed in both mitochondrial genotype and presence/absence of the Bgh plasmid. The plasmid was transmitted independently of the origin of the mitochondria. No transfer of the plasmid was observed between two Bgh isolates that were co-cultivated for 1.5 years on a common susceptible barley variety. The plasmid appears to be an autonomous replicon with no phenotypic effect on Bgh.
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Affiliation(s)
- H Giese
- Department of Ecology, Section of Genetics and Microbiology, Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, Frederiksberg C, 1871 Copenhagen, Denmark.
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14
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Nakai R, Sen K, Kurosawa S, Shibai H. Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases. FEMS Microbiol Lett 2000; 190:99-102. [PMID: 10981697 DOI: 10.1111/j.1574-6968.2000.tb09269.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Basidiomycetous fungus Flammulina velutipes R15 strain had two linear plasmids in its mitochondria designated pFV1 and pFV2. They were double-stranded DNAs, whose sizes were 8.3 and 8.9 kb, respectively. Sequencing analysis of 7364 bases of the pFV1 and 6861 bases of the pFV2 revealed that the both plasmids had one set of two open reading frames (ORFs) each of that encoded putative DNA and RNA polymerases similar to those of mitochondrial plasmids in other filamentous fungi. In phylogenetic analysis of deduced amino acid sequences of the ORFs and counterparts of other filamentous fungi, the pFV2 was expectedly clustered with plasmids of basidiomycetous fungi. whereas the pFV1 with kalilo plasmid of ascomycetous fungus Neurospora intermedia.
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Affiliation(s)
- R Nakai
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University, Nagano, Japan
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15
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Xu Y, Yang S, Turitsa I, Griffiths A. Divergence of a linear and a circular plasmid in disjunct natural isolates of the fungus Neurospora. Plasmid 1999; 42:115-25. [PMID: 10489328 DOI: 10.1006/plas.1999.1420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is known from DNA hybridization and other studies that Neurospora plasmids are widely distributed across species of this genus. However few comparisons have been performed of the structure of apparently identical plasmids in widely differing geographical and biological locations. We compare pairs of circular and linear mitochondrial plasmids from distant geographical locations. The circular plasmids (LaBelle and Harbin-1) were from different ecotypes of N. intermedia and the linear plasmids (maranhar and Harbin-3) were from different species (N. crassa and N. intermedia). The structures are highly similar at the sequence level showing that they are closely related. Most of the differences are outside the presumptive genes (coding for polymerases). Furthermore, most of the proposed functional motifs have been retained. Sequence divergence is compatible with a distribution model by vertical descent from a common ancestor, but horizontal transmission cannot be ruled out.
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Affiliation(s)
- Y Xu
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
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16
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Rao VP, Kajon AE, Spindler KR, Carayanniotis G. Involvement of Epitope Mimicry in Potentiation But Not Initiation of Autoimmune Disease. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.10.5888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
We have examined whether the peptide (368–381) from the murine adenovirus type 1 E1B sequence, exhibiting a high degree of homology with the known pathogenic thyroglobulin (Tg) T cell epitope (2695–2706), can induce experimental autoimmune thyroiditis (EAT) in SJL/J mice. The viral peptide was a poor immunogen at the T or B cell level and did not elicit EAT either directly or by adoptive transfer assays. Surprisingly, however, the viral peptide was highly antigenic in vitro, activating a Tg2695–2706-specific T cell clone and reacting with serum IgG from mice primed with the Tg homologue. The viral peptide also induced strong recall responses in Tg2695–2706-primed lymph node cells, and subsequent adoptive transfer of these cells into naive mice led to development of highly significant EAT. These data demonstrate that nonimmunogenic viral peptides can act as agonists for preactivated autoreactive T cells and suggest that epitope mimicry may at times play a potentiating rather than a precipitating role in the pathogenesis of autoimmune disease.
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Affiliation(s)
- Varada P. Rao
- †Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Adriana E. Kajon
- *Department of Genetics, University of Georgia, Athens, GA 30602; and
| | | | - George Carayanniotis
- †Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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Robison MM, Horgen PA. Widespread distribution of low-copy-number variants of mitochondrial plasmid pEM in the genus Agaricus. Fungal Genet Biol 1999; 26:62-70. [PMID: 10072320 DOI: 10.1006/fgbi.1998.1105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The incidence of the linear mitochondrial plasmid pEM in Agaricus spp. was believed to be rare, based on visualization by gel electrophoresis and Southern hybridization. However, we report in this study PCR amplification of pEM-like sequences from all but one species of Agaricus examined. Regions amplified included (1) the pEM RNA polymerase gene and (2) adjoining carboxy-termini of the DNA and RNA polymerase genes. Sequence data from the RNA polymerase-like products support a plasmid, rather than mitochondrial, origin for these sequences. Sequence variation was low, and most differences were silent or conservative at the amino acid level. Stop codons were found in two of seven sequence types suggesting that functional constraints are low. A parsimony-derived phylogeny for these sequences did not match expected phylogenies for the host species. Recent acquisition of the plasmid is presented as the most likely hypothesis explaining these observations.
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Affiliation(s)
- M M Robison
- Department of Botany, University of Toronto at Mississauga, Mississauga, Ontario, L5L 1C6, Canada
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18
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Takeda M, Hiraishi H, Takesako T, Tanase S, Gunge N. The terminal protein of the linear DNA plasmid pGKL2 shares an N-terminal domain of the plasmid-encoded DNA polymerase. Yeast 1998. [DOI: 10.1002/(sici)1097-0061(19960315)12:3<241::aid-yea907>3.0.co;2-j] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Gobbi E, Carpanelli A, Firrao G, Locci R. The Cryphonectria parasitica plasmid pUG1 contains a large ORF with motifs characteristic of family B DNA polymerases. Nucleic Acids Res 1997; 25:3275-80. [PMID: 9241241 PMCID: PMC146879 DOI: 10.1093/nar/25.16.3275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The isolation and characterization of the circular mitochondrial plasmid pUG1 from the ascomycete Cryphonectria parasitica is described. The entire sequence (4182 bp) was obtained and high similarities to DNA-dependent DNA polymerases were revealed. Strikingly common features with the DNA polymerases encoded by the Neurospora intermedia plasmids Fiji and LaBelle, such as matches to the conserved motifs A and B and the presence of TTD instead of DTD in motif C, were found, suggesting the existence of a distinct group of members of the B DNA family polymerases. These strong similarities between the plasmids might suggest a common origin of the C.parasitica and the Neurospora plasmids.
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Affiliation(s)
- E Gobbi
- Dipartimento di Biologia applicata alla Difesa delle Piante, Università di Udine, Via Scienze 208, Udine I-33100, Italy.
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20
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Fukuda K, Maebuchi M, Takata H, Gunge N. The linear plasmid pDHL1 from Debaryomyces hansenii encodes a protein highly homologous to the pGKL1-plasmid DNA polymerase. Yeast 1997; 13:613-20. [PMID: 9200811 DOI: 10.1002/(sici)1097-0061(19970615)13:7<613::aid-yea116>3.0.co;2-b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Both the linear plasmids, pDHL1 (8.4 kb) and pDHL2 (9.2 kb), of Debaryomyces hansenii TK require the presence of a third linear plasmid pDHL3 (15.0 kb) in the same host cell for their replication. A 3.5 kb Bam HI-PstI fragment of pDHL1 strongly hybridized by Southern analysis to the 3.5 kb NcoI-AccI fragment of pDHL2, suggesting the importance of this conserved region in the replication of the two smaller pDHL plasmids. The 4.2 kb pDHL1 fragment containing the above hybridized region was cloned and sequenced. The results showed that the cloned pDHL1 fragment encodes a protein of 1000 amino acid residues, having a strong similarity to the DNA polymerase coded for by ORF1 of the killer plasmid pGKL1 from Kluyveromyces lactis. The catalytic and proof-reading exonuclease domains as well as terminal protein motif were well conserved as in DNA polymerases of pGKL1 and other yeast linear plasmids. Analysis of the cloned fragment further showed that pDHL1 encodes a protein partly similar to the alpha subunit of the K. lactis killer toxin, although killer activity was not known in the DHL system. Analysis of the 5' non-coding region of the two above pDHL1-ORFs reveal the presence of the upstream conserved sequence similar to that found upstream of pGKL1-ORFs. The possible hairpin loop structure was also found just in front of the ATG start codon of the pDHL1-ORFs like pGKL1-ORFs. Thus the cytoplasmic pDHL plasmids were suggested to possess a gene expression system comparable to that of K. lactis plasmids.
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Affiliation(s)
- K Fukuda
- Kumamoto Institute of Technology, Japan
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21
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Takeda M, Hiraishi H, Takesako T, Tanase S, Gunge N. The terminal protein of the linear DNA plasmid pGKL2 shares an N-terminal domain of the plasmid-encoded DNA polymerase. Yeast 1996; 12:241-6. [PMID: 8904336 DOI: 10.1002/(sici)1097-0061(19960315)12:3%3c241::aid-yea907%3e3.0.co;2-j] [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: 02/02/2023] Open
Abstract
The 36K protein attached at the 5' end of the linear DNA plasmid pGKL2 from the yeast Kluyveromyces lactis was first purified and characterized. The terminal protein was purified from cells (1 kg wet weight) by ammonium sulphate precipitation and two rounds of centrifugation to equilibrium in CsCl gradients. The pGKL2 was present only in the post-microsomal supernatant. Approximately 10 mg of the purified pGKL2 was recovered and digested with DNase I. The terminal protein (final ca. 0 center dot 8 mg) was homogeneous by electrophoresis and we determined the N-terminal amino acid sequence up to ten residues, showing that it existed in the cryptic N-terminal domain of pGKL2-ORF2 (DNA polymerase) sequence.
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Affiliation(s)
- M Takeda
- Department of Applied Microbial Technology, Kumamoto Institute of Technology, Japan
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Structure of aGelasinospora linear plasmid closely related to the kalilo plasmid ofNeurospora intermedia. Curr Genet 1996. [DOI: 10.1007/bf02221579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Abstract
Among eukaryotes, plasmids have been found in fungi and plants but not in animals. Most plasmids are mitochondrial. In filamentous fungi, plasmids are commonly encountered in isolates from natural populations. Individual populations may show a predominance of one type, but some plasmids have a global distribution, often crossing species boundaries. Surveys have shown that strains can contain more than one type of plasmid and that different types appear to be distributed independently. In crosses, plasmids are generally inherited maternally. Horizontal transmission is by cell contact. Circular plasmids are common only in Neurospora spp., but linear plasmids have been found in many fungi. Circular plasmids have one open reading frame (ORF) coding for a DNA polymerase or a reverse transcriptase. Linear plasmids generally have two ORFs, coding for presumptive DNA and RNA polymerases with amino acid motifs showing homology to viral polymerases. Plasmids often attain a high copy number, in excess of that of mitochondrial DNA. Linear plasmids have a protein attached to their 5' end, and this is presumed to act as a replication primer. Most plasmids are neutral passengers, but several linear plasmids integrate into mitochondrial DNA, causing death of the host culture. Inferred amino acid sequences of linear plasmid ORFs have been used to plot phylogenetic trees, which show a fair concordance with conventional trees. The circular Neurospora plasmids have replication systems that seem to be evolutionary intermediates between the RNA and the DNA worlds.
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Affiliation(s)
- A J Griffiths
- Botany Department, University of British Columbia, Vancouver, Canada
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24
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Griffiths AJ, Yang X. Recombination between heterologous linear and circular mitochondrial plasmids in the fungus Neurospora. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:25-36. [PMID: 8552030 DOI: 10.1007/bf00290232] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A strain of Neurospora intermedia from China contains five prominent extragenomic mitochondrial plasmids: three linear elements called zhisi plasmids, and two circular plasmids, Harbin-1 and -2. In one subculture, levels of four plasmids (all three zhisis and Harbin-1) fell to undetectable values and two novel linear plasmids appeared, Harbin-L and -L2, as well as a new small circular plasmid, Harbin-0.9. Cross-hybridization of restriction fragments and DNA sequencing showed that the Harbin-L plasmid was composed of parts of the circular Harbin-1 plasmid and of one of the linear zhisi plasmids. A model is presented in which the Harbin-1 and zhisi plasmids are present within the same mitochondrion, and crossovers at two separate 7 bp sites of sequence identity effectively insert part of the circular Harbin-1 DNA into a zhisi linear plasmid, simultaneously deleting part of the zhisi element. The small plasmid Harbin-0.9 is a fragment of the Har-1 plasmid, and seems to be another product of the recombination process that created Har-L. Recombination of this type could have contributed to the wide array of mitochondrial plasmids found in natural populations of Neurospora.
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Affiliation(s)
- A J Griffiths
- Botany Department, University of British Columbia, Vancouver, Canada
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25
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Weber B, Börner T, Weihe A. Remnants of a DNA polymerase gene in the mitochondrial DNA of Marchantia polymorpha. Curr Genet 1995; 27:488-90. [PMID: 7586038 DOI: 10.1007/bf00311221] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- B Weber
- Lehrstuhl für Genetik, Humboldt-Universität zu Berlin, Germany
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26
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Kawano S, Takano H, Kuroiwa T. Sexuality of mitochondria: fusion, recombination, and plasmids. INTERNATIONAL REVIEW OF CYTOLOGY 1995; 161:49-110. [PMID: 7558693 DOI: 10.1016/s0074-7696(08)62496-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mitochondrial fusion, recombination, and mobile genetic elements, which are essential for mitochondrial sexuality, are well established in various organisms. The recombination of mitochondrial DNA (mtDNA) depends upon fusion between parental mitochondria, and between their mtDNA-containing areas (mt-nuclei), to allow pairing between the parental mtDNAs. Such mitochondrial fusion followed by recombination may be called "mitochondrial sex." We have identified a novel mitochondrial plasmid named mF. This plasmid is apparently responsible for promoting mitochondrial fusion and crosses over with mtDNA in successive sexual crosses with mF- strains. Only in mF+ strains carrying the mF plasmid did small spherical mitochondria fuse which subsequently underwent fusion between the mt-nuclei that contained the mtDNA derived from individual mitochondria. Several successive mitochondrial divisions followed, accompanied by mt-nuclear divisions. The resulting mitochondria contained recombinant mtDNA with the mF plasmid. Such features remind us also of the bacterial conjugative plasmids such as F plasmid. Therefore, in the final part of this chapter, we discuss the origin of sex and its relationship to the sexuality of mitochondria.
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Affiliation(s)
- S Kawano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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27
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28
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Endoh H, Yazaki K, Takahashi M, Tsukii Y. Hairpin and dimer structures of linear plasmid-like DNAs in mitochondria of Paramecium caudatum. Curr Genet 1994; 27:90-4. [PMID: 7750152 DOI: 10.1007/bf00326584] [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: 01/26/2023]
Abstract
The molecular structure of plasmid-like DNAs (designated type-II) which were isolated from mitochondria in the ciliated protozoan Paramecium caudatum was characterized. These type-II DNAs are always detected as a set of four kinds with sizes of 8.2, 4.1, 2.8 and 1.4 kb. The DNAs of 8.2 and 2.8 kb exist as dimers consisting of 4.1- and 1.4-kb monomer molecules, respectively. Electron microscopic observations indicated configurations of a hairpin structure that had a protruding end of single-stranded DNA in one terminus and a loop in the other terminus. The monomers stick together with base-pairing in opposite directions at the protruding end to form the dimers, suggesting the presence of inverted repeats. These unusual dimers may have a role in replication of the DNAs in which the monomers can serve as a primer for each other.
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Affiliation(s)
- H Endoh
- Laboratory of Biology, Hosei University, Tokyo, Japan
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29
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Hongo M, Miyasaka A, Suzuki F, Hashiba T. Expression of the linear DNA plasmid pRS64 in the plant pathogenic fungus Rhizoctonia solani. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:265-71. [PMID: 7529353 DOI: 10.1007/bf00290105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The plant pathogenic isolate RI-64 of anastomosis group 4 of Rhizoctonia solani possesses three linear DNA plasmids (pRS64-1, -2, and -3). Unique poly(A)- RNA, 0.5 kb in length and hybridizable with the pRS64 DNAs was found in mycelial cells of the isolate RI-64. The overall homology at the nucleotide level between pRS64-1, -2, and -3, and the cDNA prepared from the poly(A)- RNA was 100%, 73%, and 84%, respectively. The open reading frames found in pRS64-1, -2, and -3 (ORF1-1, ORF2-1, and ORF3-1) are 68 amino acids long. The amino acids sequence showed no significant homology with known proteins. Extracts from Escherichia coli cells expressing ORF1-1 contain a specific protein of 7 kDa. Antisera raised against the ORF1-1 product obtained from E. coli cells cross-reacted with the specific proteins found in the mycelia. The results indicate that the DNA plasmids found in R. solani contain a sequence that encodes a specific protein which may be involved in determination of plant pathogenicity.
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30
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Takano H, Kawano S, Kuroiwa T. Genetic organization of a linear mitochondrial plasmid (mF) that promotes mitochondrial fusion in Physarum polycephalum. Curr Genet 1994; 26:506-11. [PMID: 7533058 DOI: 10.1007/bf00309941] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The mF plasmid which promotes mitochondrial fusion in Physarum polycephalum is a linear molecule with complex terminal inverted repeats (TIRs). Its nucleotide sequence was determined. The mF plasmid is 14,503 bp in size, and contains ten open reading frames (ORFs). All of the ORFs except one are encoded on the same DNA strand (coding strand). The number of amino-acid residues in the putative proteins derived from the nine ORFs on the coding strand are 231, 163, 640, 235, 118, 1130, 366, 309, and 547 from left (5' end) to right (3' end) on the map. The amino-acid sequences of newly-identified ORFs on the mF plasmid did not show significant homology to any amino-acid sequences in the databases. A brief transcriptional map of the mF plasmid was constructed, and the following features were noted. (1) The transcription initiation site was located just inside the end of the left TIRs, but not within the TIRs themselves. (2) Three major transcripts of 1.0, 3.4 and 4.6 knt corresponded to the left region of the mF plasmid, and long, low-abundance (more than 4.6 knt), heterogenous transcripts corresponded to almost the entire mF plasmid. A low-abundance, 3.5-knt transcript corresponding to the coding region of ORF1 130 (a 1 130-amino-acid polypeptide) was also detected, and may be derived from the long transcripts. (3) The quantity of transcripts which included the region near the transcription initiation site was about 500-times more than that which included the region near the inner end of the right TIRs.
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Affiliation(s)
- H Takano
- Department of Plant Sciences, Graduate School of Science, University of Tokyo, Japan
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31
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Lim L, Howlett BJ. Linear plasmids, pLm9 and pLm10, can be isolated from the phytopathogenic ascomycete Leptosphaeria maculans by pulsed-field gel electrophoresis. Curr Genet 1994; 26:276-80. [PMID: 7859312 DOI: 10.1007/bf00309560] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two linear DNA plasmids (pLm9 and pLm10, sized 9 and 10 kb respectively) were isolated from the phytopathogenic ascomycete Leptosphaeria maculans, using pulsed-field gel electrophoresis. pLm9 and pLm10 are found only in aggressive isolates of L. maculans but, because aggressive and non-aggressive strains appear to be different species, these plasmids are probably not involved in pathogenicity. pLm9 and pLm10 copurify with a mitochondrially-enriched cell fraction, and do not hybridise to chromosomal or mitochondrial DNA, or to each other. Exonuclease digestions suggest that both these molecules contain covalently-bound proteins at their 5' termini. pLm9 hybridises to the RNA polymerase of a linear plasmid from the ascomycete Podospora anserina, and pLm10 hybridises to the DNA polymerase from the same P. anserina plasmid, suggesting that pLm9 and pLm10 encode their own replication and transcription enzymes.
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Affiliation(s)
- L Lim
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Victoria, Australia
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32
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Gessner-Ulrich K, Tudzynski P. Studies on function and mobility of mitochondrial plasmids from Claviceps purpurea. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s0953-7562(09)80469-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Jabaji-Hare SH, Burger G, Forget L, Lang BF. Extrachromosomal plasmids in the plant pathogenic fungus Rhizoctonia solani. Curr Genet 1994; 25:423-31. [PMID: 8082188 DOI: 10.1007/bf00351781] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Extrachromosomal DNA elements were found in field isolates of Rhizoctonia solani belonging to anastomosis groups (AG) 1-5. An isolate of AG-5 (Rh41) contains a 3.6-kbp plasmid (pRS188) which has a similar A+T content to mitochondrial DNA. pRS188 is linear and has knob structures at its ends, as revealed by electron microscopy. Exonuclease digestions show that the linear ends of pRS188 are protected, and remain protected even after proteinase K digestion. pRS188 does not hybridise to nuclear or mitochondrial DNAs of its host isolate (Rh41), to total DNAs of other plasmid-less AG-5 isolates, or to total DNA of plasmid-harbouring isolates belonging to different AGs. Cellular-fractionation experiments suggest that pRS188 is associated with mitochondria, but it remains undecided whether this occurs inside or outside of the organelles. The nucleotide sequence of about 60% of the plasmid has been determined, revealing no open reading frame longer than 91 amino acids, and no known gene or genetic element is detected in the sequence contigs of 300-1572 bp length. Similar studies were performed with the plasmid pRS104 present in an isolate of AG-4 (Rh36), the sequence of which exhibits essentially the same features as pRS188 except that its A+T content resembles that of nuclear DNA. Pathogenicity tests reveal that the isolates Rh41 and R36 are as virulent as the plasmid-less isolates of AG-4 and -5, indicating that the plasmids do not play any role in pathogenicity.
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Affiliation(s)
- S H Jabaji-Hare
- Department of Plant Science, McGill University, Ste-Anne-de Bellevue, Québec, Canada
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34
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Takano H, Kawano S, Kuroiwa T. Complex terminal structure of a linear mitochondrial plasmid from Physarum polycephalum: three terminal inverted repeats and an ORF encoding DNA polymerase. Curr Genet 1994; 25:252-7. [PMID: 7923412 DOI: 10.1007/bf00357170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The mitochondria of Physarum polycephalum have a linear plasmid (mF) which promotes mitochondrial fusion. To determine the terminal structure of the mF plasmid, restriction fragments derived from its ends were cloned and sequenced. The sequences showed that the mF plasmid has three kinds of terminal inverted repeats (TIRs). The most characteristic feature is a 144-bp repeating unit which exists between a 205-bp TIR at the extreme ends of the plasmid and another 591-bp TIR. All of the clones showed at least one of these 144-bp repeating units. The GC content of the 205-bp TIR (49%) was higher than those of the other TIRs and of another sequenced region (23%). This TIR can form three thermodynamically-stable hairpin structures based on complex internal palindromic components. Moreover, in the right terminal region of the mF plasmid, there is an open reading frame (ORF) which covers the entire 591-bp TIR and most of one of the 144-bp repeating units. This ORF encodes a 547-amino-acid polypeptide, ORF-547, and shows extensive homology with the polymerization domain of the putative DNA polymerases of linear mitochondrial plasmids from other sources.
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Affiliation(s)
- H Takano
- Department of Biology, Faculty of Science, University of Tokyo, Japan
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35
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Hermanns J, Osiewacz HD. Three mitochondrial unassigned open reading frames of Podospora anserina represent remnants of a viral-type RNA polymerase gene. Curr Genet 1994; 25:150-7. [PMID: 8087884 DOI: 10.1007/bf00309541] [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: 01/28/2023]
Abstract
The mitochondrial DNA of Podospora anserina is complex, consisting of a characteristic set of genes with a large number of introns and a substantial amount of sequence of unknown function and origin. In addition, as indicated by various types of reorganization, this genome is highly flexible. Here we report the identification of three unassigned mitochondrial open reading frames (ORF P', ORF Q', ORF 11) as remnants of a rearranged viral-type RNA polymerase gene. These ORFs are not transcribed and may be derived from the integration of a linear plasmid of the type recently identified in a mutant of P. anserina.
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Affiliation(s)
- J Hermanns
- Department of Molecular Biology of Aging Processes, German Cancer Research Center, Heidelberg
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36
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Martins A, Ribeiro G, Marques MI, Costa JV. Genetic identification and nucleotide sequence of the DNA polymerase gene of African swine fever virus. Nucleic Acids Res 1994; 22:208-13. [PMID: 8121806 PMCID: PMC307773 DOI: 10.1093/nar/22.2.208] [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: 01/28/2023] Open
Abstract
The DNA polymerase gene of African swine fever virus (ASFV) was mapped by marker rescue experiments using a phosphonoacetic acid-resistant mutant and hybridization with an oligonucleotide probe designed from the most conserved motif of family B DNA polymerases. Viral DNA fragments mapping in this region were cloned and sequenced. An open reading frame coding for a 1244 amino acid long peptide with a molecular mass of 142.5 kDa was determined from the sequence. A unique feature of ASFV DNA polymerase is the presence of 13 tandem repeats of the sequence Ala-Gly-Asp-Pro near the carboxyl end of the molecule. Comparison with 30 sequences of alpha-like DNA polymerases of cellular and viral origin showed that ASFV DNA polymerase has all the conserved motifs of family B DNA polymerases. A 3.9 kb transcript was detected by Northern hybridization and the transcription initiation and termination sites were mapped by S1 analysis and primer extension. Late transcription was initiated at a site different from the early transcription initiation site. A 145 kDa protein, consistent with the size of the gene, was identified by an in situ enzyme assay after gel electrophoresis of infected cell extracts.
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Affiliation(s)
- A Martins
- Laboratory of Virology II, Gulbenkian Institute of Science, Oeiras, Portugal
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37
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TSUKII Y, ENDOH H, YAZAKI K. Distribution and genetic variabilities of mitochondrial plasmid-like DNAs in Paramecium. ACTA ACUST UNITED AC 1994. [DOI: 10.1266/jjg.69.685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Dohmen G, Tudzynski P. A DNA-polymerase-related reading frame (pol-r) in the mtDNA of Secale cereale. Curr Genet 1994; 25:59-65. [PMID: 8082167 DOI: 10.1007/bf00712969] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial (mt)DNA of Secale cereale contains an open reading frame (pol-r), the potential translation product of which shows significant homology to the type-B DNA polymerase encoded by the S1 plasmid of Zea mays; it contains the highly-conserved domains IIa to V of family B polymerases. The pol-r ORF is transcribed, as proven by RT-PCR, but the transcript is not edited. Upstream of the putative start codon a potential promoter motif was detected, fitting well into the postulated consensus sequence of the transcription initiation regions of Z. mays and Triticum aestivum. The pol-r ORF occurs in mtDNA of the fertile rye variety "Halo" and the cytoplasmic male-sterile (CMS) line "Pampa". Both ORFs are almost identical, apart from the 3' terminus; pol-r from Halo can code for 289 amino acids, pol-r from Pampa for 312 amino acids. Based on codon usage and the lack of editing, pol-r is considered to be a "young" gene, probably introduced in the mtDNA of rye by recombination with an mt plasmid.
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Affiliation(s)
- G Dohmen
- Institut für Botanik, Westfälische Wilhelms-Universität, Münster, Germany
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39
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Abstract
The single subunit DNA-dependent RNA polymerase (RNAP) that is encoded by bacteriophage T7 is the prototype of a class of relatively simple RNAPs that includes the RNAPs of the related phages T3 and SP6, as well as the mitochondrial RNAPs. The T7 enzyme has been crystallized, and recent genetic and biochemical analyses have facilitated an interpretation of this structure. A growing body of evidence suggests that the phage-like RNAPs are related to other nucleotide polymerases such as DNA polymerases, RNA-dependent RNA polymerases, and reverse transcriptases. In this work, we review information concerning the structure and function of T7 RNAP, and evidence in support of its assignment to a broader class of nucleotide polymerases.
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Affiliation(s)
- W T McAllister
- Department of Microbiology and Immunology, Morse Institute of Molecular Genetics, SUNY Health Science Center at Brooklyn 11203-2098
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40
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Li Q, Nargang FE. Two Neurospora mitochondrial plasmids encode DNA polymerases containing motifs characteristic of family B DNA polymerases but lack the sequence Asp-Thr-Asp. Proc Natl Acad Sci U S A 1993; 90:4299-303. [PMID: 8483947 PMCID: PMC46494 DOI: 10.1073/pnas.90.9.4299] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have determined the DNA sequence of the mitochondrial plasmid from Neurospora intermedia strain Fiji N6-6. The plasmid contains a 1278-codon open reading frame that is 49% identical to the open reading frame of the mitochondrial plasmid from the LaBelle strain of N. intermedia, which is known to encode a DNA-dependent DNA polymerase. The results of polymerase assays and photolabeling studies, the high degree of identity with the LaBelle plasmid polymerase, and the observation that the Fiji polymerase activity in a reaction utilizing endogenous template is not affected by removal of RNA suggest that the Fiji plasmid also encodes a DNA-dependent DNA polymerase. Comparison of regions of amino acids that are highly conserved in the two plasmid polymerases to family B polymerases reveals good correlates for the three major polymerase motifs and suggests that previously identified motifs characteristic of reverse transcriptase found in the LaBelle sequence are not significant. The polymerases encoded by the Fiji and LaBelle plasmids are unusual in that the amino acid sequence Asp-Thr-Asp, which forms the core of the third motif in family B polymerases, is not present in either Fiji or LaBelle. A version of the motif containing Thr-Thr-Asp exists in both sequences.
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Affiliation(s)
- Q Li
- Department of Genetics, University of Alberta, Edmonton, Canada
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41
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Oeser B, Rogmann-Backwinkel P, Tudzynski P. Interaction between mitochondrial DNA and mitochondrial plasmids in Claviceps purpurea: analysis of plasmid-homologous sequences upstream of the lrRNA-gene. Curr Genet 1993; 23:315-22. [PMID: 8467529 DOI: 10.1007/bf00310892] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Homology of two linear, mitochondrial (mt) Claviceps purpurea plasmids, pClK1 and pClT5, to the upstream region of the large ribosomal RNA gene in the mtDNA of three strains (W3, T5 and K) has been investigated in detail to explore the widespread phenomenon of homology between mt plasmids and mtDNA in C. purpurea. Sequence comparison indicates that recombination between free plasmids and mtDNA is the cause of the observed homology. The process is similar to the integration of the structurally related adenoviruses into the mammalian genome. As in other fungi, palindromic sequences seem to be involved in this mitochondrial recombination process.
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Affiliation(s)
- B Oeser
- Lehrstuhl für Allgemeine Botanik/Mikrobiologie, Westfälische Wilhelms-Universität, Münster, Germany
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42
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Braithwaite DK, Ito J. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res 1993; 21:787-802. [PMID: 8451181 PMCID: PMC309208 DOI: 10.1093/nar/21.4.787] [Citation(s) in RCA: 460] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- D K Braithwaite
- Department of Microbiology and Immunology, College of Medicine, Arizona Health Sciences Center, Tucson 85724
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43
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Uemori T, Ishino Y, Toh H, Asada K, Kato I. Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosus. Nucleic Acids Res 1993; 21:259-65. [PMID: 8441634 PMCID: PMC309101 DOI: 10.1093/nar/21.2.259] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We cloned the gene encoding the thermostable DNA polymerase from the archaeon Pyrococcus furiosus. The DNA fragment of 2785 base pair (bp) containing the structural gene for DNA polymerase was sequenced. DNA polymerase (Pfu polymerase), as deduced from the DNA sequence, consisted of 775 amino acids, had a molecular weight of 90, 109, and was structurally homologous to the alpha-like DNA polymerases (family B) represented by human DNA polymerase alpha and Escherichia coli DNA polymerase II. An unrooted phylogenetic tree of the alpha-like DNA polymerases based on the amino acid sequence alignment was constructed. Pfu polymerase, with two other archaeon polymerases, constitutes a group with some animal viruses. The transcription initiation sites of the pol gene were identified by analysis of in vivo transcripts of both from P. furiosus and E. coli, and the promoters were assigned upstream of the pol coding region. A typical promoter sequence for the archaeon was found at a reasonable distance from the transcription initiation site in P. furiosus.
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Affiliation(s)
- T Uemori
- Biotechnology Research Laboratories, Takara Shuzo Co., Ltd, Shiga, Japan
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44
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Wu X, Roy KL. Complete nucleotide sequence of a linear plasmid from Streptomyces clavuligerus and characterization of its RNA transcripts. J Bacteriol 1993; 175:37-52. [PMID: 8416908 PMCID: PMC196095 DOI: 10.1128/jb.175.1.37-52.1993] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The complete nucleotide sequence of a small linear plasmid (pSCL1) from Streptomyces clavuligerus has been determined. This plasmid is 11,696 bp in length, has a 72% G+C content, and has approximately 900-bp inverted terminal repeat sequences. A comparison of the inverted terminal repeats of pSCL1 with those of a linear plasmid from S. rochei shows that the two terminal sequences have a high degree of similarity (approximately 70%). Several small inverted repeats found in the long terminal sequences of both plasmids are also conserved. An analysis of the sequence and codon preferences indicates that pSCL1 has seven or eight highly probable protein-coding open reading frames (ORFs). However, only two RNA species encoded by pSCL1 were detected in S. clavuligerus grown in liquid culture. The larger of these transcripts (900 nucleotides) corresponds to an ORF and is likely to be an mRNA for a protein similar to the KorA protein of pIJ101. The smaller transcript (460 nucleotides) does not correspond to any ORF; however, its 5' end is complementary to the 5' end of a predicted mRNA, suggesting that it may function as an antisense RNA. The larger of the two RNA species was present at a high level during the early stage of growth in liquid medium, and then its apparent rate of transcription decreased and remained at a lower level through the later stages; the level of the smaller RNA species remained relatively constant through all stages of growth.
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Affiliation(s)
- X Wu
- Department of Microbiology, University of Alberta, Edmonton, Canada
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45
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Abstract
Linear plasmids are genetic elements commonly found in yeast, filamentous fungi, and higher plants. In contrast to all other plasmids they possess terminal inverted repeats and terminal bound proteins and encode their own DNA and RNA polymerases. Here we present alignments of conserved amino acid sequences of both the DNA and RNA polymerases encoded by those linear plasmids for which DNA sequence data are available. Additionally these sequences are compared to a number of polymerases encoded by related viral and cellular entities. Phylogenetic trees have been established for both types of polymerases. These trees appear to exhibit very similar subgroupings, proving the accuracy of the method employed.
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Affiliation(s)
- F Kempken
- Ruhr-Universität Bochum, Lehrstuhl für Allgemeine Botanik, FRG
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Hermanns J, Osiewacz HD. The linear mitochondrial plasmid pAL2-1 of a long-lived Podospora anserina mutant is an invertron encoding a DNA and RNA polymerase. Curr Genet 1992; 22:491-500. [PMID: 1473181 DOI: 10.1007/bf00326415] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular characterization of an additional DNA species (pAL2-1) which was identified previously in a long-lived extrachromosomal mutant (AL2) of Podospora anserina revealed that this element is a mitochondrial linear plasmid. pAL2-1 is absent from the corresponding wild-type strain, has a size of 8395 bp and contains perfect long terminal inverted repeats (TIRs) of 975 bp. Exonuclease digestion experiments indicated that proteins are covalently bound at the 5' termini of the plasmid. Two long, non-overlapping open reading frames, ORF1 (3,594 bp) and ORF2 (2847 bp), have been identified, which are located on opposite strands and potentially encode a DNA and an RNA polymerase, respectively. The ORF1-encoded polypeptide contains three conserved regions which may be responsible for a 3'-5' exonuclease activity and the typical consensus sequences for DNA polymerases of the D type. In addition, an amino-acid sequence motif (YSRLRT), recently shown to be conserved in terminal proteins from various bacteriophages, has been identified in the amino-terminal part of the putative protein. According to these properties, this first linear plasmid identified in P. anserina shares all characteristics with invertrons, a group of linear mobile genetic elements.
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Affiliation(s)
- J Hermanns
- Deutsches Krebsforschungszentrum, Forschungsschwerpunkt: Angewandte Tumorvirologie, Abteilung: Molekularbiologie der Alterungsprozesse, Heidelberg, Federal Republic of Germany
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47
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Rohe M, Meinhardt F. Both open reading frames of the linear plasmid pMC3-2 from the ascomycete Morchella conica are transcribed in vivo. Curr Genet 1992; 22:507-9. [PMID: 1282088 DOI: 10.1007/bf00326418] [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: 12/26/2022]
Abstract
Mitochondrial RNA was isolated from the morel strain Morchella conica 3 harbouring the linear plasmid pMC3-2 and subjected to gel electrophoresis followed by a Northern analysis using cloned fragments of the plasmid pMC3-2 as probes. Hybridization was obtained only with central parts of pMC3-2 and specific bands of mtRNA. The hybridization bands (2.8 kb and 1.0 kb) correspond in size to the length of the two ORFs of pMC3-2 which were deduced from nucleotide-sequence data. Thus, both ORFs, one encoding a DNA polymerase and the other a yet unknown protein, are transcribed in the mitochondria of the plasmid-bearing Morchella conica strain.
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Affiliation(s)
- M Rohe
- Institut für Mikrobiologie, Westflische Wilhelms-Universität, Münster, Federal Republic of Germany
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48
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Gross L, Chen WJ, McAllister WT. Characterization of bacteriophage T7 RNA polymerase by linker insertion mutagenesis. J Mol Biol 1992; 228:488-505. [PMID: 1453459 DOI: 10.1016/0022-2836(92)90837-a] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thirty-four mutants of phage T7 RNA polymerase (RNAP) were generated by linker-insertion mutagenesis and characterized with respect to their ability to carry out various steps in the transcription cycle. A number of mutants with interesting biochemical properties were identified. These include: (1) Mutant RNAPs that are catalytically active but that bind weakly to a T7 promoter; one of these mutants is affected in a region of the RNAP that exhibits homology with the sigma subunit of Escherichia coli RNAP. Another is affected in a region that has been previously implicated in the discrimination of T7 versus T3 promoters (Joho, et al., 1990). (2) Mutant RNAPs that can bind to the promoter but are transcriptionally inactive; some of these RNAPs lack catalytic activity, others are catalytically active but are unable to initiate productive transcription at a T7 promoter. Among the latter class of mutants are enzymes that appear to be weakened in their ability to melt open (or to remain associated with) double-stranded DNA; these RNAPs make only abortive initiation products and are unable to proceed to the formation of a productive elongation complex. The mutations causing this phenotype affect regions of the RNAP that exhibit homology with the catalytic site of DNA polymerase I (Delarue et al., 1990). (3) A C-terminal insertion mutant with properties similar to a previously characterized "foot" mutant (Mookhtiar et al., 1991). This RNAP appears to be defective in the very early steps of transcription and may be unable to translocate and/or empty the active site. (4) A mutant that is transcriptionally active, but is unable to complement the growth of T7 gene 1- phage. This phenotype may result from disruption of a function of the RNAP that is distinct from its role in RNA synthesis.
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Affiliation(s)
- L Gross
- Morse Institute for Molecular Genetics, Department of Microbiology and Immunology State University of New York, Brooklyn 11203-2098
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Court DA, Bertrand H. Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa. Curr Genet 1992; 22:385-97. [PMID: 1423726 DOI: 10.1007/bf00352440] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nucleotide sequence of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa, was determined. The termini of the 7-kb plasmid are 349-bp inverted repeats (TIRs). Each DNA strand contains a long open reading frame (ORF) which begins within the TIR and extends toward the centre of the plasmid. ORF-1 codes for a single-subunit RNA polymerase that is not closely related to that encoded by another Neurospora plasmid, kalilo. The ORF-2 product may be a B-type DNA polymerase resembling those encoded by terminal protein-linked linear genetic elements, including linear mitochondrial plasmids and linear bacteriophages. A separate coding sequence for the terminal protein could not be identified; however, the DNA polymerase of maranhar has an amino-terminal extension with features that are also present in the terminal proteins of linear bacteriophages. The N-terminal extensions of the DNA polymerases of other linear mitochondrial plasmids contain similar features, suggesting that the terminal proteins of linear plasmids may be comprised, at least in part, of these cryptic domains. The terminal protein-DNA bond of maranhar is resistant to mild alkaline hydrolysis, indicating that it might involve a tyrosine or a lysine residue. Although maranhar and the senescence-inducing kalilo plasmid of N. intermedia are structurally similar, and integrate into mitochondrial DNA by a mechanism thus far unique to these two plasmids, they are not closely related to each other and they do not have any nucleotide sequence features, or ORFs, that distinguish them clearly from mitochondrial plasmids which are not associated with senescence and most of which are apparently non-integrative.
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Affiliation(s)
- D A Court
- Department of Microbiology, University of Guelph, Ontario, Canada
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Vierula PJ, Bertrand H. A deletion derivative of the kalilo senescence plasmid forms hairpin and duplex DNA structures in the mitochondria of Neurospora. MOLECULAR & GENERAL GENETICS : MGG 1992; 234:361-8. [PMID: 1406582 DOI: 10.1007/bf00538695] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel deletion derivative, delta kal, of the kalilo senescence plasmid from Neurospora intermedia, was recovered from a culture treated with chloramphenicol. The deletion derivative exists in mitochondria as two different, equally abundant forms: a 2.8 kb duplex DNA molecule (delta kal-2.8) and a 1.4 kb hairpin form (delta kal-1.4). The delta kal-2.8 plasmid contains the 1366 bp terminal inverted repeats and a partially duplicated 102 bp segment of the unique sequence of the 8.6 kb kalilo plasmid. In contrast, the delta kal-1.4 hairpin plasmid appears to result from the folding of single strands that are generated during the replication of delta kal-2.8. Both forms of delta kal have covalently linked terminal proteins. Sequence analysis suggests that delta kal was generated either by slippage of the tip of a growing strand during the replication of kalilo, or by illegitimate recombination between two copies of the plasmid at non-homologous palindromic sequences that might form cruciform structures. In either case, the deletion process was mediated at least in part by an inverted repeat of 5 bp in the unique region of kalilo. Since the terminal segments of kalilo DNA that are implicated in plasmid integration might also form cruciform structures, it is possible, but improbable, that the process that generated the first delta kal molecule is related to that which mediates integration of the plasmid into mitochondrial DNA.
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Affiliation(s)
- P J Vierula
- Department of Microbiology, University of Guelph, Ontario, Canada
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