Online citations, reference lists, and bibliographies.
← Back to Search

Identification And Distribution Of Sequences Having Similarity To Mitochondrial Plasmids In Mitochondrial Genomes Of Filamentous Fungi

Patrick Cahan, J. Kennell
Published 2005 · Medicine, Biology

Cite This
Download PDF
Analyze on Scholarcy
Share
Mitochondrial plasmids are autonomously replicating genetic elements commonly associated with fungal and plant species. Analysis of several plant and fungal mitochondrial genomes has revealed regions that show significant homology to mitochondrial plasmids, suggesting that plasmids have had a long-term association with their mitochondrial hosts. To assess the degree to which plasmids have invaded fungal mitochondrial genomes, BLAST search parameters were modified to identify plasmid sequences within highly AT-rich mtDNAs, and output data were parsed by E value, score, and sequence complexity. High scoring hits were evaluated for the presence of shared repetitive elements and location within plasmids and mtDNAs. Our searches revealed multiple sites of sequence similarity to four distinct plasmids in the wild-type mtDNA of Neurospora crassa, which collectively comprise more than 2% of the mitochondrial genome. Regions of plasmid similarity were not restricted to plasmids known to be associated with senescence, indicating that all mt plasmids can potentially integrate into mitochondrial DNA. Unexpectedly, plasmid-related sequences were found to be clustered in regions that have disproportionately low numbers of PstI palindromic sequences, suggesting that these repetitive elements may play a role in eliminating foreign DNA. A separate class of GC-rich palindromes was identified that appear to be mobile, as indicated by their occurrence within regions of plasmid homology. Sites of sequence similarity to mitochondrial plasmids were also detected in other filamentous fungi, but to a lesser degree. The tools developed here will be useful in assessing the contribution plasmids have made to mitochondrial function and in understanding the co-evolution of mitochondrial plasmids and their hosts.
This paper references
10.1016/0378-1119(86)90262-3
The GC clusters of the mitochondrial genome of yeast and their evolutionary origin.
M. de Zamaroczy (1986)
10.1038/345177A0
Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora
R. Collins (1990)
10.1007/BF00365640
Extrachromosomal genetics of Claviceps purpurea
P. Tudzynski (2004)
10.1007/BF00309541
Three mitochondrial unassigned open reading frames of Podospora anserina represent remnants of a viral-type RNA polymerase gene
J. Hermanns (2004)
10.1016/0092-8674(86)90525-8
An extrachromosomal plasmid is the etiological precursor of kalDNA insertion sequences in the mitochrondrial chromosome of senescent neurospora
H. Bertrand (1986)
10.1007/BF00326294
A new senescence-inducing mitochondrial linear plasmid in field-isolated Neurospora crassa strains from India
D. Court (2004)
10.1007/BF00312742
Homology between mitochondrial DNA of Agaricus bisporus and an internal portion of a linear mitochondrial plasmid of Agaricus bitorquis
M. Robison (2004)
Recombination and replication of plasmid-like derivatives of a short section of the mitochondrial chromosome of Neurospora crassa.
S. R. Gross (1989)
10.1093/NAR/25.5.0955
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
T. Lowe (1997)
10.1007/BF00312859
Heterokaryotic transmission of senescence plasmid DNA in Neurospora
A. J. Griffiths (2004)
10.1073/PNAS.90.9.4299
Two Neurospora mitochondrial plasmids encode DNA polymerases containing motifs characteristic of family B DNA polymerases but lack the sequence Asp-Thr-Asp.
Q. Li (1993)
10.1128/MCB.14.5.3094
The Mauriceville plasmid of Neurospora spp. uses novel mechanisms for initiating reverse transcription in vivo.
J. Kennell (1994)
Gapped BLAST and PSI-BLAST: A new
D. Lipman (1997)
10.1139/B95-246
Senescence is coupled to induction of an oxidative phosphorylation stress response by mitochondrial DNA mutations in Neurospora
H. Bertrand (1995)
10.1007/S002940100187
Association between variant plasmid formation and senescence in retroplasmid-containing strains of Neurospora spp.
F. An (2001)
10.1016/S1874-5334(03)80009-6
6 - Fungal Mitochondrial Genomes, Plasmids and Introns
G. Hausner (2003)
10.1146/annurev.ge.26.120192.002031
Fungal senescence.
A. J. Griffiths (1992)
10.1093/NAR/25.24.4876
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
J. Thompson (1997)
10.1038/359320A0
Deficiency of the 50K dystrophin-associated glycoprotein in severe childhood autosomal recessive muscular dystrophy
K. Matsumura (1992)
10.1016/0092-8674(88)90228-0
A novel reverse transcriptase activity associated with mitochondrial plasmids of neurospora
M. T. Kuiper (1988)
10.1007/s00294-004-0549-x
A mitochondrial plasmid and plasmid-like RNA and DNA polymerases encoded within the mitochondrial genome of carrot (Daucus carota L.)
M. Robison (2004)
10.1007/BF00419875
Extrachromosomal genetics of Claviceps purpurea
P. Tudzynski (2004)
10.1006/PLAS.1999.1448
Possible benefits of kalilo plasmids to their Neurospora hosts.
J. Bok (2000)
10.1007/s004380050763
The dynamics of pAL2-1 homologous linear plasmids in Podospora anserina
M. van der Gaag (1998)
10.1139/O98-014
The membrane domain of complex I is not assembled in the stopper mutant E35 of Neurospora.
P. C. Alves (1998)
10.1007/BF00301065
Evidence for a life span-prolonging effect of a linear plasmid in a longevity mutant of Podospora anserina
J. Hermanns (2004)
Mobility of two optional G + C-rich clusters of the var1 gene of yeast mitochondrial DNA.
J. M. Wenzlau (1990)
10.1128/MCB.14.10.6419
A mitochondrial retroplasmid integrates into mitochondrial DNA by a novel mechanism involving the synthesis of a hybrid cDNA and homologous recombination.
C. C. Chiang (1994)
10.1093/NAR/20.5.1101
Evidence that a 1.6 kilobase region of Neurospora mtDNA was derived by insertion of part of the LaBelle mitochondrial plasmid.
F. Nargang (1992)
10.1007/BF00310892
Interaction between mitochondrial DNA and mitochondrial plasmids in Claviceps purpurea: analysis of plasmid-homologous sequences upstream of the IrRNA-gene
B. Oeser (2004)
10.1016/S0092-8674(85)80068-4
Insertion of a foreign nucleotide sequence into mitochrondrial DNA causes senescence in neurospora intermedia
H. Bertrand (1985)
10.1007/978-3-662-10364-7_11
Plasmid DNA in Mycelial Fungi
F. Kempken (1995)
10.1007/BF00260864
Linear kalilo DNA is a Neurospora mitochondrial plasmid that integrates into the mitochondrial DNA
C. Myers (2004)
10.1016/0092-8674(85)90041-8
Mitochondrial DNA rearrangements associated with fertile revertants of S-type male-sterile maize
C. Schardl (1985)
The dynamics of pAL 2 - 1 homologous linear plasmids in Po - dospora anserina
Griffiths AJF (1992)
10.1201/9780203027356.CH11
Fungal Mitochondria: Genomes, Genetic Elements, and Gene Expression
J. Kennell (2003)
10.1007/BF00352440
Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa
D. Court (2004)
10.1016/0092-8674(86)90615-X
Mitochondrial plasmids of neurospora: Integration into mitochondrial DNA and evidence for reverse transcription in mitochondria
R. Akins (1986)
Plasmid DNA in mycelial fungi. In: Kück U (ed) The mycota. II. Genetics and biotechnology
F Kempken (1995)
A family of repetitive palindromic sequences found in Neurospora mitochondrial DNA is also found in a mitochondrial plasmid DNA.
F. Nargang (1983)
10.1007/s002940050325
Mitochondrial DNA rearrangements associated with mF plasmid integration and plasmodial longevity in Physarum polycephalum
Catherine Curtis Nakagawa (1998)
10.1093/nar/28.13.2571
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA)
T. Kubo (2000)
to their Neurospora hosts
CJ Braun (1986)
10.1016/J.FGB.2004.04.007
The mitochondrial plasmid pAL2-1 reduces calorie restriction mediated life span extension in the filamentous fungus Podospora anserina.
M. F. Maas (2004)
10.1002/j.1460-2075.1986.tb04281.x
The E35 stopper mutant of Neurospora crassa: precise localization of deletion endpoints in mitochondrial DNA and evidence that the deleted DNA codes for a subunit of NADH dehydrogenase.
H. Vries (1986)
10.1093/oxfordjournals.nar.a027018
Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid.
S. Mohr (2000)
10.1007/BF00418130
Characterization of inverted repeats from plasmid-like DNAs and the maize mitochondrial genome
C. Braun (2004)
10.1093/NAR/24.9.1734
Contribution of ultra-short invasive elements to the evolution of the mitochondrial genome in the genus Podospora.
F. Koll (1996)
10.1093/NAR/18.19.5871
Characterization of a novel plasmid-like element in Neurospora crassa derived mostly from the mitochondrial DNA.
A. Almasan (1990)
10.1007/BF00326237
The kalilo linear senescence-inducing plasmid of Neurospora is an invertron and encodes DNA and RNA polymerases
Benedict Shiu-Shing Chan (2004)
10.1007/BF00326306
Distribution of seven homology groups of mitochondrial plasmids in Neurospora: evidence for widespread mobility between species in nature
M. T. Arganoza (2004)
Molecular characterization of the mitochondrial DNA of a new stopper mutant ER-3 of Neurospora crassa.
A. Almasan (1988)
10.1128/MMBR.59.4.673-685.1995
Natural plasmids of filamentous fungi.
A. J. Griffiths (1995)
10.1038/339320A0
Independent transfer of mitochondrial plasmids in Neurospora crassa
G. May (1989)
10.1093/OXFORDJOURNALS.MOLBEV.A026274
Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility.
B. Paquin (2000)
10.1007/s002940100187
Association between variant plasmid formation and senescence in retroplasmid-containing strains of Neurospora spp.
A. N. Fox (2001)
10.1016/0092-8674(81)90201-4
Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria
S. Yin (1981)
10.1101/GR.361602
The Bioperl toolkit: Perl modules for the life sciences.
J. Stajich (2002)
10.1146/ANNUREV.GE.24.120190.003051
Premeiotic instability of repeated sequences in Neurospora crassa.
E. Selker (1990)
10.1007/978-3-662-07426-8
Genetics and Biotechnology
H.-U. Kück (2004)



This paper is referenced by
10.1016/j.ijbiomac.2019.12.056
The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences.
W. Liu (2019)
10.1016/j.fgb.2013.01.009
The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences.
C. Férandon (2013)
10.1534/genetics.110.117200
Deletion of a Novel F-Box Protein, MUS-10, in Neurospora crassa Leads to Altered Mitochondrial Morphology, Instability of mtDNA and Senescence
A. Kato (2010)
10.1371/journal.pone.0107536
The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications
A. Mardanov (2014)
Étude de la biodiversité microbienne associée aux champignons mycorhiziens arbusculaires dans des sites hautement contaminés par des hydrocarbures pétroliers
Bachir Iffis (2017)
Genoma de Moniliophthora perniciosa : montagem e anotação da mitocondria e desenvolvimento de sistema de anotação semi-automatico de genes
E. F. Formighieri (2006)
10.1371/journal.pone.0060768
Rapid Mitochondrial Genome Evolution through Invasion of Mobile Elements in Two Closely Related Species of Arbuscular Mycorrhizal Fungi
Denis Beaudet (2013)
An evolutionary and biochemical characterization of a self-splicing group II intron and its encoded LAGLIDADG homing endonuclease in Leptographium truncatum
S. Mullineux (2010)
mitochondrial morphology, instability of mtDNA and senescence
Akihiro Kato (2010)
10.4238/2013.June.13.3
DNA and RNA polymerase activity in a Moniliophthora perniciosa mitochondrial plasmid and self-defense against oxidative stress.
Bruno S. Andrade (2013)
10.1002/biot.200800005
Mitochondrial pAL2-1 plasmid homologs are senescence factors in Podospora anserina independent of intrinsic senescence.
A. van Diepeningen (2008)
10.1016/j.fgb.2009.07.005
The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases.
C. B. Monteiro-Vitorello (2009)
10.1016/j.exger.2010.01.002
Calorie restriction in the filamentous fungus Podospora anserina
A. Diepeningen (2010)
UNIVERSIDADE ESTADUAL DE FEIRA DE SANTANA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOTECNOLOGIA
Viviane Matos Galvão (2010)
10.1111/j.1574-6968.2007.01048.x
The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom).
Y. Wang (2008)
10.1128/9781555816636.CH13
Mitochondria and Respiration
F. Nargang (2010)
10.1016/j.fgb.2011.11.008
Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame.
Rasha M. Al-Reedy (2012)
10.1186/1471-2156-8-9
A mitochondrial mutator plasmid that causes senescence under dietary restricted conditions
M. F. Maas (2006)
10.1371/journal.pone.0072038
Complete Mitochondrial Genome of the Medicinal Mushroom Ganoderma lucidum
J. Li (2013)
Neurospora Bibliography Craig
C. Wilson (2017)
Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi
Maryam Nadimi (2015)
10.1007/978-3-642-22380-8_13
Introns, Mobile Elements, and Plasmids
G. Hausner (2012)
10.1007/s00122-008-0790-7
The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element
P. McDermott (2008)
Characterization of the Neurospora Varkud Satellite Plasmid and Transcript in vivo
Andrew Keeping (2012)
10.1016/j.fgb.2011.05.006
A 971-bp insertion in the rns gene is associated with mitochondrial hypovirulence in a strain of Cryphonectria parasitica isolated from nature.
D. Baidyaroy (2011)
10.1016/J.FGB.2005.10.006
Biogenesis and replication of small plasmid-like derivatives of the mitochondrial DNA in Neurospora crassa.
G. Hausner (2006)
10.1186/s12864-019-5732-z
Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species
A. I. Kolesnikova (2019)
10.1186/1471-2164-14-605
Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex
G. Fourie (2012)
Organelle Genetics: Evolution of Organelle Genomes and Gene Expression. 2011. Bullerwell C.E. (Ed.). Springer Verlag.
G. Hausner (2011)
10.1007/s00294-014-0436-z
Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes
Kajsa Himmelstrand (2014)
10.4238/2015.October.29.30
Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.
B. Andrade (2015)
Semantic Scholar Logo Some data provided by SemanticScholar