A 1100-bp sequence of mitochondrial DNA is involved in senescence process in Podospora: study of senescent and mutant cultures

Insertion of short poly d(A) d(T) sequences at recombination junctions in mitochondrial DNA of Podospora

We have characterized the DNA sequences at recombination points in the mitochondrial DNA of two independent mitochondrial mutants of Podospora anserina. These sequences reveal the presence of foreign DNA at each recombination border, consisting of short stretches of A and T residues. We discuss the possible origin of this DNA and suggest the involvement of a reverse transcriptase activity.

Mitochondrial functions and aging

In the filamentous ascomycete Podospora anserina mitochondria play a major role in lifespan control. Since the function of these organelles depends on a large number of individual components it is no surprise that a complex network of interacting branches of individual molecular pathways is involved in this process. Recently, the nuclear encoded transcription factor GRISEA was found to significantly affect mitochondrial functions. GRISEA is involved in the control of cellular copper homeostasis. Most importantly, the high affinity uptake of copper from the environment is controlled by this transcription factor. Once copper has entered the cell, it becomes distributed to different compartments and different target molecules. This process depends on a group of proteins, termed copper chaperones. PaCOX17, a homologue of the yeast copper chaperone yCOX17, appears to be involved in copper delivery to mitochondria. Most importantly, the metal is crucial for the assembly and the function of complex IV of the respiratory chain. However, although P. anserina is an obligate aerobe and therefore depends on mitochondrial energy transduction, impairments in the copper delivery pathway are not lethal. This is due to the induction of a molecular back-up system able to compensate for deficiencies in complex IV. The system utilizes an alternative oxidase (PaAOX) which uses iron instead of copper as a cofactor. The alternative respiratory pathway is characterized by a decreased ATP generation but, most significantly, also a decrease in the production of reactive oxygen species. Consequently, molecular damage is reduced which contributes to an increased lifespan of this type of mutant. In addition, modifications in the availability of cellular copper have other relevant consequences. Most significantly, the characteristic age-related rearrangements occurring in the mitochondrial DNA of wild-type strains of P. anserina were found to be dependent on the availability of copper.

Role of Mitochondrial DNA in the Senescence and Hypovirulence of Fungi and Potential for Plant Disease Control

The unique coenocytic anatomy of the mycelia of the filamentous fungi and the formation of anastomoses between hyphae from different mycelia enable the intracellular accumulation and infectious transmission of plasmids and mutant mitochondrial DNAs (mtDNAs) that cause senescence. For reasons that are not fully apparent, mitochondria that are rendered dysfunctional by so-called "suppressive" mtDNA mutations proliferate rapidly in growing cells and gradually displace organelles that contain wild-type mtDNA molecules and are functional. The consequence of this process is senescence and death if the suppressive mtDNA contains a lethal mutation. Suppressive mtDNA mutations and mitochondrial plasmids can elicit cytoplasmically transmissible "mitochondrial hypovirulence" syndromes in at least some of the phytopathogenic fungi. In the chestnut-blight fungus Cryphonectria parasitica, the pattern of asexual transmission of mutant mtDNAs and mitochondrial plasmids resembles the pattern of "infectious" transmission displayed by the attenuating virus that is most commonly used for the biological control of this fungus. At least some of the attenuating mitochondrial hypovirulence factors are inherited maternally in crosses, whereas the viruses are not transmitted sexually. The natural control of blight in an isolated stand of chestnut trees has resulted from the invasion of the local population of C. parasitica by a senescence-inducing mutant mtDNA. Moreover, a mitochondrial plasmid, pCRY1, attenuates at least some virulent strains of C. parasitica, suggesting that such factors could be applied to control plant diseases caused by fungi.

Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility

Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements which, during evolution, have colonized pre-existing introns converting them into invasive elements. This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities which recognize and cut the insertion site of the optional sequence. This constitutes the first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss the role that such a mobile sequence could have played during evolution.

What triggers senescence in Podospora anserina?

Senescence of Podospora anserina is triggered by a cytoplasmic and infectious factor (the determinant of senescence) and is always correlated with mitochondrial DNA modifications, especially with the accumulation of small circular subgenomic DNA molecules, the senDNAs. Several observations have suggested that the senDNAs could be the cytoplasmic and infectious determinant. However, we show here (1) that senDNA molecules can be transferred to a young culture without the cotransmission of the determinant of senescence and (2) that the determinant of senescence does not segregate as a mitochondrial DNA mutation. Overall, our data strongly argue that amplification of senDNA molecules in the mitochondria is not an intrinsic property of these small DNA molecules. They question the nature of the actual determinant of senescence.

Contribution of ultra-short invasive elements to the evolution of the mitochondrial genome in the genus Podospora

In the filamentous fungus Podospora anserina, senescence is associated with major rearrangements of the mitochondrial DNA. The undecamer GGCGCAAGCTC has been described as a preferential site for these recombination events. We show that: (i) copies of this short sequence GGCGCAAGCTC are present in unexpectedly high numbers in the mitochondrial genome of this fungus; (ii) a short cluster of this sequence, localised in a group II intronic ORF, encodes amino acids that disrupt a protein domain that is otherwise highly conserved between various species; (iii) most of the polymorphisms observed between three related species, P.anserina, P.curvicolla and P.comata, are associated with the presence/absence of this sequence; (iv) this element lies at the boundaries of major rearrangements of the mitochondrial genomes; (v) at least two other short elements in the Podospora mitochondrial genomes display similar features. We suggest that these short elements, called MUSEs (mitochondrial ultra-short elements), could be mobile and that they contribute to evolution of the mitochondrial genome in the genus Podospora. A model for mobility involving a target DNA-primed reverse transcription step is discussed.

Senescence-specific mitochondrial DNA molecules in P. anserina: evidence for transcription and normal processing of the RNA

In Podospora anserina the phenomenon of senescence was previously shown to be correlated with the presence of senescence-specific circular DNAs (senDNAs), resulting from the amplification of distinct regions (alpha, beta, gamma and epsilon) of the mitochondrial chromosome. The beta region gives rise to senDNAs with variable sizes, but sharing a 1-kb common sequence. Here, we present a molecular analysis of five beta senDNAs. We have determined the nucleotide sequence around the circularization site of each senDNA monomer. In two cases, the presence of a tRNA gene, very close to the 3' end of the monomer, has been observed. This suggests that some beta senDNAs could be generated via a reverse transcription step. We have furthermore shown that the beta senDNAs produce specific transcripts which undergo normal processing of their introns. We propose that a transcription start site, located in the beta common region, is involved in mitochondrial replication allowing the amplification of the beta senDNAs.

The role of mitochondrial DNA rearrangements in aging and human diseases

Instabilities and point mutations of the high molecular weight mitochondrial DNA (mtDNA) were shown to be correlated with various degenerative processes in both lower eukaryotes as well as in mammals. In filamentous fungi, circular and linear plasmids were demonstrated to be involved in mtDNA rearrangements and in the genetic control of senescence. In addition, in these eukaryotic microorganisms, which have proved to be ideal model systems in experimental gerontology, a number of nuclear genes were identified controlling the stability of the mitochondrial genome. Although the mitochondrial genome of mammals, including humans, appears to be quite stable in comparison to other species, mtDNA instabilities of the type described in fungi were observed in mitochondria of patients with different mitochondrial degenerative disorders (CPEO, KSS, Pearson syndrome, LHON, MERRF, MELAS). It was later demonstrated that such mtDNA rearrangements appear to accumulate progressively during aging in human subjects. These data suggest that instabilities of the mitochondrial genome may play an important role in the control of life span not only in lower eukaryotes, but also in humans.

Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells

The ability of eukaryotic organisms of the same genotype to vary in developmental pattern or in phenotype according to varying environmental conditions is frequently associated with changes in extrachromosomal circular DNA (eccDNA) sequences. Although variable in size, sequence complexity, and copy number, the best characterized of these eccDNAs contain sequences homologous to chromosomal DNA which indicates that they might arise from genetic rearrangements, such as homologous recombination. The abundance of repetitive sequence families in eccDNAs is consistent with the notion that tandem repeats and dispersed repetitive elements participate in intrachromosomal recombination events. There is also evidence that a fraction of this DNA has characteristics similar to retrotransposons. It has been suggested that eccDNAs could reflect altered patterns of gene expression or an instability of chromosomal sequences during development and aging. This article reviews some of the findings and concepts regarding eccDNAs and sequence plasticity in eukaryotic genomes.

Unstable mitochondrial DNA in natural-death nuclear mutants of Neurospora crassa

The natural-death mutant of Neurospora crassa has an accelerated senescence phenotype caused by a recessive mutation, nd, in a nuclear gene that is located in linkage group I. An examination of mitochondrial functions, however, revealed that the mutant has phenotypic and molecular defects similar to those commonly associated with maternally transmitted fungal senescence syndromes, including (i) deficiencies in cytochromes aa3 and b; (ii) a deficit in small subunits of mitochondrial ribosomes, and hence defective mitochondrial protein synthesis; and (iii) accumulation of gross rearrangements, including large deletions, in the mitochondrial chromosome of vegetatively propagated cells. These traits indicate that the nd+ allele codes for a function that is essential for stable maintenance of the mitochondrial chromosome, possibly a protein involved in replication, repair, or recombination.

Unstable mitochondrial DNA in natural-death nuclear mutants of Neurospora crassa

The natural-death mutant of Neurospora crassa has an accelerated senescence phenotype caused by a recessive mutation, nd, in a nuclear gene that is located in linkage group I. An examination of mitochondrial functions, however, revealed that the mutant has phenotypic and molecular defects similar to those commonly associated with maternally transmitted fungal senescence syndromes, including (i) deficiencies in cytochromes aa3 and b; (ii) a deficit in small subunits of mitochondrial ribosomes, and hence defective mitochondrial protein synthesis; and (iii) accumulation of gross rearrangements, including large deletions, in the mitochondrial chromosome of vegetatively propagated cells. These traits indicate that the nd+ allele codes for a function that is essential for stable maintenance of the mitochondrial chromosome, possibly a protein involved in replication, repair, or recombination.

Multipartite structure of mitochondrial DNA in a fungal longlife mutant

Rearrangements in the mitochondrial genome of the longlife mutant ex1 of the ascomycete Podospora anserina have led to a heterogeneous population of subgenomic molecules. The restriction maps of individual subcircles were established using overlapping recombinant lambda phages isolated from an ex 1 mtDNA/EMBL3 library. The formation of the subcircles and the resulting multipartite organization of the ex1 mtDNA are discussed.

Senescence in Podospora anserina: a possible role for nucleic acid interacting proteins suggested by the sequence analysis of a mitochondrial DNA region specifically amplified in senescent cultures

In Podospora anserina, the phenomenon of senescence was previously shown to be correlated with the presence of a senescence-specific DNA (sen-DNA) resulting from the amplification of some regions (alpha, beta, gamma, epsilon) of the mitochondrial chromosome. The beta region gives rise to sen-DNAs with variable sizes and junctions which share a 1,100-bp common sequence. Here we report the complete nucleotide sequence of one 4-kb beta sen-DNA. Included in the sequence are a large part of the first intron open reading frame (ORF) of the gene ND4L and three short unidentified ORFs more precisely located in the common beta region. The primary structure of the polypeptide possibly encoded by one of them is very similar to the glycine-rich domains present in various single-stranded DNA-binding proteins. The comparison of the information content of this beta sen-DNA with that of other previously sequenced sen-DNAs suggests that the role in the senescence process attributed to the sen-DNAs could be related to the overproduction of a variety of proteins which interact with nucleic acids.

Characterization of repetitive sequence families in mouse heart small polydisperse circular DNAs: age-related studies

Using alkaline denaturation-renaturation, exonuclease III digestion and density gradient centrifugations, we have isolated covalently closed circular DNA (cccDNA) molecules from 1-, 8-, 16-, and 24-month C57BL/6 mouse heart tissues. Electron microscopic analyses demonstrated that all these preparations contained small polydisperse circular DNAs (spcDNAs). spcDNAs showed similar size distributions at all ages, but more discrete size classes and slightly larger circles were observed in the 24-month heart spcDNA preparations. Based upon the final yields of spcDNAs, there appeared to be no age-related changes in the quantity of these circular molecules in vivo. Furthermore, [3H]-pBR322 recovery studies revealed no endogenous factors that might have affected the yield of spcDNAs from young and old tissues. To determine if there were any age-related changes in the quantity of repetitive sequences in spcDNAs, we probed heart spcDNAs with B1, B2, IAP, L1 and satellite sequences of the mouse genome. The hybridization results showed that these sequence families were differentially represented at all ages in spcDNAs. B2 sequences were the highest across all the age groups while L1 sequences were the lowest. The quantity of B1-, B2-, IAP-, and L1-spcDNAs appeared to decrease at 24-months. Satellite sequences appeared to decrease from 1-month to 8-months, but no change beyond 8-months.

A Podospora anserina longevity mutant with a temperature-sensitive phenotype for senescence

A Podospora anserina longevity mutant was identified with a temperature-sensitive phenotype for senescence. This mutant, termed TS1, grew for over 3 m at 27 degrees C, but when shifted to 34 degrees C, it underwent senescence between 10 and 18 cm. A previously described senescence-associated plasmid, alpha senDNA, derived from the mitochondrial genome, was not detected in TS1 at 27 degrees C but was present in senescent cultures at 34 degrees C. A similar result was observed in progeny strains obtained by crossing the TS1 mutant with a wild-type strain. Other mitochondrial excision-amplification DNAs in addition to alpha senDNA were also observed in the senescent cultures. Most were derived from a specific region of the mitochondrial genome. These results provide evidence that alpha senDNA is involved in TS1 senescence and suggest that this plasmid may play a role in the formation of other mitochondrial excision-amplification plasmids.

A Podospora anserina longevity mutant with a temperature-sensitive phenotype for senescence

A Podospora anserina longevity mutant was identified with a temperature-sensitive phenotype for senescence. This mutant, termed TS1, grew for over 3 m at 27 degrees C, but when shifted to 34 degrees C, it underwent senescence between 10 and 18 cm. A previously described senescence-associated plasmid, alpha senDNA, derived from the mitochondrial genome, was not detected in TS1 at 27 degrees C but was present in senescent cultures at 34 degrees C. A similar result was observed in progeny strains obtained by crossing the TS1 mutant with a wild-type strain. Other mitochondrial excision-amplification DNAs in addition to alpha senDNA were also observed in the senescent cultures. Most were derived from a specific region of the mitochondrial genome. These results provide evidence that alpha senDNA is involved in TS1 senescence and suggest that this plasmid may play a role in the formation of other mitochondrial excision-amplification plasmids.