The complete mitochondrial genome of <i>Yarrowia lipolytica</i>

Kerscher, Stefan; Durstewitz, Gregor; Casarégola, Serge; Gaillardin, Claude; Brandt, Ulrich

doi:10.1002/cfg.72

Cited by 61 publications

(63 citation statements)

References 44 publications

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“…Since others have shown previously that ScAbf2p affects mtDNA recombination in S. cerevisiae mitochondria (23), we hypothesized that the smaller amount of mtDNA released from the ⌬mhb1 cells could be due to the formation of recombination intermediates unable to enter the gel. We therefore treated the DNA in agarose blocks with ApaI, which has a single recognition site within the mtDNA of Y. lipolytica (72). Although the DNA was efficiently digested, the difference in the amount of mtDNA between the wild-type and mutant strains remained the same (Fig.…”

Section: Resultsmentioning

confidence: 99%

The Strictly Aerobic Yeast Yarrowia lipolytica Tolerates Loss of a Mitochondrial DNA-Packaging Protein

et al. 2014

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bMitochondrial DNA (mtDNA) is highly compacted into DNA-protein structures termed mitochondrial nucleoids (mt-nucleoids). The key mt-nucleoid components responsible for mtDNA condensation are HMG box-containing proteins such as mammalian mitochondrial transcription factor A (TFAM) and Abf2p of the yeast Saccharomyces cerevisiae. To gain insight into the function and organization of mt-nucleoids in strictly aerobic organisms, we initiated studies of these DNA-protein structures in Yarrowia lipolytica. We identified a principal component of mt-nucleoids in this yeast and termed it YlMhb1p (Y. lipolytica mitochondrial HMG box-containing protein 1). YlMhb1p contains two putative HMG boxes contributing both to DNA binding and to its ability to compact mtDNA in vitro. Phenotypic analysis of a ⌬mhb1 strain lacking YlMhb1p resulted in three interesting findings. First, although the mutant exhibits clear differences in mt-nucleoids accompanied by a large decrease in the mtDNA copy number and the number of mtDNA-derived transcripts, its respiratory characteristics and growth under most of the conditions tested are indistinguishable from those of the wild-type strain. Second, our results indicate that a potential imbalance between subunits of the respiratory chain encoded separately by nuclear DNA and mtDNA is prevented at a (post)translational level. Third, we found that mtDNA in the ⌬mhb1 strain is more prone to mutations, indicating that mtHMG box-containing proteins protect the mitochondrial genome against mutagenic events. Individual eukaryotic cells contain a population of mitochondrial DNA (mtDNA) molecules, the number of which may reach several thousand copies. For example, aerobically grown diploid cells of the yeast Saccharomyces cerevisiae contain, on average, 100 molecules of 85-kbp mtDNA. With a distance of 0.34 nm between base pairs in DNA, the total length of mtDNA reaches almost 3 mm per cell, while the diameter of the cell does not exceed 3 to 4 m. Analogously to its nuclear counterpart, mtDNA must be packaged into condensed nucleoprotein structures termed mitochondrial nucleoids (mt-nucleoids) (1-6). The size of mt-nucleoids in S. cerevisiae ranges from 0.2 to 0.9 m, meaning that mtDNA in yeasts undergoes compaction of roughly 3 orders of magnitude. Although it is known that the size and shape (oval versus globular) of mt-nucleoids, the number of mt-nucleoids (ranging from 50 to 70) per diploid cell (2), and the number of copies (up to 9) of mtDNA per mt-nucleoid (3) in S. cerevisiae depend on physiological conditions, the molecular mechanisms mediating nucleoid maintenance, dynamics, and roles in mtDNA distribution/segregation during cell division are largely not understood. This is also true for mammalian mt-nucleoids, which, in contrast to their yeast counterparts, contain a relatively small number of mtDNA molecules and are thus more solitary in nature (7,8). Description of these intra-and interspecific differences in the organization of mt-nucleoids would greatly facilitate our understanding of the m...

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Section: Resultsmentioning

confidence: 99%

The Strictly Aerobic Yeast Yarrowia lipolytica Tolerates Loss of a Mitochondrial DNA-Packaging Protein

et al. 2014

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“…In mammals and obligate aerobic yeasts, such as Yarrowia lipolytica, Neurospora crassa, and Debaryomyces hansenii, components of the respiratory chain are contained in four large iron-rich protein complexes embedded in the inner mitochondrial membrane. Of these complexes, the last three are conserved in budding and fission yeasts, whereas complex I is absent from these organisms (24,45). Instead, these yeasts have specialized NADH-Q oxidoreductases that are distinct yet able to oxidize mitochondrial NADH to NAD (57).…”

Section: Exposure Of Cells To Low Concentrations Of Iron Triggers Dowmentioning

confidence: 99%

Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast

et al. 2008

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The fission yeast Schizosaccharomyces pombe responds to the deprivation of iron by inducing the expression of the php4 ؉ gene, which encodes a negative regulatory subunit of the heteromeric CCAAT-binding factor. Once formed, the Php2/3/4/5 transcription complex is required to inactivate a subset of genes encoding iron-using proteins. Here, we used a pan-S. pombe microarray to study the transcriptional response to iron starvation and identified 86 genes that exhibit php4 ؉ -dependent changes on a genome-wide scale. One of these genes encodes the iron-responsive transcriptional repressor Fep1, whose mRNA levels were decreased after treatment with the permeant iron chelator 2,2-dipyridyl. In addition, several genes encoding the components of iron-dependent biochemical pathways, including the tricarboxylic acid cycle, mitochondrial respiration, amino acid biosynthesis, and oxidative stress defense, were downregulated in response to iron deficiency. Furthermore, Php4 repressed transcription when brought to a promoter using a yeast DNA-binding domain, and iron deprivation was required for this repression. On the other hand, Php4 was constitutively active when glutathione levels were depleted within the cell. Based on these and previous results, we propose that iron-dependent inactivation of Php4 is regulated at two distinct levels: first, at the transcriptional level by the iron-responsive GATA factor Fep1 and second, at the posttranscriptional level by a mechanism yet to be identified, which inhibits Php4-mediated repressive function when iron is abundant.

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“…A slightly different promoter motif (TTATAAGTA) is characteristic for tRNA gene transcription (Edwards et al 1983;Tabak et al 1983;Burke et al 1987). Identical or very similar promoter sequences have been identified in mitochondria of Kluyveromyces lactis (Ragnini and Frontali 1994), Torulopsis glabrata (ClarkWalker et al 1985;Koszul et al 2003), Williopsis (Hansenula) mrakii (Drissi et al 1993(Drissi et al , 1994, and Yarrowia lipolytica (Kerscher et al 2001). In contrast, mitochondrial promoters of the distantly related ascomycete fungus Neurospora crassa are only marginally similar to the nonanucleotide motif of S. cerevisiae (Kubelik et al 1990).…”

Section: Introductionmentioning

confidence: 99%

Transcription and RNA-processing in fission yeast mitochondria

Schäfer¹,

Hansen²,

Lang³

2005

RNA

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We systematically examined transcription and RNA-processing in mitochondria of the petite-negative fission yeast Schizosaccharomyces pombe. Two presumptive transcription initiation sites at opposite positions on the circular-mapping mtDNA were confirmed by in vitro capping of primary transcripts with guanylyl-transferase. The major promoter (P ma ) is located adjacent to the 5-end of the rnl gene, and a second, minor promoter (P mi ) upstream from cox3. The primary 5-termini of the mature rnl and cox3 transcripts remain unmodified. A third predicted accessory transcription initiation site is within the group IIA1 intron of the cob gene (cobI1). The consensus promoter motif of S. pombe closely resembles the nonanucleotide promoter motifs of various yeast mtDNAs. We further characterized all mRNAs and the two ribosomal RNAs by Northern hybridization, and precisely mapped their 5-and 3-ends. The mRNAs have leader sequences with a length of 38 up to 220 nt and, in most instances, are created by removal of tRNAs from large precursor RNAs. Like cox2 and rnl, cox1 and cox3 are not separated by tRNA genes; instead, transcription initiation from the promoters upstream from rnl and cox3 compensates for the lack of tRNA-mediated 5-processing. The 3-termini of mRNAs and of SSU rRNA are processed at distinct, C-rich motifs that are located at a variable distance (1-15 nt) downstream from mRNA and SSU-rRNA coding regions. The accuracy of RNAprocessing at these sites is sequence-dependent. Similar 3-RNA-processing motifs are present in species of the genus Schizosaccharomyces, but not in budding yeasts that have functionally analogous A+T-rich dodecamer processing signals.

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The complete mitochondrial genome of Yarrowia lipolytica

Cited by 61 publications

References 44 publications

The Strictly Aerobic Yeast Yarrowia lipolytica Tolerates Loss of a Mitochondrial DNA-Packaging Protein

The Strictly Aerobic Yeast Yarrowia lipolytica Tolerates Loss of a Mitochondrial DNA-Packaging Protein

Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast

Transcription and RNA-processing in fission yeast mitochondria

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