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

Abstract

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...

Further characterization of the role of the mitochondrial high-mobility group box protein in the intracellular redox environment of Aspergillus nidulans

“…Unexpectedly, the respiration of conidia and mycelia was very similar in the mutant and WT. Very recently, the mitochondrial nucleoid organizer HMGB protein Ylmhb1 was identified in Y. lipolytica, and despite the mtDNA copy number and mitochondrial transcription level being reduced in the mhb1-deleted strain, the mitochondrial respiration of the mutant was shown not to differ from WT (Bakkaiova et al, 2014). These results on Yarrowia support our findings and we propose that either HmbB functions do not influence respiratory activity or, if they do, this is compensated for by the action of other proteins.…”

“…In mitochondria, HMGB proteins regulate mitochondrial DNA (mtDNA) compaction, and affect mitochondrial recombination and replication processes (Brewer et al, 2003;Diffley & Stillman, 1991;MacAlpine et al, 1998;Miyakawa et al, 2010). Mitochondrial HMGB proteins with similar functions are well known from yeasts to mammals, such as Abf2 in Saccharomyces cerevisiae (sorting of mtDNA in zygotes, ensuring mitochondrial recombination frequency, regulating mtDNA replication and compaction of mitochondrial nucleoid) (Brewer et al, 2003;Miyakawa et al, 2010;Zelenaya-Troitskaya et al, 1998), Mthmg1 in Podospora anserina (maintaining mitochondrial genome stability, ensuring female fertility and ascospore germination) (Dequard-Chablat & Alland, 2002), Gcf1 in Candida albicans and Candida parapsilosis (participating in mtDNA packaging, mtDNA replication and recombination) (Miyakawa et al, 2009;Visacka et al, 2009), Ylmhb1 in Yarrowia lipolytica (mtDNA packaging and mtDNA copy number) (Bakkaiova et al, 2014) and Tfam in metazoans (participating in mtDNA replication, recombination and mitochondrial transcription) (Kaufman et al, 2007;Ngo et al, 2011;Rubio-Cosials et al, 2011).…”

Organization and dynamics of yeast mitochondrial nucleoids

“…78) The yeast S. cerevisiae is able to grow by fermentation without mitochondrial respiration. This characteristic is different from human cells because almost all energy production of human cells depends on aerobic respiration of mitochondria.…”

A dually located multi‐HMG‐box protein of Aspergillus nidulans has a crucial role in conidial and ascospore germination

“…This protein is extant in the genomes of relatives of C. albicans (Miyakawa et al, 2009;Visacka et al, 2009). When this article was under revision, the characterization of the Yarrowia lypolitica orthologue of Abf2p was published (Bakkaiova et al, 2014).…”