Mitochondrial genome evolution in yeasts: an all-encompassing view

Mitochondria are important organelles that harbor their own genomes encoding a key set of proteins that ensure respiration and provide the eukaryotic cell with energy. Recent advances in high-throughput sequencing technologies present a unique opportunity to explore mitochondrial (mt) genome evolution. The Saccharomycotina yeasts have proven to be the leading organisms for mt comparative and population genomics. In fact, the explosion of complete yeast mt genome sequences has allowed for a broader view of the mt diversity across this incredibly diverse subphylum, both within and between closely related species. Here, we summarize the present state of yeast mitogenomics, including the currently available data and what it reveals concerning the diversity of content, organization, structure and evolution of mt genomes.

Evolution of intraspecific transcriptomic landscapes in yeasts

Variations in gene expression have been widely explored in order to obtain an accurate overview of the changes in regulatory networks that underlie phenotypic diversity. Numerous studies have characterized differences in genomic expression between large numbers of individuals of model organisms such as Saccharomyces cerevisiae. To more broadly survey the evolution of the transcriptomic landscape across species, we measured whole-genome expression in a large collection of another yeast species: Lachancea kluyveri (formerly Saccharomyces kluyveri), using RNAseq. Interestingly, this species diverged from the S. cerevisiae lineage prior to its ancestral whole genome duplication. Moreover, L. kluyveri harbors a chromosome-scale compositional heterogeneity due to a 1-Mb ancestral introgressed region as well as a large set of unique unannotated genes. In this context, our comparative transcriptomic analysis clearly showed a link between gene evolutionary history and expression behavior. Indeed, genes that have been recently acquired or under function relaxation tend to be less transcribed show a higher intraspecific variation (plasticity) and are less involved in network (connectivity). Moreover, utilizing this approach in L. kluyveri also highlighted specific regulatory network signatures in aerobic respiration, amino-acid biosynthesis and glycosylation, presumably due to its different lifestyle. Our data set sheds an important light on the evolution of intraspecific transcriptomic variation across distant species.

Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast

Yeast species represent an ideal model system for population genomic studies but large-scale polymorphism surveys have only been reported for species of the Saccharomyces genus so far. Hence, little is known about intraspecific diversity and evolution in yeast. To obtain a new insight into the evolutionary forces shaping natural populations, we sequenced the genomes of an expansive worldwide collection of isolates from a species distantly related to Saccharomyces cerevisiae: Lachancea kluyveri (formerly S. kluyveri). We identified 6.5 million single nucleotide polymorphisms and showed that a large introgression event of 1 Mb of GC-rich sequence in the chromosomal arm probably occurred in the last common ancestor of all L. kluyveri strains. Our population genomic data clearly revealed that this 1-Mb region underwent a molecular evolution pattern very different from the rest of the genome. It is characterized by a higher recombination rate, with a dramatically elevated A:T → G:C substitution rate, which is the signature of an increased GC-biased gene conversion. In addition, the predicted base composition at equilibrium demonstrates that the chromosome-scale compositional heterogeneity will persist after the genome has reached mutational equilibrium. Altogether, the data presented herein clearly show that distinct recombination and substitution regimes can coexist and lead to different evolutionary patterns within a single genome.

Population genomic analysis reveals highly conserved mitochondrial genomes in the yeast species Lachancea thermotolerans

The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species.

Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae

Understanding the molecular basis of how reproductive isolation evolves between individuals from the same species offers valuable insight into patterns of genetic differentiation as well as the onset of speciation [1, 2]. The yeast Saccharomyces cerevisiae constitutes an ideal model partly due to its vast ecological range, high level of genetic diversity [3-6], and laboratory-amendable sexual reproduction. Between S. cerevisiae and its sibling species in the Saccharomyces sensu stricto complex, reproductive isolation acts postzygotically and could be attributed to chromosomal rearrangements [7], cytonuclear incompatibility [8, 9], and antirecombination [10, 11], although the implication of these mechanisms at the incipient stage of speciation remains unclear due to further divergence in the nascent species. Recently, several studies assessed the onset of intraspecific reproductive isolation in S. cerevisiae by evaluating the effect of the mismatch repair system [12-14] or by fostering incipient speciation using the same initial genetic background [15-18]. Nevertheless, the overall genetic diversity within this species was largely overlooked, and no systematic evaluation has been performed. Here, we carried out the first species-wide survey for postzygotic reproductive isolation in S. cerevisiae. We crossed 60 natural isolates sampled from diverse niches with the reference strain S288c and identified 16 cases of reproductive isolation with reduced offspring viabilities ranging from 44% to 86%. Using different mapping strategies, we identified reciprocal translocations in a large fraction of all isolates surveyed, indicating that large-scale chromosomal rearrangements might play a major role in the onset of reproductive isolation in this species.

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Intestinal infections in Germany due to enterohemorrhagic E. coli bacteria (EHEC) between 1998 and 2001 reveal a large scale of biological diversity of their pathogens. However, no dramatic increase of their clinical importance and public health implications has been observed. As strains of serovar O157:H7 have continuously declined as causative agents, other serovars such as O26:H11 and O103:H2 have replaced them. The great diversity of the EHEC pathogens might point to a great number of various infection routes and sources. Since recently new pathogenic factors of EHEC bacteria have been detected (especially by the sequencing of the genome of EHEC), it is currently not possible to define a clear-cut difference between human pathogens and nonhuman pathogens. The enhanced surveillance of EHEC pathogens with respect to their biological diversity and dynamics, their epidemic spread, and their infection routes and sources remain an essential task of the public health authorities.

Genome-wide analysis of intraspecific transposon diversity in yeast

Background

In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding to remnants of former transposition events. Although the biological features of Ty elements have been studied in detail in S. cerevisiae and the Ty content of the reference strain (S288c) was accurately annotated, the Ty-related intra-specific diversity has not been closely investigated so far.

Results

In this study, we investigated the Ty contents of 41 available genomes of isolated S. cerevisiae strains of diverse geographical and ecological origins. The strains were compared in terms of the number of Ty copies, the content of the potential transpositionally active elements and the genomic insertion maps. The strain repertoires were also investigated in the closely related Ty1 and Ty2 families and subfamilies.

Conclusions

This is the first genome-wide analysis of the diversity associated to the Ty elements, carried out for a large set of S. cerevisiae strains. The results of the present analyses suggest that the current Ty-related polymorphism has resulted from multiple causes such as differences between strains, between Ty families and over time, in the recent transpositional activity of Ty elements. Some new Ty1 variants were also identified, and we have established that Ty1 variants have different patterns of distribution among strains, which further contributes to the strain diversity.

Comparative mitochondrial genomics within and among yeast species of the Lachancea genus

Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.

Oral contraception enhances growth hormone responsiveness to hyper- and hypoglycaemia

AIMS

Plasma glucose levels influence growth hormone concentrations. Oral contraceptives are known to affect circulating growth hormone levels and glucose metabolism. While growth hormone plays an important role in hypoglycaemia counter-regulation, it has been shown that oral contraceptives increase growth hormone concentrations. In this context, we tested if serum growth hormone concentrations display a differential response on glycaemic variations in healthy women using oral contraceptives and those not using contraceptives.

METHODS

Fifteen healthy women with oral contraceptive treatment and 10 without participated in a stepwise hyper- and hypoglycaemic glucose clamp procedure. Serum growth hormone concentrations were measured at euglycaemic baseline and subsequently at plasma glucose plateaus of 8.8, 6.8, 4.8 and 2.8 mmol/l.

RESULTS

Growth hormone values were significantly higher in women using oral contraceptives throughout the experiments (P = 0.001). Hyperglycaemia decreased growth hormone concentrations in women using oral contraceptives (P = 0.009), but not in those who were not using oral contraceptives (P = 0.241). Hypoglycaemia significantly elevated growth hormone concentrations in women using oral contraceptives (P = 0.009), but not in those not using oral contraceptives (P = 0.094). Maximum growth hormone values were reached at the end of the hypoglycaemic plateau, with significantly higher concentrations in the group using oral contraceptives than in the group not using oral contraceptives (P = 0.016).

CONCLUSION

Healthy women on oral contraceptive treatment display an increased responsiveness of growth hormone to hypoglycaemic, as well as hyperglycaemic conditions and generally higher serum growth hormone concentrations than women without oral contraceptives. Given the known boosting effects of growth hormone on hypoglycaemic hormonal counter-regulation, oral contraceptives may thus be a pharmacological candidate contributing to combat hypoglycaemia unawareness in women with diabetes in the future.

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.

[Traumatic atlanto-occipital dislocation in a calf]

In a 7-week-old calf neurologic symptoms occurred after an accident in the feeding grid. The calf was alert but in left lateral recumbency. After having been placed on its right side it showed a sideward drift to the left. Following head movement, an asynchronous movement of the eyes could be observed. Lesions of the upper motor neuron system, N. vestibulocochlearis, Nn. oculomotorius, trochlearis and/or abducens as well as N. vagus were suspected. Radiological examination of the occipital region and cervical spine revealed an atlanto-occipital subluxation of the atlas. Based on all these findings, the diagnosis of traumatic atlanto-occipital dislocation was made and the calf was euthanized. The pathological findings confirmed this diagnosis.

Traumatische atlantookzipitale Dislokation bei einem Kalb

Bei einem 7 Wochen alten Kalb traten nach einem Unfall im Fanggitter neurologische Symptome auf. Das aufmerksame Tier lag in linker Seitenlage fest und zeigte nach Umlagern in rechte Seitenlage einen Seitwärtsdrang nach links. Nach Lageveränderung des Kopfes bewegten sich die Bulbi asynchron. Es wurde eine Schädigung des oberen motorischen Neuronsystems, des N. vestibulocochlearis, der Nn. oculomotorius, trochlearis und/oder abducens sowie des N. vagus vermutet. Bei einer Röntgenuntersuchung des Okzipitalbereichs und der Halswirbelsäule ließ sich eine Subluxation des Atlas darstellen. Aufgrund sämtlicher Befunde wurde die Diagnose atlantookzipitale Dislokation infolge Trauma gestellt und das Kalb euthanasiert. Die pathologische Untersuchung bestätigte die Diagnose.