Comparative genomics of protoploid Saccharomycetaceae

Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii

Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well-studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non-centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution.

Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts

The genetic basis of organisms' adaptation to different environments is a central issue of molecular evolution. The budding yeast Saccharomyces cerevisiae and its relatives predominantly ferment glucose into ethanol even in the presence of oxygen. This was suggested to be an adaptation to glucose-rich habitats, but the underlying genetic basis of the evolution of aerobic fermentation remains unclear. In S. cerevisiae, the first step of glucose metabolism is transporting glucose across the plasma membrane, which is carried out by hexose transporter proteins. Although several studies have recognized that the rate of glucose uptake can affect how glucose is metabolized, the role of HXT genes in the evolution of aerobic fermentation has not been fully explored. In this study, we identified all members of the HXT gene family in 23 fully sequenced fungal genomes, reconstructed their evolutionary history to pinpoint gene gain and loss events, and evaluated their adaptive significance in the evolution of aerobic fermentation. We found that the HXT genes have been extensively amplified in the two fungal lineages that have independently evolved aerobic fermentation. In contrast, reduction of the number of HXT genes has occurred in aerobic respiratory species. Our study reveals a strong positive correlation between the copy number of HXT genes and the strength of aerobic fermentation, suggesting that HXT gene expansion has facilitated the evolution of aerobic fermentation.

Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres

The G + C content at synonymous codon positions (GC3s) in genes varies along chromosomes in most eukaryotes. In Saccharomyces cerevisiae, regions of high GC3s are correlated with recombination hot spots, probably due to biased gene conversion. Here we examined how GC3s differs among groups of related yeast species in the Saccharomyces and Candida clades. The chromosomal locations of GC3s peaks and troughs are conserved among four Saccharomyces species, but we find that there have been highly consistent small shifts in their GC3s values. For instance, 84% of all S. cerevisiae genes have a lower GC3s value than their S. bayanus orthologs. There are extensive interspecies differences in the Candida clade both in the median value of GC3s (ranging from 22% to 49%) and in the variance of GC3s among genes. In three species—Candida lusitaniae, Pichia stipitis, and Yarrowia lipolytica—there is one region on each chromosome in which GC3s is markedly reduced. We propose that these GC-poor troughs indicate the positions of centromeres because in Y. lipolytica they coincide with the five experimentally identified centromeres. In P. stipitis, the troughs contain clusters of the retrotransposon Tps5. Likewise, in Debaryomyces hansenii, there is one cluster of the retrotransposon Tdh5 per chromosome, and all these clusters are located in GC-poor troughs. Locally reduced G + C content around centromeres is consistent with a model in which G + C content correlates with recombination rate, and recombination is suppressed around centromeres, although the troughs are unexpectedly wide (100–300 kb).

Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts

Background

Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms underlying the generation of alternative transcripts in Yarrowia lipolytica, a yeast highly divergent from S. cerevisiae.

Results

Experimental investigation of Y. lipolytica gene models identified several cases of alternative splicing, mostly generated by intron retention, principally affecting the first intron of the gene. The retention of introns almost invariably creates a premature termination codon, as a direct consequence of the structure of intron boundaries. An analysis of Y. lipolytica introns revealed that introns of multiples of three nucleotides in length, particularly those without stop codons, were underrepresented. In other organisms, premature termination codon-containing transcripts are targeted for degradation by the nonsense-mediated mRNA decay (NMD) machinery. In Y. lipolytica, homologs of S. cerevisiae UPF1 and UPF2 genes were identified, but not UPF3. The inactivation of Y. lipolytica UPF1 and UPF2 resulted in the accumulation of unspliced transcripts of a test set of genes.

Conclusions

Y. lipolytica is the hemiascomycete with the most intron-rich genome sequenced to date, and it has several unusual genes with large introns or alternative transcription start sites, or introns in the 5' UTR. Our results suggest Y. lipolytica intron structure is subject to significant constraints, leading to the under-representation of stop-free introns. Consequently, intron-containing transcripts are degraded by a functional NMD pathway.

A polyploid population of Saccharomyces cerevisiae with separate sexes (dioecy)

Saccharomyces cerevisiae has proved to be an interesting model for studies of evolution, with whole-genome duplication shown to have played an important role in the evolution of this species. This phenomenon depends on the formation of a transient stable polyploid state. Previous studies have reported polyploidy to be an unstable state in yeast, but here, we describe a polyploid population of S. cerevisiae. The evolution of higher eukaryotes has also involved the development of different systems of sexual reproduction, the choice between self-fertilization and out-crossing becoming a key issue. Saccharomyces cerevisiae is a hermaphrodite eukaryote, despite the theoretical genetic disadvantages of this strategy, in which self-fertilization occurs. We describe, for the first time, a near-dioecious (with separate sexes) population in this species. Mating type and the MAT locus display complex segregations. Essentially, each strain produces, by meiosis, spores of only one mating type: mata or matalpha. Moreover, strains are heterothallic, and diploid nonmating clones generated from a single spore do not sporulate. These three properties limit self-fertilization and strongly favour out-crossing. We suggest that the shift in sexual strategy, from hermaphroditism to dioecy, is specific to the brewing process, which overcomes the sexual isolation probably found in natural biotopes.

Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis

Background

Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only the genome of the S. cerevisiae reference strain has been analyzed so far for pseudogenes.

Results

We present here the first comparative analysis of pseudogenes within the fully sequenced and annotated genomes of eight yeast species, spanning the entire phylogenetic range of Hemiascomycetes. A total of 871 pseudogenes were found, out of which mutational degradation patterns and consequences on the genetic repertoire of each species could be identified. We found that most pseudogenes in yeasts originate from mutational degradation of gene copies formed after species-specific duplications but duplications of pseudogenes themselves are also encountered. In all yeasts, except in Y. lipolytica, pseudogenes tend to cluster in subtelomeric regions where they can outnumber the number of functional genes from 3 to 16 times. Pseudogenes are generally not conserved between the yeast species studied (except in two cases), consistent with their large evolutionary distances, but tend to be conserved among S. cerevisiae strains. Reiterated pseudogenization of some genes is often observed in different lineages and may affect functions essential in S. cerevisiae, which are, therefore, lost in other species. Although a variety of functions are affected by pseudogenization, there is a bias towards functions involved in the adaptation of the yeasts to their environment, and towards genes of unknown functions.

Conclusions

Our work illustrates for the first time the formation of pseudogenes in different branches of hemiascomycetous yeasts, showing their limited conservation and how they testify for the adaptation of the yeasts functional repertoires.

Genome-wide computational prediction of tandem gene arrays: application in yeasts

Background

This paper describes an efficient in silico method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality.

Results

Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs.

Conclusion

The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.

Combined phylogeny and neighborhood analysis of the evolution of the ABC transporters conferring multiple drug resistance in hemiascomycete yeasts

Background

Pleiotropic Drug Resistant transporters (PDR) are members of the ATP-Binding Cassette (ABC) subfamily which export antifungals and other xenobiotics in fungi and plants. This subfamily of transmembrane transporters has nine known members in Saccharomyces cerevisiae.

We have analyzed the complex evolution of the pleiotropic drug resistance proteins (Pdrp) subfamily where gene duplications and deletions occur independently in individual genomes.

This study was carried out on 62 Pdrp from nine hemiascomycetous species, seven of which span 6 of the 14 clades of the Saccharomyces complex while the two others species, Debaryomyces hansenii and Yarrowia lipolytica, are further apart from an evolutive point of view.

Results

Combined phylogenetic and neighborhood analyses enabled us to identify five Pdrp clusters in the Saccharomyces complex. Three of them comprise orthologs of the Pdrp sensu stricto, Pdr5p, Pdr10p, Pdr12p, Pdr15p, Snq2p and YNR070wp. The evolutive pathway of the orthologs of Snq2 and YNR070w is particularly complex due to a tandem gene array in Eremothecium gossypii, Kluyveromyces lactis and Saccharomyces (Lachancea) kluyveri. This pathway and different cases of duplications and deletions were clarified by using a neighborhood analysis based on synteny.

For the two distant species, Yarrowia lipolytica and Debaryomyces hansenii, no neighborhood evidence is available for these clusters and many homologs of Pdr5 and Pdr15 are phylogenetically assigned to species-based clusters.

Two other clusters comprise the orthologs of the sensu lato Pdrp, Aus1p/Pdr11p and YOL075cp respectively. The evolutionary pathway of these clusters is simpler. Nevertheless, orthologs of these genes are missing in some species.

Conclusion

Numerous duplications were traced among the Hemiascomycetous Pdrp studied. The role of the Whole Genome Duplication (WGD) is sorted out and our analyses confirm the common ancestrality of Pdr5p and Pdr15p. A tandem gene array is observed in Eremothecium gossypii. One of the copies is the ortholog of Snq2 while the other one is lost in the post-WGD species.

The neighborhood analysis provides an efficient method to trace the history of genes and disentangle the orthology and paralogy relationships.

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

Saccharomyces cerevisiae has been used for millennia in winemaking, but little is known about the selective forces acting on the wine yeast genome. We sequenced the complete genome of the diploid commercial wine yeast EC1118, resulting in an assembly of 31 scaffolds covering 97% of the S288c reference genome. The wine yeast differed strikingly from the other S. cerevisiae isolates in possessing 3 unique large regions, 2 of which were subtelomeric, the other being inserted within an EC1118 chromosome. These regions encompass 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses showed that 1 of these regions originated from a species closely related to the Saccharomyces genus, whereas the 2 other regions were of non-Saccharomyces origin. We identified Zygosaccharomyces bailii, a major contaminant of wine fermentations, as the donor species for 1 of these 2 regions. Although natural hybridization between Saccharomyces strains has been described, this report provides evidence that gene transfer may occur between Saccharomyces and non-Saccharomyces species. We show that the regions identified are frequent and differentially distributed among S. cerevisiae clades, being found almost exclusively in wine strains, suggesting acquisition through recent transfer events. Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes. Our results suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations.

Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes

Horizontal gene transfer has been occasionally mentioned in eukaryotic genomes, but such events appear much less numerous than in prokaryotes, where they play important functional and evolutionary roles. In yeasts, few independent cases have been described, some of which corresponding to major metabolic functions, but no systematic screening of horizontally transferred genes has been attempted so far. Taking advantage of the synteny conservation among five newly sequenced and annotated genomes of Saccharomycetaceae, we carried out a systematic search for HGT candidates amidst genes present in only one species within conserved synteny blocks. Out of 255 species-specific genes, we discovered 11 candidates for HGT, based on their similarity with bacterial proteins and on reconstructed phylogenies. This corresponds to a minimum of six transfer events because some horizontally acquired genes appear to rapidly duplicate in yeast genomes (e.g. YwqG genes in Kluyveromyces thermotolerans and serine recombinase genes of the IS607 family in Saccharomyces kluyveri). We show that the resulting copies are submitted to a strong functional selective pressure. The mechanisms of DNA transfer and integration are discussed, in relation with the generally small size of HGT candidates. Our results on a limited set of species expand by 50% the number of previously published HGT cases in hemiascomycetous yeasts, suggesting that this type of event is more frequent than usually thought. Our restrictive method does not exclude the possibility that additional HGT events exist. Actually, ancestral events common to several yeast species must have been overlooked, and the absence of homologs in present databases leaves open the question of the origin of the 244 remaining species-specific genes inserted within conserved synteny blocks.

Unusual composition of a yeast chromosome arm is associated with its delayed replication

The 11.3-Mb genome of the yeast Lachancea (Saccharomyces) kluyveri displays an intriguing compositional heterogeneity: a region of approximately 1 Mb, covering almost the whole left arm of chromosome C (C-left), has an average GC content of 52.9%, which is significantly higher than the 40.4% global GC content of the rest of the genome. This region contains the MAT locus, which remains normal in composition. The excess of GC base pairs affects both coding and noncoding sequences, and thus is not due to selective pressure acting on protein sequences. It leads to a strong codon usage bias and alters the amino acid composition of the 457 proteins encoded on C-left that do not show obvious bias for functional categories, or the presence of paralogs or orthologs of essential genes of Saccharomyces cerevisiae. They share significant synteny conservation with other species of the Saccharomycetaceae, and phylogenetic analysis indicates that C-left originates from a Lachancea species. In contrast, there is a complete absence of transposable elements in C-left, whereas 18 elements per megabase are distributed across the rest of the genome. Comparative hybridization of synchronized cells using high-density genome arrays reveals that C-left is replicated later during S phase than the rest of the genome. Two possible primary causes of this major compositional heterogeneity are discussed: an ancient hybridization of two related species with very distinct GC composition, or an intrinsic mechanism, possibly associated with the loss of the silent cassettes from C-left that progressively increased the GC content and generated the delayed replication of this chromosomal arm.

KlAft, the Kluyveromyces lactis ortholog of Aft1 and Aft2, mediates activation of iron-responsive transcription through the PuCACCC Aft-type sequence

Iron homeostasis in fungi is regulated at the transcriptional level by two different mechanisms. It is mediated by a conserved GATA-type repressor in most fungi except in the yeast Saccharomyces cerevisiae, where it is controlled by the transcription activators Aft1 and Aft2. These activators are encoded by the paralogous genes AFT1 and AFT2, which result from the whole-genome duplication. Here, we explore regulation of iron homeostasis in the yeast Kluyveromyces lactis that diverged from S. cerevisiae before this event. We identify an ortholog of AFT1/AFT2, designated KlAFT, whose deletion leads to the inability to grow under iron limitation. We show with quantitative real-time PCR analysis that KlAft activates the transcription of all homologs of the Aft1-target genes involved in the iron transport at the cell surface in response to iron limitation. However, homologs of Aft2-specific target genes encoding intracellular iron transporters are regulated neither by KlAft nor by iron. Both bioinformatic and DNA binding and transcription analyses demonstrate that KlAft activates iron-responsive gene expression through the PuCACCC Aft-type sequence. Thus, K. lactis is the first documented species with a positive iron-transcriptional control mediated by only one copy of the Aft-type regulator. This indicates that this function was acquired before the whole-genome duplication and was then diversified into two regulators in S. cerevisiae.