Conflicting phylogenetic position of Schizosaccharomyces pombe

Kodamaeahongheensis f.a., sp. nov., Kodamaeaovata f.a., sp. nov. and Kodamaeayamadae f.a., sp. nov., three new yeast species of Kodamaea (Saccharomycetales, Debaryomycetacae) from China

Kodamaea includes a growing number of interesting yeasts of the family Debaryomycetacae that are widely distributed in temperate, subtropical and tropical regions of different continents. During recent yeast collections in Henan and Yunnan Province in China, several isolates of Kodamaea were obtained from rotting wood, all of which represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and LSU rDNA), three new species are proposed: K.hongheensis f.a., sp. nov., K.ovata f.a., sp. nov. and K.yamadae f.a., sp. nov. In addition, sixteen Candida species, which are members of the Kodamaea clade based on phylogenetic analysis, are transferred to Kodamaea as new combinations. Our results indicate high species diversity of Kodamaea waiting to be discovered in rotting wood from tropical and subtropical China.

Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes

Fungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.

Pleiotropic Effects of Caffeine Leading to Chromosome Instability and Cytotoxicity in Eukaryotic Microorganisms

Caffeine, a methylxanthine analog of purine bases, is a compound that is largely consumed in beverages and medications for psychoactive and diuretic effects and plays many beneficial roles in neuronal stimulation and enhancement of anti-tumor immune responses by blocking adenosine receptors in higher organisms. In single-cell eukaryotes, however, caffeine somehow impairs cellular fitness by compromising cell wall integrity, inhibiting target of rapamycin (TOR) signaling and growth, and overriding cell cycle arrest caused by DNA damage. Among its multiple inhibitory targets, caffeine specifically interacts with phosphatidylinositol 3-kinase (PI3K)-related kinases causing radiosensitization and cytotoxicity via specialized intermediate molecules. Caffeine potentiates the lethality of cells in conjunction with several other stressors such as oxidants, irradiation, and various toxic compounds through largely unknown mechanisms. In this review, recent findings on caffeine effects and cellular detoxification schemes are highlighted and discussed with an emphasis on the inhibitory interactions between caffeine and its multiple targets in eukaryotic microorganisms such as budding and fission yeasts.

In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h

BACKGROUND

The crucial factor in the production of bio-fuels is the choice of potent microorganisms used in fermentation processes. Despite the evolving trend of using bacteria, yeast is still the primary choice for fermentation. Molecular characterization of many genes from baker's yeast (Saccharomyces cerevisiaea), and fission yeast (Schizosaccharomyces pombe), have improved our understanding in gene structure and the regulation of its expression. This in silico study was done with the aim of analyzing the promoter regions, transcription start site (TSS), and CpG islands of genes encoding for alcohol production in S. cerevisiaea S288C and S. pombe 972h-.

RESULTS

The analysis revealed the highest promoter prediction scores (1.0) were obtained in five sequences (AAD4, SFA1, GRE3, YKL071W, and YPR127W) for S. cerevisiaea S288C TSS while the lowest (0.8) were found in three sequences (AAD6, ADH5, and BDH2). Similarly, in S. pombe 972h-, the highest (0.99) and lowest (0.88) prediction scores were obtained in five (Adh1, SPBC8E4.04, SPBC215.11c, SPAP32A8.02, and SPAC19G12.09) and one (erg27) sequences, respectively. Determination of common motifs revealed that S. cerevisiaea S288C had 100% coverage at MSc1 with an E value of 3.7e-007 while S. pombe 972h- had 95.23% at MSp1 with an E value of 2.6e+002. Furthermore, comparison of identified transcription factor proteins indicated that 88.88% of MSp1 were exactly similar to MSc1. It also revealed that only 21.73% in S. cerevisiaea S288C and 28% in S. pombe 972h- of the gene body regions had CpG islands. A combined phylogenetic analysis indicated that all sequences from both S. cerevisiaea S288C and S. pombe 972h- were divided into four subgroups (I, II, III, and IV). The four clades are respectively colored in blue, red, green, and violet.

CONCLUSION

This in silico analysis of gene promoter regions and transcription factors through the actions of regulatory structure such as motifs and CpG islands of genes encoding alcohol production could be used to predict gene expression profiles in yeast species.

The evolutionary appearance of signaling motifs in PGRMC1

A complex PGRMC1-centred regulatory system controls multiple cell functions. Although PGRMC1 is phosphorylated at several positions, we do not understand the mechanisms regulating its function. PGRMC1 is the archetypal member of the membrane associated progesterone receptor (MAPR) family. Phylogentic comparison of MAPR proteins suggests that the ancestral metazoan "PGRMC-like" MAPR gene resembled PGRMC1/PGRMC2, containing the equivalents of PGRMC1 Y139 and Y180 SH2 target motifs. It later acquired a CK2 site with phosphoacceptor at S181. Separate PGRMC1 and PGRMC2 genes with this "PGRMC-like" structure diverged after the separation of vertebrates from protochordates. Terrestrial tetrapods possess a novel proline-rich PGRMC1 SH3 target motif centred on P64 which in mammals is augmented by a phosphoacceptor at PGRMC1 S54, and in primates by an additional S57 CK2 site. All of these phosphoacceptors are phosphorylated in vivo. This study suggests that an increasingly sophisticated system of PGRMC1-modulated multicellular functional regulation has characterised animal evolution since Precambrian times.

The Expanding Landscape of Moonlighting Proteins in Yeasts

Moonlighting proteins are multifunctional proteins that participate in unrelated biological processes and that are not the result of gene fusion. A certain number of these proteins have been characterized in yeasts, and the easy genetic manipulation of these microorganisms has been useful for a thorough analysis of some cases of moonlighting. As the awareness of the moonlighting phenomenon has increased, a growing number of these proteins are being uncovered. In this review, we present a crop of newly identified moonlighting proteins from yeasts and discuss the experimental evidence that qualifies them to be classified as such. The variety of moonlighting functions encompassed by the proteins considered extends from control of transcription to DNA repair or binding to plasminogen. We also discuss several questions pertaining to the moonlighting condition in general. The cases presented show that yeasts are important organisms to be used as tools to understand different aspects of moonlighting proteins.

Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways

Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.

Sporadic distribution of prion-forming ability of Sup35p from yeasts and fungi

Sup35p of Saccharomyces cerevisiae can form the [PSI+] prion, an infectious amyloid in which the protein is largely inactive. The part of Sup35p that forms the amyloid is the region normally involved in control of mRNA turnover. The formation of [PSI+] by Sup35p's from other yeasts has been interpreted to imply that the prion-forming ability of Sup35p is conserved in evolution, and thus of survival/fitness/evolutionary value to these organisms. We surveyed a larger number of yeast and fungal species by the same criteria as used previously and find that the Sup35p from many species cannot form prions. [PSI+] could be formed by the Sup35p from Candida albicans, Candida maltosa, Debaromyces hansenii, and Kluyveromyces lactis, but orders of magnitude less often than the S. cerevisiae Sup35p converts to the prion form. The Sup35s from Schizosaccharomyces pombe and Ashbya gossypii clearly do not form [PSI+]. We were also unable to detect [PSI+] formation by the Sup35ps from Aspergillus nidulans, Aspergillus fumigatus, Magnaporthe grisea, Ustilago maydis, or Cryptococcus neoformans. Each of two C. albicans SUP35 alleles can form [PSI+], but transmission from one to the other is partially blocked. These results suggest that the prion-forming ability of Sup35p is not a conserved trait, but is an occasional deleterious side effect of a protein domain conserved for another function.

Use of gene sequence analyses and genome comparisons for yeast systematics

Detection, identification and classification of yeasts have undergone a major transformation in the past decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined gene sequences from domains 1 and 2 (D1/D2) of large subunit rRNA and from the internal transcribed spacer (ITS) now permits many laboratories to identify species accurately and this has led to a doubling in the number of known species of yeasts over the past decade. Phylogenetic analysis of gene sequences has resulted in major revision of yeast systematics, resulting in redefinition of nearly all genera. Future work calls for application of genomics to refine our understanding of the species concept and to provide a better understanding of the boundaries of genera and higher levels of classification. This increased understanding of phylogeny is expected to allow prediction of the genetic potential of various clades and species for biotechnological applications and adaptation to environmental changes.

The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved

Coordinated replication of eukaryotic genomes is intrinsically asymmetric, with continuous leading strand synthesis preceding discontinuous lagging strand synthesis. Here we provide two types of evidence indicating that, in fission yeast, these two biosynthetic tasks are performed by two different replicases. First, in Schizosaccharomyces pombe strains encoding a polδ-L591M mutator allele, base substitutions in reporter genes placed in opposite orientations relative to a well-characterized replication origin are strand-specific and distributed in patterns implying that Polδ is primarily involved in lagging strand replication. Second, in strains encoding a polε-M630F allele and lacking the ability to repair rNMPs in DNA due to a defect in RNase H2, rNMPs are selectively observed in nascent leading strand DNA. The latter observation demonstrates that abundant rNMP incorporation during replication can be tolerated and that they are normally removed in an RNase H2-dependent manner. This provides strong physical evidence that Polε is the primary leading strand replicase. Collectively, these data and earlier results in budding yeast indicate that the major roles of Polδ and Polε at the eukaryotic replication fork are evolutionarily conserved.

Complex evolution of the DAL5 transporter family

BACKGROUND

Genes continuously duplicate and the duplicated copies remain in the genome or get deleted. The DAL5 subfamily of transmembrane transporter genes has eight known members in S. cerevisiae. All are putative anion:cation symporters of vitamins (such as allantoate, nicotinate, panthotenate and biotin). The DAL5 subfamily is an old and important group since it is represented in both Basidiomycetes ("mushrooms") and Ascomycetes ("yeast"). We studied the complex evolution of this group in species from the kingdom of fungi particularly the Ascomycetes.

RESULTS

We identified numerous gene duplications creating sets of orthologous and paralogous genes. In different lineages the DAL5 subfamily members expanded or contracted and in some lineages a specific member could not be found at all. We also observed a close relationship between the gene YIL166C and its homologs in the Saccharomyces sensu stricto species and two "wine spoiler" yeasts, Dekkera bruxellensis and Candida guilliermondi, which could possibly be the result of horizontal gene transfer between these distantly related species. In the analyses we detect several well defined groups without S. cerevisiae representation suggesting new gene members in this subfamily with perhaps altered specialization or function.

CONCLUSION

The transmembrane DAL5 subfamily was found to have a very complex evolution in yeast with intra- and interspecific duplications and unusual relationships indicating specialization, specific deletions and maybe even horizontal gene transfer. We believe that this group will be important in future investigations of evolution in fungi and especially the evolution of transmembrane proteins and their specialization.

Natural history and evolutionary principles of gene duplication in fungi

Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.

Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom

BACKGROUND

The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL) and barcoding projects by comparing the cophenetic correlation coefficients (CCC) among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40-45 concatenated proteins seem needed to resolve fungal TOL.

RESULTS

In total 4852 orthologous proteins (KOGs) were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before 14 were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular processes and signaling KOG category seem more informative than those belonging to the other three categories: information storage and processing; metabolism; and the poorly characterized category. After concatenation of 40 proteins the topology of the phylogenetic tree remained stable, but after concatenation of 60 or more proteins the bootstrap support values of some branches decreased, most likely due to the inclusion of proteins with lowers CCC values. The selection of protein sequences to be used in various TOL projects remains a critical and important process. The method described in this paper will contribute to a more objective selection of phylogenetically informative protein sequences.

CONCLUSION

This study provides candidate protein sequences to be considered as phylogenetic markers in different branches of fungal TOL. The selection procedure described here will be useful to select informative protein sequences to resolve branches of TOL that contain few or no species with completely sequenced genomes. The robust phylogenetic trees resulting from this method may contribute to our understanding of organismal diversification processes. The method proposed can be extended easily to other branches of TOL.

Fungal CSL transcription factors

Background

The CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) transcription factor family members are well-known components of the transmembrane receptor Notch signaling pathway, which plays a critical role in metazoan development. They function as context-dependent activators or repressors of transcription of their responsive genes, the promoters of which harbor the GTG(G/A)GAA consensus elements. Recently, several studies described Notch-independent activities of the CSL proteins.

Conclusion

Our findings support the evolutionary origin of the CSL transcription factor family in the last common ancestor of fungi and metazoans. We hypothesize that the ancestral CSL function involved DNA binding and Notch-independent regulation of transcription and that this function may still be shared, to a certain degree, by the present CSL family members from both fungi and metazoans.