A Role for Gene Duplication and Natural Variation of Gene Expression in the Evolution of Metabolism

Background: Most eukaryotic genomes have undergone whole genome duplications during their evolutionary history. Recent studies have shown that the function of these duplicated genes can diverge from the ancestral gene via neo- or subfunctionalization within single genotypes. An additional possibility is that gene duplicates may also undergo partitioning of function among different genotypes of a species leading to genetic differentiation. Finally, the ability of gene duplicates to diverge may be limited by their biological function. Methodology/Principal Findings: To test these hypotheses, I estimated the impact of gene duplication and metabolic function upon intraspecific gene expression variation of segmental and tandem duplicated genes within Arabidopsis thaliana. In all instances, the younger tandem duplicated genes showed higher intraspecific gene expression variation than the average Arabidopsis gene. Surprisingly, the older segmental duplicates also showed evidence of elevated intraspecific gene expression variation albeit typically lower than for the tandem duplicates. The specific biological function of the gene as defined by metabolic pathway also modulated the level of intraspecific gene expression variation. The major energy metabolism and biosynthetic pathways showed decreased variation, suggesting that they are constrained in their ability to accumulate gene expression variation. In contrast, a major herbivory defense pathway showed significantly elevated intraspecific variation suggesting that it may be under pressure to maintain and/or generate diversity in response t

Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

<p>Abstract</p> <p>Background</p> <p>To date very few incidences of interdomain gene transfer into fungi have been identified. Here, we used the emerging genome sequences of <it>Candida albicans </it>WO-1, <it>Candida tropicalis, Candida parapsilosis, Clavispora lusitaniae, Pichia guilliermondii</it>, and <it>Lodderomyces elongisporus </it>to identify recent interdomain HGT events. We refer to these as CTG species because they translate the CTG codon as serine rather than leucine, and share a recent common ancestor.</p> <p>Results</p> <p>Phylogenetic and syntenic information infer that two <it>C. parapsilosis </it>genes originate from bacterial sources. One encodes a putative proline racemase (PR). Phylogenetic analysis also infers that there were independent transfers of bacterial PR enzymes into members of the Pezizomycotina, and protists. The second HGT gene in <it>C. parapsilosis </it>belongs to the phenazine F (PhzF) superfamily. Most CTG species also contain a fungal PhzF homolog. Our phylogeny suggests that the CTG homolog originated from an ancient HGT event, from a member of the proteobacteria. An analysis of synteny suggests that <it>C. parapsilosis </it>has lost the endogenous fungal form of PhzF, and subsequently reacquired it from a proteobacterial source. There is evidence that <it>Schizosaccharomyces pombe </it>and Basidiomycotina also obtained a PhzF homolog through HGT.</p> <p>Conclusion</p> <p>Our search revealed two instances of well-supported HGT from bacteria into the CTG clade, both specific to <it>C. parapsilosis</it>. Therefore, while recent interkingdom gene transfer has taken place in the CTG lineage, its occurrence is rare. However, our analysis will not detect ancient gene transfers, and we may have underestimated the global extent of HGT into CTG species.</p

Integrating Information Technology into Curricula Activities: Participant Observation of Laptop Use

This paper presents descriptive use of laptops as a lecturer and students engage in curricula activities over one hour of instruction. Lave and Wenger\u27s (1991) theory of situated learning (SL) is used to contextualise laptop use in teaching and learning, inside the undergraduate business classroom. We examine how laptops are used to support teaching and learning practice and influence the curricula process, as laptops are introduced into instruction. Interpretive ethnography and participant observation capture lecturer and student descriptive narrative as they use laptops. Analysis is presented in time order and documents lecturer / student laptop use inside the undergraduate classroom

Virtual patients: an effective educational intervention to improve paediatric basic specialist trainee education in the management of suspected child abuse?

Child abuse is a particularly difficult subject to teach at both undergraduate and postgraduate level. Most doctors are dissatisfied with their training in child abuse recognition and management. We developed an interactive video based Virtual Patient to provide formal training for paediatric Basic Specialist Trainees in the recognition of suspected child abuse. The Virtual Patient case revolves around the management of suspected physical abuse in a seven month old child, who initially presents to the Emergency Department with viral upper respiratory tract symptoms. This Virtual Patient was used to facilitate a case discussion with Basic Specialist Trainees. A questionnaire was developed to determine their perception of the value of the Virtual Patient as an educational tool. Twenty five Basic Specialist Trainees completed the questionnaire. Upon completion of the case, 23/25 (92%) participants reported greater self confidence in their ability to recognize cases of suspected child abuse and 24/25 (96%) of participants reported greater self confidence in their ability to report cases of suspected child abuse. Basic Specialist Trainees perceived the Virtual Patient to be a useful educational tool. Virtual Patients may have a role to play in enhancing postgraduate training in the recognition of suspected child abuse

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

<p>Abstract</p> <p>Background</p> <p><it>Candida </it>species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of <it>Candida </it>genomic data. We have developed the <it>Candida </it>Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of <it>Candida </it>species. CGOB incorporates all available <it>Candida </it>clade genome sequences including two <it>Candida albicans </it>isolates (SC5314 and WO-1) and 8 closely related species (<it>Candida dubliniensis</it>, <it>Candida tropicalis</it>, <it>Candida parapsilosis</it>, <it>Lodderomyces elongisporus</it>, <it>Debaryomyces hansenii</it>, <it>Pichia stipitis</it>, <it>Candida guilliermondii </it>and <it>Candida lusitaniae</it>). <it>Saccharomyces cerevisiae </it>is also included as a reference genome.</p> <p>Results</p> <p>CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved <it>Candida </it>gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all <it>Candida </it>species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in <it>C. albicans</it>.</p> <p>Conclusions</p> <p>Our analysis provides an important resource that is now available for the <it>Candida </it>community. CGOB is available at <url>http://cgob.ucd.ie</url>.</p

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)

Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata

BACKGROUND: Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains many genes apparently involved in sexual reproduction. RESULTS: By genome survey sequencing, we find that genes involved in mating and meiosis are as numerous in C. glabrata as in the sexual species Kluyveromyces delphensis, which is its closest known relative. C. glabrata has a putative mating-type (MAT) locus and a pheromone gene (MFALPHA2), as well as orthologs of at least 31 other Saccharomyces cerevisiae genes that have no known roles apart from mating or meiosis, including FUS3, IME1 and SMK1. CONCLUSIONS: We infer that C. glabrata is likely to have an undiscovered sexual stage in its life cycle, similar to that recently proposed for C. albicans. The two Candida species represent two distantly related yeast lineages that have independently become both pathogenic and 'asexual'. Parallel evolution in the two lineages as they adopted mammalian hosts resulted in separate but analogous switches from overtly sexual to cryptically sexual life cycles, possibly in response to defense by the host immune system

Mitochondrial Voltage-Dependent Anion Channel Protein Por1 Positively Regulates the Nuclear Localization of Saccharomyces cerevisiae AMP-Activated Protein Kinase

ABSTRACT Snf1 protein kinase of the yeast Saccharomyces cerevisiae is a member of the highly conserved eukaryotic AMP-activated protein kinase (AMPK) family, which is involved in regulating responses to energy limitation. Under conditions of carbon/energy stress, such as during glucose depletion, Snf1 is catalytically activated and enriched in the nucleus to regulate transcription. Snf1 catalytic activation requires phosphorylation of its conserved activation loop threonine (Thr210) by upstream kinases. Catalytic activation is also a prerequisite for Snf1’s subsequent nuclear enrichment, a process that is mediated by Gal83, one of three alternate β-subunits of the Snf1 kinase complex. We previously reported that the mitochondrial voltage-dependent anion channel (VDAC) proteins Por1 and Por2 play redundant roles in promoting Snf1 catalytic activation by Thr210 phosphorylation. Here, we show that the por1Δ mutation alone, which by itself does not affect Snf1 Thr210 phosphorylation, causes defects in Snf1 and Gal83 nuclear enrichment and Snf1’s ability to stimulate transcription. We present evidence that Por1 promotes Snf1 nuclear enrichment by promoting the nuclear enrichment of Gal83. Overexpression of Por2, which is not believed to have channel activity, can suppress the localization and transcription activation defects of the por1Δ mutant, suggesting that the regulatory role played by Por1 is separable from its channel function. Thus, our findings expand the positive roles of the yeast VDACs in carbon/energy stress signaling upstream of Snf1. Since AMPK/Snf1 and VDAC proteins are conserved in evolution, our findings in yeast may have implications for AMPK regulation in other eukaryotes, including humans. IMPORTANCE AMP-activated protein kinases (AMPKs) sense energy limitation and regulate transcription and metabolism in eukaryotes from yeast to humans. In mammals, AMPK responds to increased AMP-to-ATP or ADP-to-ATP ratios and is implicated in diabetes, heart disease, and cancer. Mitochondria produce ATP and are generally thought to downregulate AMPK. Indeed, some antidiabetic drugs activate AMPK by affecting mitochondrial respiration. ATP release from mitochondria is mediated by evolutionarily conserved proteins known as voltage-dependent anion channels (VDACs). One would therefore expect VDACs to serve as negative regulators of AMPK. However, our experiments in yeast reveal the existence of an opposite relationship. We previously showed that Saccharomyces cerevisiae VDACs Por1 and Por2 positively regulate AMPK/Snf1 catalytic activation. Here, we show that Por1 also plays an important role in promoting AMPK/Snf1 nuclear localization. Our counterintuitive findings could inform research in areas ranging from diabetes to cancer to fungal pathogenesis

Genetic adaptive mechanisms mediating response and tolerance to acetic acid stress in the human pathogen Candida glabrata: role of the CgHaa1-dependent signaling pathway

The increased resilience of Candida glabrata to azoles and the continuous emergence of strains resistant to other antifungals demands the development of new therapeutic approaches focused on non-conventional biological targets. Genes contributing to increase C. glabrata competitiveness in the different infection sites are an interesting and unexplored cohort of therapeutic targets. To thrive in the vaginal tract and avoid exclusion C. glabrata cells have evolved dedicated responses rendering them capable of tolerating multiple environmental challenges, including the presence of acetic and lactic acids produced by the commensal microbiota. In this work a cohort of vaginal clinical isolates were phenotyped for their tolerance to acetic acid stress at a low pH as well as for several traits that are known to influence sensitivity to this organic acid, including the structure of the cell envelope and the ability to consume the acid in the presence of glucose. The role played by the ORF CAGL0L09339g, an homologue of the ScHaa1, a critical regulator of acetic acid resistance in S. cerevisiae[1], in C. glabrata response and tolerance to acetic acid stress at pH 4 was also scrutinized using a transcriptomic analysis. The role of CgHaa1 as well as of several of its target genes in mediating virulence of C. glabrata against epithelial vaginal cells was also studied.Funding received by the Institute for Bioengineering and Biosciences from the Portuguese Foundation for Science and Technology (FCT) (UID/BIO/04565/2013) and from Programa Operacional Regional de Lisboa 2020 (project no. 007317) is acknowledged. FCT is also acknowledged for funding the Centre of Biological Engineering through contracts FCOMP-01-0124-FEDER- 020243 and PTDC/EBB-EBI/120495/2010info:eu-repo/semantics/publishedVersio

TUF factor binds to the upstream region of the pyruvate decarboxylase structural gene ( PDC1 ) of Saccharomyces cerevisiae

The upstream activation site of the pyruvate decarboxylase gene, PDC1 , of Saccharomyces cerevisiae contains an RPG box, and mediates the increase in expression of a PDC1-lacZ fusion gene during growth on glucose. Oligonucleotide replacement experiments indicate that the RPG box functions as an absolute activator of expression, but other elements (possibly CTTCC repeats) are required for carbon source regulation, and maximal expression. Gel retardation and oligonucleotide competition experiments suggest that the DNA binding factor TUF interacts with the RPG box in the upstream region of PDC1 . Binding of TUF factor is not carbon source dependent in in vitro experiments, and is probably not responsible for glucose induction of PDC1 expression.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47573/1/438_2004_Article_BF00264453.pd