Signalogs: orthology-based identification of novel signaling pathway components in three metazoans

Background

Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integration. Recently, functional annotation of orthologs was transferred across organisms to predict novel roles for proteins. Despite the wide use of these methods, annotation of complete signaling pathways has not yet been transferred systematically between species.

Principal Findings

Here we introduce the concept of ‘signalog’ to describe potential novel signaling function of a protein on the basis of the known signaling role(s) of its ortholog(s). To identify signalogs on genomic scale, we systematically transferred signaling pathway annotations among three animal species, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Using orthology data from InParanoid and signaling pathway information from the SignaLink database, we predict 88 worm, 92 fly, and 73 human novel signaling components. Furthermore, we developed an on-line tool and an interactive orthology network viewer to allow users to predict and visualize components of orthologous pathways. We verified the novelty of the predicted signalogs by literature search and comparison to known pathway annotations. In C. elegans, 6 out of the predicted novel Notch pathway members were validated experimentally. Our approach predicts signaling roles for 19 human orthodisease proteins and 5 known drug targets, and suggests 14 novel drug target candidates.

Conclusions

Orthology-based pathway membership prediction between species enables the identification of novel signaling pathway components that we referred to as signalogs. Signalogs can be used to build a comprehensive signaling network in a given species. Such networks may increase the biomedical utilization of C. elegans and D. melanogaster. In humans, signalogs may identify novel drug targets and new signaling mechanisms for approved drugs.     

Historical range contraction,and not taxonomy,explains the contemporary genetic structure of the Australian tree <Emphasis Type="Italic">Acacia dealbata</Emphasis> Link

Irrespective of its causes, strong population genetic structure indicates a lack of gene flow. Understanding the processes that underlie such structure, and the spatial patterns it causes, is valuable for conservation efforts such as restoration. On the other hand, when a species is invasive outside its native range, such information can aid management in the non-native range. Here we explored the genetic characteristics of the Australian tree Acacia dealbata in its native range. Two subspecies of A. dealbata have previously been described based on morphology and environmental requirements, but recent phylogeographic data raised questions regarding the validity of this taxonomic subdivision. The species has been widely planted within and outside its native Australian range and is also a highly successful invasive species in many parts of the world. We employed microsatellite markers to investigate the population genetic diversity and structure among 42 A. dealbata populations from across the species’ native range. We also tested whether environmental variables purportedly relevant for the putative separation of subspecies are linked with population genetic differentiation. We found no relationship between population genetic structure of A. dealbata in Australia and these environmental features. Rather, we identified two geographically distinct genetic clusters that corresponded with populations in the northeastern part of mainland Australia, and the southern mainland and Tasmanian range of the species. Our results do not support the taxonomic subdivision of the species into two distinct subspecies based on environmental features. We therefore assume that the observed morphological differences between the putative subspecies are plastic phenotypic responses. This study provides population genetic information that will be useful for the conservation of the species within Australia as well as to better understand the invasion dynamics of A. dealbata.     

Molecular data support the existence of two species of the Antarctic fish genus <Emphasis Type="Italic">Cryodraco</Emphasis> (Channichthyidae)

Antarctic notothenioids represent one of the few strongly supported examples of adaptive radiation in marine fishes. The extent of population connectivity and structure is unknown for many species, thereby limiting our understanding of the factors that underlie speciation dynamics in this radiation. Here, we assess the population structure of the widespread species Cryodraco antarcticus and its sister species Cryodraco atkinsoni, whose taxonomic status is currently debated. Combining both population genetic and phylogenetic approaches to species delimitation, we provide evidence that C. atkinsoni is a distinct species. Our analyses show that C. atkinsoni and C. antarcticus are recently diverged sister lineages, and the two species differ with regard to patterns of population structure. A systematic and accurate account of species diversity is a critical prerequisite for investigations into the complex processes that underlie the history of speciation in the notothenioid adaptive radiation.     

AutoEPG: Software for the Analysis of Electrical Activity in the Microcircuit Underpinning Feeding Behaviour of Caenorhabditis elegans

Background

The pharyngeal microcircuit of the nematode Caenorhabditis elegans serves as a model for analysing neural network activity and is amenable to electrophysiological recording techniques. One such technique is the electropharyngeogram (EPG) which has provided insight into the genetic basis of feeding behaviour, neurotransmission and muscle excitability. However, the detailed manual analysis of the digital recordings necessary to identify subtle differences in activity that reflect modulatory changes within the underlying network is time consuming and low throughput. To address this we have developed an automated system for the high-throughput and discrete analysis of EPG recordings (AutoEPG).

Methodology/Principal Findings

AutoEPG employs a tailor made signal processing algorithm that automatically detects different features of the EPG signal including those that report on the relaxation and contraction of the muscle and neuronal activity. Manual verification of the detection algorithm has demonstrated AutoEPG is capable of very high levels of accuracy. We have further validated the software by analysing existing mutant strains with known pharyngeal phenotypes detectable by the EPG. In doing so, we have more precisely defined an evolutionarily conserved role for the calcium-dependent potassium channel, SLO-1, in modulating the rhythmic activity of neural networks.

Conclusions/Significance

AutoEPG enables the consistent analysis of EPG recordings, significantly increases analysis throughput and allows the robust identification of subtle changes in the electrical activity of the pharyngeal nervous system. It is anticipated that AutoEPG will further add to the experimental tractability of the C. elegans pharynx as a model neural circuit.     

Contrasting patterns of genetic structure and evolutionary history as revealed by rnitochondrial DNA and nuclear gene-enzyme variation betweenDrosophila melanogaster andDrosophila simulans

Drosophila melanogaster and its sibling speciesD. simulans have a cosmopolitan distribution. Studies on nuclear gene-enzyme variation from natural populations of these species reveal that the two have almost equal overall heterozygosity, yetD. simulans populations are significantly less differentiated. However, it is not clear whether this difference in population structure represents a difference in the genetic strategy with which they respond to the same adaptive challenges, or is the result of difference in species history. To help answer this question, we have undertaken an intensive survey of restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) fromD. simulans; the results are compared with those fromD. melanogaster. We surveyed 69 isofemale lines ofD. simulans from four continents and seven lines from the Seychelles Islands. Ten restriction enzymes detected 104 restriction sites in the continental mtDNAs, of which only threeHinf1 sites were variable and account for fourHlnf1 (restriction variants) haplotypes. These four variants were all found in geographically distant locations. By contrast, twenty-three haplotypes were observed inD. melanogaster, many of which were observed in only one population. It would seem, therefore, that these two species have had different histories. Specifically, cosmopolitan populations ofD: simulans are probably products of a comparatively recent expansion from a source population in Africa. These results do not negate differences in their genetic strategy of adaptation, but they do show the importance of historical contingency in the present-day pattern of geographic variation.     

Conservation genetic assessment of four plant species in a small replica of a steppe ecosystem &gt;30 years after establishment

To counter species loss living ex situ collections in botanic gardens became important elements of robust conservation programs. Several limitations, problems, and risks associated with living ex situ collections have been reported such as appropriate cultivation management to maintain genetic diversity and stochastic effects in small isolated populations in artificial habitats. However, not all small and isolated populations exhibit these predicted genetic changes. In a multi-species in situ/ex situ comparison of sand dune steppe- and grassland vegetation >30 years after the ex situ population establishment, we compared four different species’ population genetic diversities (Alyssum montanum ssp. gmelinii, Gypsophila fastigiata, Helianthemum nummularium ssp. obscurum, Onosma arenaria) by means of ISSR. We observed different species-specific genetic responses to quite similar abiotic selective forces concerning different neutral genetic diversities of wild versus botanic garden populations. The genetic divergence was kept relatively low in two of the four investigated species between the model steppe plant community within the botanic garden where human interference was kept at a minimum and the wild population. However, the moderate genetic divergence of the two other species kept under the same conditions highlights the importance of species-specific intrinsic responses and stochastic effects to ecosystem changes and provides data on population genetic dynamics in small and isolated populations. This contributes to further improve recommendations on how to best conserve endangered plant species in ex situ environments (cultivation in near nature-like replicas of the original site with as little human inference as possible over only certain periods of time, >30 years).     

Genetic Differentiation of the Mitochondrial Cytochrome Oxidase c Subunit I Gene in Genus Paramecium (Protista,Ciliophora)

Background

The mitochondrial cytochrome c oxidase subunit I (COI) gene is being used increasingly for evaluating inter- and intra-specific genetic diversity of ciliated protists. However, very few studies focus on assessing genetic divergence of the COI gene within individuals and how its presence might affect species identification and population structure analyses.

Methodology/Principal findings

We evaluated the genetic variation of the COI gene in five Paramecium species for a total of 147 clones derived from 21 individuals and 7 populations. We identified a total of 90 haplotypes with several individuals carrying more than one haplotype. Parsimony network and phylogenetic tree analyses revealed that intra-individual diversity had no effect in species identification and only a minor effect on population structure.

Conclusions

Our results suggest that the COI gene is a suitable marker for resolving inter- and intra-specific relationships of Paramecium spp.     

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.     

Identification of Mob2, a Novel Regulator of Larval Neuromuscular Junction Morphology,in Natural Populations of Drosophila melanogaster

Although evolutionary changes must take place in neural connectivity and synaptic architecture as nervous systems become more complex, we lack understanding of the general principles and specific mechanisms by which these changes occur. Previously, we found that morphology of the larval neuromuscular junction (NMJ) varies extensively among different species of Drosophila but is relatively conserved within a species. To identify specific genes as candidates that might underlie phenotypic differences in NMJ morphology among Drosophila species, we performed a genetic analysis on one of two phenotypic variants we found among 20 natural isolates of Drosophila melanogaster. We discovered genetic polymorphisms for both positive and negative regulators of NMJ growth segregating within the variant line. Focusing on one subline, that displayed NMJ overgrowth, we mapped the phenotype to Mob2 [Monopolar spindle (Mps) one binding protein 2)], a gene encoding a Nuclear Dbf2 (Dumbbell formation 2)-Related (NDR) kinase activator. We confirmed this identification by transformation rescue experiments and showed that presynaptic expression of Mob2 is necessary and sufficient to regulate NMJ growth. Mob2 interacts in a dominant, dose-dependent manner with tricornered but not with warts, to cause NMJ overgrowth, suggesting that Mob2 specifically functions in combination with the former NDR kinase to regulate NMJ development. These results demonstrate the feasibility and utility of identifying genetic variants affecting NMJ morphology in natural populations of Drosophila. These variants can lead to discovery of new genes and molecular mechanisms that regulate NMJ development while also providing new information that can advance our understanding of mechanisms that underlie nervous system evolution.     

The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations

Seed dispersal mechanisms should have a direct impact on the genetic structure of populations. Species whose seeds are dispersed near the maternal plant (e.g. gravity or wind dispersal) or species whose seeds are deposited in clumps or patches should have more fine-scale genetic structure than species whose seeds are dispersed singly by mobile animals. Furthermore, due to the overlap of seed shadows, species with high adult densities should have less genetic structure than species with lower densities. Allozyme analyses of three tropical tree species belonging to the moist tropical forest of Barro Colorado Island, Republic of Panama, were used to describe variation in the scale and intensity of genetic structure within their populations. The genetic structure of seedlings and immature trees in the low-density, wind-dispersed species (Platypodium elegans) was the coarsest and strongest whereas genetic structure in a population of Swartzia simplex var. ochnacea (high density, bird-dispersed) was both the finest and the weakest. The genetic structure of Alseis blackiana, a high-density, wind-dispersed species was intermediate in both degree and scale. In P. elegans and A. blackiana, which had J shaped size distributions, the significant genetic structure seen in the smaller and intermediate diameter classes disappeared in the largest diameter class. The loss of genetic structure was not observed in S. simplex, a species with a more even size distribution.     

Complete killing of Caenorhabditis elegans by Burkholderia pseudomallei is dependent on prolonged direct association with the viable pathogen

Background

Burkholderia pseudomallei is the causative agent of melioidosis, a disease of significant morbidity and mortality in both human and animals in endemic areas. Much remains to be known about the contributions of genotypic variations within the bacteria and the host, and environmental factors that lead to the manifestation of the clinical symptoms of melioidosis.

Methodology/Principal Findings

In this study, we showed that different isolates of B. pseudomallei have divergent ability to kill the soil nematode Caenorhabditis elegans. The rate of nematode killing was also dependent on growth media: B. pseudomallei grown on peptone-glucose media killed C. elegans more rapidly than bacteria grown on the nematode growth media. Filter and bacteria cell-free culture filtrate assays demonstrated that the extent of killing observed is significantly less than that observed in the direct killing assay. Additionally, we showed that B. pseudomallei does not persistently accumulate within the C. elegans gut as brief exposure to B. pseudomallei is not sufficient for C. elegans infection.

Conclusions/Significance

A combination of genetic and environmental factors affects virulence. In addition, we have also demonstrated that a Burkholderia-specific mechanism mediating the pathogenic effect in C. elegans requires proliferating B. pseudomallei to continuously produce toxins to mediate complete killing.     

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans.     

Candida albicans Hyphal Formation and Virulence Assessed Using a Caenorhabditis elegans Infection Model

Candida albicans colonizes the human gastrointestinal tract and can cause life-threatening systemic infection in susceptible hosts. We study here C. albicans virulence determinants using the nematode Caenorhabditis elegans in a pathogenesis system that models candidiasis. The yeast form of C. albicans is ingested into the C. elegans digestive tract. In liquid media, the yeast cells then undergo morphological change to form hyphae, which results in aggressive tissue destruction and death of the nematode. Several lines of evidence demonstrate that hyphal formation is critical for C. albicans pathogenesis in C. elegans. First, two yeast species unable to form hyphae (Debaryomyces hansenii and Candida lusitaniae) were less virulent than C. albicans in the C. elegans assay. Second, three C. albicans mutant strains compromised in their ability to form hyphae (efg1Δ/efg1Δ, flo8Δ/flo8Δ, and cph1Δ/cph1Δ efg1Δ/efg1Δ) were dramatically attenuated for virulence. Third, the conditional tet-NRG1 strain, which enables the external manipulation of morphogenesis in vivo, was more virulent toward C. elegans when the assay was conducted under conditions that permit hyphal growth. Finally, we demonstrate the utility of the C. elegans assay in a screen for C. albicans virulence determinants, which identified several genes important for both hyphal formation in vivo and the killing of C. elegans, including the recently described CAS5 and ADA2 genes. These studies in a C. elegans-C. albicans infection model provide insights into the virulence mechanisms of an important human pathogen.Candida albicans is the most common human fungal pathogen; however, our knowledge of its virulence mechanisms is incomplete, and our best antifungal agents are often ineffective in treating severe candidiasis (3). Infections with Candida species account for 70 to 90% of all invasive mycoses (32) and can be associated with devastating consequences, particularly in intensive care units where mortality rates reach 40% (24, 34). The drug resistance of pathogenic fungi exacerbates this problem and often limits therapeutic options (35). The identification of virulence pathways that can be targeted with novel antifungal therapies is urgently needed (31, 38, 46).One approach to understand the genetic mechanisms of virulence is to use invertebrates, such as the nematode Caenorhabditis elegans, as model hosts (43). Studies of C. elegans infection with Pseudomonas aeruginosa and Cryptococcus neoformans, for example, have led to the identification of evolutionarily conserved mechanisms of host immunity and microbial virulence (1, 21, 50). However, efforts to design an accurate nonmammalian model of C. albicans pathogenesis have been stymied, in part because it has been difficult to capture the role of Candida dimorphism in these systems.Morphogenesis in C. albicans is intricately related to pathogenesis and thus has been intensively studied. C. albicans hyphae are important for tissue destruction and host invasion (3). As such, C. albicans mutants and non-albicans Candida species that are unable to form true hyphae are attenuated for virulence (3, 37). However, C. albicans yeast cells also have virulence attributes (4, 33) that are likely involved in dissemination of the fungus through the bloodstream, and the establishment of infection at distant sites. To date, genetic screens to identify the determinants of Candida morphology have been conducted in vitro. Determining the role of these genes in virulence has traditionally involved separate and often laborious studies in mammals. Therefore, an expedient system to study morphogenesis of C. albicans in vivo and accurately model pathogenesis would offer many important advantages.Here, we study C. albicans pathogenesis using the invertebrate host C. elegans. C. albicans yeast cells are ingested into the gastrointestinal tract. In liquid media, the yeast cells form hyphae, which results in an aggressive infection that ultimately kills the nematode. Fungal hyphae destroy worm tissues and pierce the collagenous cuticle of the animal, a phenotype that is easily visible using a dissecting microscope. By studying mutants and genetically engineered C. albicans strains, we show that hyphal formation is required for full virulence in this system. Finally, we illustrate the utility of the C. elegans-C. albicans infection assay in a screen for genes involved in Candida morphogenesis and virulence.     

Status of research on Drosophila ananassae at global level

Drosophila, a dipteran insect, has been found to be the best biological model for different kinds of studies. D melanogaster was first described by Meigen in 1830, is most extensively studied species of the genus Drosophila and a number of investigations employing this species have been documented in areas such as genetics, behaviour, evolution, development, molecular biology, ecology, population biology, etc. Besides D. melanogaster, a number of other species of the genus Drosophila have also been used for different kinds of investigations. Among these, D. ananassae, a cosmopolitan and domestic species endowed with several unusual genetic features, is noteworthy. Described for the first time from Indonesia (Doleschall 1858), this species is commonly distributed in India. Extensive research work on D. ananassae has been done by numerous researchers pertaining to cytology, genetics, mutagenesis, gene mapping, crossing-over in both sexes, population and evolutionary genetics, behaviour genetics, ecological genetics, sexual isolation, fluctuating asymmetry, trade-offs etc. Genome of D. ananassae has also been sequenced. The status of research on D. ananassae at global level is briefly described in this review. Bibliography on this species from different countries worldwide reveals that maximum contribution is from India.     

Bioinformatics Analysis Identify Novel OB Fold Protein Coding Genes in C. elegans

Background

The C. elegans genome has been extensively annotated by the WormBase consortium that uses state of the art bioinformatics pipelines, functional genomics and manual curation approaches. As a result, the identification of novel genes in silico in this model organism is becoming more challenging requiring new approaches. The Oligonucleotide-oligosaccharide binding (OB) fold is a highly divergent protein family, in which protein sequences, in spite of having the same fold, share very little sequence identity (5–25%). Therefore, evidence from sequence-based annotation may not be sufficient to identify all the members of this family. In C. elegans, the number of OB-fold proteins reported is remarkably low (n = 46) compared to other evolutionary-related eukaryotes, such as yeast S. cerevisiae (n = 344) or fruit fly D. melanogaster (n = 84). Gene loss during evolution or differences in the level of annotation for this protein family, may explain these discrepancies.

Methodology/Principal Findings

This study examines the possibility that novel OB-fold coding genes exist in the worm. We developed a bioinformatics approach that uses the most sensitive sequence-sequence, sequence-profile and profile-profile similarity search methods followed by 3D-structure prediction as a filtering step to eliminate false positive candidate sequences. We have predicted 18 coding genes containing the OB-fold that have remarkably partially been characterized in C. elegans.

Conclusions/Significance

This study raises the possibility that the annotation of highly divergent protein fold families can be improved in C. elegans. Similar strategies could be implemented for large scale analysis by the WormBase consortium when novel versions of the genome sequence of C. elegans, or other evolutionary related species are being released. This approach is of general interest to the scientific community since it can be used to annotate any genome.     

Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses

Parasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance for most of these drugs. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.     

Mitochondrial Dysfunction Confers Resistance to Multiple Drugs in Caenorhabditis elegans

In a previous genetic screen for Caenorhabditis elegans mutants that survive in the presence of an antimitotic drug, hemiasterlin, we identified eight strong mutants. Two of these were found to be resistant to multiple toxins, and in one of these we identified a missense mutation in phb-2, which encodes the mitochondrial protein prohibitin 2. Here we identify two additional mutations that confer drug resistance, spg-7 and har-1, also in genes encoding mitochondrial proteins. Other mitochondrial mutants, isp-1, eat-3, and clk-1, were also found to be drug-resistant. Respiratory complex inhibitors, FCCP and oligomycin, and a producer of reactive oxygen species (ROS), paraquat, all rescued wild-type worms from hemiasterlin toxicity. Worms lacking mitochondrial superoxide dismutase (MnSOD) were modestly drug-resistant, and elimination of MnSOD in the phb-2, har-1, and spg-7 mutants enhanced resistance. The antioxidant N-acetyl-l-cysteine prevented mitochondrial inhibitors from rescuing wild-type worms from hemiasterlin and sensitized mutants to the toxin, suggesting that a mechanism sensitive to ROS is necessary to trigger drug resistance in C. elegans. Using genetics, we show that this drug resistance requires pkc-1, the C. elegans ortholog of human PKCε.     

Differential sexual survival of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> on copper sulfate

Based on studies of the influence of X-chromosomes on the viability of Drosophila melanogaster exposed to cadmium, and on the role of X-linked genes on copper homeostasis, we examined the effect of copper sulfate (CuSO₄) on offspring viability using three independent, inbred D. melanogaster crosses (ensuring identical autosomes for males and females within each cross). Each cross was performed with attached X-chromosome females and males with a single X-chromosome. As female D. melanogaster have less metallothionein RNA expression than males, we predicted fewer female offspring than male offspring in crosses exposed to CuSO₄, even though females have two copies of X-chromosome genes, possibly resulting in overdominant heterozygosity. In two of three crosses, CuSO₄ caused significantly higher numbers of male offspring compared to female offspring. We hypothesized that these gender-based viability differences to copper exposure are caused by X-chromosome ploidy and X-linked genetic variation affecting metallothionein expression. Observed differential offspring viability responses among crosses to copper exposure also showed that different genetic backgrounds (autosomal and/or X-chromosome) can result in significant differences in heavy metal and metallothionein regulation. These results suggest that the effect of copper on offspring viability depends on both genetic background and gender, as both factors can affect the regulation of metallothionein proteins as well as homeostasis of biologically necessary heavy metals.     

A Pathogenesis Assay Using Saccharomyces cerevisiae and Caenorhabditis elegans Reveals Novel Roles for Yeast AP-1, Yap1, and Host Dual Oxidase BLI-3 in Fungal Pathogenesis

Treatment of systemic fungal infections is difficult because of the limited number of antimycotic drugs available. Thus, there is an immediate need for simple and innovative systems to assay the contribution of individual genes to fungal pathogenesis. We have developed a pathogenesis assay using Caenorhabditis elegans, an established model host, with Saccharomyces cerevisiae as the invading fungus. We have found that yeast infects nematodes, causing disease and death. Our data indicate that the host produces reactive oxygen species (ROS) in response to fungal infection. Yeast mutants sod1Δ and yap1Δ, which cannot withstand ROS, fail to cause disease, except in bli-3 worms, which carry a mutation in a dual oxidase gene. Chemical inhibition of the NADPH oxidase activity abolishes ROS production in worms exposed to yeast. This pathogenesis assay is useful for conducting systematic, whole-genome screens to identify fungal virulence factors as alternative targets for drug development and exploration of host responses to fungal infections.Nosocomial microbial infections are a growing health problem. Among these, fungal infections are especially threatening, with an estimated mortality rate of 40% (47). The key reason for this alarming mortality rate is the limited range of antifungal agents. Identification of new drug targets requires high-throughput infection assays that are complicated by the very fact that they involve two organisms: a host and a pathogen.We have taken a reductionistic approach to studying host-pathogen interactions and have developed a Saccharomyces cerevisiae-based assay to understand the genetic and molecular mechanisms of fungal pathogenesis. Using Caenorhabditis elegans as a model host, we have found that S. cerevisiae infects the worm, producing visible disease phenotypes. The two organisms used in our study are specifically suited for host-pathogen infection studies because both genomic sequences have been completely determined and mutants are readily available. A complete genome knockout collection is available for S. cerevisiae, a resource that does not exist for any fungal pathogen. Likewise an RNA interference (RNAi)-mediated knockdown genomic library is available for C. elegans. These unique tools are key in the context of a genetic screen and allow us to systematically scan the entire genomes to identify fungal virulence factors and modulators of host immunity that combat a fungal pathogen.The budding yeast S. cerevisiae has recently been described as an emerging pathogen and has been isolated from human patients (34, 35). It is routinely used as a model for pathogenic fungi because a large proportion of its genes are conserved in pathogenic fungi (for a review, see reference 32). Homologs of genes and pathways identified in S. cerevisiae have been shown to be important in bona fide pathogens. It has also been used for the identification of gene products important for fungal survival in the mammalian host environment (21, 46). For example, the SSD1 allele type affects pathogenicity of yeast, indicating that allelic variation at the SSD1 locus may be important for survival under various conditions (46). This has allowed investigators to use reverse genetic approaches to study contributions of genes whose importance has been established in S. cerevisiae.Caenorhabditis elegans has emerged as a valuable model host in which to study pathogenesis and innate immunity (for a review, see reference 22). Microbial genes essential for virulence in mammalian models have been shown to be required for pathogenicity in nematodes (43). These studies have primarily explored bacterial species and have tested only a few fungi, such as Cryptococcus neoformans and Candida albicans, to explore virulence strategies. These studies focus on a killing assay using C. elegans and have identified several virulence factors with homologs in S. cerevisiae (4, 37), suggesting that genes and pathways we have identified in S. cerevisiae are likely to be found in pathogens. Moreover, other pathogenic fungi tested are limited in the repertoire of laboratory tools available for their study, making them recalcitrant to genetic manipulation and inappropriate for whole-genome high-throughput approaches to studying fungal virulence. Recently, Breger et al. described the application of a C. elegans-based infection assay as a tool to screen a chemical library for candidate antifungal compounds (9). Our investigation complements these studies in two significant ways. First, it allows us to identify genes that exacerbate as well as attenuate the pathogenic process, because we use an intermediate disease phenotype, while most other studies have used death as an end point phenotype. This aspect, taken together with the fact that S. cerevisiae shares significant genetic identity with pathogenic fungi, suggests that our study will yield a basic understanding of fungal pathogenesis. Second, it allows us to conduct a systematic, unbiased, whole-genome screen, which is currently not available for pathogenic fungi. Furthermore, genes and pathways identified may be targeted for antimycotic drug development.Facets of innate immunity are evolutionarily conserved from nematodes to mammals. For example, a common defense strategy of mammals (phagocytes), (14), plants (3), and insects (23) is to produce reactive oxygen species (ROS), which directly damage pathogens. In human phagocytes, an NADPH oxidase enzyme complex produces ROS in host defense (19, 41). In Drosophila melanogaster, ROS are generated in the intestine by a NADPH oxidase to combat ingested bacteria (23). Loss of NADPH oxidase activity makes the fly susceptible to the bacterial infection (23, 24). Likewise, C. elegans has also been shown to produce ROS, such as superoxide and/or hydrogen peroxide, when it ingests bacterial pathogens (12). In each case, pathogen death can be abrogated by the addition of enzymes such as catalase that break down ROS (8, 27, 36), suggesting that ROS production plays a key role in a variety of pathogenic interactions.We have found that S. cerevisiae can cause infection and death in C. elegans. Our data indicate that the nematode host produces ROS in response to fungal infection. We demonstrate that mutant yeast carrying deletions of genes that mediate oxidative stress responses fail to induce the Dar disease phenotype except in mutant worms with an altered dual oxidase gene, suggesting that the generation of ROS is a part of the defense strategy for the host and the neutralization of ROS is needed for persistent fungal infection.