A critical challenge in genomic medicine is identifying the genetic and environmental risk factors for disease. Currently, the available data links a majority of known coding human genes to ...phenotypes, but the environmental component of human disease is extremely underrepresented in these linked data sets. Without environmental exposure information, our ability to realize precision health is limited, even with the promise of modern genomics. Achieving integration of gene, phenotype, and environment will require extensive translation of data into a standard, computable form and the extension of the existing gene/phenotype data model. The data standards and models needed to achieve this integration do not currently exist.
Our objective is to foster development of community-driven data-reporting standards and a computational model that will facilitate the inclusion of exposure data in computational analysis of human disease. To this end, we present a preliminary semantic data model and use cases and competency questions for further community-driven model development and refinement.
There is a real desire by the exposure science, epidemiology, and toxicology communities to use informatics approaches to improve their research workflow, gain new insights, and increase data reuse. Critical to success is the development of a community-driven data model for describing environmental exposures and linking them to existing models of human disease. https://doi.org/10.1289/EHP7215.
CFEM, an eight cysteine-containing domain, has been identified by analyzing over 25 fungal sequences selected from database sequence searches. Features of CFEM suggest that it is a novel domain with ...characteristics distinct from known cysteine-rich domains. Some CFEM-containing proteins (e.g. Pth11 from
Magnaporthe grisea) are proposed to have important roles in fungal pathogenesis.
The G-protein-coupled receptors (GPCRs) are one of the largest protein families in human and other animal genomes, but no more than 10 GPCRs have been characterized in fungi. Do fungi contain only ...this handful or are there more receptors to be discovered? We asked this question using the recently sequenced genome of the fungal plant pathogen Magnaporthe grisea.
Proteins with significant similarity to fungus-specific and other eukaryotic GPCRs were identified in M. grisea. These included homologs of known fungal GPCRs, the cAMP receptors from Dictyostelium, and a steroid receptor mPR. We also identified a novel class of receptors typified by PTH11, a cell-surface integral membrane protein required for pathogenicity. PTH11 has seven transmembrane regions and an amino-terminal extracellular cysteine-rich EGF-like domain (CFEM domain), a characteristic also seen in human GPCRs. Sixty-one PTH11-related proteins were identified in M. grisea that shared a common domain with homologs in Neurospora crassa and other fungi belonging to this subphylum of the Ascomycota (the Pezizomycotina). None was detected in other fungal groups (Basidiomycota or other Ascomycota subphyla, including yeasts) or any other eukaryote. The subclass of PTH11 containing the CFEM domain is highly represented in M. grisea.
In M. grisea we identified homologs of known GPCRs and a novel class of GPCR-like receptors specific to filamentous ascomycetes. A member of this new class, PTH11, is required for pathogenesis, thus suggesting roles in pathogenicity for other members. The identified classes constitute the largest number of GPCR-like proteins reported in fungi to date.
We have used a luciferase reporter gene and continuous automated monitoring of bioluminescence to demonstrate unequivocally that cyanobacteria exhibit circadian behaviors that are fundamentally the ...same as circadian rhythms of eukaryotes. We also show that these rhythms can be studied by molecular methods in Synechococcus sp. PCC7942, a strain for which genetic transformation is well established. A promoterless segment of the Vibrio harveyi luciferase structural genes (luxAB) was introduced downstream of the promoter for the Synechococcus psbAI gene, which encodes a photosystem II protein. This reporter construction was recombined into the Synechococcus chromosome, and bioluminescence was monitored under conditions of constant illumination following entrainment to light and dark cycles. The reporter strain, AMC149, expressed a rhythm of bioluminescence which satisfies the criteria of circadian rhythms: persistence in constant conditions, phase resetting by light/dark signals, and temperature compensation of the period. Rhythmic changes in levels of the native psbAI message following light/dark entrainment supported the reporter data. The behavior of this prokaryote disproves the dogma that circadian mechanisms must be based on eukaryotic cellular organization. Moreover, the cyanobacterial strain described here provides an efficient experimental system for molecular analysis of the circadian clock.
Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft ...sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.
MerR, the metalloregulator of the mercury resistance (mer) operon, binds the operator (merO) between −10 and −35 of the merTPCAD promoter (P T ) and sequesters RNA polymerase (RNAP) in a closed ...complex. MerR represses P T until Hg(II) induces it to underwind merO DNA and thus facilitate open complex formation. We used cross-linking to determine if direct contacts between MerR and RNAP also occur during this process. MerR cross-linked to the α, β, and σ70 subunits of RNAP alone, indicating stable contacts which were further stabilized upon forming the preinitiation complex at P T . Hg(II) did not eliminate any of the MerR−RNAP cross-links but did increase the relative abundance of a MerR dimer conformer. Interference by MerR with self-cross-links among RNAP subunits and the formation of an electrophoretically stable association between MerR and RNAP also indicated MerR−RNAP interactions. This is the first evidence for stable physical contacts between MerR and RNAP and for a Hg(II)-induced allosteric change in MerR in the transcription-competent complex.
The psbAI and psbAIII transcripts in Synechococcus sp. strain PCC 7942 are subject to accelerated turnover when cells are exposed to high light intensities, but psbAII message stability is ...unaffected. We used a psbAI‘minigene’ which has a part of the coding sequence removed as a reporter gene in order to identify the cis‐acting elements of the transcript that determine stability. While engineering the minigene to optimally mimic the native gene, we identified a stabilizer element within the open reading frame, corresponding to the coding region for the first membrane span of the D1 protein, the presence of and translation through which was essential for normal psbA mRNA stability. We propose that this stabilizer is a site for ribosome pausing, and that accumulation of ribosomes on the transcript upstream of the pause site increases stability. To identify the elements that regulate the differential responses of the psbA transcripts to high‐light growth, sequences from psbAII and psbAIII were substituted in the psbAI minigene reporter. The chimeric reporter transcripts established that the psbAI and psbAIII untranslated leaders determine the faster turnover of these messages. The untranslated leader regions of the psbA transcripts may regulate mRNA stability by modulating translation and thereby stability, or by recruiting RNA‐binding proteins that affect mRNA turnover more directly.
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