Biology subjects

Speyer, G.

Publications and source records attributed to Speyer, G..

3 recordsLinked to original sources

bioRxiv2024

Divergence in poxvirus-encoded E3-like proteins can dictate poxvirus activation of cellular necroptosis

Poxviruses encode a plethora of proteins to modulate diverse cellular responses against viruses. Poxvirus-encoded E3-like proteins are multifunctional, regulating diverse cellular antiviral responses. The canonical Vaccinia E3-like proteins have two domains: an N-terminal Z-form nucleic acid binding domain (Z-BD) and a C-terminal double-stranded RNA binding domain (dsRNA-BD)-.Using protein sequence and structural homology modeling, we identified the presence of dsRNA- BD-containing proteins in all the poxviruses except Avipoxviruses, Salmon poxvirus and Entemopoxviruses. However, the acquisition of these proteins likely happened under three distinct events. Using structural homology modeling and FATCAT score, we can classify E3-like proteins in three distinct categories: i) the E3-like proteins with highly conserved dsRNA-BD but with or without the N-terminal domain, present in most poxviruses; ii) unconventional E3-like proteins with highly diverged dsRNA-BD, present in Macropoxvirus and Molluscipoxvirus and iii) E3-like protein with dsRNA-BD that may have different origin present in Crocodilepoxvirus.12-52-6 Members of Leporipoxvirus, Waddenpoxvirus, Cetaceanpoxvirus, and selected members of Orthopoxvirus contain E3-like proteins missing the N-terminal Z-BD required for necroptosis inhibition. Additionally, using Alphafold, we show that the Z-BD of Chordopoxviruses E3-like proteins is structurally more variable than the ds-RNA binding domain. Compared to members of Orthopoxviruses-Vaccinia virus (VACV) and Cowpox virus (CPXV) that have been shown to inhibit necroptosis and contain an N-terminus Z-BD of the canonical E3 protein, our results show that members of leporipoxviruses induce necroptosis in human and mouse necroptosis competent cell lines. Furthermore, myxoma virus (MYXV) infection activates RIP1 and RIP3-mediated necroptosis in both human and mouse necroptosis-competent cells. These data suggest that Leporipoxviruses lack countermeasures to necroptosis compared to Orthopoxviruses that encode multiple key regulators of necroptosis, possibly due to a lack of selective pressure within the viral host species (Lagomorphs). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/627069v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@132ce9borg.highwire.dtl.DTLVardef@9a459borg.highwire.dtl.DTLVardef@4fc88dorg.highwire.dtl.DTLVardef@1f7ac6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

The Divergence of Mean Phenotypes Under Persistent Directional Selection

Numerous organismal traits, particularly at the cellular level, are likely to be under persistent directional selection across phylogenetic lineages. For such traits, unless all mutations affecting such traits have large enough effects to be efficiently selected in all species, gradients in mean phenotypes are expected to arise as a consequence of differences in the power of random genetic drift, which varies by approximately five orders of magnitude across the Tree of Life. Prior theoretical work examining the conditions under which such gradients can arise focused on the simple situation in which all genomic sites affecting the trait have identical and constant mutational effects. Here, we extend this theory to incorporate the more biologically realistic situation in which mutational effects on a trait differ among nucleotide sites. Pursuit of such modifications lead to the development of semi-analytic expressions for the ways in which selective interference arises via linkage effects in single-effect models, which then extend to more complex scenarios. The theory developed clarifies the conditions under which mutations of different selective effects mutually interfere with each others fixation, and shows how variance in effects among sites can substantially modify and extend the expected scaling relationships between mean phenotypes and effective population sizes.

evolutionary biology↗

bioRxiv2017

Sex-specific gene and pathway modeling of inherited glioma risk

BackgroundGenome-wide association studies (GWAS) have identified 25 risk variants for glioma, which explain ~30% of heritable risk. Most glioma histologies occur with significantly higher incidence in males. A sex-stratified analysis ide7ntified sex-specific glioma risk variants, and further analyses using gene- and pathway-based approaches may further elucidate risk variation by sex.\n\nMethodsResults from the Glioma International Case-Control Study were used as a testing set, and results from three GWAS were combined via meta-analysis and used as a validation set. Using summary statistics for autosomal SNPs found to be nominally significant (p<0.01) in a previous meta-analysis and X chromosome SNPs with nominally significant association (p<0.01), three algorithms (Pascal, BimBam, and GATES) were used to generate gene-scores, and Pascal was used to generate pathway scores. Results were considered significant when p<3.3x10-6 in [2/3] algorithms.\n\nResults25 genes within five regions and 19 genes within six regions reached the set significance threshold in at least 2/3 algorithms in males and females, respectively. EGFR and RTEL1-TNFRSF6B were significantly associated with all glioma and glioblastoma in males only, and a female-specific association in TERT, all of which remained nominally significant after conditioning on known risk loci. There were nominal associations with the Telomeres, Telomerase, Cellular Aging, and Immortality pathway in both males and females.\n\nConclusionsThese results suggest that there may be biologically relevant significant differences by sex in genetic risk for glioma. Additional gene- and pathway-based analyses may further elucidate the biological processes through which this risk is conferred.

epidemiology↗