Evolutionary identification of residues related to G protein coupling selectivity in aminergic GPCRs/

G protein-coupled receptors (GPCRs) are coupled to four different subfamilies of G proteins namely Gs, Gi, Gq, and G12/13, in a selective way. However, receptor-wide determinants of selective G protein coupling and G protein specific activation mechanisms remained under investigated. Here, we analyzed aminergic receptors and its orthologs from different phylogenetic levels to reveal positions that are specifically evolved and conserved for the receptors that are coupled to similar G proteins. By co-analyzing these evolutionary conserved amino acids with available structures of the receptors, we revealed specific activation mechanisms for Gs, Gi1, Go, and Gq. To verify that these pathways could play role in determining coupling selectivity we investigated Gs-specific activation mechanism further. By the help of molecular dynamics simulations, we demonstrated that G7x41 is important for receptor activation and it might determine Gs coupling selectivity by promoting outwards movement of TM6. Lastly, we summarized our findings into a model of G protein selectivity called “sequential switches of activation” explaning three major molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms, and G protein contact

Common and selective signal transduction mechanisms of GPCRs

G protein-coupled receptors (GPCRs) are coupled by four major subfamilies of G proteins. GPCR coupling is processed through a combination of common and selective activation mechanisms together. Common mechanisms are shared for a group of receptors. Recently, researchers managed to identify shared activation pathways for the GPCRs belonging to the same subfamilies. On the other hand, selective mechanisms are responsible for the variations within activation mechanisms. Selective processes can regulate subfamily-specific interactions between the receptor and the G proteins, and intermediate receptor conformations are required to couple particular G proteins through G protein-specific activation mechanisms. Moreover, G proteins can also selectively interact with RGS (regulators of G protein signaling) proteins as well. Selective processes modulate the signaling profile of the receptor and the tissue they are present. This chapter summarizes the recent research conducted on common and selective signal transduction mechanisms within GPCRs from an evolutionary perspective

Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder

Major Depressive Disorder (MDD) is a commonly observed psychiatric disorder that affects more than 2% of the world population with a rising trend. However, disease-associated pathways and biomarkers are yet to be fully comprehended. In this study, we analyzed previously generated RNA-seq data across seven different brain regions from three distinct studies to identify differentially and co-expressed genes for patients with MDD. Differential gene expression (DGE) analysis revealed that NPAS4 is the only gene downregulated in three different brain regions. Furthermore, co-expressing gene modules responsible for glutamatergic signaling are negatively enriched in these regions. We used the results of both DGE and co-expression analyses to construct a novel MDD-associated pathway. In our model, we propose that disruption in glutamatergic signaling-related pathways might be associated with the downregulation of NPAS4 and many other immediate-early genes (IEGs) that control synaptic plasticity. In addition to DGE analysis, we identified the relative importance of KEGG pathways in discriminating MDD phenotype using a machine learning-based approach. We anticipate that our study will open doors to developing better therapeutic approaches targeting glutamatergic receptors in the treatment of MDD

Evolutionary association of receptor-wide amino acids with G protein-coupling selectivity in aminergic GPCRs

G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, and G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed extensive phylogenetic analysis and identified specifically conserved residues for the aminergic receptors having similar coupling profiles. By integrating our methodology of differential evolutionary conservation of G protein-specific amino acids with structural analyses, we identified specific activation networks for Gs, Gi1, Go, and Gq. To validate that these networks could determine coupling selectivity we further analyzed Gs-specific activation network and its association with Gs selectivity. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7x41 plays an important role in receptor activation and it may determine Gs coupling selectivity by facilitating a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called “sequential switches of activation” describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms, and G protein contact

Phylogenetic analysis of sars-cov-2 genomes in Turkey

COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first 30 SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find 2 of the seventeen subclusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide

A case report of a rare nonsense ZP1 variant in a patient with oocyte maturation defect

Introduction: Oocyte maturation defect (OOMD) is a rare condition causing female infertility that can be diagnosed during assisted reproduction techniques (ART). OOMD related genes are ZP1, ZP2, ZP3, PANX1, PATL2, TUBB8, WEE2 (OMIM, 2020). We report a case of a 31-year-old woman who had four ART failures diagnosed as empty follicle syndrome and OOMD. She has short stature (-3 SD), bilateral limited extension-exion on elbows. Materials and Methods: Chromosome analysis and uorescence in-situ hybridization (FISH) using X chromosome centromeric and SHOX-probe on interphase nuclei of lymphocytes and mucosal cells was investigated. Whole-exome sequencing (WES) performed via the Illumina platform. Conrmation and familial segregation analysis were performed by Sanger sequencing. Results: Karyotyping and FISH resulted in normal, possible mosaicism was excluded. WES analysis revealed a known, rare, pathogenic homozygous variant in exon 3 (c.628C>T; p.Q210*) of ZP1 gene, and her parents being rst degree cousins were carriers for this variant. Conclusions: ZP1 with autosomal recessive inheritance is related to OOMD-1 (MIM_615774). Zona pellucida (ZP) is a glycoprotein structure surrounding oocytes and is essential for oocyte development. ZP contains four types of receptor proteins (ZP1-4). Our variant in ZP1 is nonsense, premature stop codon causes to truncate ZP1 receptor proteins. This is the rst homozygous occurrence of this variant associated with OOMD. WES ndings were also analyzed for known genes related to short stature and no pathogenic variant has been observed. WES is a valuable method to identify the genetic origin in complex, multigenic conditions like in infertility.Istanbul University ProjectNumber:TSA-2018-3213

A case report of a rare nonsense ZP1 variant in a patient with oocyte maturation defect

Introduction: Oocyte maturation defect (OOMD) is a rare condition causing female infertility that can be diagnosed during assisted reproduction techniques (ART). OOMD related genes are ZP1, ZP2, ZP3, PANX1, PATL2, TUBB8, WEE2 (OMIM, 2020). We report a case of a 31-year-old woman who had four ART failures diagnosed as empty follicle syndrome and OOMD. She has short stature (-3 SD), bilateral limited extension-exion on elbows. Materials and Methods: Chromosome analysis and uorescence in-situ hybridization (FISH) using X chromosome centromeric and SHOX-probe on interphase nuclei of lymphocytes and mucosal cells was investigated. Whole-exome sequencing (WES) performed via the Illumina platform. Conrmation and familial segregation analysis were performed by Sanger sequencing. Results: Karyotyping and FISH resulted in normal, possible mosaicism was excluded. WES analysis revealed a known, rare, pathogenic homozygous variant in exon 3 (c.628C>T; p.Q210*) of ZP1 gene, and her parents being rst degree cousins were carriers for this variant. Conclusions: ZP1 with autosomal recessive inheritance is related to OOMD-1 (MIM_615774). Zona pellucida (ZP) is a glycoprotein structure surrounding oocytes and is essential for oocyte development. ZP contains four types of receptor proteins (ZP1-4). Our variant in ZP1 is nonsense, premature stop codon causes to truncate ZP1 receptor proteins. This is the rst homozygous occurrence of this variant associated with OOMD. WES ndings were also analyzed for known genes related to short stature and no pathogenic variant has been observed. WES is a valuable method to identify the genetic origin in complex, multigenic conditions like in infertility.Istanbul University ProjectNumber:TSA-2018-3213

CSB-independent, XPC-dependent transcription-coupled repair in Drosophila

Drosophila melanogaster has been extensively used as a model system to study ionizing radiation and chemical-induced mutagenesis, double-strand break repair, and recombination. However, there are only limited studies on nucleotide excision repair in this important model organism. An early study reported that Drosophila lacks the transcription-coupled repair (TCR) form of nucleotide excision repair. This conclusion was seemingly supported by the Drosophila genome sequencing project, which revealed that Drosophila lacks a homolog to CSB, which is known to be required for TCR in mammals and yeasts. However, by using excision repair sequencing (XR-seq) genome-wide repair mapping technology, we recently found that the Drosophila S2 cell line performs TCR comparable to human cells. Here, we have extended this work to Drosophila at all its developmental stages. We find TCR takes place throughout the life cycle of the organism. Moreover, we find that in contrast to humans and other multicellular organisms previously studied, the XPC repair factor is required for both global and transcription-coupled repair in Drosophila

Clinical and demographic features of hidradenitis suppurativa: A multicentre study of 1221 patients with an analysis of risk factors associated with disease severity

Background Hidradenitis suppurativa (HS) is a chronic, relapsing and debilitating inflammatory disease associated with profound morbidity. Aim In this multicentre study, we investigated the demographic and clinical features of HS, and determined risk factors of disease severity. Methods In total, 1221 patients diagnosed with HS from 29 centres were enrolled, and the medical records of each patient were reviewed. Results The mean age of disease onset was 26.2 +/- 10.4 years, and almost 70% (n = 849) of patients were current or former smokers. Mean disease duration was 8.9 +/- 8.4 years with a delay in diagnosis of 5.8 +/- 3.91 years. Just over a fifth (21%; n = 256) of patients had a family history of HS. The axillary, genital and neck regions were more frequently affected in men than in women, and the inframammary region was more frequently affected in women than in men (P < 0.05 for all). Acne (40.8%), pilonidal sinus (23.6%) and diabetes mellitus (12.6%) were the most prevalent associated diseases. Of the various therapies used, antibiotics (76.4%) were most common followed by retinoids (41.7%), surgical interventions (32.0%) and biologic agents (15.4%). Logistic regression analysis revealed that the most important determinants of disease severity were male sex (OR = 2.21) and involvement of the genitals (OR = 3.39) and inguinal region (OR = 2.25). More severe disease was associated with comorbidity, longer disease duration, longer diagnosis delay and a higher number of smoking pack-years. Conclusions Our nationwide cohort study found demographic and clinical variation in HS, which may help broaden the understanding of HS and factors associated with disease severity