Orthologous Proteins Research Articles

Phylogenetic history and temperature adaptation contribute to structural and functional stability of proteins in marine mollusks

Teasing apart the influences of phylogenetic history from thermal adaptation is a focal challenge in understanding the factors driving change in protein stability. This study conducted comprehensive comparative analyses between the phylogenetic relationships and functional/structural stabilities at protein and mRNA levels of cytosolic malate dehydrogenase (cMDH) orthologs of 41 marine mollusks living at widely different environmental temperatures. At the protein level, a significant negative correlation between adaptation temperature and heat-induced movements of the cMDH backbone was found. The movement fluctuation of individual residue varied similarly among cMDH orthologs. At the mRNA level, the free energy that occurs during the formation of the ensemble of mRNA secondary structure was significantly positively correlated with adaptation temperature. The fraction of guanine and cytosine increased with adaptation temperature. The proportion of variance in adaptation temperature that can be explained by the thermal stability (R2) was decreased after phylogenetic generalized least squares but was almost significant at both protein and mRNA levels (P < 0.05). Those analyses reveal the phylogenetic influence on the thermal adaptation of species. Our findings indicated that multi-level analysis of orthologous proteins should be considered alongside phylogenetic history to permit the development of a more comprehensive understanding of protein thermal adaptation.

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.

Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

Eggs-posed: revision of Schistosoma mansoni venom allergen-like proteins unveils new genes and offers new insights into egg-host interactions

BackgroundVenom allergen-like proteins (VALs) are abundant in the excretory-secretory products (ESPs) of numerous parasitic helminths and have been extensively studied for over 30 years because of their potential to interact with host systems. Despite substantial research, however, the precise functions of these proteins remain largely unresolved. Schistosomes, parasites of the circulatory system, are no exception, with 29 SmVAL genes identified in the genome of Schistosoma mansoni to date. The eggs of these parasites, as primary pathogenic agents, interact directly with host tissues and release excretory-secretory products that aid their egress from the host. Although SmVALs have been detected in the egg secretome in the past, direct evidence of their secretion and functional interaction with host molecules has never been demonstrated. These findings fuel the ongoing debate as to whether egg-expressed SmVALs interact with the mammalian host or are rather miracidial proteins synthesized within the egg during larval development.ResultsBased on complete revision of the SmVAL family and an associated robust transcriptomic meta-analysis of gene expression across the life cycle, we show that many of SmVAL genes, including 6 newly identified genes, are expressed in the infective larvae-producing stages (eggs and sporocysts). Following localization of two “egg-specific” SmVAL9 and SmVAL29 did not prove active secretion of these molecules into surrounding tissues but were aligned with miracidial structures interfacing with the molluscan host, specifically the larval surface and penetration glands. Finally, we show the complete lack of interactions between candidate SmVAL proteins and an array of 755 human cell receptors via a state-of-the-art SAVEXIS screen.ConclusionsOverall, we conclude that these “egg” SmVALs are not involved in direct host‒parasite interactions in the mammalian host and are rather proteins employed during intermediate host invasion. Our study revisits and updates the SmVAL gene family, highlighting the limitations of in silico protein function predictions while emphasizing the need for up-to-date datasets and tools together with experimental validation in host-parasite interactions. By uncovering the diversity, expression patterns, and interaction dynamics of SmVALs, we open new avenues for understanding host manipulation and reevaluating orthologous proteins in other helminths.

Probiogenomic analysis of Limosilactobacillus fermentum SD7, a probiotic candidate with remarkable aggregation abilities.

Probiogenomic analysis of Limosilactobacillus fermentum SD7, a probiotic candidate with remarkable aggregation abilities.

In Silico Discovery of Antigenic-Secreted Proteins to Diagnostic Human Toxocariasis

BackgroundHuman toxocariasis is a helminthic zoonosis caused by infection of Toxocara canis or T. cati. Humans can be infected by through ingestion of embryonated eggs from contaminated water, food or soil. Diagnosis is challenging, immunodiagnosis tests are commonly implemented with major pitfalls in the cross-reactivity with other pathogens, particularly in endemic areas.MethodsWith the aim of identify species-specific genes encoding for highly expressed antigenic proteins, a list of parasites that may infect humans and that might present similar clinical symptoms to T. canis infections was built. Only organisms whose genomes were completely sequenced and the proteome predicted were included. First, orthologous proteins were detected and the subcellular localization of T. canis proteins was predicted. In order to identify differentially expressed genes encoding proteins in larvae L3, pair-wise comparisons among transcriptomes from body parts and genders were performed. Finally, all secreted proteins classified as species-specific of T. canis, whose genes were upregulated in larvae L3 were included in an antigenic prediction.ResultsTwenty-eight parasites were included in the analyses, proteins of T. canis were clustered in 11,399 groups, however, 279 were species-specific groups which represent 816 proteins. Three hundred and twenty-two proteins were predicted to be secreted and upregulated in larvae L3, however, after filtering these proteins by their orthology inference, only three proteins met all the features included in this study (species-specific, upregulated, secreted, and antigenic potential). To conclude, our strategy in the study is a rational approach for discovering antigenic proteins to be used in diagnosis.

Comparative analyses of odorant binding protein orthologues in three sympatric Tomicus bark beetles provide insights into functional differentiation of OBPs to ecologically relevant odorants and insecticides.

Comparative analyses of odorant binding protein orthologues in three sympatric Tomicus bark beetles provide insights into functional differentiation of OBPs to ecologically relevant odorants and insecticides.

Toll-like receptor 4 pathway evolutionary trajectory and functional emergence.

Toll-like receptors 4 (TLR4) recognize lipopolysaccharides (LPS) from bacteria as their conventional ligands and undergo downstream signaling to produce cytokines. They mediate the signaling either by the TIRAP-MyD88 complex or by the TRAM-TRIF complex. The MyD88 pathway is common to all other TLRs, whereas the TRAM-TRIF complex is largely exclusive to TLR4. Here we study the TIR domain of TRAM and TRIF ortholog proteins that are crucial for downstream signaling. Our previous work on pan-genome-wide survey, indicates Callorhincus milli to be the ancestral organism with both TRAM and TRIF proteins. To gain a deeper insight into the protein function and to compare them with Homo sapiens adaptor proteins, we modeled the docking of the TRAM-TRIF complex of representative organisms across various taxa. These modeling experiments provide insights to ascertain a possible interaction surface and calculate the energetics and electrostatic potential of the complex. Furthermore, this enables us to employ normal mode analysis (NMA) to examine fluctuating, interacting, and other specific residue clusters that could have a role in protein functioning in both C. milli and H. sapiens. We also performed molecular dynamics simulations of these complexes and cross-validated the functionally important residues using network parameters. We compared the stoichiometry of TRAM-TRIF complexes and found that the tetrameric models (TRAM and TRIF dimer) were more stable than the trimeric model (TRAM dimer and TRIF monomer). While the critical residues of TIRAP, TRIF, and MyD88 were preserved, we also found that the important residues of TRAM signaling were not conserved in C. milli. This suggests the presence of functional TIRAP-MyD88-mediated TLR4 signaling and TRIF-mediated TLR3 signaling in the ancestral species. The overall biological function of this signaling domain appears to be gradually acquired through the orchestration of several motifs through an evolutionary scale.

Generation of antagonistic biparatopic anti-CD30 antibody from an agonistic antibody by precise epitope determination and utilization of structural characteristics of CD30 molecule.

CD30 is a member of the tumor necrosis factor receptor superfamily. Recently, blocking CD30-dependent intracellular signaling has emerged as potential strategy for immunological regulation. Development of antibody-based CD30 antagonists is therefore of significant interest. However, a key challenge is that the bivalent form of natural antibody can crosslink CD30 molecules, leading to signal transduction even in the absence of specific ligand, CD153. Biparatopic antibodies (BpAbs) offer a solution, using two different variable fragments (Fvs) to bind distinct epitopes on a single antigen molecule. BpAbs format is an attractive alternative of natural antibody by potentially avoiding unwanted crosslinking and signaling induction. We systematically characterized 36 BpAbs, each designed with pairs of Fvs binding to nine distinct epitopes across the CD30 extracellular domain. We first identified the precise epitope sites of the nine antibodies by assessing the binding to multiple orthologous CD30 proteins and mutants. We then produced the 36 BpAbs and analyzed their biological activities and binding modes. Among 36 BpAbs, we identified both potent ligand-independent agonists and ligand-blocking antagonists, with many displayed reduced signal activation, including 1:1-binding antagonists derived from AC10, a strong agonist developed for lymphoma therapy. Epitope dependency in reduced signaling activity was observed and associated with the flexible nature of CD30 protein. We successfully developed antagonistic BpAbs against CD30 by controlling the stoichiometry of antibody-antigen binding mode. This study elucidated the mechanism of signaling induction, informing the design strategies of the development of biparatopic antibodies.

Cross-Species Epitope Sequence Analysis for Discovery of Existing Antibodies Useful for Phospho-Specific Protein Detection in Model Species.

Signaling pathways play key roles in many important biological processes, such as cell division, differentiation, and migration. Phosphorylation site-specific antibodies specifically target proteins phosphorylated on a given tyrosine, threonine, or serine residue. The use of phospho-specific antibodies facilitates the analysis of signaling pathway regulation and activity. Given the usefulness of phospho-specific antibodies, a number of collections of these antibodies have been generated, typically for the detection of phosphorylated mammalian proteins. Anecdotal evidence shows that some of these are also useful for the detection of phosphorylated forms of orthologous proteins in model organisms. We propose that anti-phospho-mammalian protein antibody collections comprise an untapped resource for research in other species. To systematically analyze the potential utility of anti-phospho-mammalian protein antibodies in other species, we developed the Cross-species Epitope Sequence Analysis software tool (CESA). CESA identifies and aligns orthologous proteins in model species and then analyzes the conservation of antibody target sites. We used CESA to predict what phospho-specific antibodies in a collection from Cell Signaling Technology (CST) might be useful for studies in Drosophila melanogaster and other species. CESA predicts that more than 232 sites on 116 Drosophila proteins can potentially be targeted by the antibodies initially developed at CST to detect human, mouse, or rat phosphoproteins.

Proteomic characterization and comparison of the infective and adult life stage secretomes from Necator americanus and Ancylostoma ceylanicum.

More than 470 million people globally are infected with the hookworms Ancylostoma ceylanicum and Necator americanus, resulting in an annual loss of 2.1 to 4 million disability-adjusted-life-years. Current infection management approaches are limited by modest drug efficacy, the costs associated with frequent mass drug administration campaigns, and the risk of reinfection and burgeoning drug resistance. Subunit vaccines based on proteins excreted and secreted (ES) by hookworms that reduce worm numbers and associated disease burden are a promising management strategy to overcome these limitations. However, studies on the ES proteomes of hookworms have mainly described proteins from the adult life stage which may preclude the opportunity to target the infective larva. Here, we employed high resolution mass spectrometry to identify 103 and 57 ES proteins from the infective third larvae stage (L3) as well as 106 and 512 ES proteins from the adult N. americanus and A. ceylanicum respectively. Comparisons between these developmental stages identified 91 and 41 proteins uniquely expressed in the L3 ES products of N. americanus and A. ceylanicum, respectively. We characterized these proteins based on functional annotation, KEGG pathway analysis, InterProScan signature and gene ontology. We also performed reciprocal BLAST analysis to identify orthologs across species for both the L3 and adult stages and identified five orthologous proteins in both life stages and 15 proteins that could be detected only in the L3 stage of both species. Last, we performed a three-way reciprocal BLAST on the L3 proteomes from both hookworm species together with a previously reported L3 proteome from the rodent hookworm Nippostrongylus brasiliensis, and identified eight L3 proteins that could be readily deployed for testing using well established rodent models. This novel characterization of L3 proteins and taxonomic conservation across hookworm species provides a raft of potential candidates for vaccine discovery for prevention of hookworm infection and disease.

Cloning and Recombinant Expression of the Caspase‐Activated DNase Orthologous Gene of Giardia lamblia

In eukaryotic cells, mitochondria play a key role in apoptosis; however, ancestral eukaryotic cells such as Giardia lamblia only possess a mitochondrial remnant, the mitosome. Interestingly, this protozoan still undergoes an apoptosis‐like process; therefore, we focused primarily on the search for the mitochondria‐independent executor DNase. Here, we identified, cloned, expressed, and characterized the caspase‐activated DNase (CAD) from Giardia lamblia. Using a commercial polyclonal antibody that recognizes mouse, rat, and human caspase‐activated DNase (hCAD), we developed an immunoproteomic analysis using a crude extract of curcumin‐treated Giardia lamblia trophozoites (CEGl) and detected a spot of 42 kDa and pI 9.4, similar to hCAD and sequenced by LC‐MS. The proteomic profile matched a novel protein of 383 residues, with a predicted 42 kDa, pI 9.4, a CIDE‐N domain, and putative H‐K‐H catalytic motif. Afterward, we cloned the full‐length gene (GenBank: ON707040), expressed it, and purified it as a 6‐His tag‐recombinant protein in Escherichia coli, which was also recognized by commercial anti‐CAD. In conclusion, genetic, proteomic, and structural analyses showed that the identified gCAD is an orthologous protein of hCAD, and its DNase role in the apoptosis‐like signaling pathway of Giardia lamblia can be further analyzed.

Apoptotic proteins in Leishmania donovani: in silico screening, modeling, and validation by knock-out and gene expression analysis.

Visceral leishmaniasis, a life-threatening vector-borne illness that disproportionately affects children and elderly immunocompromised people, is a primary tropical neglected disease. No apoptotic partner proteins have yet been reported in Leishmania donovani, while their identification could contribute to knowledge on parasite cell death and the establishment of alternative therapeutics. We searched for mammalian Bcl-2 family protein orthologs and found one anti-apoptotic and two pro-apoptotic orthologs in L. donovani. A pro-death aquaporin protein, due to its characteristic BH3 domain known to interact with pro-apoptotic proteins in mammalian Bcl-2 family proteins, was also included in this study. Molecular docking and molecular dynamics simulations were conducted to assess protein-protein interactions between the identified apoptotic proteins and mimic mammalian intrinsic apoptotic pathways. The results showed that both pro-apoptotic proteins interacted with the hydrophobic pocket of the anti-apoptotic ortholog, forming a stable complex. This interaction may represent a critical event in an apoptotic pathway in L. donovani. To further characterise it, we used CRISPR-Cas9 approaches to target the identified proteins. Pure knocked population mutants, and episomal over-expressing mutant cells were exposed to apoptotic stimuli. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and quantitative expression profiling suggested that these proteins are involved in the parasite's apoptosis and could play a role in its survival.

CESA: Cross-species Epitope Sequence Analysis for discovery of existing antibodies useful for phospho-specific protein detection in model species.

Signaling pathways play key roles in many important biological processes such as cell division, differentiation, and migration. Phosphorylation site-specific antibodies specifically target proteins phosphorylated on a given tyrosine, threonine, or serine residue. Use of phospho-specific antibodies facilitates analysis of signaling pathway regulation and activity. Given the usefulness of phospho-specific antibodies, a number of collections of these antibodies have been generated, typically for detection of phosphorylated mammalian proteins. Anecdotal evidence shows that some of these are also useful for detection of phosphorylated forms of orthologous proteins in model organisms. We propose that anti-phospho-mammalian protein antibody collections comprise an untapped resource for research in other species. To systematically analyze the potential utility of anti-phospho-mammalian protein antibodies in other species, we developed the Cross-species Epitope Sequence Analysis software tool (CESA). CESA identifies and aligns orthologous proteins in model species, then analyzes conservation of antibody target sites. We used CESA to predict what phospho-specific antibodies in a collection from Cell Signaling Technology (CST) might be useful for studies in Drosophila melanogaster and other species. CESA predicts that more than 232 sites on 116 Drosophila proteins can potentially be targeted by the antibodies initially developed at CST to detect human, mouse, or rat phosphoproteins.

An in-silico study of FIKK9.5 protein of Plasmodium falciparum for identification of therapeutics

The FIKK protein family, encompassing 21 serine-threonine protein kinases, is a distinctive cluster exclusive to the Apicomplexa phylum. Predominantly located in Plasmodium falciparum which is a malarial parasite, with a solitary gene identified in a distinct apicomplexan species, this family derives its nomenclature from - phenylalanine, isoleucine, lysine, lysine (FIKK), a conserved amino acid motif. Integral to the parasite’s life cycle and consequential to malaria pathogenesis, the absence of orthologous proteins in eukaryotic organisms designates it as a promising antimalarial drug target. Among the FIKKs, FIKK9.5 plays a pivotal role in the parasite’s development within red blood cells (RBCs). This investigation acquired the three-dimensional structure of FIKK9.5 and its ligands through extensive database searches and literature review. Computational screening of natural phytochemicals derived from plants traditionally used in antimalarial remedies was conducted by employing the Glide docking suite. AutoDock Vina was utilized to discern the inhibitor exhibiting optimal binding affinity. Subsequently, Molecular Dynamics (MD) simulations employing GROMACS validated Rufigallol as the most potent inhibitory compound against FIKK9.5. The robustness of the protein-ligand complex was scrutinized through a 200 nanosecond molecular dynamics (MD) trajectory. Trajectory analysis and determination of binding free energies were accomplished using MM-GBSA and MM-PBSA approaches. The ligand-binding exhibited sustained stability throughout the simulation, manifesting an approximate binding free energy of −25.5986 kcal/mol. This comprehensive computational study lays the groundwork for potential experimental validation in the laboratory, paving the way for the development of novel therapeutics targeting FIKK9.5 in the pursuit of innovative antimalarial.

Comparative Genomics and Pathogenicity Analysis of Three Fungal Isolates Causing Barnyard Grass Blast.

Barnyard grass is one of the most serious rice weeds, often growing near paddy fields and therefore potentially serving as a bridging host for the rice blast fungus. In this study, we isolated three fungal strains from diseased barnyard grass leaves in a rice field. Using a pathogenicity assay, we confirmed that they were capable of causing blast symptoms on barnyard grass and rice leaves to various extents. Based on morphology characterization and genome sequence analyses, we confirmed that these three strains were Epicoccum sorghinum (SCAU-1), Pyricularia grisea (SCAU-2), and Exserohilum rostratum (SCAU-6). The established Avirulence (Avr) genes Avr-Pia, Avr-Pita2, and ACE1 were detected by PCR amplification in SCAU-2, but not in SCAU-1 or SCAU-6. Furthermore, the whole-genome sequence analysis helped to reveal the genetic variations and potential virulence factors relating to the host specificity of these three fungal pathogens. Based on the evolutionary analysis of single-copy orthologous proteins, we found that the genes encoding glycoside hydrolases, carbohydrate esterases, oxidoreductase, and multidrug transporters in SCAU-1 and SCAU-6 were expanded, while expansion in SCAU-2 was mainly related to carbohydrate esterases. In summary, our study provides clues to understand the pathogenic mechanisms of fungal isolates from barnyard grass with the potential to cause rice blast.

Distinct Proteomic Brain States Underlying Long-Term Memory Formation in Aversive Operant Conditioning.

Long-term memory (LTM) formation relies on de novo protein synthesis; however, the full complement of proteins crucial to LTM formation remains unknown in any system. Using an aversive operant conditioning model of aerial respiratory behavior in the pond snail mollusk, Lymnaea stagnalis (L. stagnalis), we conducted a transcriptome-guided proteomic analysis on the central nervous system (CNS) of LTM, no LTM, and control animals. We identified 366 differentially expressed proteins linked to LTM formation, with 88 upregulated and 36 downregulated in LTM compared to both no LTM and controls. Functional annotation highlighted the importance of balancing protein synthesis and degradation for LTM, as indicated by the upregulation of proteins involved in proteasome activity and translation initiation, including EIF2D, mRNA levels of which were confirmed to be upregulated by conditioning and implicated nuclear factor Y as a potential regulator of LTM-related transcription in this model. This study represents the first transcriptome-guided proteomic analysis of LTM formation ability in this model and lays the groundwork for discovering orthologous proteins critical to LTM in mammals.

Comparative analysis of the primary structure and production of recombinant poly(ADP-ribose)polymerase 1 of long-lived Heterocephalus glaber.

DNA repair is a most important cellular process that helps maintain the integrity of the genome and is currently considered by researchers as one of the factors determining the maximum lifespan. The central regulator of the DNA repair process is the enzyme poly(ADP-ribose)polymerase 1 (PARP1). PARP1 catalyzes the synthesis of poly(ADP-ribose) polymer (PAR) upon DNA damage using nicotinamide adenine dinucleotide (NAD+) as a substrate. This polymer covalently attaches to PARP1, which leads to its dissociation from the complex with damaged DNA and stimulation of the repair process. Despite intensive research on PARP1, its properties as an isolated protein have not been practically studied in mammals that demonstrate a long maximum lifespan, such as, for example, the naked mole rat (Heterocephalus glaber). High activity of DNA repair systems is observed in the cells of the naked mole rat, which ensures their high resistance to oxidative stress, as well as to genotoxic effects. The revealed features may be due to the high activity of PARP1 in the cells of the naked mole rat; however, this issue remains poorly understood and, thus, requires more detailed research, including one with the use of isolated protein PARP1 of the naked mole rat, the isolation and characterization of which have not been carried out before. In the present work, the amino acid sequence of PARP1 of the naked mole rat is compared with the amino acid sequences of orthologous proteins of other mammals. In contrast to human PARP1, 13 evolutionarily conservative amino acid substitutions in various functional domains of the protein have been identified in the amino acid sequence of naked mole rat PARP1. Using the cDNA of the naked mole rat's Parp1 gene, a vector was created for the expression of the target protein in Escherichia coli cell culture. For the first time, a detailed description of the procedure for the expression and purification of the recombinant protein PARP1 of the long-lived naked mole rat is presented. In addition, poly(ADP-ribose)polymerase activity of the obtained protein was evaluated. The results presented in this paper are the basis for further detailed characterization of the properties of purified recombinant naked mole rat PARP1.

Discovery of Alanomyces manoharacharyi: A Novel Fungus Identified Using Genome Sequencing and Metabolomic Analysis.

In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen-Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses.

Regulation of BCR-dependent germinal center B-cell formation by HGAL and insight into its emerging myeloid ortholog, C1ORF150.

The specificity of cytokine and immunoreceptor signaling frequently depends upon receptor recruitment of select adaptor proteins and specifically engaged effectors. This review focuses on the orthologous adaptor proteins, HGAL and C1ORF150, and aims to provide insight into their respective modulation of lymphoid and myeloid cell signaling, formation, and function. HGAL acts predominantly within germinal center B cells as an important BCR signal transducer. Effects on BCR signalosome assembly involve HGAL's localization to the plasma membrane via its lipidation, initial interactions with SYK, the pY-phosphorylation of HGAL including its recruitment of GRB2, and HGAL engagement of PDZ-RhoGEF and RhoA signaling. At ligated BCRs, this includes HGAL(-GRB2) stimulation of SYK kinase, attenuation of calcium flux-dependent and NF-κB expression, promotion of cSMAC formation, and cytoskeletal remodeling associated with HGAL-attenuated cell migration. HGAL and partnered effectors also impact on DLBCL pathogenesis, and studies are summarized on HGAL's actions (using DLBCL and Burkitt lymphoma B cells) including cell migration effects, HGAL modulation of cytoskeletal components, and insightful HGAL transgenic mouse and xenograft models. For C1ORF150, its HGAL-homologous subdomains are considered, together with studies that demonstrate C1OR150's FcϵRI- and KIT-mediated expression and phosphorylation in primary human mast cells. Intriguingly, recent GWAS studies have identified a C1ORF150 in-frame splice variant that is strongly associated with urticaria. Candidate mechanisms via which the encoded "C1ORF150-Δexon2" isoform affects mast cell degranulation are considered, including FcϵR1 and/or KIT receptor connections, and candidate "myristoylation switch" mechanisms.

Dysfunctional copper homeostasis in Caenorhabditis elegans affects genomic and neuronal stability

Dysfunctional copper homeostasis in Caenorhabditis elegans affects genomic and neuronal stability