Domain Sequences Research Articles

A Novel Genotype of Orientia tsutsugamushi in Human Cases of Scrub Typhus from Southeastern India

Scrub typhus is a mite-borne, re-emerging public health problem in India, particularly in Tamil Nadu, South India. More than 40 serotypes of Orientia tsutsugamushi have been documented worldwide. However, the information on the circulation of its molecular sub-types in India is scanty. A retrospective study was conducted among serologically confirmed cases of scrub typhus. DNA isolated from blood was screened by a nested polymerase chain reaction (nPCR) targeting the GroEL and the 56 kDa type-specific antigen (TSA) genes. Out of 59 samples, 14 partial fragments of GroEL and the twelve 56 kDa genes were PCR-amplified and DNA-sequenced. The neighbor-joining (NJ) analysis indicated three distinct phylogenetic clades, including a novel genotype designated as Ot-Thanjavur-Tamil Nadu (Ot-TJTN, 9 nos. 64.3%); Karp-like (4 nos. 28.6%); and Kuroki-Gilliam type (1 no. 7.1%). Also, phylogenetic analysis of twelve 56 kDa variable domains (VDΙ-ΙΙΙ) of TSA gene sequences revealed a distinctive new genotypic cluster of eight samples (66.6%), and the remaining four (33.4%) were Karp-like genotypes. The Simplot analysis for the similarity and event of recombination testing elucidated the existence of the new genotype of the Ot-TJTN cluster, which was undescribed so far, in the Kato and TA716 lineages. The significant findings recommend further studies to understand the ongoing transmission dynamics of different O. tsutsugamushi strains in vector mites, rodent hosts, and humans in this region.

Roles of the EF-Hand Domain of PLCZ1 in Establishing Species-Specific Ca 2+ Oscillations in Mouse and Rat Fertilization†.

Periodic increases in cytosolic calcium concentration (Ca2+ oscillations) during mammalian fertilization induce all the events collectively known as egg activation. The sperm-specific phospholipase C, PLC zeta 1 (PLCZ1) represents the "sperm factor" vital for initiating the persistent Ca2+ oscillations in mammals. Despite sequence conservation, the Ca2+ oscillation-inducing properties of the enzyme differ vastly among species, and this is particularly salient between mouse and rat PLCZ1, where the activities vary at least one order of magnitude in favor of the former. As previously shown, injecting wild-type (WT) rat Plcz1 mRNA into metaphase II (MII) mouse eggs induced delayed Ca2+ oscillations with low specific activity compared to the homologous mouse Plcz1 mRNA. We, therefore, sought to uncover the factor(s) diversifying these enzymes by swapping functional domains between species, creating chimeric PLCZ1s. When injected into mouse MII eggs, mouse Plcz1 mRNA with the whole- or part of the EF-hand domains swapped with the rat showed a substantial reduction in activity compared to WT. Consistently, the opposite exchange enhanced the rat's enzyme activity. EF-hand domains 1 and 2 seemed to underlie most differences, and mutations of the divergent amino acids within these domains, substitutions for Glu(m-30; r-29) and Gln(m-58; r-57), changed the activity of both species' PLCZ1s in opposite directions. Collectively, our findings support the view that differences in the sequences of EF-hand domains, especially in several of its charged residues, underpin the distinct PLCZ1 activities between these species, revealing the gametes and species' adaptability to optimize the fertilization signal and early development.

Antigen receptor ITAMs provide tonic signaling by acting as guanine nucleotide exchange factors to directly activate R-RAS2.

The small GTPase R-RAS2 regulates homeostatic proliferation and survival of T and B lymphocytes and, when present in high amounts, drives the development of B cell chronic lymphocytic leukemia. In normal and leukemic lymphocytes, R-RAS2 constitutively binds to antigen receptors through their immunoreceptor tyrosine-based activation motifs (ITAMs) and promotes tonic activation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway. Here, we examined the molecular mechanisms underlying this direct interaction and its consequences for R-RAS2 activity. R-RAS2 exhibited direct, high-affinity interactions with ITAM peptides derived from B and T cell receptors through a proline-rich sequence in the hypervariable domain of R-RAS2. In resting T and B cells, the presence of antigen receptors at the plasma membrane was sufficient to promote the activation of R-RAS2 and PI3K, and mutations that abolished the interaction of R-RAS2 with ITAMs reduced R-RAS2 signaling. Binding to ITAMs increased GDP-GTP exchange on R-RAS2 through a mechanism distinct from that by which conventional cytosolic guanosine nucleotide exchange factors (GEFs) activate RAS proteins. These results define antigen receptors as noncanonical GEFs involved in the basal activation state of R-RAS2 in lymphocytes. Such a mechanism may underlie the leukemic transformation of B cells that occurs when wild-type R-RAS2 is present in high amounts.

The potential role of domain vectors in optimizing digital data structure

Each piece of information represents a selection from a set of possibilities. This set is the “domain of information”, which must be uniformly known before any information transport. The components of digital information are also sequences of numbers that represent a selection from a domain of information. So far, however, there is no guarantee that this domain is uniformly known. There is still no infrastructure that makes it possible to publish the domain of digital information in a uniform manner. Therefore, a standardized machine-readable online definition of the binary format and the domain of digital number sequences is proposed. These are uniquely identified worldwide as domain vectors (DVs) by an efficient Internet address of the online definition. As a result, optimized, language-independent digital information can be uniformly defined, identified, efficiently exchanged and compared worldwide for more and more applications.

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing.

NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defense mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self/non-self recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The het-d and het-e NLRs in Podospora anserina are highly polymorphic incompatibility genes (het genes) whose products recognize different alleles of the het-c gene via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here we demonstrate that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic het-d and het-e incompatibility reactions. Protein structure models suggest that their WD40 domain folds into two 7-blade β-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular het-e allele does not have an incompatibility reaction with common het-c alleles, despite being 11-repeats long. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of het NLRs, while also highlighting both the fragility and the flexibility of β-propellers as immune sensor domains.

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism.

Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4's AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4's β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates. NMR and X-ray scattering (SAXS) solution measurements, mutational analyses, and biochemistry show that the substrate-mimicking AIF-interaction domain shields CHCHD4's redox-sensitive active site. Disrupting this shield critically activates CHCHD4 substrate affinity and chaperone activity. Regulatory-domain sequestration by NADH-activated AIF directly stimulates chaperone binding and folding, revealing how AIF mediates CHCHD4 mitochondrial import. These results establish AIF as an integral component of the metazoan disulfide relay and point to NADH-activated dimeric AIF as an organizational import center for CHCHD4 and its substrates. Importantly, AIF regulation of CHCHD4 directly links AIF's cellular NAD(H) sensing to CHCHD4 chaperone function, suggesting a mechanism to balance tissue-specific oxidative phosphorylation (OXPHOS) capacity with NADH availability.

Ribotyping Staphylococcus epidermidis Using Probabilistic Sequence Analysis and Levenshtein Distance Algorithm

Staphylococcus epidermidis (S. epidermidis) live in different human locations and natural environments. For ribotyping S. epidermidis sub-species, 2507 PCR-amplified reads of 16S rRNA genes of S. epidermidis in a public dataset were used for probabilistic sequence analysis. A sequence probability logo (sequence pLogo) as a reference sequence of 16S rRNA genes of S. epidermidis was constructed. Through implementation of Levenshtein Distance algorithm, two 20-base pairs (bp) motifs, commonly present in 2507 PCR-amplified reads, were identified. The top 38 S. epidermidis isolates, which carried 16S rRNA nucleotide domains that were made of different sequences but have high similarity scores to two 20-bp motifs, were found from 11 human, 8 animal, 9 plant and 10 environmental samples, indicating that these two 20-bp motifs were broadly present in diverse S. epidermidis isolates. Thirty-one PCR-amplified reads of 16S rRNA genes, which were currently not in the dataset, were utilized to verify the feasibility of using two 20-bp motifs for ribotyping S. epidermidis sub-species. S. epidermidis S1, S3, but not S2, isolates on the human scalp carried a 20-bp sequence domain with high similarities to a 20-bp motif in the sequence pLogo. The phylogenetic tree showed that S. epidermidis S1, S2 and S3 were not from a single common ancestor. Two newly identified 20-bp motifs here, thus, provided reference nucleotide residues for ribotyping S. epidermidis.

Noise Elimination for Wide Field Electromagnetic Data via Improved Dung Beetle Optimized Gated Recurrent Unit

Noise profoundly affects the quality of electromagnetic data, and selecting the appropriate hyperparameters for machine learning models poses a significant challenge. Consequently, the current machine learning denoising techniques fall short in delivering precise processing of Wide Field Electromagnetic Method (WFEM) data. To eliminate the noise, this paper presents an electromagnetic data denoising approach based on the improved dung beetle optimized (IDBO) gated recurrent unit (GRU) and its application. Firstly, Spatial Pyramid Matching (SPM) chaotic mapping, variable spiral strategy, Levy flight mechanism, and adaptive T-distribution variation perturbation strategy were utilized to enhance the DBO algorithm. Subsequently, the mean square error is employed as the fitness of the IDBO algorithm to achieve the hyperparameter optimization of the GRU algorithm. Finally, the IDBO-GRU method is applied to the denoising processing of WFEM data. Experiments demonstrate that the optimization capacity of the IDBO algorithm is conspicuously superior to other intelligent optimization algorithms, and the IDBO-GRU algorithm surpasses the probabilistic neural network (PNN) and the GRU algorithm in the denoising accuracy of WFEM data. Moreover, the time domain of the processed WFEM data is more in line with periodic signal characteristics, its overall data quality is significantly enhanced, and the electric field curve is more stable. Therefore, the IDBO-GRU is more adept at processing the time domain sequence, and the application results also validate that the proposed method can offer technical support for electromagnetic inversion interpretation.

Ig or Not Ig? That Is the Question: The Nucleating Supersecondary Structure of the Ig-Fold and the Extended Ig Universe.

Observing the omnipresence of the Ig-fold in all domains of life, one may wonder why this fold among all is such a wunderkind of evolution. Culminating in vertebrates, it enables a myriad of functions at the heart of the immune, nervous, vascular, and muscular systems. We suggest the Ig-fold resilience lies in the robust folding of a core supersecondary structure (SSS) that can accommodate a myriad of topological variations. In this chapter, we focus on the core supersecondary structure common to all topostructural variants of the Ig-fold and will see that this pattern can also be found in other β-sandwich folds. It represents a highly resilient central SSS that accommodates a very high plasticity observed among β-sandwiches. We have recently developed a universal numbering system to identify and annotate Ig-domains, Ig-like domains, and what we now call Ig-extended domains, i.e., β-sandwiches that contain and extend the Ig-fold topology (to be published). A universal numbering scheme, common to all topological and structural variants of any domain sharing the Ig-fold, allows a direct comparison of any Ig, Ig-like, and Ig-extended domain in sequence, topology, and structure. This can therefore help understand the robust patterns in Ig-folding and interactions with other Ig or non-Ig proteins, as well as help trace evolutionary patterns of immunoglobulin domains. The universal numbering scheme, called IgStrand, is now at the heart of an algorithm that can label secondary structure elements of the Ig-fold for any topological variant. It is implemented in the open-source web-based iCn3D program from NCBI (Wang, Youkharibache, Zhang, Lanczycki, Geer, Madej, Phan, Ward, Lu, Marchler, Bioinformatics 36:131-135, 2020). Interestingly, that algorithm captures SSS homologies across a very large spectrum of β-sandwiches, and one can envision classifying numerous such sandwiches as "Ig-extended" domains and their variable topological arrangements. In this chapter, we go through examples of Ig, Ig-like, and Ig-extended domains as in a journey through cells: in the cell nucleus, in the cytoplasm, or on extracellular regions of cell surface receptors, and in viruses.

Beta Sandwich-Like Folds: Sequences, Contacts, Classification of Invariant Substructures and Beta Sandwich Protein Grammar.

This chapter addresses the following fundamental question: Do sequences of protein domains with sandwich architecture have common sequence characteristics even though they belong to different superfamilies and folds? The analysis was carried out in two stages: (1) determination of domain substructures shared by all sandwich proteins and (2) detection of common sequence characteristics within the substructures. Analysis of supersecondary structures in domains of proteins revealed two types of four-strand substructures that are common to sandwich proteins. At least one of these common substructures was found in proteins of 42 sandwich-like folds (per structural classification in the CATH database). A comparison of sequence fragments and residue-residue contacts constituting common substructures revealed specific distributions of hydrophobic residues in these chains. The shared sequences and structural characteristics can be conceptualized as the "grammatical rules of beta protein linguistics." Understanding the structural and sequence commonalities of sandwich proteins may prove useful for rational protein design.

Isolating high-quality RNA for RNA-Seq from 10-year-old blood samples

There is much interest in analysing RNA, particularly with RNA Sequencing, across both research and diagnostic domains. However, its inherent instability renders it susceptible to degradation. Given the imperative for RNA integrity in such applications, proper storage and biobanking of blood samples and successful subsequent RNA isolation is essential to guarantee optimal integrity for downstream analyses. Especially for larger collections, it would be particularly beneficial if these methods would additionally offer affordability, minimal blood volume requirements and also long-term storage. In this study, RNA of high quality, suitable for transcriptomics, has been successfully isolated from 400 µL of EDTA and citrated whole blood samples in Boom’s lysis buffer stored at −85 °C for 10 years. Isolation was carried out using a modified Zymo Research Quick-RNA kit protocol. This isolation method showed significant improvement in RNA integrity when compared to RNA extracted using the original Boom method. RNA Sequencing provided high-quality data comparable to that of other studies using recently frozen blood in RNA stabilisation tubes. Additionally, sequencing data from blood collected in citrate and EDTA anticoagulants also showed excellent correlation.

Optimizing encephalomyocarditis virus VP1 protein assembly on pseudorabies virus envelope via US9 protein anchoring

ABSTRACT Live herpesvirus-vectored vaccines are critical in veterinary medicine, but they can sometimes offer insufficient protection due to suboptimal antigen expression or localization. Encephalomyocarditis virus (EMCV) is a significant zoonotic threat, with VP1 protein as a key immunogen on its capsid. To enhance immunogenicity, we explored the use of recombinant pseudorabies virus (rPRV) as a vaccine vector against EMCV. In silico analysis indicated that fusing VP1 with US9 enhances the formation of a type II transmembrane heterodimer. We constructed six rPRV groups expressing different VP1 variants and found that VP1 fused with US9’s C-terminal (US9-VP1) enhances VP1’s membrane localization and its incorporation into the PRV envelope, unlike wild-type VP1. Immunogold electron microscopy illustrated that rPRV with deleted US8 and US9, supplemented with US8 regulatory sequence (rΔ89-U9VP1), improved VP1 incorporation into the viral envelope. Post-immunization, only rΔ89-U9VP1 provided 100% protection against EMCV in mice and induced high levels of virus-neutralizing antibodies in piglets. Additionally, rPRV expressing VP1 stimulated robust T-cell responses, as demonstrated by flow cytometry and ELISpot assays. This study introduces rPRV as a potential EMCV vaccine, demonstrating that the selection of the US9 C-terminal domain and US8 regulatory sequence significantly enhances the presentation of heterologous antigens, improving vaccine efficacy.

Toward a Complete Elucidation of the Primary Structure-Activity in Pentaerythritol-Based One-Component Ionizable Amphiphilic Janus Dendrimers for In Vivo Delivery of Luc-mRNA.

Four-component lipid nanoparticles (LNPs) and viral vectors are key for mRNA vaccine and therapeutics delivery. LNPs contain ionizable lipids, phospholipids, cholesterol, and polyethylene glycol (PEG)-conjugated lipids and deliver mRNA for COVID-19 vaccines to liver when injected intravenously or intramuscularly. In 2021, we elaborated one-component ionizable amphiphilic Janus dendrimers (IAJDs) accessing targeted delivery of mRNA. Simplified synthesis and assembly processes allow for rapid IAJD screening for discovery. The role of the primary structure of IAJDs in activity indicated, with preliminary investigations, that ionizable amine (IA), sequence, and architecture of hydrophilic and hydrophobic domains are important for in vivo targeted delivery. Here, we study the role of the interconnecting linker length between the IA and the hydrophobic domain of pentaerythritol-based IAJDs. The linker length determines, through inductive effects, the position of the IA and the pKa of the IAJDs and through flexibility, the stability of the DNPs, highlighting their extraordinarily important role in effective targeted delivery.

Functional Characterization of FgAsp, a Gene Coding an Aspartic Acid Protease in Fusarium graminearum.

Aspartic proteases (APs), hydrolases with aspartic acid residues as catalytic active sites, are closely associated with processes such as plant growth and development and fungal and bacterial pathogenesis. F. graminearum is the dominant pathogenic fungus that causes Fusarium head blight (FHB) in wheat. However, the relationship of APs to the growth, development, and pathogenesis of F. graminearum is not clear. Therefore, we selected the FGSG_09558 gene, whose function annotation is aspartate protease, for further study. In this study, FGSG_09558 was found to contain a conserved structural domain and signal peptide sequence of aspartic acid protease and was therefore named FgAsp. The function of FgAsp in F. graminearum was investigated by constructing the knockout and complementation mutants of this gene. The results showed that with respect to the wild type (PH-1), the knockout mutant showed a significant reduction in mycelial growth, asexual spore production, and sexual spore formation, highlighting the key role of FgAsp in the growth and development of F. graminearum. In addition, the mutants showed a significant reduction in the virulence and accumulation level of deoxynivalenol (DON) content on maize whiskers, wheat germ sheaths, and wheat ears. DON, as a key factor of virulence, plays an important role in the F. graminearum infection of wheat ears, suggesting that FgAsp is involved in the regulation of F. graminearum pathogenicity by affecting the accumulation of the DON toxin. FgAsp had a significant effect on the ability of F. graminearum to utilize various sugars, especially arabinose. In response to the stress, hydrogen peroxide inhibited the growth of the mutant most significantly, indicating the important function of FgAsp in the strain's response to environmental stress. Finally, FgAsp plays a key role in the regulation of F. graminearum growth and development, pathogenicity, and environmental stress response.

Rational design yields RNA-binding zinc finger domains with altered sequence specificity.

Targeting and manipulating endogenous RNAs in a sequence-specific manner is essential for both understanding RNA biology and developing RNA-targeting therapeutics. RNA-binding zinc fingers (ZnFs) are excellent candidates as designer proteins to expand the RNA-targeting toolbox, due to their compact size and modular sequence recognition. Currently, little is known about how the sequence of RNA-binding ZnF domains governs their binding site specificity. Here, we systematically introduced mutations at the RNA-contacting residues of a well-characterized RNA-binding ZnF protein, ZRANB2, and measured RNA binding of mutant ZnFs using a modified RNA-bind-n-seq (RBNS) assay. We identified mutant ZnFs with an altered sequence specificity, preferring to bind a GGG motif instead of the GGU preferred by wild-type ZRANB2. Further, through a series of all-atom molecular dynamics (MD) simulations with ZRANB2 and RNA, we characterized changes in the hydrogen-bond network between the protein and RNA that underlie the observed sequence specificity changes. Our analysis of ZRANB2-RNA interactions both in vitro and in silico expands the understanding of ZnF-RNA recognition rules and serves as a foundation for eventual use of RNA-binding ZnFs for programmable RNA targeting.

Structural bioinformatic study of six human olfactory receptors and their AlphaFold3 predicted water-soluble QTY variants and OR1A2 with an odorant octanoate and TAAR9 with spermidine

Abstract The molecular mechanism of olfaction, namely, how we smell with limited olfactory receptors to recognize exceedingly diverse and large numbers of scents remains unknown despite the recent advances in chemistry, chemical, structural, and molecular biology. Olfactory receptors are notoriously difficult to study because they are fully embedded in the cell membrane. After decades of efforts and significant funding, there are only three olfactory receptor structures known. To understand olfaction, we carried out the structural bioinformatic study of six human olfactory receptors including OR51E1, OR51E2, OR52cs, OR1A1, OR1A2, TAAR9, and their AlphaFold3 predicted water-soluble QTY variants with odorants. We applied the QTY code to replace leucine (L) with glutamine (Q), isoleucine (I) and valine (V) with threonine (T), and phenylalanine (F) with tyrosine (Y) only in the transmembrane helices. Therefore, these QTY variants become water-soluble. We also present the superimposed structures of native olfactory receptors and their water-soluble QTY variants. The superimposed structures show remarkable similarity with RMSDs between 0.441 and 1.275 Å despite significant changes to the protein sequence of the transmembrane domains (43.03%–50.31%). We also show the differences in hydrophobicity surfaces between the native olfactory receptors and their QTY variants. Furthermore, we also used AlphaFold3 and molecular dynamics to study the odorant octanoate with OR1A2 and spermidine with TAAR9. Our bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices, and will likely further stimulate designs of water-soluble integral transmembrane proteins and other aggregated proteins.

An Evaluation of the Cellular and Humoral Response of a Multi-Epitope Vaccine Candidate Against COVID-19 with Different Alum Adjuvants.

SARS-CoV-2 (Betacoronavirus pandemicum) is responsible for the disease identified by the World Health Organization (WHO) as COVID-19. We designed "CHIVAX 2.1", a multi-epitope vaccine, containing ten immunogenic peptides with conserved B-cell and T-cell epitopes in the receceptor binding domain (RBD) sequences of different SARS-CoV-2 variants of concern (VoCs). We evaluated the immune response of mice immunized with 20 or 60 µg of the chimeric protein with two different alum adjuvants (Alhydrogel® and Adju-Phos®), plus PHAD®, in a two-immunization regimen (0 and 21 days). Serum samples were collected on days 0, 21, 31, and 72 post first immunization, with antibody titers determined by indirect ELISA, while lymphoproliferation assays and cytokine production were evaluated by flow cytometry. The presence of neutralizing antibodies was assessed by surrogate neutralization assays. Higher titers of total IgG, IgG1, and IgG2a antibodies, as well as increased proliferation rates of specific CD4+ and CD8+ T cells, were observed in mice immunized with 60 μg of protein plus Adju-Phos®/PHAD®. This formulation also generated the highest levels of TNF-α and IFN-γ, in addition to the presence of neutralizing antibodies against Delta and Omicron VoC. These findings indicate the potential of this chimeric multi-epitope vaccine with combined adjuvants as a promising platform against viral infections, eliciting a TH1 or TH1:TH2 balanced cell response.

A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice.

The continued emergence of SARS-CoV-2 variants and the threat of future Sarbecovirus zoonoses have spurred the design of vaccines that can induce broad immunity against multiple coronaviruses. Here, we use computational methods to infer ancestral phylogenetic reconstructions of receptor binding domain (RBD) sequences across multiple Sarbecovirus clades and incorporate them into a multivalent adenoviral-vectored vaccine. Mice immunized with this pan-Sarbecovirus vaccine are protected in the upper and lower respiratory tracts against infection by historical and contemporary SARS-CoV-2 variants, SARS-CoV, and pre-emergent SHC014 and Pangolin/GD coronavirus strains. Using genetic and immunological approaches, we demonstrate that vaccine-induced protection unexpectedly is conferred principally by CD4+ and CD8+ Tcell-mediated anamnestic responses. Importantly, prior mRNA vaccination or SARS-CoV-2 respiratory infection does not alter the efficacy of the mucosally delivered pan-Sarbecovirus vaccine. These data highlight the promise of a phylogenetic approach for antigen and vaccine design against existing and pre-emergent Sarbecoviruses with pandemic potential.

Evolution of CEACAM pathogen decoy receptors inprimates.

CEACAM1 in leukocytes controls cell activation during inflammation. This and its expression in epithelial cells led to frequent independent appropriation of CEACAM1 as receptor by pathogens in humans and other species to gain host access and to downregulate its immune response. As a countermeasure, decoy receptors with CEACAM1-like pathogen-binding domains evolved. The granulocyte-specific human CEACAM3 endocytic receptor diverts CEACAM1-binding pathogens to neutrophils for internalization and destruction. The role of the glycosylphosphatidylinositol-anchored CEACAM5 and CEACAM6 which can also bind CEACAM1-targeting pathogens in humans is less clear. We analyzed the selection of CEACAMs to avoid pathogen binding and to maintain similarity between pathogen receptors and decoy receptors in 148 primate species. Notably, functional CEACAM3 genes were not found in gibbons and New World monkeys. Interestingly, CEACAM6 in these primates exhibits similar high ratios of rates of nonsynonymous and synonymous substitution (dN/dS) in their pathogen-binding N domain exons as found for CEACAM1. High dN/dS ratios are indicative of selection for diversification typically seen in pathogen receptors. Human CEACAM6 is expressed on granulocytes and epithelial cells. Therefore, CEACAM6 could substitute for the missing endocytic receptor CEACAM3. In nearly all investigated primate groups also N exons of the epithelially expressed CEACAM5 exhibit selection for diversification. In African populations, five high-frequency polymorphisms are observed in the pathogen-binding region of CEACAM5 (I80V, V83A, I100T, I112V, I113T) with 3-4 polymorphisms combined in the same individual. These polymorphisms correspond to CEACAM1 pathogen-binding domain sequences. The glycosylphosphatidylinositol-anchored CEACAM5 and CEACAM6 are under selection to maintain similarity to the pathogen receptor CEACAM1 in most primate species, indicating a function as decoy receptors.

Exploring the biosynthesis potential of permafrost microbiomes

BackgroundPermafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.ResultsPermafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.ConclusionWe have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.