Nonadditivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the ...importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds.
To answer this question, we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways using this fitness profile, we were able to characterize the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (ΔΔGU). This enabled determination of the importance of stability effects in functional epistasis.
Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis.
•A double-mutant affinity screen enabled quantitation of ΔΔG folding•Strong negative epistasis mostly results from two destabilizing substitutions•A conformationally dynamic group of residues displays pervasive positive epistasis•Cryptically beneficial substitutions are found at 43 of 55 positions in GB1
Olson et al. analyzed how the first two steps of all mutational pathways alter the affinity of GB1 for IgG, thereby quantifying pairwise epistasis. While strong epistasis is rare, numerous cryptically beneficial substitutions are found in alternative mutational backgrounds. Thus, epistasis expands the fraction of sequence space that is functional.
Immediately from the outset of the COVID-19 pandemic, researchers from diverse biomedical and biological disciplines have united to study the novel pandemic virus, SARS-CoV-2. The antibody response ...to SARS-CoV-2 has been a major focus of COVID-19 research due to its clinical relevance and importance in vaccine and therapeutic development. Isolation and characterization of antibodies to SARS-CoV-2 have been accumulating at an unprecedented pace. Most of the SARS-CoV-2 neutralizing antibodies to date target the spike (S) protein receptor binding domain (RBD), which engages the host receptor ACE2 for viral entry. Here we review the binding sites and molecular features of monoclonal antibodies that target the SARS-CoV-2 RBD, including a few that also cross-neutralize SARS-CoV.
•The receptor binding domain is a major target of antibodies to SARS-CoV-2.•Neutralizing antibodies target various epitopes on the receptor binding domain.•Convergent antibody responses to SARS-CoV-2 are observed.•Cross-neutralization of SARS-CoV-2 and SARS-CoV maps to two RBD epitopes.•Antibody avidity can be crucial for neutralization potency against SARS-CoV-2.
Plastic pollution is a global environmental concern. In particular, the endocrine‐disrupting chemical bisphenol A (BPA) is nearly ubiquitous in aquatic environments globally, and it continues to be ...produced and released into the environment in large quantities. BPA disrupts hormone signalling and can thereby have far‐reaching physiological and ecological consequences. However, it is not clear whether BPA has consistent effects across biological traits and phylogenetic groups. Hence, the aim of this study was to establish the current state of knowledge of the effect of BPA in aquatic organisms. We show that overall BPA exposure affected aquatic organisms negatively. It increased abnormalities, altered behaviour and had negative effects on the cardiovascular system, development, growth and survival. Early life stages were the most sensitive to BPA exposure in invertebrates and vertebrates, and invertebrates and amphibians seem to be particularly affected. These data provide a context for management efforts in the face of increasing plastic pollution. However, data availability is highly biased with respect to taxonomic groups and traits studies, and in the geographical distribution of sample collection. The latter is the case for both measurements of the biological responses and assessing pollution levels in water ways. Future research effort should be directed towards biological systems, such as studying endocrine disruption directly, and geographical areas (particularly in Africa and Asia) which we identify to be currently undersampled.
Plastic pollution is a global environmental concern. In particular, bisphenol A (BPA) is nearly ubiquitous in all aquatic environments. BPA disrupts hormone signalling and can thereby have far‐reaching physiological and ecological consequences. This study aimed to establish the current state‐of‐knowledge on global environmental BPA levels and their effects on aquatic organisms. We show that BPA exposure affected a myriad of biological functions in aquatic organisms. Early life stages were the most sensitive to BPA exposure, and invertebrates and amphibians seem to be particularly affected. Our meta‐analysis identified important gaps in knowledge and we suggest future research directions.
The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in ...effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passaging. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Influenza virus evolves rapidly to constantly escape from natural immunity. Most humoral immune responses to influenza virus target the hemagglutinin (HA) glycoprotein, which is the major antigen on ...the surface of the virus. The HA is composed of a globular head domain for receptor binding and a stem domain for membrane fusion. The major antigenic sites of HA are located in the globular head subdomain, which is highly tolerant of amino acid substitutions and continual addition of glycosylation sites. Nonetheless, the evolution of the receptor-binding site and the stem region on HA is severely constrained by their functional roles in engaging the host receptor and in mediating membrane fusion, respectively. Here, we review how broadly neutralizing antibodies (bnAbs) exploit these evolutionary constraints to protect against diverse influenza strains. We also discuss the emerging role of other epitopes that are conserved only in subsets of viruses. This rapidly increasing knowledge of the evolutionary biology, immunology, structural biology, and virology of influenza virus is invaluable for development and design of more universal influenza vaccines and novel therapeutics.
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•Antigenic variation is a major challenge for influenza vaccine design.•Comprehending evolutionary constraints for influenza function is critical for vaccine development.•Broadly neutralizing antibodies reveal conserved epitopes.•Eliciting long-term heterosubtypic immunity is the ultimate goal for vaccine design.
The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has now become a pandemic, but there is currently very little understanding ...of the antigenicity of the virus. We therefore determined the crystal structure of CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient, in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein at 3.1-angstrom resolution. CR3022 targets a highly conserved epitope, distal from the receptor binding site, that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding epitope can only be accessed by CR3022 when at least two RBDs on the trimeric S protein are in the "up" conformation and slightly rotated. These results provide molecular insights into antibody recognition of SARS-CoV-2.
The progression of infectious disease depends on the intensity of and sensitivity to pathogen infection. Understanding commonalities in trait sensitivity to pathogen infection across studies through ...meta‐analytic approaches could provide insight to the pathogenesis of infectious diseases. The globally devastating amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), offers a good case system due to the widely available dataset on disruption to functional traits across species.
Here, I systematically conducted a phylogenetically controlled meta‐analysis to test how infection intensity affects different functional traits (e.g. behaviour, physiology, morphology, reproduction) and the survival in amphibians infected with Bd.
There was a consistent effect of Bd infection on energy metabolism, while traits related to body condition, osmoregulation, and behaviour generally decreased with Bd infection. Skin integrity, hormone levels, and osmoregulation were most sensitive to Bd infection (minimum Bd load ln 2.5 zoospore equivalent), while higher minimum Bd loads were required to influence reproduction (ln 10.6 zoospore equivalent). Mortality differed between life stages, where juvenile mortality was dependent on infection intensity and exposure duration, while adult mortality was dependent on infection intensity only. Importantly, there were strong biases for studies on immune response, body condition and survival, while locomotor capacity, energy metabolism and cardiovascular traits were lacking.
The influence of pathogen load on functional disruption can help inform pathogen thresholds before the onset of irreversible damage and mortality. Meta‐analytic approaches can provide quantitative assessment across studies to reveal commonalities, differences and biases of panzootic diseases, especially for understanding the ecological relevance of disease impact.
Read the free Plain Language Summary for this article on the Journal blog.
Read the free Plain Language Summary for this article on the Journal blog.
Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 ...anti-SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53-neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)-binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.
Cellular lipid requirements are achieved through a combination of biosynthesis and import programs. Using isotope tracer analysis, we show that type I interferon (IFN) signaling shifts the balance of ...these programs by decreasing synthesis and increasing import of cholesterol and long chain fatty acids. Genetically enforcing this metabolic shift in macrophages is sufficient to render mice resistant to viral challenge, demonstrating the importance of reprogramming the balance of these two metabolic pathways in vivo. Unexpectedly, mechanistic studies reveal that limiting flux through the cholesterol biosynthetic pathway spontaneously engages a type I IFN response in a STING-dependent manner. The upregulation of type I IFNs was traced to a decrease in the pool size of synthesized cholesterol and could be inhibited by replenishing cells with free cholesterol. Taken together, these studies delineate a metabolic-inflammatory circuit that links perturbations in cholesterol biosynthesis with activation of innate immunity.
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•Identification of a cholesterol metabolism-type I interferon (IFN) inflammatory circuit•Type I interferon reprograms cholesterol homeostasis•Perturbing cholesterol synthesis engages type I IFN signaling•STING/TBK1 links cholesterol metabolism with type I interferon pathway
Cholesterol metabolism and type I interferon response are co-regulated in macrophages, creating an immuno-metabolic circuit that allows innate immune cells to coordinate metabolism changes with immune activation required for antiviral responses.
Abstract
The recently discovered layered kagome metals AV
3
Sb
5
(A = K, Rb, Cs) exhibit diverse correlated phenomena, which are intertwined with a topological electronic structure with multiple van ...Hove singularities (VHSs) in the vicinity of the Fermi level. As the VHSs with their large density of states enhance correlation effects, it is of crucial importance to determine their nature and properties. Here, we combine polarization-dependent angle-resolved photoemission spectroscopy with density functional theory to directly reveal the sublattice properties of
3d
-orbital VHSs in CsV
3
Sb
5
. Four VHSs are identified around the M point and three of them are close to the Fermi level, with two having sublattice-pure and one sublattice-mixed nature. Remarkably, the VHS just below the Fermi level displays an extremely flat dispersion along MK, establishing the experimental discovery of higher-order VHS. The characteristic intensity modulation of Dirac cones around K further demonstrates the sublattice interference embedded in the kagome Fermiology. The crucial insights into the electronic structure, revealed by our work, provide a solid starting point for the understanding of the intriguing correlation phenomena in the kagome metals AV
3
Sb
5
.
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