Biology subjects

Ricci, F.

Publications and source records attributed to Ricci, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Microorganisms consume trace gases present throughout the Mariana Trench water column

Dark waters harbour two-thirds of the ocean's bacterial and archaeal cells, yet the energy sources sustaining microbial life at these depths remain poorly understood. Here we integrate hydrographic profiles with metagenomic analyses and ex situ activity measurements to investigate whether carbon monoxide (CO) and molecular hydrogen (H2) are viable energy sources for epipelagic and mesopelagic microbial populations in the Mariana Trench region. Both gases were detected from 5 to 9,371 m, with concentrations generally higher in the photic zone but anomalously high in several deeper waters. Metagenomic analyses indicate a shift from phototrophic towards lithotrophic energy acquisition with depth. Microbial populations encoding CO dehydrogenases increased from 6.1% at 5 m to 45% at 1,000 m, while those encoding uptake hydrogenases were much less abundant, but increased from 0.34% to 0.63%. Ex situ incubations revealed that in situ cell-specific CO oxidation rates declined with depth, whereas corresponding H2 oxidation rates were significantly higher at 1,000 m than at the surface. At 1,000 m, cell-specific H2 oxidation rates were approximately 4,500-fold higher than those of CO. These contrasting trends suggest that CO oxidation is a widespread auxiliary energy-acquisition strategy, whereas H2 oxidation may sustain hydrogenotrophic growth in dark waters. Together, our results suggest H2 and CO are readily available to pelagic microbial populations and are biologically oxidised in the dark zone, supporting microbial energy acquisition and oceanic biogeochemical cycling.

microbiology↗

bioRxiv2026

Light-harvesting strategies and competition drive niche partitioning among Ostreobium lineages in the spectral architecture of the coral reef

Ostreobium, a siphonous green alga capable of living inside of calcium carbonate substrates, including the skeletons of reef-building corals. This study investigates spectral niche preferences and physiological strategies of Ostreobium using community-wide experiments. We exposed natural Ostreobium communities from Porites lutea collected across shallow, mid, and deeper-water sites to three light conditions: far-red, blue, and white light, simulating healthy shallow-water corals, deeper water conditions, and bleached coral skeletons respectively. Using 16S rRNA metabarcoding and chlorophyll analysis, we assessed community changes and physiological responses over 16 weeks. We show significant variation in spectral preferences among Ostreobium OTUs, with clear evidence for both generalist and specialist strategies. Chlorophyll analysis showed photoacclimation responses through changes in pigment compositions. Our work shows that the spectral architecture of the reef plays a role in structuring Ostreobium communities, but the many mismatches between spectral preferences of OTUs and their observed presence in nature, suggests that inter-species competition is likely to be an even stronger contributor to community structure across the reefs microhabitats. We show that physiological heterogeneity within Ostreobium is strongly phylogenetically structured, and our results clearly highlight the importance of considering OTU-level differences when predicting community responses to environmental disturbances such as coral bleaching. While generalist OTUs dominate natural communities, these do poorly in incubations, and we hypothesise that white light specialists may become key players during coral bleaching events. Our work is a substantial advance in our understanding of Ostreobium ecology and provides a framework for interpreting future environmental sequencing data, offering insights into the functional roles of the different OTUs.

ecology↗

bioRxiv2026

Structural and dynamic embedding of the mouse functional connectome revealed by functional ultrasound imaging (fUSI)

Functional ultrasound imaging (fUSI) is an emerging hemodynamic neuroimaging modality whose potential for connectome-scale network mapping remains largely untested. Here, we establish a non-invasive transcranial fUSI protocol and an fMRI-inspired preprocessing framework that enable robust resting-state functional connectomics in the mouse. We show that fUSI resolves canonical brain-wide cortical and subcortical networks with high spatial concordance to fMRI, including a default-mode (DMN) and a laterocortical network. Notably, fUSI networks are robustly embedded within the structural connectome, with structure-function coupling being parsimoniously described by four dominant axes that differentially relate functional systems to known anatomical substrates. We also show that, beyond static organization, fUSI reproduces hallmark resting state fMRI dynamics, including dominant anti-correlated coactivation patterns (CAPs) and a structured transition architecture that converges onto three stable attractor modes. Together, these results establish transcranial fUSI as a portable and scalable complement to fMRI for connectome-scale mapping of mouse brain networks.

neuroscience↗

bioRxiv2025

Flavobacteria buffer nitrous oxide emissions from partial denitrifiers in coastal sediments

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling revealed both clade II nosZ flavobacterial isolates and whole sand communities exhibit a low affinity for N2O, contrary to previous reports that clade II N2O reducers generally have a high substrate affinity. This indicates adaptation to the high residence times of N2O within production and consumption zones in the sands. Collectively, these N2O reducers remove most N2O produced in permeable sediments, supporting lower-than-expected coastal emissions predicted by biogeochemical models. We conclude that permeable sediments host specialised microbial communities that mitigate N2O emissions and buffer marine nitrogen cycling amid rising nutrient pollution.

microbiology↗

bioRxiv2025

Integrated cross-sectoral surveillance of antimicrobial resistance genotypes and phenotypes across disparate reservoirs

Antimicrobial-resistant (AMR) bacteria and genes are continually exchanged among humans, animals, and environmental reservoirs. Disparate and siloed surveillance methods present a major challenge for tracing and disrupting AMR transmission, with clinical monitoring focusing on detecting specific pathogens or specific genes of interest, and environmental surveys often relying on inferences drawn from indicator organisms. Here, we demonstrate that, following sample-specific pre-processing, common surveillance approaches can be applied consistently to profile AMR abundance, distribution, and phenotypes across diverse reservoirs, including soil, sediment, water, wastewater, and faecal samples from both urban and agricultural settings. Across all sample types, three core methods provided complementary insights: (i) quantitative PCR (qPCR) arrays to measure multiple AMR genes, (ii) gene- and genome-centric metagenomics for comprehensive resistome profiling, and (iii) culture-based genomics with susceptibility testing to link genotypes to phenotypes. We applied this approach to profile 1,032 metagenome-assembled genomes, 66 bacterial isolate genomes, and 78 and 6,442 AMR genes/reference sequences via qPCR and metagenomics, respectively. This integrated framework revealed a moderate prevalence but high diversity of resistance mechanisms in both pathogens and non-pathogenic bacteria with potentially transmissible genes, with wastewater especially enriched in AMR genes. We detected mismatches between genotype and phenotype predictions and a prevalence of intermediate resistance phenotypes, highlighting how many mechanisms of environmental resistance remain poorly understood. Overall, this study demonstrates that unified field-leading surveillance methods can be extended beyond clinical contexts into diverse environmental and animal samples, while highlighting that multiple methods are needed to capture the diverse AMR genotypes and phenotypes in these settings to enable comprehensive monitoring and adaptive solutions to restrict transmission.

microbiology↗

bioRxiv2025

Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem

Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of sedimentary microorganisms within a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across its entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.

ecology↗

bioRxiv2025

Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges

Polar desert soils host diverse microbial communities despite limited nutrients and frequent temperature and light fluctuations. Adapting to these extremes, most bacteria possess high-affinity hydrogenases and carbon monoxide dehydrogenases, enabling them to use atmospheric trace gases such as hydrogen (H2) and carbon monoxide (CO) to generate energy and fix carbon. Despite the foundational importance of this process in polar desert ecosystems, little is known about the thermal sensitivity of trace gas oxidation or how this process will respond to climate warming. Here, we show through in situ and ex situ incubations that H2 consumption is an exceptionally thermally resilient process that can occur from -20 to +75{degrees}C, at rates comparable to temperate ecosystems (peaking at 8.56 nmol H2 h-1 g dry soil-1 at 25{degrees}C). Temperature ranges of CO (-20 to 42{degrees}C) and CH4 (-20 to 30{degrees}C) oxidation are also wider than expected, though the pattern of thermal sensitivity conforms with general theory. Metagenomic analyses support these data, revealing that atmospheric H2 and CO oxidisers are widespread, diverse, and abundant, and suggesting most Antarctic bacteria function below their temperature optima for these processes. Modelling of seasonal temperatures across ice-free Antarctica under current and future emissions scenarios indicates that H2 and CO oxidation can occur year-round, increasing by up to 35% or 44%, respectively, by 2100. Our results indicate constitutive aerotrophic activity contributing to Antarctic ecosystem functioning and biodiversity across spatial and temporal scales, with further studies required to understand how it interacts with photosynthesis in a changing climate.

microbiology↗

bioRxiv2025

Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems

An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, genome-resolved metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonize both forelands and persist across soil depth and decadal chronosequences that serve as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using both organic and inorganic compounds, including atmospheric trace gases and sulfur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including photosynthetic Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation both by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable soil environment for subsequent colonisation.

microbiology↗

bioRxiv2025

Metatranscriptomics sheds light on 'who is doing what' in the coral Porites lutea

Global decline of coral reefs due to climate change necessitates nature-based protection strategies for these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions occurring within the coral holobiont. Using RNAseq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides first transcriptomic evidence of Ostreobiums ability to transfer fixed carbon to other holobiont members and the coral host. Additionally, we highlight critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour distinct microbiomes with wide-ranging functions.

microbiology↗

bioRxiv2025

Abundant and active acetogens enhance the carbon dioxide sink of Blue Carbon ecosystems

Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO2) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal for chemosynthetic microbes such as acetogens. Here, we show that acetogens are abundant and active mediators of carbon sequestration in tidal wetland soils by pairing gene-and genome-resolved metagenomic analysis with isolation and analysis of gas-fermenting acetogens in bioreactors. Metagenomic profiling revealed that diverse microbes can mediate carbon fixation, primarily through the Calvin-Benson-Bassham cycle and Wood-Ljungdahl pathways. These include various bacteria and archaea capable of reductive acetogenesis. On this basis, we grew bacterial enrichment cultures from tidal wetland soils using the gases hydrogen and CO2 as the sole energy and carbon sources. Bioreactor analysis revealed that these enrichments are dominated by clostridial acetogens that grow rapidly by converting CO2 into acetate and other products. Collectively, these results reveal Blue Carbon ecosystems harbour communities that can exclusively subsist by using CO2 as their sole electron acceptor and for carbon fixation, thereby providing evidence of a novel carbon sink pathway within these ecosystems beyond the known mechanisms of photosynthetic carbon fixation and soil sequestration. Additionally, the discovery and isolation of these chemosynthetic communities provide opportunities for developing further mechanisms of CO2 removal through industrial gas fermentation.

microbiology↗

bioRxiv2025

Chemosynthesis enhances carbon fixation in an active microbialite ecosystem

Microbialites--carbonate structures formed under the influence of microbial action-- are the earliest macroscopic evidence of life. For three billion years, the microbial mat communities responsible for these structures fundamentally shaped Earths biogeochemical cycles. In photosynthetic microbial communities, light energy ultimately drives primary production and the ensuing cascade of daisy-chained metabolisms. However, reduced compounds such as trace gases and those released as metabolic byproducts in deeper, anoxic regions of the mat, could also fuel chemosynthetic processes. Here, we investigated the intricate metabolic synergies that sustain microbialite community nutrient webs. We recovered 331 genomes spanning 40 bacterial and archaeal phyla, revealing a staggering diversity fuelled by the biogeochemistry of these ecosystems. While phototrophy is an important metabolism encoded by 17% of the genomes, over half encode enzymes to harness energy from reduced compounds and 12% co-encode carbon fixation pathways, using sulfide and hydrogen as major electron donors. Consistent with these genomic predictions, we experimentally demonstrated that microbialite communities oxidise ferrous iron, ammonia, sulfide and gas substrates aerobically and anaerobically. Furthermore, carbon isotopic assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and ecosystem organic matter production alongside photosynthesis. Chemosynthesis in microbialite communities represents a complex interplay of metabolic synergies and continuous nutrient cycling, which decouples community carbon fixation from the diurnal cycle. As a result, this process mitigates the loss of organic carbon from respiration, enhancing the net productivity of these highly efficient ecosystems. SignificanceMicrobialite ecosystems are among the most ancient on Earth, having dominated the biosphere for over three billion years and persisting into the present. They serve as critical models for studying past and present Earth-biosphere interactions. In this study, we challenge the paradigm that photosynthesis is the main driver of microbialite primary productivity, emphasizing the fundamental role of chemosynthesis in the global element cycle both in modern extreme environments and throughout Earths history. Altogether, our findings provide novel insight into these unique microbial ecosystems, which may have functioned as hotspots for metabolic innovation over geological time.

microbiology↗

bioRxiv2024

Aerotolerant methanogens use seaweed and seagrass metabolites to drive marine methane emissions

Methanogenesis is classically thought to be limited to strictly anoxic environments. While oxygenated oceans are a known methane source, it is argued that methanogenesis is driven by methylphosphonate-degrading bacteria or potentially is associated to zooplankton gut microbiomes rather than by methanogenic archaea. Here we show through in situ monitoring and ex situ manipulations that methane is rapidly produced by archaea in frequently oxygenated sandy sediments. By combining biogeochemical, metagenomic, and culture-based experiments, we show this activity is driven by aerotolerant methylotrophic methanogens (Methanococcoides spp.) broadly distributed in surface layers of sandy sediments, providing evidence of a hidden process contributing to marine methane emissions. Moreover, we show that methane emissions are driven by methylated seaweed and seagrass metabolites, revealing an unexpected feedback loop between eutrophication-driven algal blooms and greenhouse gas emissions.

microbiology↗

bioRxiv2024

Enzyme-Responsive DNA Condensates

Membrane-less compartments and organelles are widely acknowledged for their role in regulating cellular processes, and there is an urgent need to harness their full potential as both structural and functional elements of synthetic cells. Despite rapid progress, synthetically recapitulating the nonequilibrium, spatially distributed responses of natural membrane-less organelles remain elusive. Here we demonstrate that the activity of nucleic-acid cleaving enzymes can be localised within DNA-based membrane-less compartments by sequestering the respective DNA or RNA substrates. Reaction-diffusion processes lead to complex nonequilibrium patterns, dependent on enzyme concentration. By arresting similar dynamic patterns, we spatially organise different substrates in concentric sub-compartments, which can be then selectively addressed by different enzymes, demonstrating spatial distribution of enzymatic activity. Besides advancing our ability to engineer advanced biomimetic functions in synthetic membrane-less organelles, our results may facilitate the deployment of DNA-based condensates as microbioreactors or platforms for the detection and quantitation of enzymes and nucleic acids.

synthetic biology↗

bioRxiv2024

CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflicts

Oncogene-induced replicative stress is a potent tumor-suppressive mechanism that must be kept in check for cancer cells to thrive. Thus, the identification of genes and pathways involved in replicative stress is key to understand cancer evolution and to identify prospective therapeutic targets. Here, we investigated factors that modulate replicative stress upon deregulation of the MYC oncogene. We identified the cyclin-dependent kinase CDK12 as selectively required to prevent transcription-replication conflicts and the activation of a cytotoxic DNA-damage response (DDR). At the mechanistic level, CDK12 was recruited to damaged genes by PARP-dependent DDR-signaling and elongation-competent RNAPII. Once recruited, CDK12 repressed transcription by preventing the association of CDK9 with RNAPII. Either loss or chemical inhibition of CDK12 led to DDR-resistant transcription at damaged genes. Genome-wide profiling revealed that loss of CDK12 exacerbated transcription-replication conflicts in MYC-overexpressing cells and led to the accumulation of double-strand DNA breaks (DSBs), occurring preferentially between early- replicating regions and transcribed genes, organized in a co-directional head-to-tail orientation. Overall, our data demonstrate that CDK12 protects genome integrity by repressing transcription of damaged genes, which is required for proper resolution of DSBs at oncogene-induced transcription-replication conflicts. This provides a rationale that explains both how CDK12 deficiency can promote tandem duplications of early-replicated regions during tumor evolution, and how CDK12 targeting can exacerbate replicative-stress in tumors.

cancer biology↗

bioRxiv2024

Developmental assembly of multi-component polymer systems through interconnected gene networks in vitro

Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter "nicking" and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.

synthetic biology↗

bioRxiv2022

FGF10 triggers de novo alveologenesis in a BPD model: impact on the resident mesenchymal niche cells

Bronchopulmonary dysplasia (BPD) is a neonatal lung disease developing in premature babies characterized by arrested alveologenesis and associated with decreased Fibroblast growth factor 10 (FGF10) expression. One-week hyperoxia (HYX) exposure of newborn mice leads to a permanent arrest in alveologenesis. To test the role of Fgf10 signaling to promote de novo alveologenesis following hyperoxia, we used transgenic mice allowing inducible expression of Fgf10 and recombinant FGF10 (rFGF10) protein delivered intraperitoneally. We carried out morphometry analysis, and IF on day 45. Alveolospheres assays were performed co-culturing AT2s from normoxia (NOX) with FACS-isolated Sca1Pos resident mesenchymal cells (rMC) from animals exposed to NOX, HYX+PBS, or HYX+FGF10. scRNAseq between rMC-Sca1Pos isolated from NOX and HYX+PBS were also carried out. Transgenic overexpression of Fgf10 and rFGF10 administration rescued the alveologenesis defects following HYX. Alveolosphere assays indicate that the activity of rMC-Sca1Pos is negatively impacted by HYX and partially rescued by rFGF10 treatment. Analysis by IF demonstrates a significant impact of rFGF10 on the activity of resident mesenchymal cells. scRNAseq results identified clusters expressing Fgf10, Fgf7, Pdgfra, and Axin2, which could represent the rMC niche cells for the AT2 stem cells. In conclusion, we demonstrate that rFGF10 administration is able to induce de-novo alveologenesis in a BPD mouse model and identified subpopulations of rMC-Sca1Pos niche cells potentially representing its cellular target.

cell biology↗

bioRxiv2022

Antibody affinity and concentration of convalescent sera provide context for reduced SARS-CoV-2 Omicron spike affinity of therapeutic antibodies

We assessed the affinities of the therapeutic monoclonal antibodies (mAbs) cilgavimab, tixagevimab, sotrovimab, casirivimab, and imdevimab to the receptor binding domain (RBD) of wild type, Delta, and Omicron spike. The Omicron RBD affinities of cilgavimab, tixagevimab, casirivimab, and imdevimab decreased by at least two orders of magnitude relative to their wild type equivalents, whereas sotrovimab binding was less severely impacted. These affinity reductions correlate with reduced antiviral activities of these antibodies, suggesting that simple affinity measurements can serve as an indicator for activity before challenging and time-consuming virus neutralization assays are performed. We also compared the properties of these antibodies to serological fingerprints (affinities and concentrations) of wild type RBD specific antibodies in 74 convalescent sera. The affinities of the therapeutic mAbs to wild type and Delta RBD were in the same range as the polyclonal response in the convalescent sera indicative of their high antiviral activities against these variants. However, for Omicron RBD, only sotrovimab retained affinities that were within the range of the polyclonal response, in agreement with its high activity against Omicron. Serological fingerprints thus provide important context to affinities and antiviral activity of mAb drugs and could guide the development of new therapeutics.

biochemistry↗

bioRxiv2021

Mutations in two SARS-CoV-2 variants of concern reflect two distinct strategies of antibody escape

Understanding the factors that contribute to antibody escape of SARS-CoV-2 and its variants is key for the development of drugs and vaccines that provide broad protection against a variety of virus variants. Using microfluidic diffusional sizing, we determined the dissociation constant (KD) for the interaction between receptor binding domains (RBDs) of SARS-CoV-2 in its original version (WT) as well as alpha and beta variants with the host-cell receptor angiotensin converting enzyme 2 (ACE2). For RBD-alpha, the ACE2-binding affinity was increased by a factor of ten when compared with RBD-WT, while ACE2-binding of RBD-beta was largely unaffected. However, when challenged with a neutralizing antibody that binds to both RBD-WT and RBD-alpha with low nanomolar KD values, RBD-beta displayed no binding, suggesting a substantial epitope change. In SARS-CoV-2 convalescent sera, RBD-binding antibodies showed low nanomolar affinities to both wild-type and variant RBD proteins--strikingly, the concentration of antibodies binding to RBD-beta was half that of RBD-WT and RBD-alpha, again indicating considerable epitope changes in the beta variant. Our data therefore suggests that one factor contributing to the higher transmissibility and antibody evasion of SARS-CoV-2 alpha and beta is a larger fraction of viruses that can form a complex with ACE2. However, the two variants employ different mechanisms to achieve this goal. While SARS-CoV-2 alpha RBD binds with greater affinity to ACE2 and is thus more difficult to displace from the receptor by neutralizing antibodies, RBD-beta is less accessible to antibodies due to epitope changes which increases the chances of ACE2-binding and infection.

biochemistry↗