Biology subjects

Ma, C.

Publications and source records attributed to Ma, C..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Massive expansion of the pig gut virome based on global metagenomic mining

The pig gut virome plays a crucial role in the gut microbial ecosystem of pigs, yet a comprehensive reference database is still lacking. To address this gap, we established the Pig Virome Database (PVD) of the gut that comprises 5,566,804 viral contig sequences from 4,650 publicly available gut metagenomic samples using a pipeline named "metav" developed in this study. The majority of viral operational taxonomic units (vOTUs) were identified as Caudoviricetes (65.36%). By clustering sequences, we identified 48,299 vOTU genomes, of which 92.83% were not found in existing major databases. The PVD database contains a total of 18,161,503 protein-coding genes that can be used to explore the functional potential of the pig gut virome. Our study showed that the PVD can improve the detection of viruses that carry antibiotic/metal resistance genes, mobile genetic elements, virulence factor genes, and quorum sensing systems. These findings highlight the extensive diversity of viruses in the pig gut and provide detailed insight into host-virus interactions.

microbiology↗

bioRxiv2023

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. While tools exist to answer this question, all existing approaches to date return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, no tools to date account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. In this work, we present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of average nucleotide identity, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power as well as quantify theoretically how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. Code implementing this approach, as well as all experiments performed, is available at https://github.com/KoslickiLab/YACHT.

bioinformatics↗

bioRxiv2023

Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations

AbstractHost-microbiome interaction is known to play a pivotal role in the cancer ecosystem, yet the associations have not been systematically investigated at the pan-cancer and the multi-omics level. Here, we evaluated nearly 10,000 samples across 32 cancer types collected from The Cancer Genome Atlas (TCGA), to investigate the association between the tumor microbiome (taxa, n=1,630) and tumor microenvironment composition (cell types, n=20), epigenome (CpG island methylation, n=30,716), transcriptome (gene expression, n=10,216) and proteome (protein expression, n=193). We identified 836,738 candidate associations between the tumor microbiome and host molecular aberrations across multiple cancers. Besides cancer-specific associations, we also revealed recurrent pan-cancer associations between microbes (Lachnoclostridium, Flammeovirga, Terrabacter and Campylobacter) and immune cells, as well as between microbes (Collimonas and Sutterella) and fibroblasts, which were further validated by cell type estimations derived from pathological images and methylation data. We also identified several potential microbe and gene/protein expression associations mediated by DNA methylation using the sequential mediation analysis. Furthermore, our survival analysis demonstrated that tumor microbes may affect the patients overall survival and progression-free survival. Finally, a user-friendly web portal, Multi-Omics and Microbiome Associations in Cancer (MOMAC) was constructed for users to explore potential host-microbe interactions in cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/536730v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@70f74eorg.highwire.dtl.DTLVardef@7c3078org.highwire.dtl.DTLVardef@152354dorg.highwire.dtl.DTLVardef@299282_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

6mA-Sniper: Quantifying 6mA Sites in Eukaryotes at Single-Nucleotide Resolution

While N6-methyldeoxyadenine (6mA) modification has been linked to fundamental regulatory processes in prokaryotes, its prevalence and functional implications in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution. With 6mA-Sniper, we delineated an accurate 6mA profile in C. elegans with 2,034 sites, significantly enriched on sequences of [GC]GAG motif. Twenty-six of 39 6mA events with MnlI restriction endonuclease sites were experimentally verified, demonstrating the feasibility of this method. Notably, the enrichment of these 6mA sites on a specific sequence motif, their within-population conservation and the combinatorial patterns, and the selective constrains on them jointly support an active model for the shaping of the profile by some undiscovered methyltransferases. In a joint study (Cell Research, in revision), Ma et al. reported METL-9 as a new methyltransferase in shaping the basal and stress-dependent 6mA profile in C. elegans. Notably, with the 6mA profile identified by 6mA-Sniper at single-nucleotide resolution, we found that the levels of 6mAs are significantly decreased in strains with the removal of METL-9 (METL-9 KO-OP50), while generally increased after P. aeruginosa infection, further verified the efficiency of 6mA-Sniper in accurately pinpointing 6mA sites. Moreover, for the regions marked by 998 6mA sites emerged specifically after the infection, we identified an enrichment of the upregulated genes after the infection. The gene upregulations are likely mediated through a mutual exclusive crosstalk between 6mA and H3K27me3 modification, as supported by their co-occurrence, and the signal of increased H3K27me3 at regions marked by 6mAs depleted in METL-9 KO-OP50 strains. Notably, in different C. elegans strains, the cross-strain genetic variants removing 6mA sites are associated with the decreased expression of their host genes, and the removal of two randomly-selected 6mA events with genome editing directly decreased the expression of their host genes. We thus highlight 6mA regulation as a previously-neglected regulator of transcriptome in eukaryotes.

genomics↗

bioRxiv2023

An Ensemble Penalized Regression Method for Multi-ancestry Polygenic Risk Prediction

Great efforts are being made to develop advanced polygenic risk scores (PRS) to improve the prediction of complex traits and diseases. However, most existing PRS are primarily trained on European ancestry populations, limiting their transferability to non-European populations. In this article, we propose a novel method for generating multi-ancestry Polygenic Risk scOres based on enSemble of PEnalized Regression models (PROSPER). PROSPER integrates genome-wide association studies (GWAS) summary statistics from diverse populations to develop ancestry-specific PRS with improved predictive power for minority populations. The method uses a combination of [L]1 (lasso) and [L]2 (ridge) penalty functions, a parsimonious specification of the penalty parameters across populations, and an ensemble step to combine PRS generated across different penalty parameters. We evaluate the performance of PROSPER and other existing methods on large-scale simulated and real datasets, including those from 23andMe Inc., the Global Lipids Genetics Consortium, and All of Us. Results show that PROSPER can substantially improve multi-ancestry polygenic prediction compared to alternative methods across a wide variety of genetic architectures. In real data analyses, for example, PROSPER increased out-of-sample prediction R2 for continuous traits by an average of 70% compared to a state-of-the-art Bayesian method (PRS-CSx) in the African ancestry population. Further, PROSPER is computationally highly scalable for the analysis of large SNP contents and many diverse populations.

genetics↗

bioRxiv2023

A proximity-dependent biotinylation map of cytosol-facing organelle outer membrane proteome in living Arabidopsis cells

The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. Using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to map the proximity proteome of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates involved in local protein translation and translocation, membrane contact sites, and organelle quality control. This system also performed admirably for the rapid isolation of intact mitochondria and peroxisomes. Our data support the notion that TOM20-3 is a candidate for both a mitochondrial and a chloroplast receptor, and that PEX11D is a candidate for a peroxisome receptor for the coupling of protein translation and import. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.

cell biology↗

bioRxiv2023

Mass-immigration shapes the antibiotic resistome of wastewater treatment plants

Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily variations of ARG surveillance is still lacking in WWTPs. Here, 285 ARGs and ten mobile gene elements (MGEs) were monitored in seven WWTPs in Xiamen via high-throughput qPCR (HT-qPCR) for seven days. The average daily load of ARGs to WWTPs was about 1.21 x 1020 copies/d, and a total of 1.44 x 1018 copies/d was discharged to the environment across the entire city. Interestingly, no daily variations were observed in ARG richness, abundance, and community composition. Stochastic processes were the main force determining the assembly of ARG communities, with their relative importance ranked in the order of influent (INF) > effluent (EFF) > activated sludge (AS). Further analyses indicated that bacteria and ARGs from upstream treatment units played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment units. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.

microbiology↗

bioRxiv2023

Retrieved Sequence Augmentation for Protein Representation Learning

The advancement of protein representation learning has been significantly influenced by the remarkable progress in language models. Accordingly, protein language models perform inference from individual sequences, thereby limiting their capacity to incorporate evolutionary knowledge present in sequence variations. Existing solutions, which rely on Multiple Sequence Alignments (MSA), suffer from substantial computational overhead and suboptimal generalization performance for de novo proteins. In light of these problems, we introduce a novel paradigm called Retrieved Sequence Augmentation (RSA) that enhances protein representation learning without necessitating additional alignment or preprocessing. RSA associates query protein sequences with a collection of structurally or functionally similar sequences in the database and integrates them for subsequent predictions. We demonstrate that protein language models benefit from retrieval enhancement in both structural and property prediction tasks, achieving a 5% improvement over MSA Transformer on average while being 373 times faster. Furthermore, our model exhibits superior transferability to new protein domains and outperforms MSA Transformer in de novo protein prediction. This study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available at https://github.com/HKUNLP/RSA.

bioinformatics↗

bioRxiv2023

Design, evaluation and implementation of synthetic isopentyldiol pathways in Escherichia coli

Isopentyldiol (IPDO) is an important raw material in cosmetic industry. So far IPDO is exclusively produced through chemical synthesis. Growing interest in natural personal care products has inspired the quest to develop a bio-based process. We previously reported a biosynthetic route that produces IPDO via extending leucine catabolism (route A), the efficiency of which, however, is not satisfactory. To address this issue, we computational designed a novel non-natural IPDO synthesis pathway (Route B) using RetroPath RL, the state of art tool for bio-retrosynthesis based on Artificial Intelligence methods. We compared this new pathway with route A and another two intuitively designed routes for IPDO biosynthesis from various aspects. Route B, which exhibits the highest thermodynamic driving force, least non-native reaction steps and lowest energy requirements appeared to hold the greatest potential for IPDO production. All three newly designed routes were then implemented in E. coli BL21(DE3) strain. Results show that the computationally designed route B can produce 2.2 mg/L IPDO from glucose, whereas no IPDO production from routes C and D. These results highlight the importance and usefulness of in silico design and comprehensive evaluation of the potential efficiencies of candidate pathways in constructing novel non-natural pathways for the production of biochemicals.

bioengineering↗

bioRxiv2023

Assembly and operation of a cooling stage to immobilize C. elegans on their culture plates

High-resolution in vivo microscopy approaches can reveal subtle information and fine details inside the model animal Caenorhabditis elegans (C. elegans) but requires strong animal immobilization. Unfortunately, most current immobilization techniques require substantial manual effort, rendering high-resolution imaging low-throughput. We greatly simplify the C. elegans immobilization procedure by using a cooling approach that can easily immobilize entire populations of C. elegans directly on their cultivation plates. The cooling stage can establish and maintain a wide range of temperatures on the cultivation plate and ensures even temperature distribution across the agarose surface. In this article, we document the whole process of building the cooling stage from scratch. We envision that a typical researcher can build an operational cooling stage in their lab following our protocol without difficulty. We show how to utilize the cooling stage under three protocols, which have advantages for different experiments. We also show an example cooling profile of the stage as it approaches its final temperature and include some helpful tips in using cooling immobilization.

bioengineering↗

bioRxiv2023

Development of attention-based robust deep learning model for tongue diagnosis by smartphone

Compared with tongue diagnosis using tongue image analyzers, tongue diagnosis by smartphone has great advantages in convenience and cost for universal health monitoring, but its accuracy is affected by the shooting conditions of smartphones. Developing deep learning models with high accuracy and robustness to changes in the shooting environment for tongue diagnosis by smartphone and determining the influence of environmental changes on accuracy are necessary. In our study, a dataset of 9003 images was constructed after image pre-processing and labeling. Next, we developed an attention-based deep learning model (Deep Tongue) for 8 subtasks of tongue diagnosis, including the spotted tongue, teeth-marked tongue, and fissure tongue et al, which the average AUC of was 0.90, higher than the baseline model (ResNet50) by 0.10. Finally, we analyzed the objective reasons, the brightness of the environment and the hue of images, affecting the accuracy of tongue diagnosis by smartphone through a consistency experiment of direct subject inspection and tongue image inspection. Finally, we determined the influence of environmental changes on accuracy to quantify the robustness of the Deep Tongue model through simulation experiments. Overall, the Deep Tongue model achieved a higher and more stable classification accuracy of seven tongue diagnosis tasks in the complex shooting environment of the smartphone, and the classification of tongue coating (yellow/white) was found to be sensitive to the hue of the images and therefore unreliable without stricter shooting conditions and color correction.

bioinformatics↗

bioRxiv2022

Identification of a key genetic factor governing arabinan utilization in the gut microbiome suggests a novel therapeutic target for constipation

Probiotics have been widely used to improve impaired gastro-intestinal motility, yet their efficacy varied substantially across strains. Here, by a large-scale genetic screen plus in vivo measurements, we identified a key genetic factor (abfA cluster governing arabinan utilization) in probiotic Bifidobacterium longum harnessing the treatment efficacy against functional constipation (FC). Intriguingly, it also presents in a range of gut resident microbiota and played a protective role against FC. Next, our longitudinal multi-omics study in humans revealed that the exogenous abfA-cluster- carrying B. longum can well establish itself in the gut, and enrich arabinan-utilization residents and beneficial metabolites (e.g., acetate, butyrate, chenodeoxycholic acid and uracil). Finally, transplantation of abfA-cluster-enriched human microbiota to FC- induced germ-free mice recapitulated the marked gut-motility improvement and elevated production of beneficial metabolites. Collectively, our proof-of-concept study actively demonstrated a critical yet underexplored role of microbial abfA cluster in ameliorating FC, establishing generalizable principles for developing functional-genomics-directed probiotic therapies.

microbiology↗

bioRxiv2022

Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph

BackgroundComputational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action (MOAs) between repurposed drugs and their target diseases remain largely unknown, which is still a main obstacle for computational drug repurposing methods to be widely adopted in clinical settings. ResultsIn this work, we propose KGML-xDTD : a Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases. It is a two-module framework that not only predicts the treatment probabilities between drugs/compounds and diseases but also biologically explains them via knowledge graph (KG) path-based, testable mechanisms of action (MOAs). We leverage knowledge-and-publication based information to extract biologically meaningful "demonstration paths" as the intermediate guidance in the Graph-based Reinforcement Learning (GRL) path-finding process. Comprehensive experiments and case study analyses show that the proposed framework can achieve state-of-the-art performance in both predictions of drug repurposing and recapitulation of human-curated drug MOA paths. ConclusionsKGML-xDTD is the first model framework that can offer KG-path explanations for drug repurposing predictions by leveraging the combination of prediction outcomes and existing biological knowledge and publications. We believe it can effectively reduce "black-box" concerns and increase prediction confidence for drug repurposing based on predicted path-based explanations, and further accelerate the process of drug discovery for emerging diseases.

bioinformatics↗

bioRxiv2022

Encoding of spatial location by frontal orienting field neurons

The neural mechanisms of motor planning have been extensively studied in rodents. Preparatory activity in the frontal cortex predicts upcoming choice, but limitations of typical tasks have made it challenging to determine whether the spatial information is in a self-centered direction reference frame or a world-centered position reference frame. Here, we trained rats to make delayed visually-guided orienting movements to six different directions, with four different target positions for each direction, which allowed us to disentangle direction versus position tuning in neural activity. We recorded single unit activity from the rat frontal orienting field (FOF) in the secondary motor cortex, a region involved in planning orienting movements. Population analyses revealed that the FOF encodes two separate 2D maps of space. First, a 2D map of the planned and ongoing movement in a self-centered direction reference frame. Second, a 2D map of the animals current position on the port wall in a world-centered reference frame. Thus, preparatory activity in the FOF represents self-centered upcoming movement directions, but FOF neurons multiplex both self- and world-reference frame variables at the level of single neurons. Neural network model comparison supports the view that despite the presence of world-centered representations, the FOF receives the target information as self-centered input and generates self-centered planning signals.

neuroscience↗

bioRxiv2022

Regulation of adventitial interstitial fluid circulation by heartbeat and respiration

Converging studies showed interstitial fluid (ISF) adjacent to blood vessels flows along adventitia of vasculature into heart and lungs. We aim to reveal circulatory pathways and regulatory mechanism of such adventitial ISF flow in rat model. By MRI, real-time fluorescent imaging, micro-CT and histological analysis, ISF was found to flow in adventitial matrix surrounded by fascia and along systemic vessels into heart, then flow into lungs via pulmonary arteries and back to heart via pulmonary veins, which was neither perivascular tissues nor blood or lymphatic vessels. Under physiological conditions, speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, became pulsative during heavy breathing. During cardiac or respiratory cycle, each dilation or contraction of heart or lungs can generate to-and-fro adventitial ISF flow along femoral veins. Discovered regulatory mechanisms of adventitial ISF flow along vasculature by heart and lungs will revolutionize understanding of cardiovascular system. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/512678v3_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1d29c16org.highwire.dtl.DTLVardef@583f5org.highwire.dtl.DTLVardef@1a551eorg.highwire.dtl.DTLVardef@ca4780_HPS_FORMAT_FIGEXP M_FIG Graphic abstract of adventitial interstitial fluid cycle by heartbeat and respiration.The heart and lungs can work together to regulate the ISF (green arrow) adjacent to blood vessels to flow centripetally in an adventitial pathway along the major arteries and veins of the systemic vasculature to the epicardium and myocardium, then flow into the lungs via the pulmonary arteries and back to the heart via the pulmonary veins, forming an adventitial ISF circulatory network. Under physiological conditions, the speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, and became pulsative during heavy breathing. During respiratory cycle, each expansion of the lungs during inflation generates a centrifugal flow of adventitial ISF along the systemic veins, while each contraction of the lungs during deflation generates a centripetal adventitial ISF flow. During cardiac cycle, each dilation of atria or ventricles generates a centripetal flow of adventitial ISF along the systemic veins, while each contraction of atria or ventricles generates a centrifugal adventitial ISF flow. C_FIG

physiology↗

bioRxiv2022

Perturbation of mitochondrial Ca2+ homeostasis activates cross-compartmental proteostatic response in Arabidopsis

Mitochondrial Ca2+ (mtCa2+) homeostasis is essential to mitochondrial functions. However, how mtCa2+ homeostasis is achieved and the consequences of impaired mtCa2+ homeostasis in plants is poorly understood. Here, we demonstrate a critical role for mitochondrial Ca2+ uniporter (MCU) in the control of mtCa2+ uptake for mtCa2+ homeostasis in planta by characterizing MCU mutants and overexpressed plants. Impaired MCU-controlled mtCa2+ homeostasis (iMUCH) in gain-of-function and loss-of-function MCU plants causes the misregulation of mitochondrial gene expression that triggers mitonuclear protein imbalance. Transcriptome integrated with proteomics analysis reveal activation of multiple compartmental UPR gene expression and decrease of cytosolic translation with selective repression of ribosome and RNA modification protein synthesis upon iMUCH. Intriguingly, TOR signalling is not involved in cytosolic translational response to iMUCH, but the reduction of eIF phosphorylation is evident under iMUCH induced mitochondrial stress. Thus, our study unveils the essential functions of MCU proteins for mtCa2+ homeostasis, and the involvement of MCU-controlled mtCa2+ homeostasis in mitochondrial stress dependent regulation of protein synthesis for cellular proteostasis that is connected to plant growth and stress resistance.

plant biology↗

bioRxiv2022

Alternative mRNA polyadenylation bridges mitochondrion-to-nucleus communication in Arabidopsis

Mitochondria produce signals besides energy and metabolites that influence plant growth and fitness. However, how mitochondrial signals are relayed to other cellular compartments is largely unknown. By applying poly(A)-site RNA-sequencing (PAS-seq) to wildtype Arabidopsis seedlings and a mutant in the histone demethylase JMJ30 treated with the mitochondrial electron transfer chain inhibitor antimycin A (AA), we identified a previously undefined mitochondrion-to-nucleus communication pathway by which mitochondrial functional state regulates co-transcriptionally alternative polyadenylation (APA) of nuclear mRNA. We observed a global shortening of 3' untranslated regions (UTRs) as a molecular signature of AA-activated mitochondrial retrograde response (MRR), which contributed in part to translational regulation of auxin response and cell wall biogenesis. JMJ30 regulated AA-induced 3' UTR shortening, resulting in more transcripts with shortened 3' UTRs upon AA treatment in a JMJ30 gain-of-function mutant and overexpression lines. We also report on the JMJ30-interacting protein CPSF30, a cleavage and polyadenylation specificity factor that recruits JMJ30 to modulate H3K27me3 status at its target loci. Our study illustrates how epigenetic modification and APA coordinate mitochondrion-to-nucleus communication to allow cells to rapidly respond to changes in mitochondrial functional state and shape plant growth and fitness. One-sentence summaryEpigenetic modification and APA coordinate mitochondrion-to-nucleus communication to allow cells to rapidly respond to changes in mitochondrial functional state and shape plant growth and fitness.

molecular biology↗

bioRxiv2022

Determinants restricting ACE2 recognition of MERS-related coronaviruses in bats

Phylogenetically distant coronaviruses have evolved to use ACE2 as their common receptors, including NL63 and many Severe acute respiratory syndrome (SARS) coronavirus-related viruses. We recently reported two Middle East respiratory syndrome coronavirus (MERS-CoV) closely related bat merbecoviruses, NeoCoV and PDF-2180, use Angiotensin-converting enzyme 2 (ACE2) for entry. However, their host range and cross-species transmissibility remain unknown. Here, we characterized their species-specific receptor preference by testing ACE2 orthologs from 49 bats and 53 non-bat mammals. Both viruses exhibited broad receptor recognition spectra and are unable to use ACE2 orthologs from 24 species, mainly Yinpterochiropteran bats. Comparative analyses of bat ACE2 orthologs underscored four crucial host range determinants, all confirmed by subsequent functional assays in human and bat cells. Among them, residue 305, participating in a critical interaction, plays a crucial role in host tropism determination. NeoCoV-T510F, a mutation that enhances human ACE2 recognition, further expanded the potential host range via tighter interaction with an evolutionary conserved hydrophobic pocket. Our results elucidated the molecular basis for the species-specific ACE2 usage of MERS-related viruses across mammals and shed light on their zoonotic risks.

microbiology↗