Biology subjects

Wong, Y. H.

Publications and source records attributed to Wong, Y. H..

6 recordsLinked to original sources

bioRxiv2025

A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation

Long-range RNA-RNA pairing impacts the genome structure and function of SARS-CoV-2 variants. To understand the structure and function relationships of different SARS-CoV-2 variants that have emerged during the COVID-19 pandemic, we performed high-throughput structure probing and modelling of the genomic structures of the wildtype (WT), Alpha, Beta, Delta and Omicron variants of SARS-CoV-2. We observed that genomes of SARS-CoV-2 variants are generally structurally conserved, and that single-nucleotide variations and interactions with RNA binding proteins can impact RNA structures across the viruses. Importantly, using proximity ligation sequencing, we identified many conserved ultra-long-range RNA-RNA interactions, including one that spans more than 17 kb in both the WT virus and the Omicron variant. We showed that mutations that disrupt this 17 kb long-range interaction reduce viral fitness at later stages of its infection cycle, while compensatory mutations partially restore virus fitness. Additionally, we showed that this ultra-long-range RNA-RNA interaction structure binds directly to ADAR1 to alter the RNA editing levels on the viral genome. These studies deepen our understanding of RNA structures in the SARS-CoV-2 genome and their ability to interact with host factors to facilitate virus infectivity.

genomics↗

bioRxiv2024

Marseilleviruses biological properties and viral translation-associated proteins based on in silico tertiary structure

Marseilleviruses are a group of double-strand DNA viruses that infect amoeba within the Nucleocytoviricota phylum and are ubiquitous in water and soil globally. Here, we report four novel strains isolated from mangroves in Guangdong province, China, namely, futianmevirus, futianmfvirus, dashavirus str. E, and xiwanvirus. Viral particles presented about 220[~]240 nm icosahedrally shaped capsids and were wrapped by membranes to form giant vesicles. Based on stability assays, viral particles were halotolerant and acid-tolerant, but sensitive to chloroform and high temperature, while giant vesicles conferred thermal and acid/alkaline resistance to particles. Genomics and phylogenetic analyses showed that the four strains formed divergent branches within different lineages of marseillevirus. Notably, to our knowledge, futianmevirus was the first reported marseillevirus lacking translation elongation factor EF-1alpha (EF1A). Our in silico analysis of marseillevirus coded translation-associated homolgs suggested their conserved functions. Additionally, we predicted at least four novel proteins that were structurally similar to components of the protozoan ribosome. Overall, not only our data comprehensively described the diversity of marseillevirus biological properties, but also proposed a new perspective on the giant virus translation system. ImportanceThe family Marseilleviridae was the second reported family of giant viruses and distributed globally. In this work, we reported the four novel marseilleviruses isolated from saltwater samples of mangrove. Difference of biological properties between giant vesicles and viral particles revealed the environment fitness of marseillevirus. On the other hand, sensitivity to chloroform indicated the importance of lipid components for viral infection. Additionally, our comparative genomics, phylogenetic analysis, and protein structure comparison revealed the diverse translation-associated gene sets of marseilleviruses. The prediction of ribosome components expands the knowledge about the giant viral translation-associated proteins, and will be helpful in future to reveal how giant viruses hijack the amoeba translation system.

microbiology↗

bioRxiv2024

Brachiopod genome unveils the evolution of the BMP-Chordin network in bilaterian body patterning

Bone morphogenetic protein (BMP) signalling is crucial in regulating dorsal-ventral patterning and cell fate determination during early development in bilaterians. Interactions between BMP ligands and their main antagonist, Chordin, establish BMP gradients, subdivide embryos into distinct territories and organise body plans. However, the molecular control and evolutionary origins of dorsal-ventral patterning within spiralians, one of the three major bilaterian groups, have been obscured by their unique embryonic development. Here we present the chromosome-level genome of a spiralian with deuterostome-like development, the brachiopod Lingula anatina, and apply functional transcriptomics to study dorsal-ventral patterning under the control of BMP signalling. We uncover the presence of a dorsal-ventral BMP signalling gradient in the L. anatina gastrula with bmp2/4 and chordin expressed at its dorsal and ventral sides, respectively. Using small-molecule drugs, exogenous recombinant BMP proteins and RNA sequencing, we show that a high level of BMP pathway activation inhibits the expression of neural genes during gastrula and larval stages. We also show that BMP signalling splits the developing larval shell field into two valves. The discovery of a BMP-mediated dorsal-ventral patterning system in a spiralian, similar to those observed in deuterostomes and non-spiralian protostomes, suggests deep conservation of this mechanism across all three major bilaterian clades. This is further supported by striking similarities in the gene sets regulated by BMP signalling in brachiopods and the vertebrate model Xenopus. We argue that the spiralian ancestor retained the basal bilaterian mechanism of dorsal-ventral patterning, although downstream components of the BMP-Chordin network have undergone dynamic evolutionary changes.

evolutionary biology↗

bioRxiv2022

Broadly neutralizing and protective nanobodies against diverse sarbecoviruses

As SARS-CoV-2 Omicron and other variants of concern continue spreading around the world, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with exceptional breadth and potency against diverse sarbecoviruses including SARS-CoV-1, Omicron BA.1, and BA.2. Crystal structure analysis of one representative nanobody, 3-2A2-4, revealed a highly conserved epitope between the cryptic and the outer face of the receptor binding domain (RBD). The epitope is readily accessible regardless of RBD in "up" or "down" conformation and distinctive from the receptor ACE2 binding site. Passive delivery of 3-2A2-4 protected K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. This group of nanobodies and the epitope identified should provide invaluable reference for the development of next generation antibody therapies and vaccines against wide varieties of SARS-CoV-2 infection and beyond.

immunology↗

bioRxiv2021

Mapping the allosteric effects that define functional activity of SARS-CoV-2 specific antibodies

Previous studies on the structural relationship between human antibodies and SARS-CoV-2 have focused on generating static snapshots of antibody complexes with the Spike trimer. However, antibody-antigen interactions are dynamic, with significant binding-induced allosteric effects on conformations of antibody and its target antigen. In this study, we employ hydrogen-deuterium exchange mass spectrometry, in vitro assays, and molecular dynamics simulations to investigate the allosteric perturbations linked to binding events between a group of human antibodies with differential functional activities, and the Spike trimer from SARS-CoV-2. Our investigations have revealed key dynamic features that define weakly or moderately neutralizing antibodies versus those with strong neutralizing activity. These results provide mechanistic insights into the functional modes of human antibodies against COVID-19, and provide a rationale for effective antiviral strategies. TeaserDifferent neutralizing antibodies induce site-specific allosteric effects across SARS-CoV-2 Spike protein

biochemistry↗

bioRxiv2021

Structural basis for substrate recognition, ligation and activation by a hyperactive Asn peptide ligase from Viola yedoensis

Peptide asparaginyl ligases (PALs) belong to a limited class of enzymes from cyclotide-producing plants, that perform site-specific ligation reactions after a target peptide Asx (Asn/Asp) binds to the ligase active site. How PALs specifically recognize their polypeptide substrates has remained elusive especially at the prime binding side of the enzyme. Here we captured VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzymes S1 pocket and why a hydrophobic residue is required at the substrate P2 position. Beside illustrating the role played by P1 and P2 residues as primary anchors for the enzyme reaction, these results provide a mechanistic explanation for the role of the "Gatekeeper" residue at the surface of the S2 pocket, in shifting the non-prime portion of the substrate and, as a result, the activity towards either ligation or hydrolysis. These results detail the molecular events that occur during proenzyme maturation in the plant vacuolar compartment, suggest a mechanism for ligation, and will inform the design of peptide ligases with tailored specificities. One sentence summaryWe captured VyPAL2, a catalytically efficient plant peptide ligase with a bound substrate, providing the molecular basis for substrate recognition and ligation.

biochemistry↗