Biology subjects

Zou, C.

Publications and source records attributed to Zou, C..

29 records · Page 2Linked to original sources

bioRxiv2023

Redundant and distinct roles of two 14-3-3 proteins in Fusarium sacchari, pathogen of sugarcane Pokkah boeng disease

Fusarium sacchari is one of the most important sugarcane pathogens that causes Pokkah boeng disease (PBD) in China. 14-3-3 proteins have been shown to play vital roles in developmental processes in dimorphic transition, signal transduction and carbon metabolism in some phytopathogenic fungi, but were poorly understood in F. sacchari. In this study, two 14-3-3 protein-encoding genes, FsBmh1 and FsBmh2 in F. sacchari, were investigated. Although both FsBmh1 and FsBmh2 were expressed at vegetative growth stage, FsBmh1 was repressed at sporulation stage in vitro. In order to clarify the roles of FsBmh1 and FsBmh2, deletion mutants {Delta}FsBmh1 and {Delta}FsBmh2 were constructed. Phenotypic defects, including hyphal branching, hyphal septation, conidiation, spore germination and colony growth, were more severe in {Delta}FsBmh2 than in {Delta}FsBmh1, although virulence attenuation was observed in both mutants. To further explore the relationship between FsBmh1 and FsBmh2, the combination of deletion and silencing ({Delta}FsBmh/sFsBmh) and overexpression (O-FsBmh) mutants were constructed and characterized. Compared to the single allele deletion, combinations of {Delta}FsBmh1/sFsBmh2 or {Delta}FsBmh2/sFsBmh1 showed more severe manifestations in general, suggesting a redundancy in function of the two 14-3-3 genes. Comparative transcriptome analysis revealed that more functional genes were affected in {Delta}FsBmh2 than in {Delta}FsBmh1. Redundancy in function between FsBmh1 and FsBmh2 suggests that 14-3-3 is vitally important for the organism and distinction in roles between the two isoforms may be resulted from the divergence in evolution. To the best of our knowledge, this was the first report on the distinct roles of 14-3-3 protein isoforms in a pathogenic fungus. Knowledge gained from this study should be of help to further understand the regulation mechanism of pathogenicity-related traits in fungal pathogens and for the development of new strategy for control of PBD in particular.

microbiology↗

bioRxiv2023

Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders

Small molecules that induce protein-protein interactions to exert proximity-driven pharmacology such as targeted protein degradation are a powerful class of therapeutics1-3. Molecular glues are of particular interest given their favorable size and chemical properties and represent the only clinically approved degrader drugs4-6. The discovery and development of molecular glues for novel targets, however, remains challenging. Covalent strategies could in principle facilitate molecular glue discovery by stabilizing the neo-protein interfaces. Here, we present structural and mechanistic studies that define a trans-labeling covalent molecular glue mechanism, which we term "template-assisted covalent modification". We found that a novel series of BRD4 molecular glue degraders act by recruiting the CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). BRD4BD2, in complex with DCAF16, serves as a structural template to facilitate covalent modification of DCAF16, which stabilizes the BRD4-degrader-DCAF16 ternary complex formation and facilitates BRD4 degradation. A 2.2 [A] cryo-electron microscopy structure of the ternary complex demonstrates that DCAF16 and BRD4BD2 have pre-existing structural complementarity which optimally orients the reactive moiety of the degrader for DCAF16Cys58 covalent modification. Systematic mutagenesis of both DCAF16 and BRD4BD2 revealed that the loop conformation around BRD4His437, rather than specific side chains, is critical for stable interaction with DCAF16 and BD2 selectivity. Together our work establishes "template-assisted covalent modification" as a mechanism for covalent molecular glues, which opens a new path to proximity driven pharmacology.

biochemistry↗

bioRxiv2022

Genetic Diversity of Candidatus Liberibacter asiaticus Based on Four Hypervariable Genomic Regions in China

Huanglongbing (HLB; greening disease), caused by Candidatus Liberibacter asiaticus (CLas), is the most damaging citrus disease worldwide. The disease has spread throughout the citrus-producing regions of Guangxi, Guangdong, Fujian, and others in China. A total of 1,789 HLB-like symptomatic or asymptomatic samples were collected from the Guangxi and Fujian provinces of China to decipher the genetic diversity of CLas and its correlation with pathogenicity and host range. The disease was the most severe in orange and the least in pomelo. CLas bacteria associated with the specific geographical and citrus variety infected more than 50% of the HLB-like symptomatic samples. We identified a total of 6,286 minor variations by comparing 35 published CLas genomes and observed a highly heterogeneous variation distribution across the genome. Highly diverse regions, including two prophages, were generally more unstable and prone to lose. In the collected CLas strains, four highly diverse non-prophage segments and three prophage segments in the prophage region were chosen for PCR amplification and genotyping. Four hypervariable regions were used to decipher CLas diversity. A total of 100 strains were divided into four groups, of which 90 strains were clustered into two clades with 15 reported reference genomes, while 10 were grouped in two clades separately from the reported genomes. This study provides insight into the molecular characteristics and genetic variations of different CLas strains in China and might help develop HLB prevention and control strategies. ImportanceThe objective of the present study is to characterize the hypervariable genomic region sequence, decipher the genetic diversity of CLas strains from China, understand how various strains differ, and lay the foundation for developing HLB prevention and control strategies.

microbiology↗

bioRxiv2021

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that [~]30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction. HighlightOur manuscript presents a high-quality reference genome of the inbred line A188, and provides new insights into candidate genes underlying maize embryonic callus induction and other maize agronomic traits.

genetics↗

bioRxiv2021

Evolution of ACE2 and SARS-CoV-2 Interplay Across 247 Vertebrates

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause the most serious pandemics of Coronavirus Disease 2019 (COVID-19), which threatens human health and public safety. SARS-CoV-2 spike (S) protein uses angiotensin-converting enzyme 2 (ACE2) as recognized receptor for its entry into host cell that contributes to the infection of SARS-CoV-2 to hosts. Using computational modeling approach, this study resolved the evolutionary pattern of bonding affinity of ACE2 in 247 jawed vertebrates to the spike (S) protein of SARS-CoV-2. First, high-or-low binding affinity phenotype divergence of ACE2 to the S protein of SARS-CoV-2 has appeared in two ancient species of jawed vertebrates, Scyliorhinus torazame (low-affinity, Chondrichthyes) and Latimeria chalumnae (high-affinity, Coelacanthimorpha). Second, multiple independent affinity divergence events recur in fishes, amphibians-reptiles, birds, and mammals. Third, high affinity phenotypes go up in mammals, possibly implying the rapid expansion of mammals might accelerate the evolution of coronaviruses. Fourth, we found natural mutations at eight amino acid sites of ACE2 can determine most of phenotype divergences of bonding affinity in 247 vertebrates and resolved their related structural basis. Moreover, we also identified high-affinity or low-affinity-associated concomitant mutation group.The group linked to extremely high affinity may provide novel potentials for the development of human recombinant soluble ACE2 (hrsACE2) in treating patients with COVID-19 or for constructing genetically modified SARS-CoV-2 infection models promoting vaccines studies. These findings would offer potential benefits for the treatment and prevention of SARS-CoV-2.

evolutionary biology↗

bioRxiv2020

Human hepatocyte PNPLA3 148M exacerbates rapid non-alcoholic steatohepatitis development in chimeric mice

Advanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing protein 3 (PNPLA3-I148M). Here, we study how human hepatocytes with PNPLA3 148I and 148M variants engrafted in the livers of chimeric mice respond to a hypercaloric Western-style diet. As early as 4 weeks, mice developed dyslipidemia, impaired glucose tolerance, and steatohepatitis selectively in the human graft, followed by pericellular fibrosis after 8 weeks of hypercaloric feeding. The PNPLA3 148M variant, either from a homozygous 148M human donor or overexpressed in a homozygous 148I donor background, caused widespread microvesicular steatosis and even more severe steatohepatitis. We conclude that PNPLA3 148M in human hepatocytes exacerbates NAFLD. These models will facilitate mechanistic studies into human genetic variants associated with advanced fatty liver diseases.

pathology↗

bioRxiv2020

Public broadly neutralizing antibodies against hepatitis B virus in individuals with elite serologic activity

SUMMARYAlthough there is no effective cure for chronic hepatitis B virus (HBV) infection, antibodies are protective and constitute clinical correlates of recovery from infection. To examine the human neutralizing antibody response to HBV in elite neutralizers we screened 144 individuals. The top individuals produced shared clones of broadly neutralizing antibodies (bNAbs) that targeted 3 non-overlapping epitopes on the HBV S antigen (HBsAg). Single bNAbs protected humanized mice against infection, but selected for resistance mutations in mice with established infection. In contrast, infection was controlled by a combination of bNAbs targeting non-overlapping epitopes with complementary sensitivity to mutations that commonly emerge during human infection. The co-crystal structure of one of the bNAbs with a peptide epitope containing residues frequently mutated in human immune escape variants revealed a loop anchored by oppositely charged residues. The structure provides a molecular explanation for why immunotherapy for HBV infection may require combinations of complementary bNAbs.

immunology↗

bioRxiv2019

An RNA-based system to study hepatitis B virus replication and select drug-resistance mutations

Hepatitis B virus (HBV) chronically infects over 250 million people worldwide, increasing their risk of liver cirrhosis and hepatocellular carcinoma. There is a vaccine to prevent new infections, but no efficient cure for chronic infection. New insights into HBV biology are needed to improve cure rates for this widespread devastating disease. We describe a method to initiate replication of HBV, a DNA virus, using synthetic RNA. This approach has several advantages over existing systems: it eliminates contaminating background signal from input virus or plasmid DNA and can be easily adapted to multiple genotypes and mutants. Further, it can be applied to identify anti-HBV compounds, measure anti-HBV drug efficiency, study virus evolution, and, as we demonstrate, it can be uniquely applied to predict antiviral drug resistance.

microbiology↗

bioRxiv2019

High-throughput sequencing analysis of bacterial diversity in raw and pasteurized goat milk

The aim of this study was to evaluate the microbial composition of both raw and pasteurized goat milk using high-throughput DNA sequencing. This analysis revealed that the dominant phylum found in the raw milk was Proteobacteria, and the dominant genus was Kluyvera; Proteobacteria and Kluyvera constituted up to 67.66% and 28.85% of the total bacteria population, respectively. The microorganisms in goat milk predominantly consist of Gram-negative bacteria. Notably, Akkermansia and Faecalibacterium were identified in goat milk for the first time. In addition, the results also indicate that some bacteria in pasteurized goat milk may exist in a viable but nonculturable (VBNC) state. This study provides a theoretical basis that may aid the community in better understanding bacterial diversity in goat milk. The results of this study will help us to improve the quality and safety of goat milk. ImportanceThe microbial diversity in goat milk and pasteurized goat milk at different refrigeration stages was described. Several bacterial species that have not previously been reported in goat milk were identified, including many VBNC bacteria. The findings provided the necessary microbial information for quality and safety of goat milk and dairy products.

microbiology↗

bioRxiv2018

Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity

Since its outbreak in 2007, Zika virus (ZIKV) has become a global health threat that causes severe neurological conditions. Here we perform a comparative in vivo structural analysis of the RNA genomes of two ZIKV strains to decipher the regulation of their infection at the RNA level. Our analysis identified both known and novel functional RNA structural elements. We discovered a functional long-range intramolecular interaction specific for the Asian epidemic strains, which contributes to their infectivity. Our findings illuminate the structural basis of ZIKV regulation and provide a rich resource for the discovery of RNA structural elements that are important for ZIKV infection.

molecular biology↗

bioRxiv2018

Non-invasive spinal electro-magnetic stimulation (SEMS): a tool for evaluation and modulation of lower limb spinal-muscular transmission in healthy adults

ObjectiveOur earlier electrophysiological recordings using animal models revealed diminished transmission through spared fibers to motoneurons and leg muscles after incomplete spinal cord injury (SCI). Administration of spinal electro-magnetic stimulation (SEMS) at specific parameters induced transient improvement of transmission at neuro-muscular circuitry in SCI animals. In the current human study, we sought translate this knowledge to establish optimal parameters of SEMS for (i) neurophysiological evaluation via Compound Motor Action Potential (CMAP); and (ii) modulation at neuro-muscular circuitry via H-reflex and M-wave response in 12 healthy adults.\n\nMethodsSEMS application was with a coil positioned over T12-S1 spinal levels. SEMS-evoked CMAP-responses were wirelessly measured simultaneously from biceps femoris (BF), semitendinosus (ST), vastus lateralis (VL), soleus (SOL), medial gastrocnemius (MG) and lateral gastrocnemius (LG) muscles. We also examined effects of SEMS trains on H-reflex and M-wave responses. H-reflexes and M-waves were measured simultaneously from SOL, MG and LG muscles and evoked by peripheral electrical stimulation of tibial nerves before and after each SEMS session.\n\nResultsSpinal levels for SEMS application to evoke CMAP-responses in corresponding muscles and amplitude/latency of these responses have been established. SEMS applied over L4-S1 spinal levels at 0.2 Hz rate for 30 min induced facilitation of H-reflexes and M-responses. Facilitation lasted for at least 1 hour after stopping SEMS and was associated with a decrease in threshold intensity and leftward shift of recruitment curve for H-reflex and M-wave. SEMS did not alter TMS-evoked responses in hand muscles.\n\nConclusionSEMS is a novel, non-invasive approach for sustained neuromodulation of H-reflex and M-wave responses in triceps surae muscle group. The parameters of SEMS application established in this study for evaluation and neuromodulation of neural pathways innervating leg muscles in healthy individuals may be used as a reference for neurophysiological evaluation and long-lasting plasticity of the lower limb spino-neuromuscular circuitry in individuals with SCI.

neuroscience↗