Biology subjects

Zhuo, L.

Publications and source records attributed to Zhuo, L..

10 recordsLinked to original sources

bioRxiv2026

Spatial specialization of antioxidant defenses dictates predation success in Myxococcus xanthus

Redox-based chemical warfare is a primary driver of microbial community assembly. Here, we show that the predatory bacterium Myxococcus xanthus employs a spatial division of labor between two inducible monofunctional catalases, mxKatB and mxKatE, to overcome prey-derived hydrogen peroxide (H2O2). Quantitative transcript analysis revealed distinct regulatory specificities: mxkatB was the dominant transcriptional responder to exogenous H2O2, whereas mxkatE was preferentially induced by UV irradiation. Biochemical analyses demonstrated strict compartmentalization of enzymatic activity. mxKatE functioned intracellularly, consistent with a role in mitigating endogenous genotoxic stress. In contrast, mxKatB, which harbors an N-terminal Sec-dependent signal peptide, was exclusively localized to the extracellular milieu. Targeted gene deletions corroborated these non-redundant physiological roles. {Delta}katE mutant exhibited severe growth defects and heightened sensitivity to UV and H2O2 yet retained full predation proficiency. Conversely, {Delta}katB mutant displayed unaltered vegetative fitness but were severely impaired in prey lysis due to oxidative inactivation of secreted bacteriolytic enzymes. Failure of cross-complementation confirmed that spatial localization, rather than catalytic capacity, dictates enzyme function. Our findings establish that M. xanthus deploys an extracellular catalase shield to protect its exoenzyme arsenal from prey-derived oxidants. This spatial specialization of antioxidant defenses represents a sophisticated strategy that directly determines the outcome of bacterial predation and shapes interspecies interactions within microbial communities. IMPORTANCEPredatory bacteria such as M. xanthus must withstand chemical defenses deployed by their prey. We show that M. xanthus uses a spatially specialized antioxidant system: an extracellular catalase (mxKatB) secreted to shield its lytic enzymes from prey-derived hydrogen peroxide, and an intracellular catalase (mxKatE) that handles endogenous oxidative stress. This division of labor reveals that bacterial antioxidant defenses can be compartmentalized to protect extracellular weaponry rather than the cell itself, adding a new dimension to how spatial organization of stress responses influences the outcome of microbial competition.

ecology↗

bioRxiv2024

Multi-view BLUP: a promising solution for post-omics data integrative prediction

Phenotype prediction is a promising strategy for accelerating molecular plant breeding. Data from multiple sources (called multi-view data) can provide complementary information to characterize a biological object from various aspects. By integrating multi-view information into phenotype prediction, a multi-view best linear unbiased prediction (MVBLUP) method was proposed in this paper. By assigning different weights to measure the importance of different views of data and using a differential evolution algorithm with an early stopping mechanism to adjust the weight vector adaptively, a multi-view kinship matrix was obtained first and then incorporated into the BLUP model for phenotype prediction. To validate the efficiency of MVBLUP, we conducted numerical experiments on four multi-view datasets. Compared to the average performance of the single-view method, the prediction accuracy of the MVBLUP method has improved by a range of 0.038 to 0.201.The results demonstrate that the MVBLUP model is an effective method of integrating multi-view data.

genetics↗

bioRxiv2024

Pan-cistrome analysis of the leaf accessible chromatin regions of 214 maize inbred lines

Characterizing the noncoding regions of the genome, particularly the cis-regulatory elements (CREs) located in accessible chromatin regions (ACRs) in gene promoters, is crucial for understanding how gene expression is regulated and how genotype contributes to phenotypic diversity in plants.In this study, we used ATAC-seq to resequence and map the ACRs of 214 maize inbred lines. We identified 82,174 ACRs and reported that 39.55% of them exhibited significant variation across the population. Next, we used the accessibility of ACRs as a quantitative feature and performed a chromatin associability GWAS (caGWAS), resulting in 27,004 caQTLs. Among them, 2,463 were predicted to disrupt the cis-regulatory elements that TF binds in these ACRs, suggesting that TF binding affects chromatin accessibility. Specifically, we identified two caACRs that regulate the expression of fad7, which encodes a fatty acid desaturase and affects the linolenic acid content.Our findings highlight the dynamic nature of maize ACRs and demonstrate that chromatin accessibility information could be used for GWASs, offering key insights into the genetic and regulatory mechanisms of chromatin accessibility and its impact on complex traits in plants.

genomics↗

bioRxiv2024

CA1i pyramidal neurons mediate the role of NMDA receptor subunit GluN3A in depressive behavior and D-serine anti-depression

The hippocampus is a highly complex structure, defined by profound structural, functional, and molecular heterogeneity. The GluN3A subunit, which forms non-classic N-methyl-D-aspartate receptors (NMDARs), is enriched in the hippocampal CA1 subregion and has a poorly understood functional role, especially in stress-related behavioral regulation. Here, we employed chronic social defeat stress (CSDS) and GluN3A knockout (KO) mouse models combined with behavioral, molecular, genetic, pharmacological, and circuit-level analyses to investigate the role of hippocampal GluN3A in stress coping. We found that CSDS selectively reduced GluN3A expression in the intermediate CA1 (CA1i) region. Decreased GluN3A expression in CA1i, from either stress or genetic deletion, promoted passive coping behaviors, whereas overexpression of GluN3A in CA1i reversed the phenotype under both conditions. Mechanistically, consistent with GluN3A enrichment in pyramidal neurons, c-fos staining and fiber photometry revealed that GluN3A was essential for CA1i pyramidal neuronal activation during coping behaviors. Further chemogenetic manipulations demonstrated that activating CA1i neurons facilitated active coping, while inhibition induced passivity. Moreover, local administration of D-serine, an agonist of GluN3A-containing NMDARs, rapidly shifted coping behavior from passive to active by activating CA1i neurons via GluN3A-dependent mechanisms. Circuit tracing revealed that CA1i neurons project to multiple sub-hippocampal and cortico-limbic regions, and GluN3A overexpression selectively enhanced downstream neuronal activity in CA3 and infralimbic cortex, but not in the nucleus accumbens. Together, these findings identify GluN3A as a key molecule linking hippocampal subregional specialization with adaptive stress coping, and suggest that the rapid, resilience-promoting effects of D-serine are also GluN3A-dependent.

neuroscience↗

bioRxiv2024

Biallelic pathogenic variants in DNAH3 cause male infertility in humans and mice

Axonemal protein complexes, including the outer and inner dynein arms (ODA/IDA), are highly ordered structures of the sperm flagella that drive sperm motility. Deficiencies in several axonemal proteins have been associated with male infertility, which is characterized by asthenozoospermia or asthenoteratozoospermia. Dynein axonemal heavy chain 3 (DNAH3) resides in the IDA and is highly expressed in the testis. However, the relationship between DNAH3 and male infertility is still unclear. Herein, we identified biallelic variants of DNAH3 in four unrelated Han Chinese infertile men with asthenoteratozoospermia through whole-exome sequencing (WES). These variants contributed to deficient DNAH3 expression in the patients sperm flagella. Importantly, the patients represented the anomalous sperm flagellar morphology, and the flagellar ultrastructure was severely disrupted. Intriguingly, Dnah3 knockout (KO) male mice were also infertile, especially showing the severe reduction in sperm movement with the abnormal IDA and mitochondrion structure. Mechanically, nonfunctional DNAH3 expression resulted in decreased expression of IDA-associated proteins in the spermatozoa flagella of patients and KO mice, including DNAH1, DNAH6, and DNALI1, the deletion of which has been involved in disruption of sperm motility. Moreover, the infertility of patients with DNAH3 variants and Dnah3 KO mice could be rescued by intracytoplasmic sperm injection (ICSI) treatment. Our findings indicated that DNAH3 is a novel pathogenic gene for asthenoteratozoospermia and may further contribute to the diagnosis, genetic counseling, and prognosis of male infertility.

genetics↗

bioRxiv2023

Robust and Adaptive Deep Model Ensemble Framework Fine-tuned by Structural Information for Drug-Target Interactions

In the fields of new drug development and drug repositioning, drug-target interactions (DTI) play a pivotal role. Although deep learning models have already made significant contributions in this domain, the state-of-the-art models still exhibit shortcomings in predictive performance and issues of false-negative errors. Based on these observations, we constructed a streamlined yet effective base learner model. With our designed adaptive feature weight network, the model can capture key features within drugs (targets). Furthermore, by cross-partitioning the training data, multiple base learners are integrated into a powerful ensemble model named EADTN. The performance of the model is further enhanced as the number of base learners increases. Additionally, we employed a single-linkage clustering algorithm to cluster drugs and proteins and leveraged this clustering information to fine-tune the base learners, which elevates the value of EADTN in real-world applications like drug repositioning and targeted drug development. Our designed substructure importance ranking method also demonstrates the models exceptional capability to recognize key substructures. Benefiting from the models low generalization error capability, we successfully identified false-negative samples within the dataset, revealing new interaction relationships. Experimental results indicate that EADTN consistently outperforms existing state-of-the-art models across multiple datasets. More importantly, the ensemble learning and clustering fine-tuning approaches adopted by our model offer a fresh perspective for related fields.

bioinformatics↗

bioRxiv2023

DnaK duplicates and regionally evolves for the increase of proteomic complexity in bacteria

Hsp70 is important for organismic cells to maintain proteostasis and the chaperone protein is duplicated in all eukaryotes and many prokaryotes. Although the functioning mechanism of Hsp70 has been clearly illuminated, the chaperone duplication and functional evolution has been less investigated. DnaK is a highly conserved bacterial Hsp70 family. Here we showed that the dnaK gene is present in 98.9% bacteria and 6.4% bacteria possess duplicated dnaKs; the occurrence and duplication is positively corelated to the increase of proteomic complexity. We identified the interactomes of the two DnaK paralogs in Myxococcus xanthus DK1622, which are mostly nonoverlapped, but both preferring the &{beta} domain proteins. Consistent with the proteomes, the MxDnaK substrates are both significantly size-larger and pI-higher than that of the single E. coli DnaK. MxDnaK1 is heat-shock inducible, prefers to bind cytosolic proteins, while MxDnaK2 is decreased by heat shock, and is more associated with membrane proteins. The nucleotide binding domain and the substrate binding beta domain are responsible for the significant changes of DnaK substrates, and the former also determines the dimerization of MxDnaK2, but not MxDnaK1. Our work highlights that DnaK is duplicated and regionally evolved for the increase of proteomic complexity in bacteria.

microbiology↗

bioRxiv2020

The ParAs function is realized by two separate proteins in the partitioning system of Myxococcus plasmid pMF1

The par operon in the sole myxobacterial plasmid pMF1 includes a function-unknown parC gene in front of the classical parA and parB genes. Removal of parC severely reduced plasmid stability, but ex-situ compensations of parC did not restore the par system function. Individual expression of parA formed insoluble proteins, while co-expression of parC before parA produced a soluble ParC-ParA heterodimer. ParA alone had no ATPase activity and no polymerization, while ParC addition aided ParA to restore the activities. Fusing ParC and ParA in different ways all produced soluble proteins and some restored ATPase activity or increased plasmid stability. Protein interaction model analysis and experiments revealed that ParC structurally mimics the N-terminal of Ia-type SopA (ParA), endowing the Myxococcus ParA protein to play functions by shifting of ParC between two sites on ParA surface. The present results highlight that ParC functions as a part of ParA to support its soluble expression and function, and the separation of ParC and ParA into two proteins in structure enables the ParC fragment to shift in a larger range around ParA to function during partitioning. Author summaryOur work on ParC here provides a new example for the evolution of multi-domain protein. ParC and ParA are two proteins, but their expression and function act as a whole, which proposes a new regulatory model for bacterial par system, and also provides research ideas and materials for the study of functional coordination and evolution of ParA domains in the future.

microbiology↗

bioRxiv2019

Temporal regulation of prenatal embryonic development by paternal imprinted loci

H19 and Gtl2 are paternal imprinted genes that are pivotal for prenatal embryonic development. Meanwhile, mouse nongrowing oocytes and sperm- or oocyte-originated haploid embryonic stem cells (haESCs) carrying both H19 and IG-DMR (differentially DNA-methylated region) deletions (DKO) that partially mimic paternal imprinting of H19-Igf2 and Dlk1-Dio3 can be employed as sperm replacement to efficiently support full-term embryonic development. However, how H19-DMR and IG-DMR act together to regulate embryonic development is still largely unknown. Here, using androgenetic haESC (AG-haESC)-mediated semi-cloned (SC) technology, we showed that paternal H19-DMR and IG-DMR are not essential for pre-implantation development of SC embryos generated through injection of AG-haESCs into oocytes. H19-DMR plays critical roles before 12.5 days of gestation while IG-DMR is essential for late-gestation of SC embryos. Interestingly, we found that combined deletions of H19 and H19-DMR can further improve the efficiency of normal development of SC embryos at mid-gestation compared to DKO SC embryos. Transcriptome and histology analyses revealed that H19 and H19-DMR combined deletions rescue the placental defects. Furthermore, we showed that H19, H19-DMR and IG-DMR deletions (TKO) give rise to better prenatal and postnatal embryonic development of SC embryos compared to DKO. Together, our results indicate the temporal regulation of paternal imprinted loci during embryonic development.

developmental biology↗

bioRxiv2018

The landscape and diagnostic potential of T and B cell repertoire in Immunoglobulin A Nephropathy

Immunoglobulin A Nephropathy (IgAN) is the most common glomerulonephritis worldwide. In IgAN, immune complex deposite in glomerular mesangium, which induce inflammation and affect the kidneys normal functions. However, the exact pathogenesis of IgAN is still incompletely understood. Further, in current practice the clinical diagnosis relies on needle biopsy on renal tissue. Therefore, a non-invasive method for clinical diagnosis and prognosis surveillance of the disease is in high demand. In this paper, we investigated both the T cell receptor bata chain (TCRB) and immunoglobulin heavy chain (IGH) repertoire of kidney infiltrating and circulating lymphocytes of IgAN patients by immune repertoire high throughput sequencing. We found that the features of TCRB and IGH in the renal tissues were remarkably different from that in blood, including a decreased repertoire diversity and increased IgA and IgG frequency, and more activated B cells. The CDR3 length of PBMC TCRB and IGH in patients is significantly shorter than that in healthy controls, which is the result of both VDJ rearrangement and clone selection. We also found that the IgA1 frequency in the PBMC of IgAN is significant higher than that in other Nephropathy (NIgAN) and healthy control, which is consistent with the previous reports on the level of IgA1 producing B cells and serum IgA1. Significantly, we identified a set of IgAN disease related TCRB and IGH CDR3s, which can be used to distinguish IgAN from NIgAN and healthy controls from the blood with high accuracy. These results indicated that TCRB and IGH repertoire can potentially serve as non-invasive biomarkers for IgAN diagnosis. The characteristics of kidney infiltrating and circulating lymphocytes repertoire shed light on IgAN detection, treatment and surveillance.

immunology↗