Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 559 records · Page 31Linked to original sources

bioRxiv2023

Dynamic enhancer interactome promotes senescence and aging

Gene expression programs are regulated by enhancers which act in a context-specific manner, and can reside at great distances from their target genes. Extensive three-dimensional (3D) genome reorganization occurs in senescence, but how enhancer interactomes are reconfigured during this process is just beginning to be understood. Here we generated high-resolution contact maps of active enhancers and their target genes, assessed chromatin accessibility, and established one-dimensional maps of various histone modifications and transcription factors to comprehensively understand the regulation of enhancer configuration during senescence. Hyper-connected enhancer communities/cliques formed around genes that are highly expressed and within essential gene pathways in each cell state. In addition, motif analysis indicates the involvement of specific transcription factors in hyper-connected regulatory elements in each condition; importantly, MafK, a bZIP family transcription factor, was upregulated in senescence, and reduced expression of MafK ameliorated the senescence phenotypes. Because the accumulation of senescent cells is a key feature of aging, we further investigated enhancer connectomes in the liver of young and aged mice. Hyper-connected enhancer communities were identified during aging, which regulate essential genes that maintain cell differentiation and homeostasis. These findings reveal that hyper-connected enhancer communities correlate with high gene expression in senescence and aging and provide potential hotspots for therapeutic intervention in aging and age-associated diseases.

molecular biology↗

bioRxiv2023

UBL3 Interacts with Alpha-synuclein in Cells and the Interaction is Downregulated by the EGFR Pathway Inhibitor Osimertinib

Ubiquitin-like 3 (UBL3) acts as a post-translational modification (PTM) factor and regulates protein sorting into small extracellular vesicles (sEVs). sEVs have been reported as vectors for the pathology propagation of neurodegenerative diseases, such as -synucleinopathies. Alpha-synuclein (-syn) has been widely studied for its involvement in -synucleinopathies. However, it is still unknown whether UBL3 interacts with -syn, and is influenced by drugs or compounds. In this study, we investigated the interaction between UBL3 and -syn, and any ensuing possible functional and pathological implications. We found that UBL3 can interact with -syn by the Gaussia princeps based split luciferase complementation assay in cells and immunoprecipitation, while cysteine residues at its C-terminal, which are considered important as PTM factors for UBL3, were not essential for the interaction. The interaction was upregulated by 1-methyl-4-phenylpyridinium exposure. In drug screen results, the interaction was significantly downregulated by the treatment of osimertinib. These results suggest that UBL3 interacts with -syn in cells and be significantly downregulated by epidermal growth factor receptor (EGFR) pathway inhibitor osimertinib. Therefore, the UBL3 pathway may be a new therapeutic target for -synucleinopathies in the future.

molecular biology↗

bioRxiv2023

eIF2B Activator Rescues Neonatal Lethality of an eIF2Bα Sugar Phosphate Binding Mutation Associated with Vanishing White Matter Disease

eIF2B is a decameric guanine nucleotide exchange factor (GEF) that is essential for protein synthesis and a key effector of the integrated stress response (ISR). Hypomorphic mutations in any of the eIF2B subunits are associated with Vanishing White Matter Disease (VWM), a leukodystrophy characterized by ISR activation and white matter loss. Here, we showed that the VWM-associated N208Y eIF2B mutation, which abolishes sugar phosphate binding, led to a drastic reduction in its level in cells and concomitant ISR activation. We found that N208Y homozygous mice are small and die shortly after birth. Remarkably, continuous availability of 2BAct, a small molecule eIF2B activator, in food rescued the lethality and significantly extended their lifespan. 2BAct-maintained N208Y homozygous mice, however, developed motor deficits and loss of myelin with age. As is the case for milder VWM models, ISR induction was restricted to the central nervous system in treated animals. Upon 2BAct withdrawal, adult mutant mice deteriorated quickly, the ISR was induced in all peripheral tissues tested and resulted in high levels of circulating FGF21 and GDF15. This model provides a novel platform to study the impact of ISR activation across tissues with temporal control.

neuroscience↗

bioRxiv2023

Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the viability of employing PFB or SFB samples as substitute RNA sources in transcriptomic analysis and performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples in terms of protein-coding gene expression patterns, differential expression gene profiling, and immunological characterizations, suggesting that PFB can be a viable alternative for transcriptomic analysis. This contributes to the optimization of blood sample utilization and the advancement of precision medicine research.

bioinformatics↗

bioRxiv2023

Vacuolar H+-ATPase subunit a was identified as the target protein of the oomycete inhibitor fluopicolide

Approximately 240 fungicides are currently in use. However, only a few direct targets have been identified, which limits the development of fungicides and rapid resistance monitoring. Fluopicolide, which is an excellent oomycete inhibitor, is classified as delocalization of spectrin-like proteins inhibitors by FRAC. In the current study, a Pc-actinin knockout had no effect on the sensitivity of Phytophthora capsici to fluopicolide. The vacuolar H+-ATPase subunit a (PcVHA-a) was identified using a BSA-seq and DARTS assay. Four kinds of point mutations in PcVHA-a that cause fluopicolide resistance in P. capsici were confirmed using site-directed mutagenesis. The results of MST, molecular docking, and a DARTS assay indicated that PcVHA-a could bind fluopicolide. Sequence analysis and a molecular docking assay proved the specificity of fluopicolide to oomycetes or fish. Our results suggest that PcVHA-a is the target of fluopicolide, and H+-ATPase could be used as a novel target for the development of new fungicides.

pharmacology and toxicology↗

bioRxiv2023

Tailored chemical reactivity probes for systemic imaging of aldehydes in fibroproliferative diseases

During fibroproliferation, protein-associated extracellular aldehydes are formed by the oxidation of lysine residues on extracellular matrix proteins to form the aldehyde allysine. Here we report three Mn(II)-based, small molecule magnetic resonance (MR) probes that contain -effect nucleophiles to target allysine in vivo and report on tissue fibrogenesis. We used a rational design approach to develop turn-on probes with a 4-fold increase in relaxivity upon targeting. The effects of aldehyde condensation rate and hydrolysis kinetics on the performance of the probes to detect tissue fibrogenesis noninvasively in mouse models were evaluated by a systemic aldehyde tracking approach. We showed that for highly reversible ligations, off-rate was a stronger predictor of in vivo efficiency, enabling histologically validated, three-dimensional characterization of pulmonary fibrogenesis throughout the entire lung. The exclusive renal elimination of these probes allowed for rapid imaging of liver fibrosis. Reducing the hydrolysis rate by forming an oxime bond with allysine enabled delayed phase imaging of kidney fibrogenesis. The imaging efficacy of these probes, coupled with their rapid and complete elimination from the body, make them strong candidates for clinical translation.

biochemistry↗

bioRxiv2023

Organohalide respiration by a Desulforhopalus-dominated community

Despite the fact that several potential organohalide-respiring bacteria (OHRB) were discovered in metagenome-assembled genomes (MAGs) in our previous study of marine sediments from Aarhus Bay, delineation of their roles and interactions are yet to be disentangled. Henceforth, obtaining corresponding pure cultures or more defined consortia would be highly instrumental for more detailed eco-physiological studies. To this end, we isolated a colony from an anaerobic slant tube culture inoculated with a stable PCE dehalogenating enrichment. Intriguingly, the derived culture exhibited debromination only, instead of PCE dechlorination, under sulfate-reducing conditions. The culture was capable of conserving energy for growth via debromination of 2,6-dibromophenol (2,6-DBP). Analysis of 16S rRNA gene sequence data extracted from shot gun metagenome sequences revealed that a strain belonging to Desulforhopalus was the predominant member of the consortium at a relative abundance of 29 %. Moreover, five bins (completeness > 85% and contamination < 3%) were assembled and all were identified as potentially new species (average nucleotide identity, ANI < 95%). Two bins from potential OHRB, bin.3 belonging to Desulfoplanes, and bin.4 belonging to Marinifilaceae, were found to encode reductive dehalogenase (RDase) genes, whereas bin.5 was found to contain a gene coding for thiolytic tetrachloro-p-hydroquinone (TPh-) RDase bearing 23.4 % identity to TPh-RDase of Sphingobium chlorophenolicum. The expression of all three RDase genes was strongly-induced after adding 2,6-DBP. Acetylene, a known inhibitor of different redox-active metalloenzymes, was found to inhibit methanogenesis as well as reductive dehalogenation without affecting gene expression, suggesting post-transcriptional inhibition. Phylogenomic analyses revealed the ecological importance of complementary roles of community members, including complete de novo vitamin B12 biosynthesis, which agreed with physiological data. Altogether, the findings presented here provided insight into the mutualism of the consortium and provided leads for synthetic OHR community optimization strategies for in situ bioremediation.

microbiology↗

bioRxiv2023

Genome-resolved transcriptomics reveals novel organohalide-respiring bacteria from Aarhus Bay sediments

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from PCE-respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 high quality bins with over 75 % completeness and less than 5 % contamination. Sixteen bins harbored RDase genes, and were affiliated taxonomically to the class of Bacilli, and phyla of Bacteroidota, Synergistota, and Spirochaetota, that have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically closely related to the genus Vulcanibacillus, contained an unprecedented 97 RDase genes. Of these, 84 RDase genes of bin.26 were transcribed during PCE dechlorination in addition to RDase genes from members of Synergistales (bin.15 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested the RDase genes were likely under the regulation of transcriptional regulators not previously associated with OHR, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to provide evidence towards the diversity, activity and regulation of reductive dehalogenases.

microbiology↗

bioRxiv2023

ANP rescues the preeclamptic symptoms in Axl knockout mice by improving trophoblast function

Pre-eclampsia (PE) is characterized by maternal hypertension and/or proteinuria after 20 weeks of gestation. Shallow trophoblast invasion into spiral artery (SpA) and defective decidualization have been implicated in the pathogenesis of PE. However, the underlying mechanisms remain unclear. AXL receptor tyrosine kinase is a biomarker and therapeutic target for a variety of metastatic cancers while tumorigenesis and placentation share many features. In this study, a new function of AXL in promoting SpA remodeling and trophoblast invasion were demonstrated. The pregnant Axl knockout (Axl-/-) mice exhibited typical PE symptoms, including increased blood pressure and proteinuria. Artificially induced decidualization experiments showed that appeared normal, however, RNA-seq results of Axl-/- deciduoma revealed abnormal expression of a number of transcripts, including Corin, which encodes a cardiac protease that activates atrial natriuretic peptide (ANP). Treatment with ANP reversed the PE symptoms. Moreover, in decidua from women afflicted with PE, AXL level was significantly lower than that in normal pregnancies. These data show that the abnormality of decidua-derived AXL-CORIN-ANP affects maternal-fetal crosstalk and contributes to PE.

pathology↗

bioRxiv2023

FGF-21 Conducts a Liver-Brain-Kidney Axis to Promote Renal Cell Carcinoma

Metabolic homeostasis is one of the most exquisitely tuned systems in mammalian physiology. Metabolic homeostasis requires multiple redundant systems to cooperate to maintain blood glucose concentrations in a narrow range, despite a multitude of physiological and pathophysiological pressures. Cancer is one of the canonical pathophysiological settings in which metabolism plays a key role. In this study, we utilized REnal Gluconeogenesis Analytical Leads (REGAL), a liquid chromatography-mass spectrometry/mass spectrometry-based stable isotope tracer method that we developed to show that in conditions of metabolic stress, the fasting hepatokine fibroblast growth factor-21 (FGF-21)1, 2 coordinates a liver-brain-kidney axis to promote renal gluconeogenesis. FGF-21 promotes renal gluconeogenesis by enhancing {beta}2 adrenergic receptor (Adrb2)-driven, adipose triglyceride lipase (ATGL)-mediated intrarenal lipolysis. Further, we show that this liver-brain-kidney axis promotes gluconeogenesis in the renal parenchyma in mice and humans with renal cell carcinoma (RCC). This increased gluconeogenesis is, in turn, associated with accelerated RCC progression. We identify Adrb2 blockade as a new class of therapy for RCC in mice, with confirmatory data in human patients. In summary, these data reveal a new metabolic function of FGF-21 in driving renal gluconeogenesis, and demonstrate that inhibition of renal gluconeogenesis by FGF-21 antagonism deserves attention as a new therapeutic approach to RCC.

physiology↗

bioRxiv2023

A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments

Cold seeps harbor abundant and diverse microbes that represent a tremendous potential for biological applications and also have a significant influence on biogeochemical cycles. Though recent metagenomic studies have expanded our understanding of the microbial community and function of seep microorganisms, the knowledge of diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic data from 16 cold seep sites across the globe to construct comprehensive gene and genome catalogs. The non-redundant gene catalog was comprised of 147 million genes (clustered at 95% amino acid identity), and 35.72% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) are obtained, most of which (94.31%) belong to novel species. Of them, 81 ANME species are identified covering all subclades except ANME-2d, and 23 syntrophic SRB species spanning Seep-SRB1a Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAGs catalogs are a valuable resource that enables expanded knowledge of the structure and functions of cold seep microbiomes.

microbiology↗

bioRxiv2023

The BTB-ZF gene Bm-mamo regulate pigmentation in caterpillars

The color pattern of insects is one of the most diverse adaptive evolutionary phenotypes. However, the molecular regulation of this color pattern is not fully understood. In this study, we found that the transcription factor Bm-mamo is responsible for black dilute (bd) allele mutations in the silkworm. Bm-mamo belongs to the BTB zinc finger family and is orthologous to mamo in Drosophila melanogaster. This gene has a conserved function in gamete production in Drosophila and silkworms and has evolved a pleiotropic function in the regulation of color patterns in caterpillars. Using RNAi and clustered regularly interspaced short palindromic repeats (CRISPR) technology, we showed that Bm-mamo is a repressor or has dark melanin patterns in the larval epidermis. Using in vitro binding assays and gene expression profiling in wild-type and mutant larvae, we also showed that Bm-mamo likely regulates the expression of related pigment synthesis and cuticular protein genes in a coordinated manner to mediate its role in color pattern formation. This mechanism is consistent with the dual role of this transcription factor in regulating both the structure and shape of the cuticle and the pigments that are embedded within it. This study provides new insight into the regulation of color patterns as well as into the construction of more complex epidermis features in some insects.

genetics↗

bioRxiv2023

Identification of a novel MCR-1 variant displaying low level of co-resistance to β-lactam antibiotics that uncovers a potential novel antimicrobial peptide

The emerging and global spread of a novel plasmid-mediated colistin resistance gene, mcr-1, threatens human health. It is accepted that MCR-1 affects bacterial fitness, and this fitness cost correlates with bacterial membrane lipid A perturbation. However, the detailed molecular mechanism remains unclear. Here, we screened out a novel MCR-1 variant, named M6, with a two-point mutation that rendered a low level of co-resistance to {beta}-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe lipid A perturbation resulting in peptidoglycan layer remodelling and thus resulted in phenotypic co-resistance to {beta}-lactams. Moreover, we found that a lipid A loading cavity is localized at the linker domain of MCR-1 and governs colistin resistance and bacterial membrane permeability, and the mutated pocket of M6 facilitates the binding affinity of lipid A. More importantly, synthetic peptides derived from M6 achieved broad-spectrum antimicrobial activity. These findings provide insights into a potential vulnerability that could be exploited in future antimicrobial drug design.

microbiology↗

bioRxiv2023

Active-feedback 3D single-molecule tracking using a fast-responding galvo scanning mirror

Real-time three-dimensional single-particle tracking (RT-3D-SPT) allows continuous detection of individual freely diffusing objects with high spatiotemporal precision by applying closed-loop active feedback in an optical microscope. However, the current tracking speed in RT-3D-SPT is primarily limited by the response time of control actuators, impeding long-term observation of fast diffusive objects such as single molecules. Here, we present an RT-3D-SPT system with improved tracking performance by replacing the XY piezoelectric stage with a galvo scanning mirror with an approximately five-time faster response rate (~5 kHz). Based on the previously developed 3D single-molecule active real-time tracking (3D-SMART), this new implementation with a fast-responding galvo mirror eliminates the mechanical movement of the sample and allows more rapid response to particle motion. The improved tracking performance of the galvo mirror-based implementation is verified through simulation and proof-of-principle experiments. Fluorescent nanoparticles and ~ 1 kB double-stranded DNA molecules were tracked via both the original piezoelectric stage and new galvo mirror implementations. With the new galvo-based implementation, notable increases in tracking duration, localization precision, and the degree to which the objects are locked to the center of the detection volume were observed. These results suggest faster control response elements can expand RT-3D-SPT to a broader range of chemical and biological systems.

biophysics↗

bioRxiv2023

TTG2 defines trichome cell shape by modulating microtubules and actin cytoskeleton in Arabidopsis

The Arabidopsis TRANSPARENT TESTA GLABRA2 (TTG2) gene encodes a WRKY transcription factor that regulates a range of development events like trichome, seed coat, and atrichoblasts formation. Loss-of-function of TTG2 was previously shown to reduce or eliminate trichome branching. Here, we report the identification of a new allele of TTG2, ttg2-6. In contrast to the ttg2 mutants described before, ttg2-6 displays unique trichome phenotypes. Some ttg2-6 mutant trichomes are hyperbranched, whereas others are hypobranched, distorted, or clustered. Further, we found that in addition to specifically activating R3 MYB transcription factor TRIPTYCHON (TRY) to promote trichome branching, TTG2 also integrates cytoskeletal signaling to regulate trichome morphogenesis. The ttg2-6 trichomes display aberrant cortical microtubules (cMTs) and cortical actin filaments (F-actin) configurations. Moreover, genetic and biochemical analysis showed that TTG2 could directly bind and regulate the expression of BRICK1 (BRK1), a subunit of the actin nucleation promoting complex SCAR/WAVE. Collectively, taking advantage of ttg2-6, we uncovered new functions for TTG2 in facilitating cMT and F-actin cytoskeleton-dependent trichome development. Our evidence for a direct relationship between TTG2 and cytoskeletal regulators establishes an unprecedented understanding of cellular signaling events downstream of the core transcriptional regulation during trichome development in Arabidopsis.

developmental biology↗

bioRxiv2023

Re-evaluating the nuclear staining on pathological sections in Alzheimer's disease

A paper recently published on Nature Neuroscience, asserting that lysosome leakage induces neuronal cell death and the formation of senile plaques in Alzheimers disease. The study believed that flower-like perikaryal rosettes formed by packed autophagic vacuoles around central nuclei, termed "PANTHOS" neurons, are responsible for the senile plaque formation. However, all of the nuclei staining in this paper based on images in the blue fluorescence channel. We did detailed studies on the senile plaque blue autofluorescence and found that senile plaque blue autofluorescence could be easily mistaken as nuclear staining. The blue "nuclear" staining in this paper is probably inaccurate since it was not verified in red or green fluorescence channels and their "nuclei"-related data might be mis-interpreted.

neuroscience↗

bioRxiv2023

Constitutive expression of the Type VI secretion system carries no measurable fitness cost in Vibrio cholerae

The Type VI Secretion System (T6SS) is a widespread and highly effective mechanism of microbial warfare; it confers the ability to efficiently kill susceptible cells within close proximity. Due to its large physical size, complexity, and ballistic basis for intoxication it has widely been assumed to incur significant growth costs in the absence of improved competitive outcomes. In this study, we precisely examine the fitness costs of constitutive T6SS firing in the bacterium Vibrio cholerae. We find that, contrary to expectations, constitutive use of T6SS has a negligible impact on growth, reducing growth fitness by 0.025 {+/-} 0.5% (95% CI) relative to a T6SS-control. Mathematical modeling of microbial populations demonstrates that, due to clonal interference, constitutive expression of the T6SS will often be neutral, with little impact on evolutionary outcomes. Our findings underscore the importance of precisely measuring the fitness costs of microbial social behaviors, and help explain the prevalence of the T6SS across Gram negative bacteria.

microbiology↗

bioRxiv2023

De novo mutation rates in sticklebacks

Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what is the expected level of genetic diversity in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates ({micro}) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50x) whole genome re-sequencing and a high-quality reference genome. After stringent filtering, we discovered 295 germline mutations from 106 offspring translating to {micro} = 4.64 x 10-9 and {micro} = 4.08 x 10-9 per base, per generation, in the two populations, respectively. Twenty percent of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated {micro} was 3.2 times smaller than the commonly used substitution rate, recalibration with {micro} led to substantial increase in estimated divergence times between different stickleback species. Our estimates of de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

genomics↗