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Yang, J.

Publications and source records attributed to Yang, J..

At least 523 records · Page 29Linked to original sources
bioRxiv2023

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TFs DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TFs binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.

genomics↗
bioRxiv2023

Spatial transcriptomics of peach and nectarine elucidates the mechanism underlying fruit trichome development

Peach (Prunus persica) is an economically significant fruit-bearing tree. The trichomes of peach fruits are essential for their growth and development by playing a protective role against abiotic stresses, such as intense ultraviolet (UV) light, high temperature, cold-induced stress, and biotic stresses, such as pests and disease infestation. However, the mechanism underlying trichome development in peach fruits is unknown. Therefore, spatial transcriptome sequencing technology was used to compare the transcriptomic information seven days after flowering (DAF) of peach and nectarine fruits at an ultra-high resolution. The results revealed significant variations in how fruits at the early development stage responded to stress exposure. Comparatively, nectarine response to stress was significantly magnified than peach. Notably, a novel trichome-related marker gene, Prupe.7G196500, was identified in peach, which showed a robust function in response to jasmonic acid and wounding. Further, the Prupe.7G196500pro::GUS construct was found to specifically expressed in the trichomes of the true leaves of 10-day-old Arabidopsis thaliana (Arabidopsis) seedlings and induced by drought treatment. Finally, gain-of-function analysis showed that Prupe.7G196500 promoted trichomes development. In conclusion, this study identified the cell types and novel marker genes associated with peach fruit. The role of Prupe.7G196500 in positively regulating trichome development was also characterized, thereby laying the foundation for analyzing the mechanism involved in trichome development in peach fruits.

developmental biology↗
bioRxiv2023

Differential Chromatin Architecture and Risk Variants in Deep Layer Excitatory Neurons and Grey Matter Microglia Contribute to Major Depressive Disorder

Major depressive disorder (MDD) associated genetic variants reside primarily in the non-coding, regulatory genome. Here we investigate genome-wide regulatory differences and putative gene-regulatory effects of disease risk-variants by examining chromatin accessibility combined with single-cell gene-expression profiles in over 200,000 cells from the dorsolateral prefrontal cortex (DLPFC) of 84 individuals with MDD and neurotypical controls. MDD-associated accessibility alterations were prominent in deep-layer excitatory neurons characterized by transcription factor (TF) motif accessibility and binding of nuclear receptor (NR)4A2, an activity-dependent TF responsive to pathological stress. The same neurons were significantly enriched for MDD-associated genetic variation disrupting cis-regulatory sites and TF binding associated with genes involved in synaptic communication. Furthermore, a grey matter microglial cluster exhibited differentially closed chromatin in MDD affecting binding sites bound by TFs known to regulate immune homeostasis. In summary, our study points to specific cell types and regulatory mechanisms whereby genetic variation may increase predisposition to MDD.

genomics↗
bioRxiv2023

Investigation of H9N2 avian influenza immune escape mutant that lacks haemagglutination activity

H9N2 avian influenza viruses pose a global threat to animal and human health. While vaccination is essential for mitigating disease impact, these viruses evolve to evade vaccine immunity through changes in the haemagglutinin (HA) glycoprotein. In this study, we identified immune escape mutation in an H9N2 virus resulting from pressure exerted by homologous chicken antisera. The immune-escape variant acquired an amino acid substitution, replacing glycine (G) with glutamic acid (E) at position 149 in the HA protein. The G149E mutant virus lost the ability to agglutinate chicken erythrocytes, while still maintaining replication comparable to the wild-type virus in chicken embryos and cells. This led to the hypothesis that the G149E substitution, leading to a shift from a neutral to a negative charge polarity at HA position 149, might be crucial for the optimal interaction between the virus and receptors on erythrocytes. Investigation indicated that agglutination could be restored by substituting E to positively charged amino acids histidine (H), arginine (R) or lysine (K). These findings suggest that the H9N2 virus may be likely acquire the G149E mutation under immune pressure in nature. This mutation poses challenges to vaccination and surveillance efforts as it partially evades immune protection and is not easily detectable by conventional haemagglutination assays. This underscores the intricate interplay between antigenic variation and viral traits, emphasising the critical need for ongoing surveillance and research to effectively mitigate the risks associated with avian influenza H9N2 viruses. IMPORTANCEUnderstanding how avian influenza viruses evolve to persist in nature is crucial for enhancing disease mitigation tools such as vaccines, diagnostics, and risk assessment. In this study, we identified an H9N2 virus antibody escape mutant with G149E mutation in the haemagglutinin that had lost the ability to agglutinate chicken erythrocytes, while retaining infectivity and replication fitness. The lack of haemagglutination activity potentially negatively impacts routine surveillance and commonly used diagnostics such as haemagglutination assay or haemagglutination inhibition assay. Therefore, it is urgent to develop and adopt alternative methods for viral detection. Difficult to detect variants potentially that are not compatible with common surveillance techniques could circulate remain silent while reassort with other influenza viruses, which posing unpredictable risks to animal and human health. This research helps us better understand avian influenza, leading to improved disease control, diagnostics, and risk assessment to protect both animals and humans.

microbiology↗
bioRxiv2023

Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation

Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in >70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation.

systems biology↗
bioRxiv2023

Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos

In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb the long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in [~]2667 insertions throughout the mouse genome. CRISPRi robustly repressed 2485 ([~] 93%) MT2_Mm insertions and 1090 ([~]55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at the 2-cell stage and embryonic arrest mostly at the morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by OBOX proteins. Thus, through unprecedented large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesnt require transgenic animals.

developmental biology↗
bioRxiv2023

In vivo Imaging using Surface Enhanced Spatially Offset Raman Spectroscopy (SESORS): Balancing Sampling Frequency to Improve Overall Image Acquisition

Background and RationaleIn the field of optical imaging, the ability to image tumors at depth with high selectivity and specificity remains a challenge. Surface enhanced resonance Raman scattering (SERRS) nanoparticles (NPs) can be employed as image contrast agents to specifically target cells in vivo, however, this technique typically requires time-intensive point-by-point acquisition of Raman spectra, thus hindering the real-time image acquisition desired for clinical applications. Moreover, traditional approaches involving Raman spectroscopy are limited in their inability to probe through tissue depths of more than a few millimeters. Here, we combine the use of "spatially offset Raman spectroscopy" (SORS) with that of SERRS in a technique known as "surface enhanced spatially offset resonance Raman spectroscopy" (SESORRS) to image deep-seated tumors in vivo. Additionally, by accounting for the laser spot size, we report an experimental SESORRS approach for detecting both the bulk tumor, subsequent delineation of tumor margins at high speed, and the identification of a deeper secondary region of interest with fewer measurements than are typically applied. MethodsTo enhance light collection efficiency, four modifications were made to a previously described custom-built SORS system. Specifically, the following parameters were increased: (i) the numerical aperture (NA) of the lens, from 0.2 to 0.34; (ii) the working distance of the probe, from 9 mm to 40 mm; (iii) the NA of the fiber, from 0.2 to 0.34; and (iv) the fiber diameter, from 100 {micro}m to 400 {micro}m. To calculate the sampling frequency, which refers to the number of data point spectra obtained for each image, we considered the laser spot size of the elliptical beam (6 x 4 mm). Using SERRS contrast agents, we performed in vivo SESORRS imaging on a GL261-Luc mouse model of glioblastoma at four distinct sampling frequencies: par-sampling frequency (12 data points collected), and over-frequency sampling by factors of 2 (35 data points collected), 5 (176 data points collected), and 10 (651 data points collected). ResultsIn comparison to the previously reported SORS system, the modified SORS instrument showed a 300% improvement in signal-to-noise ratios (SNR). Glioblastomas were imaged in vivo using SESORRS in mice (n = 3) and tumors were confirmed using MRI and histopathology. The results demonstrate the ability to acquire distinct Raman spectra from deep-seated glioblastomas in mice through the skull using a low power density (6.5 mW/mm2) and 30-times shorter integration times than a previous report (0.5 s versus 15 s). The ability to map the whole head of the mouse and determine a specific region of interest using as few as 12 spectra (6 second total acquisition time) is achieved. Subsequent use of a higher sampling frequency demonstrates it is possible to delineate the tumor margins in the region of interest with greater certainty. In addition, SESORRS images indicate the emergence of a secondary tumor region deeper within the brain in agreement with MRI and H&E staining. ConclusionIn comparison to traditional Raman imaging approaches, this approach enables improvements in the rapid detection of deep-seated tumors in vivo through depths of several millimeters due to improvements in SNR, spectral resolution, and depth acquisition. This approach offers an opportunity to navigate larger areas of tissues in shorter time frames than previously reported, identify regions of interest, and then image such area with greater resolution using a higher sampling frequency. Moreover, using a SESORRS approach, we demonstrate that it is possible to detect secondary, deeper-seated lesions through the intact skull.

bioengineering↗
bioRxiv2023

Reinstatement of CDX2 as a differentiation therapy for colorectal cancers

Despite advances in artificial intelligence (AI) within cancer research, its application toward realizing differentiation therapy in solid tumors remains limited. Using colorectal cancer (CRC) as a model, we developed a machine learning (ML) framework, CANDiT (Cancer Associated Nodes for Differentiation Targeting), to selectively induce differentiation and death of cancer stem cells (CSCs)--a key obstacle to durable response. Centering on one node, CDX2, a master differentiation factor lost in high-risk, poorly differentiated CRCs, we built a transcriptomic network to identify therapeutic strategies for CDX2 restoration. Network-based prioritization identified PRKAB1, a stress polarity sensor, as a top target. A clinical-grade PRKAB1 agonist reprogrammed transcriptional networks, induced crypt differentiation, and selectively eliminated CDX2-low CSCs in CRC cell lines, xenografts and patient-derived organoids (PDOs). Multivariate analyses in PDOs revealed a strong therapeutic index, linking efficacy (IC) to the biomarker-defined CDX2-low state. A 50-gene response signature--derived from an integrated analyses of all three models and trained across multiple datasets--revealed that CDX2 restoration therapy may translate into a [~]50% reduction in recurrence and mortality risk. Mechanistically, treatment activated a differentiation-associated stress polarity signaling axis while dismantling Wnt and YAP-driven stemness programs essential to CSC survival. Thus, CANDiT offers a scalable path to CSC-directed therapy in solid tumors by translating transcriptomic vulnerabilities into precision treatments. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/557628v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@16eeb1eorg.highwire.dtl.DTLVardef@10e308borg.highwire.dtl.DTLVardef@9512f0org.highwire.dtl.DTLVardef@10e74eb_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIn this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk. HighlightsO_LIAn ML framework (CANDiT) identifies target for differentiation therapy for CRCs C_LIO_LITherapy induces crypt differentiation and CSC-specific cytotoxicity C_LIO_LICDX2-low state predicts therapeutic response; restoration improves prognosis C_LIO_LITherapy dismantles stemness via reactivation of stress polarity signaling C_LI

cancer biology↗
bioRxiv2023

Quantitative Learning of Cellular Features From Single-cell Transcriptomics Data Facilitates Effective Drug Repurposing

In this study, we have devised a computational framework SuperFeat that allows for the training of a machine learning model and evaluate the canonical cellular states/features in pathological tissues that underlie the progression of disease. This framework also enables the identification of potential drugs that target the presumed detrimental cellular features. This framework was constructed on the basis of an artificial neural network with the gene expression profiles serving as input nodes. The training data comprised single-cell RNA-seq datasets that encompassed the specific cell lineage during the developmental progression of cell features. A few models of the canonical cancer-involved cellular states/features were tested by such framework. Finally, we have illustrated the drug repurposing pipeline, utilizing the training parameters derived from the adverse cellular states/features, which has yielded successful validation results both in vitro and in vivo. SuperFeat is accessible at https://github.com/weilin-genomics/rSuperFeat.

cell biology↗
bioRxiv2023

New tree shrew Parkinson's model: a cost-effective alternative to monkey models

The surge in demand for experimental monkeys has led to a rapid increase in their associated costs. Consequently, there is a growing need for the development of a cost-effective model for Parkinsons disease (PD) that exhibits all core clinical and pathological phenotypes of PD. Evolutionarily, tree shrews (Tupaia belangeri) are much closer to primates in comparison to rodents and share more similar PD-related brain structures and movement ability with monkeys. As such, tree shrews represent an ideal small animal species for modeling PD. To develop a tree shrew PD model, we used the 1-Methyl-4-phenylpyridinium (MPP+) metabolite, derived from the well-established PD modeling drug 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), to induce lesions in the dopaminergic neurons of the unilateral substantia nigra. After determining the optimal modeling dosage, the tree shrews consistently exhibited and maintained all classic clinical manifestations of PD for a 5-month period. The symptoms closely resembled the ones observed in PD monkeys and included bradykinesia, rest tremor, postural instability, and apomorphine-induced rotations, a classic phenotype of unilateral PD models. Immunostaining showed a significant loss of dopaminergic neurons (approximately 95%) in the substantia nigra on the lesioned side of the brain, a crucial pathological marker of PD. Further cytomorphological analysis revealed that the size of nigral dopaminergic neurons in tree shrews exceeded that of rodents and more closely approximated that of macaques. Based on the principle that structure determines function, the morphological similarity between tree shrews and monkeys may be an important structural basis for the manifestation of the highly similar phenotypes between monkey and tree shrew PD models. Collectively, this study successfully developed a PD model in a small animal species that faithfully recapitulated the classical clinical symptoms and key pathological indicators of PD monkeys. In addition to the well-recognized monkey models, the tree shrew model provides a novel avenue for the evaluation of PD treatments and underlying mechanisms.

neuroscience↗
bioRxiv2023

Environmental factors and cultural drift influence song evolution in New World Sparrows

Variation in bird song is often assumed to be determined by sexual selection, rather than natural selection. However, most investigations to date have drawn their conclusions from a handful of species due to the challenges with manually processing sound data. Here, we use deep machine learning to investigate nearly all species of New World Sparrows. We leverage existing data to identify the processes that structure variation in bird song and to determine how this variation corresponds to patterns in genes and traits. Song variation in ~40% of species can be explained by environment, geography, and time. Across a community and global scale, the action of natural selection on the evolution of song is at least as impactful as it is on other genetically-determined traits.

evolutionary biology↗
bioRxiv2023

Resolving the climatic and ecological drivers of geographical gradients in avian sexual selection

Sexual selection, one of the central pillars of evolutionary theory, has powerful effects on organismal morphology, behaviour and population dynamics. However, current knowledge about geographical variation in this evolutionary mechanism and its underlying drivers remains highly incomplete, in part because standardized data on the strength of sexual selection is sparse even for well-studied organisms. Here we use information on mating systems - including the incidence of polygamy and extra-pair paternity - to quantify the intensity of sexual selection in 10671 (>99.9%) bird species distributed worldwide. We show that avian sexual selection varies latitudinally, peaking at higher latitudes, although the gradient is reversed in the worlds most sexually selected birds - specialist frugivores - which are strongly associated with tropical forests. Phylogenetic models further reveal that the strength of sexual selection is explained by temperature seasonality coupled with a suite of climate-associated factors, including migration, diet, and territoriality. Overall, these analyses suggest that climatic conditions leading to short, intense breeding seasons, or highly abundant and patchy food resources, increase the potential for polygamy in birds, driving latitudinal gradients in sexual selection. Our findings help to resolve longstanding debates about spatial variation in evolutionary mechanisms linked to reproductive biology, and provide a comprehensive species-level dataset for further studies of selection and phenotypic evolution in the context of global climatic change.

evolutionary biology↗
bioRxiv2023

Wall-following: phylogenetic context of an enhanced behaviour in stygomorphic Sinocyclocheilus (Cypriniformes: Cyprinidae) cavefishes

With 75 known species, the freshwater-fish genus Sinocyclocheilus is the largest cavefish radiation in the world, emerging as a model system for evolutionary studies. They show multiple adaptations for cave dwelling (stygomorphic adaptations), which include a range of traits such as eye degeneration (Normal-eyed, Micro-eyed and Eyeless), depigmentation of skin, and in some species, the presence of "horns". Their behavioural adaptations to subterranean environments, however, are poorly understood. Wall-following (WF) behaviour, where an organism remains in close contact with the boundary demarcating its habitat when in the dark, is a peculiar behaviour observed in a wide range of animals and is enhanced in some cave dwellers. Hence, we hypothesize wall-following to be present also in Sinocyclocheilus, possibly enhanced in Eyeless species compared to species with visual cues (Normal / Micro-eyed species). Using 13 species representative of Sinocyclocheilus radiation and eye-morphs, we designed a series of assays, based on pre-existing methods for Astyanax mexicanus behavioural experiments, to examine wall-following behaviour under three stimulation conditions. Our results indicate that eyeless species exhibit significantly enhanced levels of WF compared to Normal-eyed species, with Micro-eyed forms demonstrating intermediate levels. Using a mtDNA based dated phylogeny (chronogram with four clades A - D), we traced the degree of WF of these forms to outline common patterns. We show that intensity of WF behaviour is high in the subterranean clades (B & C) compared to clades with free-living species (A & D). Experiments on WF behaviour revealed that eyeless species are highly sensitive to vibrations, whereas normal-eyed species are the least sensitive. Since WF behaviour is present to some degree in all Sinocyclocheilus species, and given that these fishes evolved in the late Miocene, we identify this behaviour as being ancestral with WF enhancement related to cave occupation. Our results from this diversification-scale study of cavefish behaviour suggest that enhanced wall-following behaviour may be a convergent trait across all stygomorphic cavefish lineages. Significance statementSinocyclocheilus, a genus of 75 species of freshwater cavefish, is an emerging model system in evolutionary studies. Their adaptations for subterranean life, including eye degeneration, skin depigmentation, and horn-like structures, are well-known, but their behavioural adaptations remain understudied. Here we focus on a phenomenon, called "wall-following," where fish stay close to the cave walls in absence of light. We hypothesized that this behaviour would be more pronounced in eyeless species. We selected 13 species, representative of the diversity of the genus and eye types, and observed their wall-following behaviour under different conditions. Results were intriguing; eyeless species exhibited heightened wall-following behaviour compared to their sighted counterparts, with small-eyed species falling in between. Researchers also mapped this behaviour on a phylogenetic tree, discovering a pattern: cave-dwelling clades showed stronger wall-following than free-living ones. Wall-following is prevalent in all Sinocyclocheilus species and, given the evolutionary history of the genus, is considered an ancestral behaviour that intensified with cave adaptation. These findings contribute to our understanding of convergent evolution, suggesting that enhanced wall-following may be a shared trait among diverse cavefish lineages.

animal behavior and cognition↗
bioRxiv2023

New structural features of the APC/C revealed by high resolution cryo-EM structures of apo-APC/C and the APC/C CDH1:EMI1 complex

The multi-subunit anaphase-promoting complex/cyclosome (APC/C) is a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex (MCC). In this study, we took advantage of the latest developments in cryo-electron microscopy (cryo-EM) to determine the structures of human APC/CCDH1:EMI1 and apo-APC/C at 2.9 [A] and 3.2 [A] resolution, respectively, providing novel insights into the regulation of APC/C activity. The high-resolution maps allowed the unambiguous assignment of a previously unassigned -helix to the N-terminus of CDH1 (CDH11) in the APC/CCDH1:EMI1 ternary complex. We also identified a novel zinc-binding module in APC2 that confers structural stability to APC2, and we confirmed the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we were able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity.

cell biology↗
bioRxiv2023

PQS and pyochelin in Pseudomonas aeruginosa share inner membrane transporters to mediate iron uptake

Bacteria uptake different forms of iron through various channels to meet their needs. Our previous studies have shown that TseF, a type VI secretion system effector for Fe uptake, facilitates the delivery of outer membrane vesicle (OMV)-associated PQS-Fe3+ to bacterial cells by involving the Fe(III) pyochelin receptor FptA and the porin OprF. However, the form in which the PQS-Fe3+ complex enters the periplasm and how it is taken up into the cytoplasm remain unclear. Here, we first demonstrate that the PQS-Fe3+ complex enters the cell directly through FptA or OprF. Next, we find that inner membrane transporters such as FptX, PchHI, and FepBCDG are not only necessary for P. aeruginosa to uptake PQS-Fe3+ and PCH-Fe3+, but also necessary for the virulence of P. aeruginosa toward Galleria mellonella larvae. Furthermore, we suggest that the function of PQS-Fe3+ (but not PQS)-mediated quorum-sensing regulation is dependent on FptX, PchHI, and FepBCDG. Additionally, the findings indicate that, unlike FptX, both FepBCDG and PchHI play no role in the autoregulatory loop involving PchR, but further deletion of fepBCDG and pchHI can reverse the inactive PchR phenotype caused by fptX deletion and reactivate the expression of the PCH pathway genes under iron-limited conditions. Finally, this work detected the interaction between FptX, PchHI, and FepBCDG, indicating that a larger complex could be formed to mediate uptake of PQS-Fe3+ and PCH-Fe3+. These results pave the way for a better understanding of the PQS and PCH iron uptake pathway, and provide future directions to tackle P. aeruginosa infections. IMPORTANCEIron is a key factor for P. aeruginosa to break through the hosts defense system and successfully infect. To acquire the necessary iron from the host, P. aeruginosa has evolved a number of strategies, the most common being the synthesis, secretion, and uptake of siderophores such as pyoverdine, pyochelin, and the quorum-sensing signaling molecule PQS. However, despite intensive studies of the siderophore uptake pathways of P. aeruginosa, our understanding of how siderophores transport iron across the inner membrane into the cytoplasm is still far from complete. Here, we reveal that PQS and pyochelin in P. aeruginosa share inner membrane transporters such as FptX, PchHI and FepBCDG to mediate iron uptake. Meanwhile, PQS and pyochelin-mediated signaling operates to a large extent via these inner membrane transporters. Our study revealed an interesting phenomenon of shared uptake pathways between PQS and pyochelin, which will lead us to reexamine the role of these two molecules in the iron uptake and virulence of P. aeruginosa.

microbiology↗
bioRxiv2023

Ancient farmer and steppe pastoralist-related founding lineages contributed to the complex landscape of episodes in the diversification of Chinese paternal lineages

Ancient DNA advances have reported the complex genetic history of Eurasians, but how the knowledge of ancient subsistence strategy shifts and population movements influenced the fine-scale paternal genetic structure in East Asia has not been assessed. Here, we reported one integrated Y-chromosome genomic database of 15,530 people, including 1753 ancient people and newly-reported 919 individuals genotyped using our recently-developed targeted sequencing YHSeqY3000 panel, to explore Chinese genomic diversity, population evolutionary tracts and their genetic formation mechanism. We identified four major ancient technological innovations and population movements that shaped the landscape of Chinese paternal lineages. First, the expansion of millet farmers and early East Asians from the Yellow River Basin carrying the major O2/D subclades promoted the formation of the Sino-Tibetan peoples major composition and accelerated the Tibetan Plateaus permanent occupation. Second, rice farmers dispersal from the Yangtze River Valley carrying O1 and some sublineages of O2 contributed significantly to Tai-Kadai, Austronesian, Hmong-Mien, Austroasiatic people and southern Han Chinese. Third, Siberian-related paternal lineages of Q and C originated and boomed from Neolithic hunter-gatherers from the Mongolian Plateau and the Amur River Basin and significantly influenced the gene pools of northern Chinese. Fourth, western Eurasian-derived J, G and R lineages initially spread with Yamnaya steppe pastoralists and other proto-Indo-European people and further widely dispersed via the trans-Eurasian cultural communication along the Eurasian Steppe and the ancient Silk Road, remaining genetic trajectories in northwestern Chinese. Our work provided comprehensive modern and ancient genetic evidence to illuminate the impact of population interaction from the ancient farmer or herder-based societies on the genetic diversity patterns of modern people, revised our understandings of ancestral sources of Chinese paternal lineages, underscored the scientific imperative of the large-scale genomic resources of dense spatiotemporal underrepresented sampling populations to understand human evolutionary history.

genetics↗
bioRxiv2023

Mapping protein-exopolysaccharide binding interaction in Staphylococcus epidermidis biofilms by live cell proximity labeling

Bacterial biofilms consist of cells encased in an extracellular polymeric substance (EPS) composed of exopolysaccharides, extracellular DNA, and proteins that are critical for cell-cell adhesion and protect the cells from environmental stress, antibiotic treatments, and the host immune response. Degrading EPS components or blocking their production have emerged as promising strategies for prevention or dispersal of bacterial biofilms, but we still have little information about the specific biomolecular interactions that occur between cells and EPS components and how those interactions contribute to biofilm production. Staphylococcus epidermidis is a leading cause of nosocomial infections as a result of producing biofilms that use the exopolysaccharide poly- (1[->]6)-{beta}-N-acetylglucosamine (PNAG) as a major structural component. In this study, we have developed a live cell proximity labeling approach combined with quantitative mass spectrometry-based proteomics to map the PNAG interactome of live S. epidermidis biofilms. Through these measurements we discovered elastin-binding protein (EbpS) as a major PNAG-interacting protein. Using live cell binding measurements, we found that the lysin motif (LysM) domain of EbpS specifically binds to PNAG present in S. epidermidis biofilms. Our work provides a novel method for the rapid identification of exopolysaccharide-binding proteins in live biofilms that will help to extend our understanding of the biomolecular interactions that are required for bacterial biofilm formation.

microbiology↗