Biology subjects

Xiong, Q.

Publications and source records attributed to Xiong, Q..

29 records · Page 2Linked to original sources

bioRxiv2021

The beneficial rhizobacterium Bacillus velezensis acquires iron from roots via a type VII secretion system for colonization

Niche colonization is the key for bacterial adaptation to the environment, and competition for iron largely determines root colonization by rhizosphere microbes. Pathogenic and beneficial symbiotic bacteria use various unique secretion systems to support plant colonization or acquire limited resources from the environment. However, ubiquitous nonsymbiotic beneficial rhizobacteria have never been reported to use a unique secretion system to facilitate colonization. Here, we show that the type VII secretion system (T7SS) of the beneficial rhizobacterium Bacillus velezensis SQR9 contributes to root colonization. Knocking out T7SS and the major secreted protein YukE in SQR9 caused a significant decrease in root colonization. Moreover, the T7SS and YukE caused iron loss in plant roots in the early stage after inoculation, which contributed to root colonization by SQR9. Interestingly, purified YukE, but not inactivated YukE, could change the permeability of root cells. We speculated that secreted YukE might be directly inserted into the root cell membrane to cause iron leakage, indicating that the bacterial protein and root cell membrane interact directly. Moreover, a bacterial siderophore and the T7SS may be coordinately involved in iron acquisition by B. velezensis SQR9 for efficient root colonization. We showed that the beneficial rhizobacterium B. velezensis SQR9 could acquire iron from roots via the T7SS for rapid colonization. These findings provide the first insight into the function of the unique secretion system in nonsymbiotic beneficial rhizobacteria and reveal a novel mutualism in which plants and bacteria might share iron in a sequential manner.

microbiology↗

bioRxiv2021

Subcellular dynamics studies reveal how tissue-specific distribution patterns of iron are established in developing wheat grains

Understanding iron trafficking in plants is key to enhancing the nutritional quality of crops. Due to the difficulty of imaging iron in transit, little is known about iron translocation and distribution in developing seeds. A novel approach, combining 57Fe isotope labelling and NanoSIMS, was used to visualize iron translocation dynamics at the subcellular level in wheat grain, Triticum aestivum L. We were able to track the main route of iron from maternal tissues to the embryo through different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, as confirmed by histological staining and TEM-EDS. Virtually all iron was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Aleurone cells contained a new type of iron body, highly enriched in 57Fe, and most likely represents iron-nicotianamine being delivered to phytate globoids. Correlation with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification efforts.

plant biology↗

bioRxiv2021

A DNA-origami NanoTrap for studying the diffusion barriers formed by Phe-Gly-rich nucleoporins

DNA nanotechnology provides a versatile and powerful tool to dissect the structure-function relationship of biomolecular machines like the nuclear pore complex (NPC), an enormous protein assembly that controls molecular traffic between the nucleus and cytoplasm. To understand how the intrinsically disordered, Phe-Gly-rich nucleoporins (FG-nups) within the NPCs central transport channel impede the diffusion of macromolecules, we built a DNA-origami NanoTrap. The NanoTrap comprises precisely arranged FG-nups in an NPC-like channel, which sits on a baseplate that captures macromolecules that pass through the FG network. Using this biomimetic construct, we determined that the FG-motif type, grafting density and spatial arrangement are critical determinants of an effective diffusion barrier. Further, we observe that diffusion barriers formed with cohesive FG-interactions dominate in mixed-FG-nup scenarios. Our DNA-origami platform thus sheds light on how NPCs sieve inert macromolecules and will provide a valuable tool for studying nuclear transport.

synthetic biology↗

bioRxiv2020

Body site-specific and disease-specific virulome in the human microbiome

Human body habitats are home to a diverse array of microbes, and within these microbial ecosystems, there are exchanges of genetic material, including virulence factors (VFs). Little is known about the diversity and abundance of VFs in different body sites and different types of diseases. We developed a virulome analysis pipeline using the species-specific sequence identity inferred from intraspecies ANI values to precisely assign reads to virulence factors. We characterized the human virulome from four body habitats, including the gut, oral cavity, skin, and vagina. Specifically, the diversity and abundance of VFs in the oral cavity were significantly higher than those in other body sites, including stool. We highlight the importance of sex-specific analysis when studying the human virulome. We analyzed data from more than 4,000 samples across healthy and diseased subjects and 13 types of diseases from different metagenomic sequencing studies to characterize the disease-specific virulome. Atherosclerotic cardiovascular disease (ACVD) has a more diverse virulome than other diseases tested. Notably, many VFs, including genes for secretion systems and toxins, are more abundant in diseased subjects than in healthy controls. We present, to our knowledge, the most comprehensive healthy and diseased virulome dataset yet created.

genomics↗

bioRxiv2020

A novel high-accuracy genome assembly method utilizing a high-throughput workflow

Across domains of biological research using genome sequence data, high-quality reference genome sequences are essential for characterizing genetic variation and understanding the genetic basis of phenotypes. However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing regions. Here, we describe a high-throughput gold standard genome assembly workflow using a large-scale bacterial artificial chromosome (BAC) library with a refined two-step pooling strategy and the Lamp assembler algorithm. This strategy minimizes the laborious processes of physical map construction and clone-by-clone sequencing, enabling inexpensive sequencing of several thousand BAC clones. By applying this strategy with a minimum tiling path BAC clone library for the short arm of chromosome 2D (2DS) of bread wheat, 98% of BAC sequences, covering 92.7% of the 2DS chromosome, were assembled correctly for this species with a highly complex and repetitive genome. We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0. Our 2DS assembly represents a new benchmark for the assembly of complex genomes with both high accuracy and efficiency.

genomics↗

bioRxiv2020

A DNA-origami nuclear pore mimic reveals nuclear entry mechanisms of HIV-1 capsid

The capsid of human immunodeficiency virus 1 (HIV-1) plays a pivotal role in viral nuclear import, but the mechanism by which the viral core passages the nuclear pore complex (NPC) is poorly understood. Here, we use DNA-origami mimics of the NPC, termed NuPODs (NucleoPorins Organized by DNA), to reveal the mechanistic underpinnings of HIV-1 capsid nuclear entry. We found that trimeric interface formed via three capsid protein hexamers is targeted by a triple-arginine (RRR) motif but not the canonical phenylalanine-glycine (FG) motif of NUP153. As NUP153 is located on the nuclear face of the NPC, this result implies that the assembled capsid must cross the NPC in vivo. This hypothesis is corroborated by our observations of tubular capsid assemblies penetrating through NUP153 NuPODs. NUP153 prefers to bind highly curved capsid assemblies including those found at the tips of viral cores, thereby facilitating capsid insertion into the NPC. Furthermore, a balance of capsid stabilization by NUP153 and deformation by CPSF6, along with other cellular factors, may allow for the intact capsid to pass NPCs of various sizes. The NuPOD system serves as a unique tool for unraveling the previously elusive mechanisms of nuclear import of HIV-1 and other viruses.

microbiology↗

bioRxiv2020

Identification of a common deletion in the spike protein of SARS-CoV-2

Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development.

genetics↗

bioRxiv2020

Sorting liposomes of distinct sizes by DNA-brick assisted centrifugation

The "tiny bubbles of fluid" wrapped by lipid-bilayer membranes, termed vesicles, are abundant in cells and extracellular space, performing critical tasks including nutrient uptake, cargo transport, and waste confinement. Vesicles on different missions and transport routes are often distinct both in size and in chemical composition, which confers specificity to their interactions with other membranous compartments. Therefore, to accurately recapitulate the vesicles structure and behavior, it is important to use homogeneous liposomes (vesicles made of synthetic components) with precisely defined attributes as model membranes. Although existing methods can generate liposomes of selected sizes with reasonable homogeneity, the scalable production of uniformly-sized liposomes across a wide range of dimensions and compositions remains challenging. Here we report a streamlined, high-throughput sorting technique that uses cholesterol-modified "nanobricks" made of a few DNA oligonucleotides to differentiate hetero-sized liposomes by their buoyant densities. After DNA-brick coating, milligrams of liposomes of different origins (e.g., produced via extrusion or sonication, and reconstituted with membrane proteins) can be separated by centrifugation into six to eight homogeneous populations with mean diameters from 30 to 130 nm. In proof of concept experiments, we show that these uniform, leak-free liposomes are ideal substrates to study, with an unprecedented resolution, how membrane curvature influences the activity of peripheral (ATG3) and integral (SNARE) membrane proteins. We anticipate that our sorting technique will facilitate the quantitative understanding of membrane curvature in vesicular transport. Furthermore, adding a facile and standardized separation step to the conventional liposome preparation pipeline may benefit the formulation and prototyping of liposomal drug-carrying vehicles.

biophysics↗

bioRxiv2019

Cortical ensemble activity discriminates auditory attentional states

Selective attention modulates sensory cortical activity. It remains unclear how auditory cortical activity represents stimuli that differ behaviorally. We designed a cross-modality task in which mice made decisions to obtain rewards based on attended visual or auditory stimuli. We recorded auditory cortical activity in behaving mice attending to, ignoring, or passively hearing auditory stimuli. Engaging in the task bidirectionally modulates neuronal responses to the auditory stimuli in both the attended and ignored conditions compared to passive hearing. Neuronal ensemble activity in response to stimuli under attended, ignored and passive conditions are readily distinguishable. Furthermore, ensemble activity under attended and ignored conditions are in closer states compared to passive condition, and they share a component of attentional modulation which drives them to the same direction in the population activity space. Our findings suggest that task engagement changes sensory cortical representations across modalities in the same directions, and cross-modality attention may differentially modulates attended and ignored modalities.

neuroscience↗

bioRxiv2018

Split-miniSOG for detecting and localizing intracellular protein-protein interactions: application to correlated light and electron microscopy

A protein complementation assay (PCA) for detecting and localizing intracellular protein-protein interactions (PPIs) was built by bisection of miniSOG, a fluorescent flavoprotein derived from the light, oxygen, voltage (LOV)-2 domain of Arabidopsis phototropin. When brought together by interacting proteins, the fragments reconstitute a functional reporter that permits tagged protein complexes to be visualized by fluorescence light microscopy (LM), and then by standard as well as \"multicolor\" electron microscopy (EM) imaging methods via the photooxidation of 3-3-diaminobenzidine (DAB) and its lanthanide-conjugated derivatives.

cell biology↗

bioRxiv2018

Metabolomics and proteomics analyses of grain yield reduction in rice under abrupt drought-flood alternation

HighlightAbrupt drought-flood alteration is a frequent meteorological disaster that occurs during summer in southern China and the Yangtze river basin, which often causes a large area reduction of rice yield. We previously reported abrupt drought-flood alteration effects on yield and its components, physiological characteristics, matter accumulation and translocation, rice quality of rice. However, the molecular mechanism of rice yield reduction caused by abrupt drought-flood alternation has not been reported.\n\nIn this study, four treatments were provided, no drought and no floods (control), drought without floods (duration of drought 10 d), no drought with floods (duration of floods 8 d), and abrupt drought-flood alteration (duration of drought 10 d and floods 8 d). The quantitative analysis of spike metabolites was proceeded by LC-MS (liquid chromatograph-mass spectrometry) firstly. Then the Heat-map, PCA, PLS-DA, OPLS-DA and response ranking test of OPLS-DA model methods were used to analysis the function of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alteration. In addition, relative quantitative analysis of spike total proteins under the treatment was conducted iTRAQ (isobaric tags for relative and absolute quantification) and LC-MS. In this study, 5708 proteins were identified and 4803 proteins were quantified. The identification and analysis of DEPs function suggested that abrupt drought-flood alteration treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process, etc, during panicle differentiation stage. In this study relative quantitative proteomics, metabolomics and physiology data (soluble protein content, superoxide dismutase activity, hydrogen peroxidase activity, peroxidase activity, malondialdehyde content, free proline content, soluble sugar content and net photosynthetic rate) analysis were applied to explicit the response mechanism of rice panicle differentiation stage under abrupt drought-flood alteration and provides a theoretical basis for the disaster prevention and mitigation.\n\nAbstractAbrupt drought-flood alternation is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, a quantitative analysis of spike metabolites was conducted via liquid chromatograph-mass spectrometry (LC-MS), and Heat-map, PCA, PLS-DA, OPLS-DA, and a response ranking test of OPLS-DA model methods were used to analyze functions of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alternation. The results showed that 102 DMs were identified from the rice spike between T1 (abrupt drought-flood alternation) and CK0 (control) treatment, 104 DMs were identified between T1 and CK1 (drought) treatment and 116 DMs were identified between T1 and CK2 (flood) treatment. In addition, a relative quantitative analysis of spike total proteins was conducted using isobaric tags for relative and absolute quantification (iTRAQ) and LC-MS. The identification and analysis of DEPs functions indicates that abrupt drought-flood alternation treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process during the panicle differentiation stage. In this study, relative quantitative metabolomics and proteomics analyses were applied to explore the response mechanism of rice panicle differentiation in response to abrupt drought-flood alternation.\n\nAbbreviations

plant biology↗