Biology subjects

Zhao, Q.

Publications and source records attributed to Zhao, Q..

At least 181 records · Page 10Linked to original sources

bioRxiv2022

Pseudokinase HPO-11 inhibits nonsense-mediated decay to ensure genome stability in C. elegans

DNA double-strand breaks (DSBs) are highly toxic DNA lesions that can induce mutations and chromosome rearrangement therefore causing genome instability (GIN). In response to DSBs, cells activate the DNA damage response by hierarchical assembly of signaling and repair mechanisms. This involves recruitment of the repair factors at DSB sites, local chromatin remodeling, cell cycle arrest and, eventually, DNA repair or apoptosis. Studies investigating mechanisms ensuring genome stability have so far mostly focused on DNA-protein interactions and signal transduction in response to DNA damage. Emerging evidence in the last decade suggests that post-transcriptional control of gene expression by RNA-binding proteins also participates in maintaining genome integrity. However, how specific control of RNA fate mechanistically affects genome stability is still poorly understood. Here, we report that the pseudokinase HPO-11 ensures genome integrity in C. elegans. Loss of hpo-11 leads to accumulation of R-loops, increased DSBs and germline apoptosis, as well as an elevated mutation rate in the somatic cells. In addition, inhibition of nonsense mediated decay (NMD) reduces DSBs and germline apoptosis in the absence of hpo-11. We find that HPO-11 physically interacts with SMG-2, the core factor of NMD, and prevents degradation of specific transcripts by NMD, thus contributing to maintenance of genome stability. Furthermore, knock-down of hpo-11 human homologs NRBP1/2 also results in increased DNA DSBs, and NRBP1/2 physically interact with the human SMG-2 orthologue UPF1. In summary, our work identifies an evolutionarily conserved role of HPO-11 to protect genome stability via suppressing abnormal mRNA decay by NMD.

molecular biology↗

bioRxiv2022

Pathway and mechanism of tubulin folding mediated by TRiC/CCT conjugated with its ATPase cycle revealed by cryo-EM

The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. Our structural and XL-MS analyses suggested a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. Remarkably, in the closed TRiC-tubulin-S3 map resolved to 3.1-[A]-resolution, we captured a near-natively folded tubulin. We found the near-natively folded tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions, while the tubulin I domain was found to remain dynamic. Moreover, we also showed the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated tubulin folding conjugated with TRiC ATPase cycle, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.

biochemistry↗

bioRxiv2022

Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT

The eukaryotic chaperonin TRiC/CCT assists the folding of ~10% cytosolic proteins. The essential cytoskeletal proteins tubulin and actin are the obligate substrates of TRiC and their folding involves cochaperone and co-factors. Here, through cryo-EM analysis, we present a more complete picture of yeast TRiC-assisted tubulin and actin folding in the ATPase-cycle, under the coordination of cochaperone plp2. Our structures revealed that in the open C1 and C2 states, plp2 and substrates tubulin/actin engage with TRiC inside its chamber, one per ring. Noteworthy, we captured a ternary TRiC-plp2-tubulin complex in the closed C3 state, engaged with a full-length {beta}-tubulin in the native folded state even loaded with a GTP, and with a plp2 occupying the opposite ring, not reported before. Another closed C4 state revealed an actin in the intermediate state of folding and a plp2 occupying the other ring. Intriguingly, along with TRiC ring closure, we captured a large translocation of plp2 within TRiC chamber coordinating substrate translocation on the CCT6 hemisphere, potentially facilitating substrate stabilization and folding. Our findings provide structural insights into the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the complex biogenesis machinery TRiC and plp2, and could extend our understanding on the links between cytoskeletal proteostasis and related human diseases.

biophysics↗

bioRxiv2022

Apicosome: newly identified cell-type-specific organelle in mouse cochlear and vestibular hair cells

Cochlear and vestibular hair cells in the inner ear are highly specialized sensory receptors for sound waves and acceleration of body movements; these cells can perform their specialized functions because of their distinctive morphology and some unique organelles that they harbor. Here, we report a serendipitous identification in the mouse of a hair-cell-specific organelle, which we name "apicosome." The apicosome was recognized by anti-FLRT1 antibodies but contains no FLRT1, and the organelle presents several distinctive characteristics: (1) the apicosome typically appears as a single entity ([~]500 nm in diameter), but occasionally as two entities, in hair cells; (2) it first appears in the subapical region at the neural side at embryonic day (E) 17-18 in cochlear hair cells, subsequently descends to the perinuclear region during the first postnatal week, and completely disappears around postnatal day (P) 10; (3) in vestibular hair cells, it can be detected in the subapical region of neonatal (P3) cells and persists in adult hair cells although it becomes smaller and more distant from the subapical region; (4) the timing of apicosome translocation and disappearance during development is correlated in kinocilium maintenance; (5) the organelle is potentially associated with microtubules; and (6) the appearance of the apicosome is irregular in supernumerary hair cells and this is likely linked to anomalous lateral inhibition. Thus, our study identifies a previously undescribed organelle in sensory hair cells and lays the foundation for further characterization of this specialized structure potentially linked to hair-cell development and morphogenesis.

neuroscience↗

bioRxiv2022

Inhibiting circRNA Cdr1as expression in the ILPFC of adult male C57BL/6J mice impairs fear extinction memory

Circular RNAs (circRNAs) comprise a novel class of regulatory RNAs that are abundant in the brain, particularly within synapses. They are highly stable, dynamically regulated, and display a range of functional roles, including as decoys for miRNAs and proteins and, in some cases, translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, relatively few studies have shown a causal link between circRNA function and memory. To address this knowledge gap, we sequenced circRNAs in the synaptosome compartment of the medial prefrontal cortex of fear extinction trained male C57BL/6J mice and found 12837 circRNAs enriched at the synapse, including Cdr1as. Targeted knockdown of Cdr1as in the neural processes of the infralimbic prefrontal cortex of male C57BL/6J mice led to impaired fear extinction memory. Altogether, our findings highlight the importance of localised circRNA activity at the synapse for memory formation and suggest that circRNAs may have a more widespread effect on brain function than previously thought.

neuroscience↗

bioRxiv2022

Phase separation of Myc differentially regulates gene transcription

Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundred-fold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives proliferation and cell survival. Whether increasing N-myc levels simply mediate binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but how strongly it contributes to gene activation remains unclear. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that bear the hallmarks of transcriptional activity. We tested the contribution of phase separation to N-myc-mediated gene expression by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at identical N-myc levels, which both showed a strong impact on gene expression compared to no N-myc expression. However, we found that only a small fraction of <3% of N-myc-regulated genes is further affected by phase separation, but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell survival by [~]15% corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery.

cell biology↗

bioRxiv2022

In vivo base editing rescues photoreceptors in a mouse model of retinitis pigmentosa

Retinitis pigmentosa (RP) is a group of retinal diseases that cause the progressive death of retinal photoreceptor cells and eventually blindness. Mutations in the {beta}-domain of the phosphodiesterase 6 (Pde6b) gene are among the most identified causes of autosomal recessive RP. Here, we report a base editing approach in which adeno-associated virus (AAV)-mediated adenine base editor (ABE) delivery to postmitotic photoreceptors is used to correct the Pde6b mutation in a retinal degeneration 10 (rd10) mouse model of RP. Subretinal delivery of AAV8-ABE corrects Pde6b mutation with up to 37.41% efficiency at the DNA level and up to 91.95% efficiency at the cDNA level, restores PDE6B expression, preserves photoreceptors and rescues visual function. RNA-seq reveals upregulation of genes associated with phototransduction and photoreceptor survival. Our data demonstrate that base editing is a potential gene therapy that could provide durable protection against RP.

genetics↗

bioRxiv2022

The AI Neuropsychologist: Automatic scoring of memory deficits with deep learning

BackgroundMemory deficits are a hallmark of many different neurological and psychiatric conditions. The Rey-Osterrieth complex figure (ROCF) is the state-of-the-art assessment tool for neuropsychologists across the globe to assess the degree of non-verbal visual memory deterioration. To obtain a score, a trained clinician inspects a patients ROCF drawing and quantifies deviations from the original figure. This manual procedure is time-consuming, slow and scores vary depending on the clinicians experience, motivation and tiredness. MethodsHere, we leverage novel deep learning architectures to automatize the rating of memory deficits. For this, we collected more than 20k hand-drawn ROCF drawings from patients with various neurological and psychiatric disorders as well as healthy participants. Unbiased ground truth ROCF scores were obtained from crowdsourced human intelligence. This dataset was used to train and evaluate a multi-head convolutional neural network. ResultsThe model performs highly unbiased as it yielded predictions very close to the ground truth and the error was similarly distributed around zero. The neural network outperforms both online raters and clinicians. The scoring system can reliably identify and accurately score individual figure elements in previously unseen ROCF drawings, which facilitates explainability of the AI-scoring system. To ensure generalizability and clinical utility, the model performance was successfully replicated in a large independent prospective validation study that was pre-registered prior to data collection. ConclusionsOur AI-powered scoring system provides healthcare institutions worldwide with a digital tool to assess objectively, reliably and time-efficiently the performance in the ROCF test from hand-drawn images.

neuroscience↗

bioRxiv2022

The adipose-neural axis is critically involved in cardiac arrhythmias

Dysfunction of the sympathetic nervous system and increase of epicardial adipose tissue (EAT) have been independently associated with the occurrence of cardiac arrhythmia. However, their exact roles in triggering arrhythmia remain elusive due to a lack of appropriate human disease models. Here, using the in vitro co-culture system with sympathetic neurons, cardiomyocytes, and adipocytes, we show that adipocyte-derived leptin could activate sympathetic neurons and increase the release of NPY, which in turn trigger arrhythmia of cardiomyocytes by interaction with NPY1R and subsequently enhancing the activity of NCX and CaMKII. The arrhythmic phenotype could be partially blocked by leptin neutralizing antibody, or an inhibitor of NPY1R, NCX or CaMKII. More importantly, increased EAT thickness accompanied with higher leptin/NPY blood levels was detected in atrial fibrillation patients compared to control group. Our study provides the first evidence that adipose-neural axis would contribute to arrhythmogenesis and represent a potential therapeutic target for arrhythmia.

cell biology↗

bioRxiv2022

Discovery of synapse-specific RNA N6-methyladenosine readers associated with the consolidation of fear extinction memory

The RNA modification N6-methyladenosine (m6A) is critically involved in the regulation of gene activity underlying experience-dependent plasticity, and is necessary for the functional interplay between RNA and RNA binding proteins (RBPs) in the nucleus. However, the complete repertoire of m6A-modified RNA interacting RBPs in the synaptic compartment, and whether they are involved in fear extinction, have yet to be revealed. Using RNA immunoprecipitation followed by mass spectrometry, we discovered 12 novel, synapsespecific, learning-induced m6A readers in the medial prefrontal cortex of male C57/B6 mice. m6A RNA-sequencing also revealed a unique population of learning-related m6A-modified RNAs at the synapse, which includes a variant of the long non-coding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (Malat1). m6A-modified Malat1 binds to a subset of novel m6A readers, including cytoplasmic FMR1 interacting protein 2 (CYFIP2) and dihydropyrimidase-related protein 2 (DPYSL2) and a cell-type-specific, state-dependent, and synapse-specific reduction in m6A-modified Malat1 disrupts the interaction between Malat1 and DPYSL2 and impairs fear extinction. The consolidation of fear-extinction memory therefore relies on an interaction between m6A-modified Malat1 and select RBPs in the synaptic compartment.

neuroscience↗

bioRxiv2022

Distinct Single-cell Immune Ecosystems Distinguish True and De Novo HBV-related Hepatocellular Carcinoma Recurrences

Revealing differential tumor immune microenvironment (TIME) characteristics between true versus de novo hepatocellular carcinoma (HCC) recurrence could help optimal development and use of immunotherapies. Here, we studied the TIME of recurrent HBV-related HCCs by 5and VDJ single-cell and bulk RNA-sequencing, flow cytometry, and multiplexed immunofluorescence. Analyses of mutational profiles, evolutionary trajectories, and clonal architecture using whole-exome sequencing identified de novo versus true recurrences, some of which occurred before clinical diagnosis. The TIME of truly recurrent HCCs was characterized by an increased abundance in KLRB1+CD8+ T cells with memory phenotype and low cytotoxicity. In contrast, we found an enrichment in cytotoxic and exhausted CD8+ T cells in the TIME of de novo recurrent HCCs. Transcriptomic and interaction analyses showed an upregulated GDF15 expression level on HCC cells in proximity to dendritic cells, which may have dampened antigen presentation and inhibited anti-tumor immunity in the TIME of truly recurrent lesions. In contrast, we found that myeloid cells crosstalk with T cells mediated T cell exhaustion and immunosuppression in the TIME of de novo recurrent HCC. In conclusion, our results support genomic diagnosis and immune profiling for guiding immunotherapy implementation based on the type of HCC recurrence and TIME. HighlightsO_LITruly recurrent lesions are seeded before primary tumor diagnosis, and that de novo cancer can occur earlier than the clinically used 2-year limit. C_LIO_LIScRNA-seq unravels distinct immune ecosystems in true versus de novo HCC recurrences, highlighting the need for different immunotherapy strategies for two types of HCC recurrence. C_LIO_LICD8+ T cells in de novo recurrence displayed cytotoxic and exhausted phenotypes while those in truly recurrent lesions showed a memory phenotype with weak cytotoxicity. C_LIO_LIHCC cells expressing the inhibitory molecule GDF15 were in the proximity of DCs only in truly recurrent lesions. C_LIO_LIHigh GDF15 expression level was associated with truly recurrent HCC and worse prognosis. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/494526v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@1b76bf0org.highwire.dtl.DTLVardef@10f889aorg.highwire.dtl.DTLVardef@d16b52org.highwire.dtl.DTLVardef@dceb7a_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

Orphan C/D box snoRNAs modulate fear-related memory processes in mice

C/D box small nucleolar RNAs (snoRNAs) comprise a class of small noncoding RNAs with important regulatory effects on cellular RNA function. Although it is well established that snoRNAs coordinate the post-transcriptional modification of pre-ribosomal and small nuclear RNAs by 2-O-methylation, which leads to enhanced RNA stability, whether they are necessary for memory-related processes remains relatively unexplored. Using targeted sequencing, we have identified more than 150 C/D box snoRNAs in the prefrontal cortex of male C57BL/6J mice, 31 of which are differentially expressed in response to fear extinction learning. We have also discovered a subset of snoRNAs, including many orphans, that are enriched in the synaptic compartment, including the orphan snoRNA snord64. An extinction learning-induced increase in synapse-enriched snord64 led to increased 2-O-methylation within the 3-UTR of the mRNA encoding the ubiquitin ligase RNF146. This effect was blocked by snord64 knockdown and was accompanied by attenuated forgetting of conditioned fear and the enhanced retrieval of fear extinction memory. Localized activity of orphan snoRNAs therefore represents a novel mechanism associated with fear-related learning and memory. Significance statementWe have discovered a population of experience-dependent small nucleolar RNAs (snoRNAs), and found that several of these are recruited to the synaptic compartment in response to fear extinction learning. In particular, the orphan snoRNA, snord64, drives the methylation of the mRNA encoding the ubiquitin ligase, RNF146, with a reduction in snord64 attenuating forgetting of conditioned fear and enhancing the retrieval of fear extinction memory. This study reveals a new mechanism of gene regulation associated with fear-related memory that involves the activity of synapse-enriched snoRNAs.

neuroscience↗

bioRxiv2022

PathGPS: Discover shared genetic architecture using biobank data

The increasing availability and scale of Genome Wide Association Studies (GWAS) bring new horizons for understanding biological mechanisms. PathGPS is an exploratory method that discovers genetic architecture using GWAS summary data. It can separate genetic components from unobserved environmental factors and extract clusters of genes and traits associated with the same biological pathways. When applying to a metabolomics dataset and the UK Biobank, PathGPS confirms several known gene-trait clusters and suggest many new hypotheses for future investigations.

bioinformatics↗

bioRxiv2022

HSP90.6 is involved in grain filling via carbon and nitrogen metabolism in maize.

Carbon and nitrogen are the two most abundant nutrients in all living things, and their metabolism maintains normal plant growth. However, the molecular mechanism underlying carbon and nitrogen metabolism remains largely unknown. Here, we found that HSP90.6 is involved in the metabolism of carbon and nitrogen. We performed gene cloning and functional characterization of a maize EMS mutant ehsp90.6, whose kernels were small. HSP90.6 encodes heat shock protein 90.6, which has a single-amino acid mutation within its HATPase_c domain. Transcriptome profiling showed that the expression of amino acid biosynthesis- and carbon metabolism-related genes was significantly downregulated in hsp90.6. HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis; this occurs by interactions between HSP90.6 and the 26S proteasome subunits RPN6 and PBD2 (PRC2). The loss of HSP90.6 significantly reduced the activity of the 26S proteasome, resulting in the accumulation of ubiquitinated proteins and defects in nitrogen recycling. Moreover, HSP90.6 interacted with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Together, these findings revealed that HSP90.6 regulates nutrient metabolism in maize seeds by affecting 26S proteasome-mediated nitrogen recycling and GF14-6-mediated carbon metabolism. One sentence summaryHSP90.6 is involved in nutrient metabolism via 26S proteasome-mediated protein degradation to promote nitrogen recycling and GF14-6 protein-mediated carbon metabolism. The author responsible for the distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is Weibin Song (songwb@cau.edu.cn). HighlightsO_LIHATPase_c is necessary for HSP90.6 to regulate maize kernel development. C_LIO_LIHSP90.6 is involved in nitrogen recycling via the 26S proteasome degradation pathway. C_LIO_LIHSP90.6 interacts with the 14-3-3 protein GF14-6 to affect carbon metabolism. C_LI IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSSeeds are the main harvested organs of maize. Understanding the regulatory mechanism of grain filling is helpful to cultivate high-quality and high-yield maize. In the past few years, the regulatory network of grain filling has been explored through multiple means, including transcriptomic, proteomic and functional genomic techniques. Many genes that control grain filling through different mechanisms have been cloned, such as CTLP1 (Choline Transporter-like Protein 1), OS1 (Opaque Endosperm and Small Germ 1), and MN6 (Miniature Seed6). To identify new genes involved in maize grain filling, ethyl methanesulfonate (EMS) was used to induce mutations, and the ehsp90.6 mutant, which exhibited abnormal kernel development, was isolated by bulked segregant analysis RNA sequencing (BSR). QuestionWhy does the single-amino acid mutation of HSP90.6 affect grain size, and how does the loss of HSP90.6 affect grain filling? FindingsA single-amino acid mutant (ehsp90.6) and knockout mutant (hsp90.6) were obtained. We found that HSP90-6 was involved in the regulation of maize grain filling. A single-single amino acid mutation in the HATPase_c domain reduced the ATPase activity of HSP90.6, resulting in smaller grains. The functional loss of HSP90.6 resulted in the expression of amino acid biosynthesis- and carbon metabolism-related genes being significantly downregulated in hsp90.6. We indicated that HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis by interacting with the 26S proteasome subunits RPN6 and PBD2 (PRC2). Moreover, HSP90.6 was found to interact with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Next stepsTo further verify that the interaction between HSP90.6 and 26S proteasome subunits and GF14-6 affects grain filling, knockout validation of RPN6, PBD2 (PRC2) and GF14-6 will be performed. In addition, since GF14-6 interacts with the phosphorylated proteins, we will determine the phosphorylation site of HSP90.6. Due to the important role of HSP90 family proteins in plant development, there are other regulatory pathways that need to be explored.

plant biology↗

bioRxiv2022

Hyperactive somatostatin interneurons near amyloid plaque and cell-type-specific firing deficits in a mouse model of Alzheimer's disease

Alzheimers disease (AD) is characterized by synaptic loss and neuronal network dysfunction. These network deficits are mediated by early alterations in neuronal firing rates that coincide with amyloid plaque accumulation. Mounting evidence supports that inhibitory networks are impaired in AD, but the mechanisms driving these inhibitory deficits are poorly understood. Here we use in vivo multiphoton calcium imaging to determine the relationship between amyloid accumulation and the spontaneous activity of excitatory neurons and inhibitory interneurons in an APP/PS1 mouse model of Alzheimers disease. We show that somatostatin-expressing (SOM) interneurons are hyperactive, while parvalbumin-expressing interneurons are hypoactive in APP/PS1 mice. Only SOM interneuron hyperactivity correlated with proximity to amyloid plaque. These inhibitory deficits were accompanied by decreased excitatory neurons activity and decreased pairwise activity correlations in APP/PS1 mice. Our study identifies cell-specific interneuronal firing deficits driven by amyloid pathology in APP/PS1 mice and provides new insights for targeting inhibitory circuits in Alzheimers disease.

neuroscience↗

bioRxiv2022

Fear extinction is regulated by long noncoding RNA activity at the synapse

Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are expressed at the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq on synaptosomes, we identified a significant number of lncRNAs that accumulate at synapses within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these is a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3bp2 and Caprin1, regulates the activity-dependent trafficking and clustering of RNA granules in dendrites. In addition, we found that cell-type-specific, state-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and the coordination of RNA condensates in the synaptic compartment.

neuroscience↗

bioRxiv2022

Excited-state dynamics of the all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics

The rhodopsin mimic is a chemically synthetized complex with the retinyl Schiff base (RSB) formed between protein and the retinal chromophore, which can mimic the natural rhodopsin-like protein. The artificial rhodopsin mimic is more stable and designable than the natural protein and hence has wider uses in photon detection devices. The mimic structure RSB, like the case in the actual rhodopsin-like protein, undergoes isomerization and protonation throughout the photoreaction process. As a result, understanding the dynamics of the RSB in the photoreaction process is critical. In this study, the transient absorption spectra (TAS) of three mutants of the cellular retinoic acid-binding protein II (CRABPII)-based rhodopsin mimic at PH = 3 were recorded, from which the related excited-state dynamics of the all-trans protonated RSB (AT-PRSB) were investigated. The transient fluorescence spectra (TFS) measurements are used to validate some of the dynamic features. We find that the excited-state dynamics of AT-PRSB in three mutants share a similar pattern that differs significantly from the dynamics of 15-cis PRSB (15C-PRSB) of the rhodopsin mimic in neutral solution. By comparing the dynamics across the three mutants, we discovered that the aromatic residues near the {beta}-ionone ring structure of the retinal may help stabilize the AT-PRSB and hence slow down its isomerization rate. Furthermore, from the three mutants, we find one protein with near-infrared fluorescence emission up to 688 nm, leading to further possible applications in sensing or bioimaging.

biochemistry↗

bioRxiv2022

ScRNA-seq Identified the Metabolic Reprogramming of Human Colonic Immune Cells in Different Locations and Disease States

Different regions and states of the human colon are likely to have a distinct influence on immune cell functions. Here we studied the immunometabolic mechanisms for the spatial immune specialization and the dysregulated immune response during ulcerative colitis at single-cell resolution. We revealed that the macrophages and CD8+ T cells in the lamina propria (LP) of the human colon possessed an effector phenotype and were more activated, while their lipid metabolism was suppressed compared with those in the epithelial (Epi). Also, IgA+ plasma cells accumulated in lamina propria of the sigmoid colon were identified to be more metabolically activated versus those in the cecum and transverse colon, and the improved metabolic activity was correlated with the expression of CD27. In addition to the immunometabolic reprogramming caused by spatial localization colon, we found dysregulated cellular metabolism was related to the impaired immune functions of macrophages, dendritic cells, regulatory T cells, and ILCs in patients with ulcerative colitis. The cluster of OSM+ inflammatory monocytes was also identified to play its role in resistance to anti-TNF treatment, and we explored targeted metabolic reactions that could reprogram them to a normal state. Altogether, this study revealed a landscape of metabolic reprogramming of human colonic immune cells in different locations and disease states, and offered new insights into treating ulcerative colitis by immunometabolic modulation.

immunology↗