Biology subjects

Qian, P.

Publications and source records attributed to Qian, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of Cereibacter sphaeroides ferrochelatase reveal an oligomeric state that occludes the substrate-binding site

Protoporphyrin IX (PPIX) is the last shared intermediate of heme and (bacterio)chlorophyll ((B)Chl) biosynthesis. Insertion of iron into PPIX by the PPIX ferrochelatase (FeCh) PpfC produces heme, whereas magnesium insertion by magnesium chelatase (MgCh) initiates (B)Chl synthesis. Chlorophototrophic organisms must regulate this biosynthetic node to ensure the correct flux of PPIX to each of these crucial tetrapyrrole products, presenting a particularly acute problem for the facultative bacterium Cereibacter (previously Rhodobacter) sphaeroides, which can switch between chemotrophic (respiratory) and phototrophic (photosynthetic) growth modes. To elucidate the structural basis for the catalytic and regulatory functions of C. sphaeroides FeCh (PpfCCs), we used cryogenic electron microscopy to determine its structure, to our knowledge the first such information for a Gram-negative or phototrophic organism. We determined the 2.6 [A] structure of an active site mutant of PpfCCs, which forms a dimer with a monomer-to-monomer interface that coordinates two hemes. We also determined a 2.5 [A] structure of the wild-type enzyme, in which two dimers interact in a homotetrameric arrangement that occludes PPIX binding at the active site of each monomer. We propose that the PpfCCs dimer likely docks onto the inner membrane in a manner analogous to the human enzyme, whereas the tetramer represents a transiently inactive state whereby the hydrophobic lips and active site are both occluded. These novel oligomerization states of FeCh may have evolved to influence the flux of tetrapyrroles through the heme/BChl branchpoint in purple bacteria.

biochemistry↗

bioRxiv2026

Outer membrane 'PusCD' complexes coordinate phospho(inositol)lipid utilisation in plant Bacteroidota

Gram-negative bacteria belonging to the phylum Bacteroidota are prominent and ecologically important members of host-associated microbiomes. A feature of Bacteroidota species is the presence of diverse outer membrane TonB-dependent transporter and cognate surface exposed lipoprotein (TBDT-SLP) complexes. Many 'SusCD-like' TBDT-SLPs coordinate complex carbohydrate capture from the environment. Here, we show the model soil Bacteroidota species Flavobacterium johnsoniae synthesises two TBDT-SLP complexes (named PusCD1 and PusCD2) that are essential for growth on phosphatidylinositol, a member of an abundant lipid class within plant plasma membranes, as a phosphorus source. Structural characterisation of ligand-bound PusCD1 complex from F. johnsoniae membranes reveals a new binding mechanism for organophosphorus and broadens the known functional repertoire of this class of transporters. Diverse PusCD-like complexes are widespread among plant associated Bacteroidota, pointing to a major, previously unrecognised route for the recycling of organophosphorus compounds in the rhizosphere, with potential implications for engineering microbial-mediated phosphorus recovery from organic waste streams.

microbiology↗

bioRxiv2025

Synchronized Latency Reversal and Immune Clearance by a Multifunctional Fusion Protein Enables HIV-1 Reservoir Reduction

Strategies that concurrently reactivate latent reservoirs and enhance immune-mediated clearance hold significant promise for achieving an HIV cure. Here, we developed hyperIL-15xsCD4-Fc (15xsCD4-Fc), a fusion protein that integrates latency reactivation, targeted immune engagement, and effector-mediated killing into a single molecule. This agent not only potently reverses HIV-1 latency in CD4+ T cells from people living with HIV-1 (PLWH) through coordinated IL-15 receptor signaling and sCD4-mediated HIV-1 envelope (Env) engagement, but also enhances antigen-specific CD8+ T cell response in PBMCs derived from PLWH. Furthermore, 15xsCD4-Fc enables Env-specific elimination of reactivated latently infected cells by NK cells while preventing off-target cytotoxicity. In PBMCs from PLWH, 15xsCD4-Fc reduced replication-competent HIV-1 DNA by 93.8%. In antiretroviral treated HIV-1-infected humanized mice, the molecule demonstrated both safety and efficacy in diminishing viral reservoir in lymphoid organs. This spatiotemporally coupled approach to reservoir exposure and immune recognition establishes a clinically viable strategy for clearing the HIV-1 reservoir. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693434v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@8f8f0org.highwire.dtl.DTLVardef@10f63f7org.highwire.dtl.DTLVardef@16c1de2org.highwire.dtl.DTLVardef@11e1787_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Interplay of Anchor and Latch Residues at Enzyme Active Site in Preserving Induced Fit Configurations for Efficient Catalysis: A Case Study of CARNMT1 for Histidine Methylation

Determining the origin of high catalytic efficiency of enzymes has been a central goal in biochemical research. But our understanding of the mechanisms by which enzymes achieve enormous rate enhancements is still incomplete. One of wildly accepted strategies to achieve rate enhancements by enzymes is to position catalytic residues precisely in enzyme-substrate complexes and form reactive conformations for catalysis. Such catalytic strategy through positioning may also serve as the basis for transition state stabilization. Although considerable efforts have been made to determine relationships between enzyme activities and the formation of reactive conformations of enzyme-substrate complexes, there is considerable uncertainty concerning the ability of enzymes to preserve reactive conformations during enzyme-catalyzed reactions. The failure of properly maintaining reactive conformations during reactions may prevent residues from exerting catalytic effects and lead to significant reductions of activities. Here QM/MM MD and free energy simulations are performed for CARNMT1 to determine the importance and requirements for preservation of catalytic competent reactive conformations during enzyme-catalyzed reactions. For CARNMT1, the existence of wild-type reactive conformation is directly related to the conformation of His347. Therefore, the conformation of His347 can be used to monitor preservation or collapse of the reactive conformation during catalysis. It is found that for wild-type the reactive conformation can not only be formed in the enzyme-substrate complex but also be preserved well after the reaction passes TS. For the Tyr386Ala, Tyr396Asp and Tyr398Ala mutants, the wild-type like reactive conformations can be formed in the mutant-substrate complexes but collapse in the early stage of reaction. Such pre-mature collapse of the reactive conformation in the mutants prevents the residues to fully exert catalytic effects and leads to a significant reduction of catalytic efficiency. The results suggest that the ability of enzymes to preserve reactive conformations with well-positioned catalytic residues during enzyme-catalyzed reactions can be an important factor for efficient catalysis, and this property of enzymes deserves attention.

biochemistry↗

bioRxiv2023

Bacillus velezensis HBXN2020 alleviates Salmonella Typhimurium-induced colitis by improving intestinal barrier integrity and reducing inflammation

Bacillus velezensis is a species of Bacillus that has been widely investigated because of its broad-spectrum antimicrobial activity. However, most studies on Bacillus velezensis have focused on the biocontrol of plant diseases, with few reports on antagonizing Salmonella Typhimurium infections. In this investigation, it was discovered that Bacillus velezensis HBXN2020, which was isolated from healthy black pigs, possessed strong anti-stress and broad-spectrum antibacterial activity. Importantly, Bacillus velezensis HBXN2020 did not cause any adverse side effects in mice when administered at various doses (1 x 107, 1 x 108, and 1 x 109 CFU) for 14 d. Supplementing Bacillus velezensis HBXN2020 spores, either as a curative or preventive measure, dramatically reduced the levels of Salmonella Typhimurium ATCC14028 in the mices feces, ileum, cecum, and colon, as well as the disease activity index (DAI), in a model of infection caused by this pathogen in mice. Additionally, supplementing Bacillus velezensis HBXN2020 spores significantly regulated cytokine levels (TNF-, IL-1{beta}, IL-6, and IL-10) and maintained the expression of tight junction proteins and mucin protein. Most importantly, adding Bacillus velezensis HBXN2020 spores to the colonic microbiota improved its stability and increased the amount of beneficial bacteria (Lactobacillus and Akkermansia). All together, Bacillus velezensis HBXN2020 can improve intestinal microbiota stability and barrier integrity and reduce inflammation to help treat infection by Salmonella Typhimurium.

microbiology↗

bioRxiv2023

Study on genetic differentiation of Schistosome japonicum intermediate hosts Oncomelania hupensis robertsoni in hilly regions of China: using the complete mitochondrial genome

ObjectiveOncomelania hupensis robertsoni is the only intermediate host of Schistosoma japonicum in western China, its genetic differentiation directly impacts the susceptibility of Schistosoma japonicum. This study aimed to sequence the complete mitochondrial genome of Oncomelania hupensis robertsoni Yunnan strain and analyze the genetic differentiation of Oncomelania hupensis robertsoni in hilly regions of China. MethodsSamples were from 14 administrative villages in Yunnan Province of China, with 30 Oncomelania hupensis per village, and the complete mitochondrial genome was sequenced. Additional, we retrieved 14 other region Oncomelania hupensis of complete mitochondrial sequences from GenBank, and a comprehensive analysis of the genetic differentiation of Oncomelania hupensis robertsoni was conducted by constructing phylogenetic trees, calculating genetic distances, and analyzing homogeneity. ResultsA total of 26 complete mitochondrial sequences were determined. The length of genome ranged from 15,181 to 15,187 bp, and the base composition of the genome was A+T (67.5%) and G+C content (32.5%). This genome encoded 37 genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region rich in A+T. Using the Philippines genotypes as outgroup, the phylogenetic trees and homology analysis confirmed the existence of two distinct phylogroups, Oncomelania hupensis robertsoni and the remaining 9 provincial genotypes. Oncomelania hupensis robertsoni is subdivided into Oncomelania hupensis robertsoni Yunnan strain and Sichuan strain, with a genetic distance of 0.0834. Oncomelania hupensis robertsoni Yunnan strain is subdivided into two subbranches, "Yunnan North" and "Yunnan South", with a genetic distance of 0.0216, and the samples exhibited over 97% homology. ConclusionOncomelania hupensis robertsoni Yunnan strain exhibits a higher level of genetic homology and clear north-south differentiation, the distribution characteristics were closely associated with watershed distribution. This work reported the first mitochondrial genome of Oncomelania hupensis robertsoni Yunnan strain, which could be used as an important reference genome for Oncomelania hupensis, and also provide a theoretical basis for explaining the distribution pattern of Oncomelania hupensis robertsoni and control of schistosomiasis. Author SummaryOncomelania hupensis (O. hupensis) is the only intermediate host of Schistosoma japonicum (S. japonicum), O. hupensis residing in different geographical regions display morphological differences and genetic variations, along with varying susceptibility to S. japonicum. In this study, we sequenced 26 complete mitochondrial genome of O. hupensis robertsoni Yunnan strain (O. h. r. Yunnan strain), the length of genome ranged from 15,181 to 15,187 bp, and the base composition of the genome was A+T (67.5%) and G+C content (32.5%). This genome encoded 37 genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region rich in A+T. Additional, we retrieved 14 other region O. hupensis of complete mitochondrial sequences from GenBank. The phylogenetic trees and homology analysis confirmed that O. hupensis robertsoni is subdivided into Yunnan strain and Sichuan strain, and O. h. r. Yunnan strain is subdivided into two subbranches, "Yunnan North" and "Yunnan South", the samples exhibited over 97% homology. This work reported the first mitochondrial genome of O. h. r. Yunnan strain, which could be used as an important reference genome for O. hupensis, and also provide a molecular biology-based theoretical foundation for understanding the genetic differentiation of O. hupensis.

genomics↗

bioRxiv2023

Cell Typing and Sub-typing Based on Detecting Characteristic Subspaces of Morphological Features Derived from Neuron Images

MotivationRecent advances in reconstructing 3D neuron morphologies at the whole brain level offer exciting opportunities to study single cell genotyping and phenotyping. However, it remains challenging to define cell types and sub-types properly. ResultsAs morphological feature spaces are often too complicated to classify neurons, we introduce a method to detect the optimal subspace of features so that neurons can be well clustered. We have applied this method to one of the largest curated databases of morphological reconstructions that contains more than 9,400 mouse neurons of 19 cell types. Our method is able to detect the distinctive feature subspaces for each cell type. Our approach also outperforms prevailing cell typing approaches in terms of its ability to identify key morphological indicators for each neuron type and separate superclasses of these neuron types. the subclasses of neuronal types could supply information for brain connectivity and modeling, also promote other analysis including feature spaces. AvailabilityAll datasets used in this study are publicly available. All analyses were conducted with python package Scikitlearn 0.23.1 version. Source code used for data processing, analysis and figure generation is available as an open-source Python package, on https://github.com/SEU-ALLEN-codebase/ManifoldAnalysis Contactljliu@braintell.org

neuroscience↗

bioRxiv2023

Non-homogenous axonal bouton distribution in whole-brain single cell neuronal networks

We examined the distribution of pre-synaptic contacts in axons of mouse neurons and constructed whole-brain single-cell neuronal networks using an extensive dataset of 1891 fully reconstructed neurons. We found that bouton locations were not homogeneous throughout the axon and also among brain regions. As our algorithm was able to generate whole-brain single-cell connectivity matrices from full morphology reconstruction datasets, we further found that non-homogeneous bouton locations have a significant impact on network wiring, including degree distribution, triad census and community structure. By perturbing neuronal morphology, we further explored the link between anatomical details and network topology. In our in silico exploration, we found that dendritic and axonal tree span would have the greatest impact on network wiring, followed by synaptic contact deletion. Our results suggest that neuroanatomical details must be carefully addressed in studies of whole brain networks at the single cell level.

neuroscience↗

bioRxiv2022

Instantaneous antidepressant effect of lateral habenula deep brain stimulation in rats studied with functional magnetic resonance imaging

The available treatments for depression have substantial limitations, including low response rates and substantial lag time before a response is achieved. We applied deep brain stimulation (DBS) to the lateral habenula (LHb) of two rat models of depression (Wistar Kyoto rats and lipopolysaccharide-treated rats) and observed an immediate (within seconds to minutes) alleviation of depressive-like symptoms with a high response rate. Simultaneous functional magnetic resonance imaging (fMRI) conducted on the same sets of depressive rats used in behavioral tests revealed DBS-induced activation of multiple regions in afferent and efferent circuitry of the LHb. The activation levels of brain regions connected to the medial LHb (M-LHb) was correlated with the extent of behavioral improvements. Rats with more medial stimulation sites in the LHb exhibited greater antidepressant effects than those with more lateral stimulation sites. These results indicated that the antidromic activation of the limbic system and orthodromic activation of the monoaminergic systems connected to the M-LHb played a critical role in the rapid antidepressant effects of LHb-DBS. This study indicates that M-LHb-DBS might act as a valuable, rapid-acting antidepressant therapeutic strategy for treatment-resistant depression and demonstrates the potential of using fMRI activation of specific brain regions as biomarkers to predict and evaluate antidepressant efficacy.

neuroscience↗

bioRxiv2022

The complex roles of genomic DNA modifications of bacteriophage T4 in resistance to nuclease-based defense systems of E. coli

The interplay between defense and counter-defense systems of bacteria and phages is a major driver of evolution of both organisms, leading to their greatest genetic diversity. Bacterial restriction-modification (R-M) and CRISPR-Cas are two well-known defense systems that target phage DNAs through their nuclease activities, whereas phages have developed counter-defense systems through covalent modifications of their genomes. Recent studies have revealed many novel nuclease-containing antiphage systems, which leads to the question of whats the role of phage genome modifications in countering these systems. Here, we scanned Escherichia coli genome sequences available in the NCBI databases and found abundant nuclease-containing defense systems, indicating that phage genomic DNA could be a major target for E. coli to restrict infection. From a collection of 816 E. coli strains, we cloned and validated 14 systems. Particularly, Gabija and type III Druantia systems have broad antiphage activities. Using wild-type phage T4 and its mutants, T4 (hmC) and T4 (C), which contain glucosyl-5-hydroxymethylcytosines, 5-hydroxymethylcytosines, and unmodified cytosines in the genomic DNA respectively, we revealed the complex roles of genomic modification of phage T4 in countering the nuclease-containing defense systems other than simply blocking the degradation of genomic DNA by nuclease.

microbiology↗

bioRxiv2022

Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex

The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique nearinfrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.

biophysics↗

bioRxiv2022

Inter-brain coupling reflects disciplinary differences in real-world classroom learning

Classroom is the primary site for learning. One important feature of classroom learning is its organization into different disciplines. While disciplinary differences could substantially influence students learning processes, little is known about the neural mechanism underlying successful disciplinary learning. In the present study, wearable EEG devices were used to record a group of high school students during their classes of a soft (Chinese) and a hard (Math) discipline throughout one semester. The students with higher learning outcomes in Chinese were found to have better inter-brain neural couplings with their excellent peers, whereas the students with higher Math outcomes were found to have better couplings with the class average. Moreover, the inter-brain couplings showed distinct dominant frequencies for the two disciplines. Our results illustrate disciplinary differences in successful learning from an inter-brain perspective and suggest the neural activities of excellent peers and class average as exemplars for soft and hard disciplines. TeaserSuccessful classroom learning is associated with distinct inter-brain coupling patterns for soft and hard disciplines

neuroscience↗

bioRxiv2022

Inner membrane complex proteomics reveals a palmitoylation cascade regulating intraerythrocytic development of malaria parasite

Malaria is caused by infection of the erythrocytes by the parasites Plasmodium. Inside the erythrocytes, the parasites multiply via schizogony, an unconventional cell division mode. The Inner Membrane Complex (IMC), an organelle located beneath the parasite plasma membrane, serving as the platform for protein anchorage, is essential for schizogony. So far, complete repertoire of IMC proteins and their localization determinants remain unclear. Here we used biotin ligase (TurboID)-based proximity labelling to compile the proteome of the schizont IMC of rodent malaria parasite Plasmodium yoelii. In total, 300 TurboID-interacting proteins were identified. 19 of the 22 selected candidates were confirmed to localize in the IMC, indicating good reliability. In light of the existing palmitome of Plasmodium falciparum, 83 proteins of the P. yoelii IMC proteome are potentially palmitoylated. We further identified DHHC2 as the major resident palmitoyl-acyl-transferase of the IMC. Depletion of DHHC2 led to defective schizont segmentation and growth arrest both in vitro and in vivo. DHHC2 was found to palmitoylate two critical IMC proteins CDPK1 and GAP45 for their IMC localization. In summary, this study reports an inventory of new IMC proteins and demonstrates a central role of DHHC2 in governing IMC localization of proteins during the schizont development.

microbiology↗

bioRxiv2021

Substrate Specificity for Human Histidine Methyltransferase SETD3

Histidine methyltransferase SETD3 plays an important role in human biology and diseases. Previously, we showed that SETD3 catalyzes N3-methylation of histidine 73 in {beta}-actin (Kwiatkowski et al., 2018). Here we report integrated synthetic, biocatalytic, biostructural and computational analyses on human SETD3-catalyzed methylation of {beta}-actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N-nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free-energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic and functional insight into {beta}-actin histidine methylation by SETD3.

biochemistry↗

bioRxiv2021

5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes

5-methylcytosine (m5C) is an important epitranscriptomic modification involved in mRNA stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles of Plasmodium parasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (P. yoelii) and human (P. falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to the Plasmodium transcripts and that a Plasmodium ortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knock-out of P. yoelii nsun2 (pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in rodent and human malaria parasites. Restoration of the nsun2 gene in the knock-out parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species of Plasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites. SignificanceModifications of RNA including methylations of cytosine (m5C) and adenosine (m6A) have important roles in RNA metabolism, cellular responses to stress, and biological processes of differentiation and development. Here, we report on the profiles of m5C mRNA modifications in malaria parasites that infect rodents (Plasmodium yoelii) and humans (Plasmodium falciparum). These parasites have genes that encode homologs of human and plant NSUN2 methyltransferases (m5C "writers"). We show that one of these homologs, termed PyNSUN2, stabilizes mRNA transcripts in P. yoelii and mediates m5C-associated development of the parasite sexual stages (gametocytes). Further research on m5C and other epitranscriptomic modifications may yield new insights into molecular pathways of gametocyte development and mosquito infectivity that can be exploited to interrupt malaria transmission.

microbiology↗

bioRxiv2020

Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP

The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 [A]. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.

molecular biology↗

bioRxiv2020

Structure of the light harvesting 2 complex reveals two carotenoid energy transfer pathways in a photosynthetic bacterium

We report the 2.4 [A] resolution structure of the light harvesting 2 complex (LH2) from Marichromatium (Mch.) purpuratum determined by electron cryo-microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. Two sets of distinct carotenoids are identified in the structure, and a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules is shown. The geometry imposed by the heptameric ring controls the resonant coupling of the long wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique. One Sentence SummaryThe structure of a heptameric LH2 antenna complex reveals new energy transfer pathways and the basis for assembling LH rings.

biochemistry↗

bioRxiv2020

Single-cell RNA-seq reveals endoimmune cells in zebrafish

Endothelial cells (ECs) constitute a monolayer that covers the interior surface of blood vessels and participates in various processes. Although vascular ECs share certain common properties, they differ in both structure and function. So far, the transcriptome profile and heterogeneity of the full repertoire of ECs in vertebrates remain poorly understood. The relatively small size of zebrafish embryos and larvae allows a feasible analysis of the broad spectrum of ECs within every tissue and organ of a whole organism. ECs have been suggested to be conditional innate immune cells. Whether ECs possess the comparable capacity of involvement in immune response is so far undetermined. Currently, through single-cell RNA sequencing analysis of total ECs of zebrafish we identified a fraction of endothelial cells expressing the marker genes of innate immune cells, named "endoimmune cells". We found the percentage of these cells gradually increased along with the embryonic development. Then, we observed the patrolling mCherry+ cells displayed the morphology alike to the macrophages and neutrophils. Furthermore, we revealed that some of the kdrl:ras-mCherry ECs were labelled with coro1a:EGFP as well. In addition, we demonstrated that the mCherry+ EC from intersegmental vessel could gradually present the expression of GFP in Tg(kdrl:ras-mCherry::coro1a:GFP) line, suggesting the endoimmune cells are derived from ECs. Importantly, we showed the endoimmune cells are responsive to the inflammation in zebrafish. Taken together, these data suggested the existence of endoimmune cells, a novel type of subpopulations of ECs. It will provide novel insights for understanding endothelial roles in both normal physiological function and human diseases and enable endoimmune cells-based target therapies.

cell biology↗