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Peng, Z.

Publications and source records attributed to Peng, Z..

At least 55 records · Page 3Linked to original sources

Somites are a source of nephron progenitors in zebrafish

For over a century it has been believed that the vertebrate kidney arises exclusively from the intermediate mesoderm. Here, we overturn this paradigm by demonstrating that some nephrons, the functional units of the kidney, originate from the somites--blocks of paraxial mesoderm best known for their contribution to muscle and connective tissues. Using a combination of the GESTALT technique to assign developmental ancestry, somite transplantation experiments and Cre-lox fate-mapping, we show that somites can contribute to the nephrons in the adult zebrafish kidney. Our findings uncover an unexpected developmental connection between the somites and kidneys, potentially offering new pathways for developing regenerative treatments for kidney diseases.

developmental biology↗

Commensal-derived Trehalose Monocorynomycolate Triggers γδ T Cell-driven Protective Ocular Barrier Immunity

Commensals shape host physiology through molecular crosstalk with host receptors. Identifying specific microbial factors that causally influence host immunity is key to understanding homeostasis at the host-microbe interface and advancing microbial-based therapeutics. Here, we identify trehalose monocorynomycolate (TMCM) from Corynebacterium mastitidis (C. mast) as a potent stimulator of IL-17 production by {gamma}{delta} T cells at the ocular surface. Mechanistically, TMCM-driven IL-17 responses require both IL-1 signals and {gamma}{delta} TCR signaling, which also supports endogenous {gamma}{delta} T cell IL-1R1 expression. Notably, synthetic TMCM alone is sufficient to mimic the effect of C. mast in inducing {gamma}{delta} T cell immunity and protect against pathogenic corneal infection. Our findings establish TMCM as a key mediator of commensal-driven immune defense, highlighting its potential as a {gamma}{delta} T cell adjuvant and a microbiome-informed therapeutic to enhance IL-17-driven protection at barrier sites such as the ocular surface. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643820v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@63139forg.highwire.dtl.DTLVardef@9d6978org.highwire.dtl.DTLVardef@775e37org.highwire.dtl.DTLVardef@ca84b6_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LICorynomycolates enable ocular C. mast colonization and protective IL-17 immunity C_LIO_LITMCM drives IL-17 from {gamma}{delta} T cells through TCR and IL-1R signaling C_LIO_LI{gamma}{delta} TCR signaling maintains the expression of endogenous IL-1R1 C_LIO_LISynthetic TMCM mimics the ability of C. mast to induce {gamma}{delta} T cell immunity in the eye C_LIO_LITMCM protects against P. aeruginosa keratitis, highlighting its therapeutic potential C_LI

immunology↗

Spatial transcriptomics elucidates the central role of cerebral vasculatures in the progression of Japanese encephalitis

The cellular and molecular mechanisms underlying the neuropathology of Japanese encephalitis virus (JEV) remain obscure. Herein, we designed Stereo-seq chips to simultaneously capture the in situ transcriptomes of both the host and JEV, constructing a comprehensive spatiotemporal pathological landscape for Japanese encephalitis (JE). This study reveals the central role of the vascular system in JE pathogenesis, particularly the meninges, which displayed the strongest signal of inflammation and cell death in the JEV-infected brain. The activation of the Ackr1+ endothelial cells, disruption of the blood-brain barrier, the migration of JEV-infected monocytes, secretion of immune factors by the infected cells, and the occurrence of pyroptosis and necroptosis form a positive feedback loop, resulting in an increasing influx of immune cells and tissue damage. JEV infection leads to neurological impairments, which may be attributed to the interaction between viral proteins and host cellular factors such as Stat1, Stat3, Nfkb1, and Sp1. As the vascular system serves as a central receiver and amplifier of inflammatory signals, regulating inflammation within the vascular system is essential in mitigating JE progression.

immunology↗

Ocular immune privilege in action: the living eye imposes unique regulatory and anergic gene signatures on uveitogenic T cells

Despite ocular immune privilege, circulating retina-specific T cells can trigger autoimmune uveitis, yet intraocular bleeding--a relatively common event--rarely leads to disease. Using an in vivo immune privilege model, we previously reported that all naive retina-specific T cells entering the eye become primed in situ; about Ob% become FoxpO+ T-regulatory cells (Tregs), while the rest fail to induce pathology. Here, single-cell transcriptomics and functional validation revealed distinct phenotypes in both populations: ocular Tregs were highly suppressive, whereas non-Tregs expressed suppression- and anergy-associated genes and lacked regulatory function. Trajectory analyses suggested that Tregs and anergic cells arise from a common proliferative precursor in parallel, rather than sequentially. Our data indicate a key checkpoint governing the divergence of anergic and regulatory fates. These findings provide molecular-level insights into ocular immune privilege and may inform strategies to silence autoimmune effector cells or reverse T cell unresponsiveness in cancer, vaccination, or chronic infection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/640701v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1e13f5org.highwire.dtl.DTLVardef@b065feorg.highwire.dtl.DTLVardef@f83014org.highwire.dtl.DTLVardef@1ca8f0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIEye-primed retina-specific T cells develop distinct tolerance-associated phenotypes. C_LIO_LIEye-induced anergic T cells remain hyporesponsive to antigen re-stimulation. C_LIO_LIRegulatory and anergic T cells differentiate in parallel from a common precursor. C_LIO_LIInduction of T cell anergy is a novel feature of ocular immune privilege. C_LI

immunology↗

Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis

Background & AimsMitochondrial dysfunction has been implicated in aging and various cancer development. As highly dynamic organelles, mitochondria constantly undergo fission, mediated by dynamin-related protein 1 (DRP1, gene name Dnm1l), and fusion, regulated by mitofusin 1 (MFN1), MFN2, and optic atrophy 1 (OPA1). However, whether and how dysregulation of mitochondria dynamics would be involved in liver pathogenesis and tumorigenesis is unknown. MethodsDnm1l Flox/Flox (Dnm1lF/F), Mfn1F/F and Mfn2F/F mice were crossed with albumin-Cre mice to generate liver-specific Dnm1l knockout (L-Dnm1l KO), L-Mfn1 KO, L-Mfn2 KO, L-Mfn1, Mfn2 double KO (DKO), and L-Mfn1, Mfn2, Dnm1l triple KO (TKO) mice. These mice were housed for various periods up to 18 months. Some mice also received hydrodynamic tail vein injections of a Sleeping Beauty transposon-transposase plasmid system with c-MYC and YAP. Blood and liver tissues were harvested for biochemical and histological analysis. ResultsL-Dnm1l KO mice had elevated serum alanine aminotransferase levels and increased hepatic fibrosis as early as two months of age. By 12 to 18 months, male L-Dnm1l KO mice developed spontaneous liver tumors, primarily hepatocellular adenomas. While female L-Dnm1l KO mice also developed liver tumors, their incidence was much lower. In contrast, neither L-Mfn1 KO nor L-Mfn2 KO mice had notable liver injury or tumorigenesis. However, a small portion of DKO mice developed tumors at 15-18 month-old. Increased DNA damage, senescence and compensatory proliferation were observed in L-Dnm1l KO mice but were less evident in L-Mfn1 KO, L-Mfn2 KO or DKO mice, indicating that mitochondrial fission is more important to maintain hepatocyte homeostasis and prevent liver tumorigenesis. Interestingly, further deletion of Mfn1 and Mfn2 in L-Dnm1l KO mice markedly abolished liver injury, fibrosis, and both spontaneous and oncogene-induced tumorigenesis. RNA sequencing and metabolomics analysis revealed significant activation of the cGAS-STING-interferon pathway and alterations in the tumor microenvironment pathways, alongside increased pyrimidine synthesis and metabolism in the livers of L-Dnm1l KO mice. Notably, the changes in gene expression and pyrimidine metabolism were considerably corrected in the TKO mice. ConclusionsMitochondrial dynamics and stability are essential for maintaining hepatic mitochondrial homeostasis and hepatocyte functions. Loss of hepatic DRP1 promotes liver tumorigenesis by increasing pyrimidine metabolism and activating the cGAS-STING-mediated innate immune response.

cell biology↗

Ustilaginoidea virens suppresses floral immunity through promoting GA biosynthesis by the effector SCRE9

Rice false smut caused by Ustilaginoidea virens has become one of the most important rice diseases. U. virens specifically infects rice florets through stamen filaments. However, it is mysterious how U. virens inhibits floral immunity for successful colonization. Here, we show that a small cysteine-rich effector SCRE9 is a key virulence factor in U. virens. Expression of SCRE9 in rice not only suppresses immune responses and false smut resistance, but also significantly increases expression of expansin and gibberellin (GA) biosynthetic genes and GA content in young rice panicles. We further demonstrate that OsSIP1 (SCRE9-interacting protein 1) in rice is targeted by SCRE9 and interacts with the OsMADS63 and OsMADS68 transcription factors that transcriptionally regulate the GA synthesis gene GA3ox1. Interestingly, the chloroplast-localized OsSIP1 recruits OsMADS63/68 into the chloroplast. SCRE9 causes OsSIP1 to be translocated into the nucleus, thereby releasing OsMADS63/68 from the chloroplast into the nucleus to promote GA3ox1 transcription. Therefore, SCRE9 promotes GA biosynthesis and expression of expansins in rice florets, thus loosening cell walls and overcoming the physical barrier during U. virens infection. The finding uncovers an unidentified floret infection strategy that offsets the deficiency in cell wall degrading ability in the unique floret colonizing fungus.

plant biology↗

The comprehensive detection of hemoglobinopathy variants via long-read sequencing

BACKGROUNDThe genetic complexity of hemoglobin genes, characterized by high GC content and homologous sequences, poses significant challenges for detecting hemoglobin variants in clinical settings. METHODSA long-read indexed PCR method utilizing the novel CycloneSEQ nanopore sequencing platform was developed to detect all variant types, including single nucleotide variants (SNVs), deletions, structural variants (SVs) in HBA, HBB, HBD, and HBG genes. The method was validated using 507 clinical samples to assess its performance. RESULTSThe long-read indexed PCR system employed 13 primers targeting the hemoglobin gene clusters. This design enabled the detection of 37 types of HBA deletions, 5 SV (3 multicopies (, anti3.7, anti4.2) and 2 fusion allele (HK and anti-HK)), 37 HBB deletions, and all SNVs in the targeted regions. Validation across 507 samples (84 with HBA variants, 60 with HBB variants, 256 with both HBA and HBB variants, and 107 with no known variants) demonstrated 100.0% sensitivity and specificity. Additionally, the long-read sequencing enabled phasing of variants within hemoglobin genes, providing insights critical for clinical interpretation. CONCLUSIONSThe long-read indexed PCR method, combined with the CycloneSEQ nanopore sequencing platform, proved to be a robust and efficient solution for detecting hemoglobinopathy variants. The integration of indexed primers and barcoding enhances scalability, making this method ideal for large-scale population screening programs in the future.

genomics↗

TurboID-based proximity labeling discovers ABCF2 as an adhesion receptor for the zoonotic pathogen Pasteurella multocida

Pasteurella multocida is a zoonotic pathogen that can cause fatal infections in both animals and humans. A significant number of putative adhesive factors have been predicted to contribute to the pathogenesis of P. multocida, but their interactive proteins on host cells remain unclear. In this study, we experimentally verified the roles of three previously proposed proteins (PlpE, PtfA, Hsf-2) in the adherence of P. multocida. Through turboID-based proximity labeling screening, we identified ATP-binding cassette sub-family F member 2 (ABCF2) as a host interactive protein for PlpE/PtfA/Hsf-2. Crucial amino acid residues in PlpE, PtfA, and/or Hsf-2 that are essential for interacting with ABCF2 included Asp-123 (PlpE), Lys-88 (PtfA), Asp-136 (PtfA), Ala-464 (Hsf-2), Glu-473 (Hsf-2), and Arg-489 (Hsf-2). Knocking down or knocking out ABCF2 significantly reduced the adherence and invasion of P. multocida to host cells, while overexpression of ABCF2 markedly increased these effects. However, ABCF2 did not contribute to the adherence of other bacterial species such as Klebsiella pneumoniae and Bordetella bronchiseptica. Additionally, we demonstrated that P. multocida infection upregulated the expression of host ABCF2 by activating the p38 MAPK and NF-{kappa}B signaling pathways. Furthermore, we showed that ABCF2 was involved in the P. multocida-induced p53-dependent apoptotic signaling pathway. To the best of our knowledge, this is the first identification of ABCF2 as a host factor contributing to the adherence of P. multocida and only the second report of ABCF2s involvement in bacterial pathogenesis. ImportanceP. multocida can cause fatal infections in both animals and humans, yet the mechanisms related to its pathogenesis remain to be fully explored. In this study, we identified ABCF2 as a crucial host interactive protein for three adhesive proteins encoded by P. multocida and experimentally verified its role in the adherence and invasion of P. multocida. Furthermore, we elucidated how P. multocida modulates ABCF2 during its infection and revealed p53-dependent apoptosis as a downstream effect of ABCF2 during P. multocida infection. Given the absence of reports on ABCF2 contributing to the pathogenesis of P. multocida and only one previous report on the involvement of ABCF2 in bacterial pathogenesis prior to this study, this research could be valuable for comprehending the interactions between bacteria and hosts during bacterial infections.

microbiology↗

Improved automated model building for cryo-EM maps using CryFold

Constructing atomic models from cryogenic electron microscopy (cryo-EM) density maps is essential for interpreting molecular mechanisms. In this study, we present CryFold, an approach for de novo model building for cryo-EM maps, leveraging recent advancements in AlphaFold2 (1) to improve the state-of-the-art method ModelAngelo (2). To accommodate the cryo-EM map information, CryFold replaces the global attention mechanism in AlphaFold2 with local attention, which is further enhanced by a novel 3D rotary position embedding. CryFold produces more complete models, reduces the resolution requirement, and accelerates the modeling. The application of CryFold to three new maps with unknown structure demonstrates its ability to accurately distinguish between paralog sequences in noisy regions, detect previously uncharacterized proteins with unknown functions, precisely compartmentalize the map to isolate non-protein components, and improve the modeling of conformational changes. A particular case includes a 104-protein complex that has been modeled within a few hours, and a minor conformational change of a single protein domain has been detected at the periphery when models from two different maps were compared. CryFold stands as an accurate method currently available for model building of proteins in cryo-EM structure determination. The source code and model parameters are available at https://github.com/SBQ-1999/CryFold.

bioinformatics↗

The T-type voltage-gated Ca2+ channel CaV3.1 as a candidate receptor for Pasteurella multocida toxin and contributes to the disruption of respiratory epithelial barrier induced by the toxin

Pasteurella multocida toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen P. multocida. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we discovered that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions ({beta}-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca2+ inflow, leading to an imbalance of cellular Ca2+ homeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signaling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca2+ channel CaV3.1 was found to participate in PMT-induced cytoplasmic Ca2+ inflow. Knocking out CaV3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca2+ inflow stimulated by PMT. Further analysis identified Ser (aa92), Glu (aa155), Tyr (aa167), and Leu (aa448) as crucial sites utilized by PMT to interact with CaV3.1. These findings suggest CaV3.1 serves as an important host receptor of PMT and contributes to PMT-induced respiratory epithelial barrier disruption. ImportancePMT is a significant toxin produced by the zoonotic respiratory pathogen P. multocida, yet little is known about its pathogenesis beyond causing progressive atrophic rhinitis in pigs. In our study, we have discovered that PMT has the capacity to disrupt the integrity of the mammalian respiratory epithelial barrier. This disruption involves an imbalance in cellular Ca2+ homeostasis, endoplasmic reticulum stress, and activation of the RhoA/ROCK signaling pathway induced by PMT. Importantly, we have identified CaV3.1 as a pivotal receptor that plays a crucial role in the pathogenic effects of PMT. Our findings highlight the potential of CaV3.1 as a target for intervention strategies aimed at combating the detrimental effects of PMT.

microbiology↗

Into the Void: Cavities and Tunnels are Essential for Functional Protein Design

The design of functional proteins is crucial as it enables the creation of tailored proteins with specific capabilities, unlocking the potential solutions to various biomedical and industrial challenges. The exact relationship between structure, sequence, and function in protein design is intricate, however, a consensus has been reached that the function of a protein is mostly decided by its structure, which further decides its sequence. While the integration of biology with artificial intelligence has propelled significant advancements in protein design and engineering, structure-based functional protein design, especially de novo design, the quest for satisfactory outcomes remains elusive. In this work, we use backbone geometry to represent the cavities and tunnels of functional proteins and show that they are essential for functional protein design. Correct cavity enables specific biophysical processes or biochemical reactions, while appropriate tunnels facilitate the transport of biomolecules or ions. We also provide a package called CAvity Investigation Navigator (CAIN) to help to do the analysis, which is available at https://github.com/JiahuiZhangNCSU/CAIN.

biophysics↗

Targeting Fatty Acid Desaturase I Inhibits Renal Cancer Growth Via ATF3-mediated ER Stress Response

Monounsaturated fatty acids (MUFAs) play a pivotal role in maintaining endoplasmic reticulum (ER) homeostasis, an emerging hallmark of cancer. However, the role of polyunsaturated fatty acid (PUFAs) desaturation in persistent ER stress driven by oncogenic abnormalities remains elusive. Fatty Acid Desaturase 1 (FADS1) is a rate-limiting enzyme controlling the bioproduction of long-chain PUFAs. Our previous research has demonstrated the significant role of FADS1 in cancer survival, especially in kidney cancers. We explored the underlying mechanism in this study. We found that pharmacological inhibition or knockdown of the expression of FADS1 effectively inhibits renal cancer cell proliferation and induces cell cycle arrest. The stable knockdown of FADS1 also significantly inhibits tumor formation in vivo. Mechanistically, we show that while FADS1 inhibition induces ER stress, its expression is also augmented by ER-stress inducers. Notably, FADS1-inhibition sensitized cellular response to ER stress inducers, providing evidence of FADS1s role in modulating the ER stress response in cancer cells. We show that, while FADS1 inhibition-induced ER stress leads to activation of ATF3, ATF3-knockdown rescues the FADS1 inhibition-induced ER stress and cell growth suppression. In addition, FADS1 inhibition results in the impaired biosynthesis of nucleotides and decreases the level of UPD-N-Acetylglucosamine, a critical mediator of the unfolded protein response. Our findings suggest that PUFA desaturation is crucial for rescuing cancer cells from persistent ER stress, supporting FADS1 as a new therapeutic target.

cancer biology↗

Functional characterization of fatty acid synthase in Hermetia illucens

Fatty acid synthase (FAS) is a key role in de novo lipogenesis (DNL) in most lives. In insects, type I FAS functions in homodimer, activated by a phosphopantetheine transferase (PPT), to de novo produce essential saturated fatty acid for cellular processes. In a nova insect species Hermetia illucens (Diptera: Stratiomyidae), different from most animals and insects, lauric acid (LA) accumulates to a noticeable level, near content of that in coconut oil or palm kernel oil. However, the origin of LA, from de novo biosynthesis or as degraded products from long chain fatty acid, was still ambiguous. Here, in this study, we mined a FAS genes (HiOGS16234) from H. illucens genome and initially characterized its abilities of LA production in a free-fatty-acid producible yeast. After clear the yeast metabolites background of fatty acid by deletion of ScFAS1 and ScELO1 sequentially, which responsible for fatty acid genesis and elongation respectively, functions of HiOGS16234 from H. illucens was in vitro elucidated by analyzing its product portfolio. Through protein domain swap in HiOGS16234, we found the ketoacyl synthase domain and thioesterases domain were responsible for the different product portfolio of HiOGS16234, compared with DmFASN1. Through in vitro assay in yeast, the origin of LA in BSF was firstly elucidated at molecular level, which support DNL origin hypothesis in BSF.

synthetic biology↗

PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks

AO_SCPLOWBSTRACTC_SCPLOWProteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to model the complex features of proteins have involved the training of large and expressive protein language models (pLMs) such as ESM-2 and ProtT5, which accurately encode structural, functional, and physicochemical properties of input protein sequences. However, the over 200 million sequences that these pLMs were trained on merely scratch the surface of proteomic diversity, as they neither input nor account for the effects of PTMs. In this work, we fill this major gap in protein sequence modeling by introducing PTM tokens into the pLM training regime. We then leverage recent advancements in structured state space models (SSMs), specifically Mamba, which utilizes efficient hardware-aware primitives to overcome the quadratic time complexities of Transformers. After adding a comprehensive set of PTM tokens to the model vocabulary, we train bidirectional Mamba blocks whose outputs are fused with state-of-the-art ESM-2 embeddings via a novel gating mechanism. We demonstrate that our resultant PTM-aware pLM, PTM-Mamba, improves upon ESM-2s performance on various PTM-specific tasks. PTM-Mamba is the first and only pLM that can uniquely input and represent both wild-type and PTM sequences, motivating downstream modeling and design applications specific to post-translationally modified proteins. To facilitate PTM-aware protein language modeling applications, we have made our model available at: https://huggingface.co/ChatterjeeLab/PTM-Mamba.

bioinformatics↗

Late-Life Alcohol Exposure Does Not Exacerbate Age-Dependent Reductions in Mouse Spatial Memory and Brain TFEB Activity

Alcohol consumption is believed to affect Alzheimers disease (AD) risk, but the contributing mechanisms are not well understood. A potential mediator of the proposed alcohol-AD connection is autophagy, a degradation pathway that maintains organelle and protein homeostasis. Autophagy is in turn regulated through the activity of Transcription factor EB (TFEB), which promotes lysosome and autophagy-related gene expression. To explore the effect of alcohol on brain TFEB and autophagy, we exposed young (3-month old) and aged (23-month old) mice to two alcohol-feeding paradigms and assessed biochemical, transcriptome, histology, and behavioral endpoints. In young mice, alcohol decreased hippocampal nuclear TFEB staining but increased SQSTM1/p62, LC3-II, ubiquitinated proteins, and phosphorylated Tau. Hippocampal TFEB activity was lower in aged mice than it was in young mice, and Gao-binge alcohol feeding did not worsen the age-related reduction in TFEB activity. To better assess the impact of chronic alcohol exposure, we fed young and aged mice alcohol for four weeks before completing Morris Water and Barnes Maze spatial memory testing. The aged mice showed worse spatial memory on both tests. While alcohol feeding slightly impaired spatial memory in the young mice, it had little effect or even slightly improved spatial memory in the aged mice. These findings suggest that aging is a far more important driver of spatial memory impairment and reduced autophagy flux than alcohol consumption.

animal behavior and cognition↗

Proteus: pioneering protein structure generation for enhanced designability and efficiency

Diffusion-based generative models have been successfully employed to create proteins with novel structures and functions. However, the construction of such models typically depends on large, pre-trained structure prediction networks, like RFdiffusion. In contrast, alternative models that are trained from scratch, such as FrameDiff, still fall short in performance. In this context, we introduce Proteus, an innovative deep diffusion network that incorporates graph-based triangle methods and a multi-track interaction network, eliminating the dependency on structure prediction pre-training with superior efficiency. We have validated our models performance on de novo protein backbone generation through comprehensive in silico evaluations and experimental characterizations, which demonstrate a remarkable success rate. These promising results underscore Proteuss ability to generate highly designable protein backbones efficiently. This capability, achieved without reliance on pre-training techniques, has the potential to significantly advance the field of protein design. Codes are available at https://github.com/Wangchentong/Proteus.

bioinformatics↗

Generative Diffusion Models for Antibody Design, Docking, and Optimization

In recent years, optimizing antibody binding affinity for biomedical applications has become increasingly important. However, traditional wet-experiment-based approaches are time-consuming and inefficient. To address this issue, we propose a diffusion model-based antibody optimization pipeline to improve binding affinity. Our approach involves two key models: AbDesign for designing antibody sequences and structures, and AbDock, a paratope-epitope docking model, used for screening designed CDRs. On an independent test set, our AbDesign demonstrates the exceptional performance of an RMSD of 2.56[A] in structure design and an amino acid recovery of 36.47% in sequence design. In a paratope-epitope docking test set, our AbDock achieves a state-of-the-art performance of DockQ 0.44, irms 2.71[A], fnat 0.40, and Lrms 6.29[A]. The effectiveness of the optimization pipeline is further experimentally validated by optimizing a flaviviruse antibody 1G5.3, resulting in a broad-spectrum antibody that demonstrates improved binding to 6 out of the nine tested flaviviruses. This research offers a general-purpose methodology to enhance antibody functionality without training on data from specific antigens.

bioinformatics↗

Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani

Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria (EHB) have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. (En-Cren) isolated from the generalist fungal pathogen Rhizoctonia solani. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved. ImportanceThe genome characterization and comparative genomics analysis of En-Cren provided the foundation and resources for a better understanding of the ecology and evolution of this EHB in the rhizosphere. The ability to produce IAA and PAA may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction yet to be explored.

microbiology↗