Biology subjects

Hao, J.

Publications and source records attributed to Hao, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Repressed expression of nucleoporins and importins impairs plant defense against an infectious noncoding RNA

Plant pathogens threaten global food security and cause substantial annual economic losses. Of particular concern are host jumps, in which pathogens expand their host range to new species, often resulting in sudden and difficult-to-control disease outbreaks. However, the ability to anticipate such events remains limited by an incomplete understanding of pathogen adaptability and the mechanisms governing nonhost resistance. Here, we show that temperature modulates the infectivity and host range of potato spindle tuber viroid (PSTVd), a pathogenic noncoding RNA that severely impacts solanaceous crops such as potato and tomato. Using in vivo single-molecule RNA structure probing, we found that higher temperatures drive PSTVd into a more uniform RNA conformation associated with enhanced infectivity in tomato. Concurrently, elevated temperature suppresses key host defense pathways, including RNA silencing and NPR1-mediated immunity. Notably, these conditions enable PSTVd to overcome nonhost resistance and establish infection in Arabidopsis thaliana. Our findings reveal that elevated temperature promotes PSTVd host expansion through multiple coordinated mechanisms, linking changes in pathogen behavior with increased host susceptibility, and suggest that ongoing climate warming may heighten the risk of viroid host jumps.

plant biology↗

bioRxiv2025

scSTAR2: a multiomics integration algorithm to reveal disease specific cellular signatures by bridging single-cell resolution features and clinical metadata

Single-cell techniques, pivotal in characterizing intricate cell and spatial structures within tissues, face challenges in contextualizing clinical phenotypes. Currently, most investigations of the clinical phenotype related cell/spatial heterogeneities relied on the phenotype information from single-cell data. However, a wealth of underutilized clinical metadata exists within conventional bulk sequencing data. Current methods for correlating clinical information with individual cells or spatial regions remain limited and lack robustness. Here we present scSTAR2, a novel algorithm that transcends existing limitations by reconstructively integrating multiomics data to identify cells associated with clinical phenotypes. Unlike existing methods, scSTAR2 reconstructs single-cell data guided by specific phenotypes, significantly reducing interference from irrelevant noise. By employing scSTAR2 to integrate scRNA-seq, scATAC-seq, and spatial transcriptomics and bulk RNA-seq, we not only confirmed a new heat-shock Treg subtype in tumors but also more sensitively identified TLS (tertiary lymphoid structure) areas than traditional methods. In conclusion, scSTAR2 has proven to significantly enhance single-cell data interpretation across diverse clinical scenarios.

bioinformatics↗

bioRxiv2025

Subtype-specific neutralizing antibodies promote antigenic shift during influenza virus co-infection

Reassortment between different influenza strains occurs when they co-infect the same host cell. The emergence of a reassortant virus depends on both its intrinsic fitness and extrinsic factors, including pre-existing humoral immunity. The generation of pandemic strains, such as H2N2 and H3N2, and zoonotic influenza A viruses, like H5N6, H5N8, and H7N9, in birds is suggested to be the result of extensive selection by pre-existing antibodies. To further explore the role of humoral immunity in reassortment, we generated two divergent fluorescent protein-expressing viruses and used strain-specific and cross-reactive monoclonal antibodies (mAbs) to assess the impact of cross-immunity on reassortment. Our results indicate that all mAbs altered the genotypic diversity and significantly reduced the release of progeny virions in co-infected cells both in vitro and in vivo. Moreover, antibody transfer studies in mice revealed protection from challenge with divergent pathogenicity profiles. Notably, selection driven by a strain-specific mAb depended on its neutralizing specificity, whereas the selection driven by broadly reactive mAbs was independent of neutralization specificity. Our findings demonstrate that pre-existing neutralizing antibodies shape reassortment and that strain-specific neutralizing antibodies promote antigenic shift during co-infection, which is not the case for broadly cross-reactive antibodies that recognize influenza viruses from different subtypes.

microbiology↗

bioRxiv2025

Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids

A bioengineered kidney using a decellularized kidney scaffold (DKS) offers a promising solution to the kidney shortage. However, the transplantation of bioengineered kidneys using DKS recellularized with human endothelial, renal cells or others has not yet successfully achieved the vascular and renal reconstruction in vivo. In this study, we identified another type of stem cells, designated as human placenta-derived angiogenic stem cells (hPASCs), which serve as seeding cells for the vascularization of DKS. These hPASCs encompass angiogenic subpopulations, exhibit both stem cell properties and the capacity for vascular differentiation. Human fetal kidney organoids (KIO) were established as a source of renal parenchymal cells, comprising renal, immune, and vascular cell populations. We developed a vascularized bioengineered kidney by recellularizing DKS with hPASCs and KIO using a circulation perfusion culture system. The hPASCs bioengineered kidney demonstrated enhanced angiogenesis and reconstructed renal architecture in vivo, by transplantation into rat models of renal subcapsular and partial nephrectomy. Furthermore, immunofluorescence and single-cell analyses revealed that the hPASCs revascularized bioengineered kidney regenerated both vascular and renal parenchymal cells within the host. This study offers another strategy for kidney bioengineering and regeneration.

bioengineering↗

bioRxiv2025

Cross-Platform Omics Pipeline for Integrated Transcriptomics

The fragmentation of single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) tools across Python/R ecosystems, coupled with escalating computational demands for million-cell datasets, creates critical barriers to reproducible analysis. To overcome this, we present CrosPIT (Cross-Platform Omics Pipeline for Integrated Transcriptomics), a cloud-native framework that unifies cross-language analysis in Google Colab with versioned storage on Google Drive. Pre-configured environments enable rapid switching between CPU/GPU/R runtimes, eliminating local hardware constraints. To demonstrate biological utility, we embedded several modules, such as a module for precision detection of malignant epithelial cells in colorectal cancer. CrosPIT thus delivers a scalable, language-agnostic solution that standardizes workflows through native AnnData/Seurat object interoperability, accelerates integrative omics research, and democratizes access to high-performance transcriptomic analysis.

bioinformatics↗

bioRxiv2025

Genome-wide CRISPR/Cas9 knockout screen identifies host factors essential for Bovine Parainfluenza Virus Type 3 replication

Bovine Parainfluenza Virus Type 3 (BPIV3) is a leading cause of respiratory illness in cattle and a primary component of Bovine Respiratory Disease Complex (BRDC), resulting in significant economic losses. Understanding the mechanisms of BPIV3 infection, particularly the entry process, is essential for developing effective control measures. Identifying specific host factors that viruses exploit during their life cycle can reveal critical vulnerabilities for potential antiviral targets. We established a genome-wide CRISPR/Cas9 knockout screen in bovine cells to identify host factors involved in viral infections. Our screen identified several key host factors required for BPIV3 infection, including the sialic acid transporter SLC35A1 and the protein LSM12. Further mechanistic analysis revealed that these factors play critical roles at distinct stages of the BPIV3 entry process. These findings not only advance our understanding of how BPIV3 infects host cells, but also identify potential host targets for inhibiting infection and developing novel antiviral strategies.

microbiology↗

bioRxiv2025

Structural insights into the remodeled RNA polymerase II complex on an RNA template

DNA-dependent RNA polymerases (DdRPs) recognize not only DNA but also RNA templates. This RNA-dependent RNA polymerase (RdRP) activity is exploited by viroids in plants and human hepatitis delta virus in animals. A major knowledge gap exists regarding the molecular basis conferring this RdRP activity. Here, we provide evidence supporting the reorganization of the 12-subunit Pol II to 7-subunit in vivo for PSTVd transcription. Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9 are not involved in PSTVd transcription in planta. A splicing variant of transcription factor IIIA with seven zinc finger domains (TFIIIA-7ZF) aids the remodeled Pol II in transcribing PSTVd. Using AlphaFold3, the structure of the remodeled Pol II with PSTVd RNA and TFIIIA-7ZF was generated. The predicted structure and experimental data both show that the N-terminus of TFIIIA-7ZF binds to the left terminal domain of PSTVd, while the C-terminus interacts with Rpb2. Interestingly, AlphaFold3 also predicts the bending at PSTVd loop 8 in the TFIIIA-7ZF/PSTVd complex. Replacing this loop 8 with a rigid double-stranded conformation impairs the TFIIIA-7ZF/PSTVd interaction. Altogether, our demonstrate an active form of heterogenous organization of the essential Pol II enzyme in vivo and provide structural insights into the organization of Pol II transcription complex on RNA template.

molecular biology↗

bioRxiv2025

Oncogene SETDB1s Dual Role in Endometrial Cancer: Driving Tumor Progression and Immune Escape

Oncogene SETDB1, an H3K9 methyltransferase, drives tumorigenesis in various cancers. Using endometrial cancer (EC) as a model, we discovered SETDB1s dual mechanisms in driving EC tumorigenesis and mediating immune evasion. SETDB1 knockout (SETDB1-/-) tumor-bearing mice exhibited prolonged survival of up to 100 days. Transcriptomic profiling of SETDB1-/- EC cells revealed decreased expression of oncogenes (POLR2A, MSH6, FLNA) and increased expression of tumor suppressor genes (PGR, RERG, ZNF582), which indicates that SETDB1 intrinsically promotes EC tumor proliferation by regulating these downstream genes. SETDB1 repressed repeat elements and the interferon pathway, mediating immune evasion extrinsically by inhibiting anti-tumor macrophage infiltration. ChIP-seq analysis showed SETDB1 binding at pericentromeric regions on many chromosomes and numerous ZNFs. Loss of SETDB1 resulted in abnormal cell division. SETDB1-/- tumors displayed reduced proliferation markers (Ki67, pHH3) and increased macrophage infiltration. Mechanistically, SETDB1 promotes CD47 (a dont-eat-me signal) and represses CCL5 and CXCL9 (macrophage and T-cell recruiting chemokines), contributing to immune evasion. M1-like macrophages killed more SETDB1-/- cells in co-culture. Additionally, SETDB1 knockout in mouse EC cells reduced tumor growth in C57BL/6 mice, with increased macrophage and CD4+ T-cell infiltration. Our results indicates that elevated SETDB1 and its target genes can predict higher tumor grade and worse survival, suggesting that targeting SETDB1 could be a promising therapeutic strategy for EC.

cancer biology↗

bioRxiv2025

Synergistic neuroprotective and cognitive-enhancing effects of Walnut Peptide and Theanine in human brain organoid and mouse stress models

Stress is a prevalent mental health concern emerging predominantly in late adolescence or early adulthood. Since 2007, the Food and Drug Administration (FDA) has not approved any novel anxiolytic pharmaceuticals, fueling interest in nutritional supplements as alternative therapies for stress management. Building on prior zebrafish research, this study investigates the synergistic effects of Theanine (Th) and Walnut Peptide (WP) on stress mitigation and cognitive enhancement. Utilizing the human brain organoid stress (BO-stress) model, WP+ Th were observed to reduce stress and regulate expression of neurotransmitters, including Gamma-Aminobutyric Acid (GABA), serotonin (5-HT), dopamine (DA), and acetylcholine (Ach), as well as brain-derived neurotrophic factor (BDNF) and serotonin transporter (SERT). Subsequent in vivo study using C57BL/6J mouse-stress model demonstrated that the treatment (Th 85 mg/mL + WP 200 mg/mL), or administrated with vehicles, significantly improved their performance in stress and cognitive assessments, partially normalized neurotransmitter imbalances by modulating SERT and BDNF expression. These findings highlighted the potential of using WP + Th, particularly when delivered with vehicles (eg: powder/yogurt/milk), as a novel combined therapeutic approach for stress management and cognitive enhancement. We performed a correlation analysis between BO-stress model and mouse-stress model, revealing a alignement in the SERT levels.In addition, SERT was highly correlated with other markers in the mouse hippocampus and may represent a key target for modulating the balance between stress and cognition. Significance StatementThis study established an innovative human brain organoid-stress model and, in conjunction with mouse-stress model, elucidated the synergistic actions of Theanine and Walnut Peptide in mitigating stress and augmenting cognitive function. Their beneficial effects were mediated through the regulation of SERT and BDNF, presenting a promising non-pharmacological avenue for mental health care. In addition, species differences between humans and mice were also examined through correlation analysis of brain organoids and mouse models. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/640260v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1a81886org.highwire.dtl.DTLVardef@e2281dorg.highwire.dtl.DTLVardef@1b7b167org.highwire.dtl.DTLVardef@dff9aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

The membrane skeleton density of red blood cells in MYH9-related disease patients is decreased

MYH9-related disease (MYH9-RD) is a rare autosomal dominant disorder caused by mutations in MYH9 gene, which encodes the heavy chain of nonmuscle myosin IIA. Nearly all MYH9-RD patients present with macrothrombocytopenia, characterized by decreased platelet count and increased platelet size. In this study, we collected blood samples from three MYH9-RD patients (R702S, D1424N, and R1464C) and unexpectedly found that the actin levels in the red blood cells (RBCs) from all three MYH9-RD patients are substantially lower than the healthy controls. We further revealed that the levels of two RBC membrane skeleton proteins, -spectrin and tropomodulin, are also reduced in MYH9-RD RBCs. We showed that the membrane skeleton of MYH9-RD RBCs was more porous and that MYH9-RD RBCs produced more severe deformation under hyperosmotic pressure compared to healthy controls. We conclude that MYH9-RD mutations reduce the RBC membrane skeleton density and impair its mechanical properties, and propose that defects in the membrane skeleton network in RBCs may be a common symptom in MYH9-RD. Key pointsThe levels of membrane skeleton proteins and the density of membrane skeleton network in RBCs of MYH9-RD patients are reduced. MYH9-RD RBCs produce greater deformation under hypertonic conditions compared to healthy controls.

pathology↗

bioRxiv2025

OPTN protects retinal ganglion cells and ameliorates neuroinflammation in optic neuropathies

Optineurin (OPTN) is a crucial component of the homeostatic pathway, playing a pivotal role in regulating a number of essential signaling pathways including NF-{kappa}B, interferon, autophagy, and vesicular trafficking. The dysfunction of OPTN has been implicated in the pathogenesis of several diseases, such as primary open angle glaucoma (POAG), amyotrophic lateral sclerosis (ALS), frontotemporal lobar dementia, and Pagets disease of bone. Interestingly, mutations in OPTN are implicated as gain-of-function in glaucoma pathology and loss-of-function in ALS. However, the role of loss-of-function OPTN in glaucoma pathology remains unclear. Here, we demonstrate that OPTN dysfunction contributes to chronic neuroinflammation, leading to sustained RGC death, which may represent a shared pathological mechanism in both normal tension glaucoma (NTG) and high-tension glaucoma (HTG). Retinal conditioned OPTN knockout contributes to short-term astrogliosis and long-term microglia activation, with the propagation of microglia activation spreading to the optic nerve. Moreover, OPTN loss of function does not further exacerbate RGC death in the ocular hypertension mouse model induced by viscobead injection. Combined with the downregulation of OPTN in glaucoma patients, we have revealed an IOP-independent mechanism of glaucoma pathogenesis. Furthermore, we found that OPTN-driven NPY upregulation may suppress the CHOP-associated neurodegeneration. Our findings reveal a neuroprotective role for the OPTN-NPY signaling pathway, and its dysfunction promotes RGC loss in glaucoma pathology. The OPTN-NPY-mediated neuroinflammatory pathway provides a potential therapy for IOP-resistant glaucoma and highlights a druggable target for CHOP-associated neurodegeneration.

neuroscience↗

bioRxiv2024

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.

biophysics↗

bioRxiv2024

FABP5 in Skin Macrophages Mediates Saturated Fat-Induced IL-1β Signaling in Obesity-Associated Psoriasis Development

High fat diet (HFD)-induced obesity increases the risk and severity of psoriasis. However, the immunoregulatory effects of different HFD-induced obesity on psoriasis pathogenesis remains poorly understood. Here, mimicking human dietary fat profiles, four HFDs - saturated, monounsaturated, omega-6 and omega-3 fats - were designed and used to induce obesity in mice. Despite comparable obesity levels across groups, only the saturated HFD exacerbated imiquimod (IMQ)-induced psoriasis. This exacerbation correlated with elevated levels of IL-1{beta}-producing macrophages, IL-17A-producing {gamma}{delta} T cells, and neutrophils within psoriatic lesions. Mechanistically, saturated fatty acids (FAs) promoted IL-1{beta}/IL-17 signaling via fatty acid-binding protein 5 (FABP5)-mediated mitochondrial FA oxidation and extracellular ATP release in skin macrophages. Deletion of FABP5, either globally or specifically in macrophages, attenuated IL-1{beta}/IL-17A signaling and alleviated IMQ-induced psoriasis. These findings identify FABP5 as a key mediator of saturated HFD-driven psoriasis via the IL-1{beta}/IL-17 axis, offering insights into the interplay between dietary fats, obesity and psoriasis. HighlightsO_LISaturated, but not unsaturated, high-fat diets (HFDs) drive the development of obesity-associated psoriasis. C_LIO_LISaturated fats enhance IL-1{beta}/IL-17 signaling in psoriatic skin. C_LIO_LIFABP5 mediates saturated fat-induced IL-1{beta} signaling by promoting ATP production and release. C_LIO_LIDeletion of FABP5 in macrophages alleviates the development of saturated HFD-associated psoriasis. C_LI Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/628705v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@93fedaorg.highwire.dtl.DTLVardef@409fa2org.highwire.dtl.DTLVardef@b08362org.highwire.dtl.DTLVardef@81abcc_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Adaptation to cystine limitation stress promotes PDAC tumor growth and metastasis through translational upregulation of OxPPP

Cystine/cysteine is critical for antioxidant response and sulfur metabolism in cancer cells and is one of the most depleted amino acids in the microenvironment of pancreatic ductal adenocarcinoma (PDAC). The effects of cystine limitation stress (CLS) on PDAC progression are poorly understood. Here we report that adaptation to CLS (CLSA) promotes PDAC cell proliferation and tumor growth through translational upregulation of the oxidative pentose phosphate pathway (OxPPP). OxPPP activates the de novo synthesis of nucleotides and fatty acids to support tumor growth. On the other hand, CLSA-mediated lipidomic reprogramming depends on triacylglycerides synthesis and lipid droplet formation to mitigate lipotoxicity. Through drug screening, we identify lomitapide as an inhibitor of CLSA PDAC tumor growth and a potent sensitizer of chemotherapy. Lomitapide inhibits triacylglycerides synthesis to interfere with CLSA and chemotherapy-induced lipidomic reprogramming. Taken together, we demonstrate that CLSA promotes PDAC tumor growth through metabolic reprogramming and lomitapide could be used to target the dysregulated lipid metabolism in PDAC.

cancer biology↗

bioRxiv2024

Molecular epidemiology of carbapenem-resistant hypervirulent Klebsiella pneumoniae: Risk factors and resistance mechanism of ceftazidime/avibactam in China

The high morbidity and mortality rates associated with carbapenem-resistant hypervirulent Klebsiella pneumoniae have become a global public health problem. We analyzed the whole genome sequence and epidemiological data of 81 carbapenem-resistant Klebsiella pneumoniae strains and conducted sensitivity experiments to explore the optimal concentration of carbapenem-resistant Klebsiella pneumoniae. We verified the resistance and virulence genes of carbapenem-resistant Klebsiella pneumoniae using polymerase chain reaction and compared virulence between carbapenem-resistant hypervirulent Klebsiella pneumoniae a ndcarbapenem-resistant-non-hypervirulent Klebsiella pneumoniae through Galleria mellonella assays.The prevalent types of multilocus sequence typing in our carbapenem-resistant Klebsiella pneumoniae strains were ST11 (69.14%, 56/81). ST11-K64-O1/O2v1 has become an epidemic type in our hospital, with drug-resistance genes dominated by blaKPC-2 (90.12%, 73/81). Ceftazidime/avibactam has better antibacterial effects on carbapenem-resistant Klebsiella pneumoniae, and its resistance is mainly mediated by a resistance plasmid containing the blaKPC-2 gene. 52 carbapenem-resistant hypervirulent Klebsiella pneumoniae strains carry the blaKPC-2, with a high detection rate of siderophore. Further research has shown that the genetic environment of the blaKPC-2 contains TnpR_Tn3 and ISKpn27 upstream and ISKpn6 insertion sequences downstream. Galleria mellonella revealed that the survival rate of carbapenem-resistant hypervirulent Klebsiella pneumoniae was lower than that of carbapenem-resistant-non-hypervirulent Klebsiella pneumoniae, and the survival rate of carbapenem-resistant hypervirulent Klebsiella pneumoniae-K64 was lower than that of carbapenem-resistant hypervirulent Klebsiella pneumoniae-K47.The spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains is alarming, necessitating molecular monitoring of hypervirulent strains and strengthening the nosocomial infection prevention and control measures. Antibiotics should be used reasonably based on patients infection status and local epidemiological data. ImportanceCarbapenem-resistant Klebsiella pneumonia is a global public health concern. We conducted a molecular epidemiological analysis of 81 carbapenem-resistant hypervirulent Klebsiella pneumoniae strains from our hospital and explored the resistance mechanism of ceftazidime/avibactam. We identified the blaKPC-2 gene to be primarily responsible for carbapenem resistance in our hospital, and ST11-K64 was the dominant clone. A high-risk clone, ST307-K102, was detected, necessitating strengthened surveillance to prevent its spread. This studys findings contribute to the optimization of antimicrobial management and indicate that genomic research can assist with the tracking of hospital infection outbreaks and the improvement of infection-control measures.

microbiology↗

bioRxiv2024

SOQ1 functions as a methionine sulfoxide reductase in the chloroplast lumen for regulation of photoprotective qH in Arabidopsis

Photosynthetic organisms must balance light absorption and energy dissipation to prevent photo-oxidative damage. Non-photochemical quenching (NPQ) dissipates excess light energy as heat, with the quenching component qH providing sustained photoprotection. However, the molecular mechanism underlying qH induction remains unclear. Our study focuses on the thylakoid membrane protein SUPPRESSOR OF QUENCHING 1 (SOQ1) and its inhibition of qH through interaction with LIPOCALIN IN THE PLASTID (LCNP) in Arabidopsis thaliana. Structural homology of SOQ1 lumenal domains with bacterial disulfide bond protein D suggested potential thiol-disulfide exchange activity. In vitro assays determined that both SOQ1 thioredoxin-like (Trx-like) and C-terminal (CTD) domains contain a redox-active cysteine pair and evidenced electron transfer from Trx-like to CTD. Importantly, we found that SOQ1 lumenal domains exhibit methionine sulfoxide reductase (Msr) activity converting oxidized methionine residues in LCNP back to methionine, which thereby inactivates LCNP and prevents qH formation. Mutational analyses identified cysteine residues in SOQ1-CTD and methionine residues in LCNP as critical for qH suppression, supporting their role in redox regulation. Additionally, we found that the redox state of SOQ1 in vivo is light-dependent, shifting from reduced to oxidized under stress conditions, indicating a dynamic regulation of its activity. We conclude that the Trx-like domain of SOQ1 provides reducing power to its CTD displaying Msr activity. SOQ1 is therefore an unusual example of a protein possessing both a disulfide reductase and Msr domain in tandem. Our findings elucidate the redox-regulation mechanism of qH involving SOQ1-mediated methionine reduction of LCNP, providing insights into the intricate control of photoprotective processes in chloroplasts and enhancing our understanding of plant resilience under environmental stress.

plant biology↗

bioRxiv2024

Evidence for high-frequency parallel evolution in virulent A. baumannii cultures

Acinetobacter baumannii, is a gram-negative opportunistic pathogen notorious for its antibiotic resistance and adaptability. These attributes present significant challenges in clinical infection management and failure to manage infection results in around 1,000,000 global deaths per year. A greater knowledge of the layers of regulation employed by such a versatile pathogen may yield an improved understanding of the factors important for A. baumannii survival in diverse conditions and then facilitate the development of countermeasures. This study initially began with the investigation of phenotypic changes in colony opacity under varying environmental conditions with experiments designed to probe aspects of virulence, motility, biofilm formation, and antibiotic resistance. Our initial data also suggest evidence for a phenotype driving mutation system which simultaneously occurred in multiple lineages at the same time. This genetic alteration was observed at higher than expected frequencies, seemingly providing a striking example of parallel evolution. Using proteomic profiling and PacBio sequencing, we characterized lineages of AB5075 which, following changes in culture conditions, grew into colonies of a split translucent/ opaque phenotype which was inherited by translucent and opaque progeny lineages. A genetic alteration in the capsule operon gene wzy, marked by an ISAba13 transposon insert, led to the downregulation of the wzy gene product. Translucent variants demonstrated denser sedimentation and reduced biofilm formation, whereas both opaque and translucent variants showed unexpectedly similar antibiotic resistance profiles, challenging the assumptions that capsule formation and antibiotic resistance are always linked. Our findings suggest that the adaptability and resistance mechanisms of A. baumannii are related but distinct, where capsule loss is part of a broader, adaptive strategy rather than a sole determinant of antibiotic susceptibility. These insights highlight the need for a nuanced therapeutic approach, considering the dynamic interplay of environmental cues, phenotypic changes, and genetic rearrangements. We believe that this study further opens a path for understanding the adaptability of A. baumannii and lays the groundwork for developing innovative therapeutic strategies against this resilient pathogen. Significance StatementThis study advances our understanding of the adaptability mechanisms of Acinetobacter baumannii, a pathogen notorious for its antibiotic resistance in clinical settings. We initially focused on the role of phenotype switches and identified genetic alterations in the Wzy operon that impact capsule production. Our studies led us to the surprising realization that we were observing multiple identical but independent evolution events. In addition, contrary to the traditional view that capsule variability directly correlates with antibiotic resistance, our findings revealed that susceptibility to aminoglycosides can occur independently of capsule loss, indicating capsule loss may be part of multiple survival strategies. These insights challenge existing paradigms and underscore the necessity for multiple therapeutic and preventative strategies that address the pathogens multifaceted adaptability for survival. Ultimately, this research contributes significantly to our knowledge of the biology of A. baumannii, paving the way for more effective management of infections caused by this formidable pathogen.

microbiology↗

bioRxiv2024

Warming treatments shift the temporal dynamics of diversity and composition of bacteria in wild blueberry soils.

Soil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. In Maine, wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. To elucidate the response of bacterial communities to warming during the growing season, we employed passive and active open-top chambers to simulate climate warming scenarios in wild blueberry fields. Warming treatments elevated atmospheric temperatures by 1.2 and 3.3 {degrees}C (passive and active warming), respectively, but did not affect soil temperatures. Nevertheless, soils in the active warming treatment exhibited significantly lower water content than ambient conditions. Overall, soil bacterial diversity and richness (June, July, and August data combined) under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after two years of experimental warming. However, significantly higher bacterial evenness and diversity under warming treatments were observed in the early growing season (June). Our study also reveals pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soil, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity during the growing season than by warming treatments. The increased bacterial evenness and diversity under warming treatments in June may be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.

microbiology↗