Biology subjects

Qi, M.

Publications and source records attributed to Qi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Harmine Plus Exendin-4 Enhances Remission of Recent-Onset Type 1 Diabetes Following Anti-CD3 Therapy

Type 1 diabetes (T1D) results from autoimmune destruction of pancreatic {beta}-cells. While anti-CD3 therapy can delay disease progression and preserve residual {beta}-cell function, disease reversal will likely require both immune modulation and {beta}-cell regeneration. We found that the combination of harmine and exendin-4 (H+E) reduced inflammation-induced human {beta}-cell apoptosis, suppressed cytokine signaling and immunogenicity pathways, and improved {beta}-cell function. Although H+E alone did not reverse diabetes in NOD mice, low-dose anti-CD3 followed by H+E normalized blood glucose, increased insulin levels, improved glucose tolerance, expanded {beta}-cell mass, and enhanced diabetes remission. These effects were associated with reduced pro-inflammatory T-cell responses, increased regulatory T cells, and greater expression of exhaustion-related T-cell markers, without broad lymphocyte depletion. Similar immunomodulatory effects were observed in activated human PBMCs. Transcriptomic analyses identified the lncRNA SNHG6 as a key mediator of H+E action; SNHG6 protected {beta}-cells from cytokine-induced stress, apoptosis, and immunogenicity. Together, these findings demonstrate that H+E promotes {beta}-cell recovery and resilience while reducing {beta}-cell immunogenicity, enabling remission of recent-onset T1D when combined with anti-CD3 therapy. SNHG6 emerges as a novel regulator of {beta}-cell protection during inflammation.

cell biology↗

bioRxiv2026

Spatiotemporal biogenesis of thylakoid membranes in the green alga Chlamydomonas reinhardtii

Thylakoid membranes are essential for oxygenic photosynthesis, yet the mechanisms underlying their spatial and temporal biogenesis remain poorly understood. Here, using a light-induced membrane regeneration system in Chlamydomonas reinhardtii, we generate a time-resolved map of thylakoid formation and photosynthetic complex assembly at unprecedented spatial and temporal resolution by integrating super-resolution fluorescence microscopy, cryo-electron tomography, proteomics, and spectroscopy. We show that thylakoid biogenesis is globally distributed and multipolar, with new membrane formation occurring at multiple sites across the chloroplast, including regions adjacent to the inner envelope membranes in both basal and lobe regions. We identify F-ATP synthase storage membranes and map the redistribution of translating ribosomes from T-zone enrichment to a chloroplast-wide distribution at early stages of thylakoid formation, consistent with decentralized synthesis of photosynthetic complexes. We further delineate the hierarchical assembly of photosystem supercomplexes, starting with formation of reaction centers. Together, these findings refine the spatial organization of photosynthetic membrane biogenesis and establish a unified spatiotemporal framework linking thylakoid formation, translational activation, and functional maturation, providing a mechanistic basis for plastid engineering to enhance photosynthetic efficiency.

Cell Biology↗

bioRxiv2026

Beyond Fixation: Persistent Genetic Variation Under Intense Selection

Understanding how and why genetic variation is maintained under sustained selection remains a central question in evolutionary genetics. Experimental evolution shows that adaptation in sexually reproducing populations is often highly polygenic, proceeding through coordinated, genome-wide allele frequency shifts from standing variation rather than classic hard sweeps. Recent explanations emphasize highly polygenic architectures, optimizing-selection, and genetic redundancy, which can slow fixation by distributing selection across many loci during adaptation. However, observations from long-term selection experiments reveal a pattern these frameworks do not fully explain: substantial genetic variation persists after hundreds of generations of intense directional selection in constant environments. Here, we use long-term experimental evolution in Drosophila melanogaster to test whether balancing-selection actively maintains genetic variation under strong life-history selection and preserves evolutionary reversibility. Longstanding populations selected for accelerated or delayed reproduction were shifted to the opposing regime, imposing age-structured fitness trade-offs. Notably, selection for early reproduction is associated with substantial loss of genetic variation, providing a stringent test of whether standing variation is truly depleted. Following reciprocal shifts, populations showed rapid phenotypic convergence toward the target regime. At the genomic level, allele-frequency trajectories were strongly antiparallel and highly repeatable across replicates, revealing coordinated polygenic responses. Relaxing long-standing early-life selection produced a pronounced rebound in genome-wide heterozygosity. Deep sequencing uncovered ultra-rare alleles at sites appearing fixed under standard coverage, indicating low-frequency functional variation persists below detection thresholds. These results suggest that substantial genetic variation can persist under intense directional selection and be rapidly redeployed when selection reverses, consistent with widespread balancing-selection.

evolutionary biology↗

bioRxiv2026

Tipping Points and Emergent Phases of Species Diversity in Mutualistic Ecological Networks under Global Warming

Global warming poses a severe threat to ecosystem resilience and biodiversity, potentially driving species loss, declining diversity, and ecosystem collapse. Accurately predicting tipping points of ecological resilience under global warming remains a fundamental challenge. Here, we develop a theoretical framework to identify climate-induced tipping points in mutualistic ecological networks, capturing critical transitions under warming scenarios. We show that rising temperatures, increasing intraspecific competition, and deteriorating mutualistic interaction can drive ecosystems through three distinct dynamical phases of species diversity: stable full coexistence, stable partial coexistence, and total extinction. Notably, ecosystems with low species abundances are particularly vulnerable, facing heightened risks of diversity loss and extinction. Moreover, the warming rate modulates these transitions, as slower warming grants endangered species a window of time within which to adjust and attenuate the loss of resilience. Applying this framework to assess various emission mitigation pathways, we find that "pollute first, clean up later" scenarios pose a threat to biodiversity, leading to irreversible biodiversity losses even after subsequent emission reductions. Our findings offer critical insights into the timing and mechanisms of ecological tipping points under climate change and underscore the urgency of proactive mitigation strategies.

ecology↗

bioRxiv2025

Large-language-model-based antibiotic resistance gene prediction and resistomes mining in cyanobacterial blooms

The rapid spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious public health threat. Conventional ARG detection methods, including sequence-alignment and machine learning, are limited by high false-negative or false-positive rates, especially due to sequence diversity and class imbalance in metagenomic data. Moreover, few tools offer comprehensive solutions for ARG identification, classification, and functional annotation. To address these limitations, we developed ESMARG, a novel protein language model framework based on ESM1v, for accurate ARG identification, classification, and annotation. Trained with both ARG and abundant non-ARG sequences from real-world metagenomes to enhance robustness and reduce false positives, ESMARG significantly outperformed traditional alignment-based (BLAST, DIAMOND) and recent deep learning models (ARGNet, ARG-SHINE), achieving 0.998 precision, 0.939 recall, and 0.968 F1-score for ARG identification. Functional and mechanism classification modules also demonstrated high accuracy (0.986 and 0.987) and computational efficiency. We applied ESMARG to analyze 26 cyanobacterial aggregate (CA) metagenomes collected from Lake Taihu across a full annual cyanobacterial harmful algal bloom (CyanoHAB) cycle. A total of 110 ARGs, spanning 24 drug classes and multiple resistance mechanisms, were detected, with seasonal shifts in ARG abundance and composition. Strong correlations were identified between CA resistomes and microbial community structure, especially with cyanobacteria. Further, ARG abundance was shaped by both biotic factors--such as cyanobacterial dominance and bacterial functional profiles--and abiotic variables, including biochemical oxygen demand and water temperature. Our findings demonstrate the power of ESMARG for high-resolution ARG profiling and reveal complex ecological interactions between resistomes, microbiomes, and environmental factors in CyanoHAB. HighlightsO_LIDeveloped ESMARG model outperforms BLAST/other deep learning models in ARG detection C_LIO_LIARG showed seasonal dynamics in cyanobacterial metagenomes across algal bloom cycle C_LIO_LIARG was strongly correlate with microbiome structure and cyanobacteria dominance C_LIO_LIARG abundance was shaped by cyanobacteria, bacterial functions, BOD and temperature C_LI

bioinformatics↗

bioRxiv2025

Impact of Inactivation Methods on Biosafety and Antigen Reactivity of Brucella melitensis from the Perspective of Astral-DIA Proteomics Based on Antibody Immunoprecipitation Mass Spectrometry

Effective Brucella inactivation is imperative for safe vaccine development, diagnostics, and sample handling, particularly in resource-limited regions lacking high-level containment facilities. This study investigated inactivation methods using the Rev.1 vaccine strain and three Brucella melitensis field isolates from Gansu (GS-XG, GS-SN, GS-MQ). Heat (80{degrees}C/95{degrees}C, 10-20 min) and formaldehyde (0.4%/0.6%, 48-72 h) inactivation were evaluated for biosafety and antigenicity. Rev.1 was completely inactivated by 80{degrees}C/95{degrees}C for 20 min or 0.6% formaldehyde for 48-72 h. Superior antigenicity, compared to phenol inactivation, was confirmed by ELISA and Western Blot. However, field isolates demonstrated greater resistance, surviving 80{degrees}C for 20 min and 0.4% formaldehyde for 72 h, necessitating stricter conditions (95{degrees}C, 20 min; 0.6% formaldehyde, 72 h) for their complete inactivation. Astral-DIA proteomics analyzed approximately 60% of the proteome ([~]2000/3300 proteins), revealing 256, 311, and 318 differentially expressed proteins between 80{degrees}C/95{degrees}C heat, 48-h/72-h formaldehyde, and heat/formaldehyde methods, respectively. Gene Ontology and KEGG analyses indicated heat inactivation upregulated cellular structure proteins but downregulated metabolic pathways, with 95{degrees}C potentially damaging conformational epitopes. Formaldehyde treatment (48 h) stabilized soluble antigens, preserving ribosomal and regulatory protein epitopes, while 72-h treatment induced organelle disintegration. Protein-Protein Interaction networks suggested heat inactivation enhanced immunogenicity of membrane and stress proteins, suitable for targeted studies, whereas formaldehyde preserved broader epitopes, beneficial for whole-cell vaccines and multi-epitope screening. Inactivation methods must be tailored to specific strain characteristics and applications. Astral-DIA provides molecular insights into antigenicity loss, guiding future research on protein functions and epitope dynamics for precise brucellosis control.

microbiology↗

bioRxiv2025

Glutamatergic heterogeneity in the neuropeptide projections from the lateral hypothalamus to the mouse olfactory bulb

The direct pathway from the lateral hypothalamus to the mouse olfactory bulb (OB) includes neurons that express the neuropeptide orexin-A, and others that do not. The OB-projecting neurons that do not express orexin-A are present in an area of the lateral hypothalamus known to contain neurons that express the neuropeptide melanin-concentrating hormone (MCH). We used virally mediated anterograde tract tracing and immunohistochemistry for orexin-A and MCH to demonstrate that the OB is broadly innervated by axon projections from both populations of neurons. Orexin-A and MCH were expressed in each OB layer across its anterior to posterior axis. Both orexin-A and MCH neurons are genetically heterogeneous, with subsets that co-express an isoform of vesicular glutamate transporter (VGLUT). We used high-resolution confocal imaging to test whether the projections from orexin-A and MCH neurons to the OB reflect this glutamatergic heterogeneity. The majority ([~]57%) of putative orexin-A axon terminals overlapped with VGLUT2, with smaller proportions that co-expressed VGLUT1, or that did not overlap with either VGLUT1 or VGLUT2. In contrast, only [~]26% of putative MCH axon terminals overlapped with VGLUT2, with the majority not overlapping with either VGLUT. Therefore, the projections from the lateral hypothalamus to the OB are genetically heterogeneous and include neurons that can release two different neuropeptides. The projections from both populations are themselves genetically heterogeneous with distinct ratios of glutamatergic and non-glutamatergic axon terminals. Three Key PointsO_LIA direct anterograde projection from orexin-A-expressing neurons in the hypothalamus to the mouse olfactory bulb (OB) was confirmed using virally mediated tract tracing. C_LIO_LIOrexin-A and melanin-concentrating hormone (MCH), two neuropeptides primarily produced in the lateral hypothalamus are broadly expressed throughout the mouse OB. C_LIO_LIApproximately 64% of putative orexin-A axon terminals overlapped with vesicular glutamate transporter type 1 (VGLUT1) or type 2 (VGLUT2). In contrast, only 25% of putative MCH axon terminals overlapped with VGLUT2. C_LI

neuroscience↗

bioRxiv2024

Multi-omics analysis of long-term cultured human islets

Beta-cell dysfunction in pancreatic islets, characterized as either the loss of beta-cell mass or the resistance of beta-cell to glucose, is the leading cause of progression to diabetes. Islet transplantation became a promising approach to replenish functional beta-cell mass. However, not much known about changes in islets used for transplantation after isolation. We have subjected human islets into long-term in vitro culture (LTC) and characterized those survived islets. While most of the dysregulated genes were downregulated during LTC, specific groups of mRNA or miRNA were upregulated, and they are involved in specific pathways. In general, alpha-cells and beta-cells of LTC-islets have elevated expressions of MAFB and MAFA genes, respectively. We also found that exocrine cells were eliminated faster than endocrine cells, and beta-cells were lost at a higher rate than alpha-cells. Interestingly, one specific group of cells that have characteristics of immature alpha-cells or beta-cells, were enriched in LTC-islets, revealing the possibility of transdifferentiation of alpha-cells to beta-cells, or dedifferentiation of beta-cells to alpha-cells, under in vitro culture. Our results suggest that there are intrinsic cellular and molecular mechanisms in pancreatic cells that are associated with their maturity and correlated with their survival ability under unfavorable living conditions.

molecular biology↗

bioRxiv2024

Single MAPT knock-in mouse models of frontotemporal dementia for sharing with the neurodegenerative research community

We recently reported development of human MAPT knock-in mice that carry single or double pathogenic mutations of frontotemporal dementia. However, it takes more than 14 months for the line with the most aggressive phenotypes to exhibit tau pathology without forming high-order tau oligomers, along with concomitant abnormal behavior. We thus generated MAPT knock-in mice carrying triple mutations, among which the MAPTP301S;Int10+3;S320F line exhibited robust pathology starting earlier than 6 months. Tau accumulation took place mainly in the thalamus, hypothalamus, amygdala and entorhinal cortex, but less so in the hippocampus, leading to synaptic loss, atrophy and behavioral abnormalities. Crossbreeding MAPTP301S;Int10+3;S320F with App knock-in mice AppNL-G-F resulted in the manifestation of tau pathology in the hippocampus and cortex. These mutant mice will be valuable tools for understanding the mechanisms of frontotemporal dementia, Alzheimers disease and other tauopathies.

neuroscience↗

bioRxiv2024

Variation in precipitation drives differences in interactions and short-term transient instability between grassland functional groups: a stage-structured community approach

Climate change is expected to increase the frequency and severity of precipitation extremes, causing droughts and flooding. Consequently, grassland communities are forecasted to become increasingly unstable. To predict grassland responses, we need empirical information together with models that reliably extrapolate community dynamics from those observations. However, such prediction is challenging because community models typically simulate long-term (asymptotic) performance, and thus potentially neglect their short-term (transient) performance. Here, we use data from a precipitation experiment performed over eight years to model both short- and long-term responses of three functional groups - grasses, legumes, and non-leguminous forbs - to precipitation extremes. We use multi-functional-group Integral Projection Models and pseudospectral theory, to track grassland community dynamics. We show that the percentage-cover-stage-structure of functional groups shapes their transient instability, and that inter-functional-group interactions are competitive under increased precipitation but facilitative under decreased precipitation. IPMs and pseudospectra enable forecasting of how functional-group-stage-structure drives responses to climatic extremes.

ecology↗

bioRxiv2024

Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response

Diabetes mellitus (DM) significantly accelerates vascular diseases like peripheral arterial disease (PAD). Endothelial cells (ECs) and macrophages (M{Phi}s) singularly and synergistically are important contributors to DM-associated vascular dysfunction. Single-cell (sc) profiling technologies are revealing the true heterogeneity of ECs and M{Phi}s, but how this cellular diversity translates to cell-cell interactions, and consequentially vascular function, remains unknown. We leveraged scRNA sequencing and spatial transcriptome (ST) profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We generated a transcriptome and interactome map encompassing the major arterial cells and highlighted Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) as a top T2D-induced gene in mononuclear phagocytes (MPs), with concomitant increases of TREM2 ligands in ECs. We verified DM-associated TREM2 induction in cell and mouse models, and found that TREM2 inhibition decreases pro-inflammatory responses in MPs and ECs, as well as increases EC migration in vitro. Furthermore, TREM2 inhibition using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in DM mice subjected to hindlimb ischemia, suggesting that TREM2 promotes ischemic injury in DM. Finally, in human PAD, co-existing DM was associated with greater expression of TREM2 and its interaction with ECs, with a further increase in ischemic tissue compared to patient-matched non-ischemic tissue. Collectively, our study presents the first atlas of human diabetic vessels with single cell and spatial resolution, and identifies TREM2-EC interaction as a key driver of diabetic vasculopathies, the targeting of which may offer an opportunity to ameliorate vascular dysfunction associated with DM-PAD.

cell biology↗

bioRxiv2024

CD74+ fibroblasts proliferate upon mechanical stretching to promote angiogenesis in keloid

The healing of human skin wounds is susceptible to perturbation caused by excessive mechanical stretching, resulting in enlarged scars, hypertrophic scars, or even keloids in predisposed individuals. Keloids are fibro-proliferative scar tissues that extend beyond the initial wound boundary, consisting of the actively progressing leading edge and the quiescent center. The stretch-associated outgrowth and enhanced angiogenesis are two features of the leading edge of keloids. However, which cell population is responsible for transducing the mechanical stimulation to the pathological alterations of keloid tissues remains unclear. Herein, through joint analysis of single-cell RNA sequencing of keloid specimens and RNA sequencing of stretched keloid fibroblasts, we identified CD74+ fibroblasts, a previously unappreciated subset of fibroblasts, as a key player in stretch-induced keloid progression. Examination of macrophage markers suggested a possible myeloid origin of the CD74+ fibroblasts. Immunostaining of keloid cryosections depicted a predominant distribution of CD74+ fibroblasts in the leading edge, interacting with vasculature. CD74+ fibroblasts possessed pro-angiogenic and migratory capacities, as revealed by in vitro transwell and tube formation assays on purified CD74+ fibroblasts. Additionally, these cells underwent proliferation upon stretching, through PIEZO1-mediated calcium influx and the downstream ERK and AKT signaling. Collectively, our findings propose a model wherein CD74+ fibroblasts serve as pivotal drivers of stretch-induced keloid progression, fueled by their proliferative, pro-angiogenic, and migratory capacities. Targeting the attributes of CD74+ fibroblasts hold promise as a therapeutic strategy for keloid management. Significance statementKeloids are fibro-proliferative scars resulting from aberrant skin wound healing processes, consisting of the actively progressing leading edge and the quiescent center. Mechanical stretching and neo-vascularization have both been implicated in keloid progression, yet little is known about whether they are interconnected. Herein, we demonstrated that CD74+ fibroblasts, a previously undiscovered fibroblast subset, possessed heightened pro-angiogenic and migratory capacities, and underwent proliferation upon mechanical stretching, thereby facilitating the progression of the leading edge of keloids. Examination of macrophage markers suggested a possible myeloid origin of CD74+ fibroblasts. Our findings uncover the connection between stretch-induced keloid progression and neo-vascularization through CD74+ fibroblasts and provide valuable insights into potential therapeutic interventions.

cell biology↗

bioRxiv2024

Ubiquitin-mediated stabilization of SlPsbS regulates low night temperature tolerance in tomatoes

Non-photochemical quenching (NPQ) plays a fundamental role in safely operating photosynthesis under low night temperatures (LNT). PsbS protein is essential for the rapid induction of NPQ, and its stability is often affected by adverse environmental conditions. However, the regulatory mechanism for the stability of PsbS or chloroplast proteins remains to be fully characterized. We showed that LNT decreased NPQ levels and SlPsbS protein abundance in tomato leaves. COP9 signalosome subunit 5A (SlCSN5A) facilitated SlPsbS ubiquitination and degradation in the cytosol. Further, tomato chloroplast vesiculation (SlCV) was activated by LNT. Under LNT, SlCV targeted the chloroplasts and induced the formation of CV-containing vesicles (CCVs) containing SlPsbS, which were exported from the chloroplasts. Subsequently, SlCV and SlPsbS contact SlCSN5A in the cytosol and are ubiquitinated and degraded. Genetic evidence demonstrated that overexpression of SlCV aggravated SlPsbS protein degradation, whereas silencing of SlCSN5 and SlCV delayed LNT-induced NPQ reduction and SlPsbS protein turnover. This study provides evidence that CSN5A is associated with chloroplast proteins, and reveals a ubiquitin-dependent degradation pathway of chloroplast proteins co-mediated by CV and CSN5A, thereby providing new insights into the regulation of chloroplast protein stability under stress conditions.

plant biology↗

bioRxiv2024

A video-rate hyperspectral camera for monitoring plant health and biodiversity

Hyperspectral cameras are a key enabling technology in precision agriculture, biodiversity monitoring, and ecological research. Consequently, these applications are fuelling a growing demand for devices that are suited to widespread deployment in such environments. Current hyperspectral cameras, however, require significant investment in post-processing, and rarely allow for live-capture assessments. Here, we introduce a novel hyperspectral camera that combines live spectral data and high-resolution imagery. This camera is suitable for integration with robotics and automated monitoring systems. We explore the utility of this camera for applications including chlorophyll detection and live display of spectral indices relating to plant health. We discuss the performance of this novel technology and associated hyperspectral analysis methods to support an ecological study of grassland habitats at Wytham Woods, UK.

ecology↗

bioRxiv2023

Climate change has desynchronized insect and vegetation phenologies across Europe

Climate change is drastically affecting the phenologies of species worldwide, including shifts in development1-3. The potential impact of climate change on the synchronicity of plant-insect phenology is particularly concerning since the stability of pollination networks and food chains depends on their tight temporal dependencies4-6. Furthermore, the recently reported "insect armageddon"7 makes it urgent to establish trends and identify primary drivers of plant-insect phenological synchrony. Here, coupling high-resolution remote sensing and citizen science data across Europe over 34 years, we examine the differences in occurrence dates of 1,584 herbivorous insects across four orders and the corresponding dates of leaf unfolding. We find that 61.2% of the vegetation and insect phenologies have become highly asynchronous, with vegetation phenology advancing four-fold faster than insect phenology. These trends were modulated by insects life-cycles and taxonomic order. A primary driver of this phenological mismatch is the higher sensitivity of vegetation phenology than insect phenology to climate, which has prevented insects from matching the pace of plant phenological advance in the growing season. Our analyses provide a unique continental overview and underlying mechanisms of the asynchronicity between vegetation and insect phenologies, thus enhancing our ability to predict and manage its potential cascading ecological effects.

ecology↗

bioRxiv2023

Elevation, drainage, and spatially heterogeneous vulnerability of tidal marshes to sea level rise

Tidal marsh stability under Sea Level Rise (SLR) is driven by feedbacks between marsh macrophyte productivity, sediment accretion, and surface elevation gain. Predictive models and empirical studies often assume a spatially uniform tidal regime across the marsh platform, neglecting hydrological variations caused by tidal attenuation, drainage efficiency and terrestrial groundwater influences. This oversimplification can result in misleading estimates of marsh stability, especially in interior marsh of microtidal systems, which are more vulnerable to SLR-induced deterioration. Here we investigated how spatial variation in hydrology alters marsh vulnerability by comparing groundwater and surface water fluctuations between interior marsh zones and tidal creek edges at two microtidal marshes in the Chesapeake Bay. We assessed the deviation between observed and elevation- and tidally-derived estimates of hydroperiod, daily inundation duration, and soil saturation index (SSI). Using growth-hydroperiod response curves of marsh macrophytes, we assessed how these deviations alter marsh vulnerability predictions. We found that both tidal attenuation and weak drainage play dominant roles in shaping interior marsh hydrology. Due to tidal attenuation, water level fluctuations were muted from a 60 cm range at the marsh edge to a 20 [~] 30 cm range in marsh interior 500 m away. Therefore, interior marsh exhibits greater hydrological sensitivity to even minor elevation loss, which presents amplified hydrological stress and accelerated vegetation diebacks. Poor drainage in interior marsh result in a persistently higher water level, and slower recession at low tide, leading to prolonged inundation and soil saturation in interior marshes. As a result, assuming a spatially uniform tidal regime underestimated the hydroperiod (by 22-50%) and soil saturation (by 40-50%), and overestimated plant performance (by 10-25%) in interior marsh zones. Our findings highlight the critical need to incorporate tidal attenuation and drainage heterogeneity into empirical studies and numerical simulations to improve marsh resilience prediction and guide adaptive management strategies.

ecology↗

bioRxiv2023

A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase

The devastating soybean rust (SBR) pathogen, Phakopsora pachyrhizi, encodes many secreted proteins, but only two have been functionally characterized for their roles in rust virulence. Here, we demonstrate that transient expression of P. pachyrhizi effector candidate 15 (PpEC15), an aspartic protease, leads to enhanced bacterial growth in planta, suppression of callose deposition, reduced expression of plant defense-related marker genes and suppression of pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species (ROS). Stable expression of PpEC15 in soybean suppresses PAMP-induced ROS production and enhances bacterial growth, indicating that, collectively, PpEC15 suppresses host and non-host innate immune responses. Yeast-two-hybrid and proximity labeling identified putative PpEC15 interacting partners including a peptide-chain release factor (PCRF), a NAC83 (NAM, ATAF, and CUC) transcription factor, and a DAHP (3-deoxy-7-phosphoheptulonate) synthase. We further show that PpEC15 can cleave DAHP but does not cleave PCRF or NAC83. Virus-induced gene silencing of NAC83, PCRF and DAHP altered PAMP-induced ROS production and salicylic acid production, indicating that these proteins may be involved in immune signaling. Collectively, our data show that PpEC15 is conserved across P. pachyrhizi isolates and other economically important rust species and is involved in the suppression of plant basal defense responses. Understanding the role of PpEC15 in P. pachyrhizi virulence will provide a foundation for designing targeted intervention strategies to generate rust-resistant crops.

plant biology↗

bioRxiv2023

Insights into Phakopsora pachyrhizi effector-effector interactions

The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, where some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast-two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRP), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions.

plant biology↗