Biology subjects

Oda, Y.

Publications and source records attributed to Oda, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Digital pathological classification of peripheral neuroblastic tumors across multi-continent cohorts

Peripheral neuroblastic tumors (pNTs) are embryonal tumors of neural crest origin with highly variable clinical behaviors, ranging from spontaneous regression to aggressive and fatal disease. The International Neuroblastoma Pathology Classification (INPC) defines four diagnostic categories and stratifies tumors into Favorable Histology (FH) or Unfavorable Histology (UH) group based on age-linked assessment of tumor differentiation/maturation and the Mitosis-Karyorrhexis Index (MKI). Prognostic distinction according to INPC offers significant prediction of clinical outcomes, with patients harboring FH tumors demonstrating longer overall and event-free survival than those with UH tumor. Here, we assembled the largest multi-continental whole-slide histology imaging dataset of pNTs to date, comprising 2,030 tumors from the United States, Canada, Australia, New Zealand, Germany and Japan. Using this dataset, we developed NB-PathAssist, a computational pathology framework for automated INPC-based classification from digitized whole-slide images. NB-PathAssist integrates foundation-model-based feature extraction with an archetype-guided SummaryMixing architecture that compresses whole-slide morphology into representative histologic tokens for tumor-level classification. To automate MKI assessment, we manually annotated 14,049 nuclei, classifying them as mitotic-karyorrhectic (MK) tumor cells, non-MK tumor cells, or non-tumor cells. The resulting model was applied to phenotype cells in whole-slide images across 1,649 tissue sections. Across geographically and institutionally diverse cohorts, NB-PathAssist reproducibly assessed key diagnostic features and generated prognostic classifications concordant with reference INPC annotations. The average balanced accuracy for classifying tumor categories, grade of neuroblastic differentiation, MKI and prognostic groups achieved 0.84, 0.86, 0.89 and 0.96, respectively. We packaged the NB-PathAssist algorithms into an end-to-end online platform for scalable and standardized AI-assisted assessment of pNTs.

pathology↗

bioRxiv2026

COPAL: An ensemble of protein-ligand co-folding models enriches preferred ligand predictions for the LuxR-family of quorum sensing receptors

Acyl-homoserine lactone (AHL) quorum sensing enables many species of proteobacteria to coordinate collective behaviors. In such systems, a synthase produces an AHL signal, which is sensed by a LuxR-family receptor. Despite extensive genomic annotation of LuxR homologs, preferred AHLs for most receptors remain unknown, limiting functional understanding of quorum sensing across diverse bacteria. Here, we present the COPAL (combining ordered predictions of audited ligands) pipeline, which integrates multiple protein-ligand co-folding models to identify preferred AHLs for a specific LuxR. Benchmarking on a leakage-controlled subset of 96 experimentally characterized LuxR-AHL pairs shows that COPAL places the preferred AHL within the top-6 candidates (out of 58) for 68% of receptors, outperforming every individual co-folding model. Further, inter-model agreement correlates with ranking accuracy, offering an indication of confidence. We show that COPAL resolves the specificity shift induced by three-point mutations in LasR and correctly nominates C8-HSL as the preferred ligand for the previously uncharacterized Mesorhizobium sp. NJ3 receptor, which we verified experimentally. Finally, we release the Ranked AHL-LuxR Prediction Hub (RALPH), comprising precomputed rankings for about 10,000 unique LuxR homologs. More broadly, COPAL shows that unweighted rank aggregation of complementary co-folding models offers a general strategy for predicting receptor-ligand specificity in data-scarce biological systems.

biochemistry↗

bioRxiv2026

Trajectory inference of epithelial-centered neighborhood profiles reconstructs a pseudo-temporal continuum in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by complex lung architecture and spatially heterogeneous remodeling, which have hindered integrated analysis of cell-intrinsic activity and intercellular communication during disease progression. Here we profiled six IPF lung specimens comprising more than 630,000 cells using the Xenium 5k panel and developed an epithelial-centered neighborhood profiling framework based on the local cellular composition around each epithelial cell. This approach captured fibrosis-associated variation in epithelial niches without requiring predefined histological regions. Pseudo-temporal continuum inference of these profiles reconstructed a continuous axis that reflected the spatial progression of fibrotic remodeling from relatively preserved alveolar regions to fibrotic and airway-like remodeled regions. Within this spatial dataset, we mapped coordinated changes in epithelial states, local microenvironments, epithelial intracellular pathway activities, and directional interactions with neighboring cell types along the same axis. Our findings provide a spatial framework that generates testable hypotheses for progressive epithelial niche remodeling in IPF.

bioinformatics↗

bioRxiv2026

MAP70-2 is required for division plane orientation during 3D differential growth within a tissue

Communication between tissues and cell division orientation are essential for organ development. During lateral root formation in Arabidopsis thaliana, three-dimensional differential growth is established within a tissue of interconnected and pressurized cells. To emerge, the new organ needs to overcome the mechanical constraints provided by the overlying tissues. How the division plane orientation within the growing organ encountering mechanical constrains is coordinated remains unclear. Here, we show that MICROTUBULE ASSOCIATED PROTEIN 70-2 contributes to this integration of mechanical feedback during lateral root development by being associated with division plane orientation during primordium formation. MAP70-2 expression in the lateral root primordium is dynamic, localizing to cell corners and the cortical division zone prior to cytokinesis. Loss of MAP70-2 leads to misoriented cell divisions in the early stage of lateral root development and defective morphogenesis. Here we propose that MAP70-2 integrates biochemical and mechanical cues to establish correct division plane orientation during three-dimensional differential growth to facilitate lateral root organogenesis.

plant biology↗

bioRxiv2025

Induction of meningioma stem signature via hydrogel reprogramming and application of meningioma stem cell marker CXCR4 to pathological diagnosis and treatment.

BackgroundsMeningioma accounts for about 40% of brain tumors, but there was no effective treatment for recurrent or inoperable cases. We have previously found that when cancer cells are cultured on certain hydrogels, cancer stem cells are efficiently induced in various cancer types and we named this process as hydrogel activated reprogramming (HARP) phenomenon. In this study, we aimed to identify a key molecule that induced meningioma stem cells via hydrogels. MethodsMeningioma cells cultured on hydrogels were analyzed for expression of regular stem cell markers and their tumor genericity. Microarray analysis was performed to identify meningioma stem cell specific markers and to examine the application of such marker molecules as a therapeutic targets or pathological diagnosis for grading. ResultsRegular stem cell markers such as Nanog, and Oct3/4 were induced by culturing meningioma cells on hydrogels, and comprehensive gene expression analysis identified molecules involved in cancer stem cell activity. Among them, CXCR4 was selected as a therapeutic target molecule. Stimulation of CXCR4 via CXCL12 led to an increase in stem cell markers. In human meningioma pathological specimens and cultured cell lines, there was a correlation between CXCR4 expression levels and NF2 mutations and/or deletions. CXCR4 immunohistochemistry also detected along with the brain invasion. Thus, CXCR4 immunohistochemistry may be useful to suggest typical CNS WHO grade 1 meningioma, that do not require molecular analysis. ConclusionsWe have defined meningioma stem cell signature via HARP phenomenon and identified CXCR4 with biological significance as being diagnostic target. Key PointsO_LIWe induce meningioma stem signature via Hydrogel activated reprogramming (HARP) phenomena. C_LIO_LIWe identified CXCR4 as a candidate molecule as stemness marker and therapeutic target. C_LIO_LITranslational research using pathological specimens reveal CXCR4 immunohistochemistry has been shown to play an auxiliary role in the diagnosis of meningiomas. C_LI Importance of the StudyIn addition to morphology, immunohistochemistry and gene alteration are being adopted as diagnostic criteria for CNS tumors. From CNS5 onwards, epigenetic changes such as methylation analysis are being adopted as diagnostic criteria. We induced epigenetic changes in meningioma cells and induced cancer stemness, and this technique will be of great importance in the research and diagnosis of meningioma. In addition, microarray analysis was used to select CXCR4 from the molecules that increased simultaneously during stem cell induction on the three hydrogels, and further analysis revealed that CXCR4 immunostaining may indicate the distribution of meningioma stem cells, also making it useful for diagnosis. This report will contribute to the advancement of meningioma research and diagnosis by conducting basic research and using histopathological specimens.

bioengineering↗

bioRxiv2025

Evolution of BA.2.86 to JN.1 reveals functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), is still circulating among humans, leading to the continuous evolution. SARS-CoV-2 Omicron JN.1 evolved from a distinct SARS-CoV-2 lineage, BA.2.86, spread rapidly worldwide. It is unclear why BA.2.86 did not become dominant and was quickly replaced by JN.1, which possesses one amino acid substitution in the spike protein (S:L455S) and two in the non-spike proteins NSP6 and ORF7b (NSP6:R252K and ORF7b:F19L) compared to BA.2.86. Here, we utilized recombinant viruses to elucidate the impact of these mutations on the virological characteristics of JN.1. We found that the mutation in the spike attenuated viral replication, but the non-spike mutations enhanced replication, suggesting the mutations in the non-spike proteins compensate for the one in the spike to improve viral fitness, as the mutations in the spike contribute to further immune evasion. Our findings suggest that functional changes in both the spike and non-spike proteins are necessary in the evolution of SARS-CoV-2 to enable evasion of adaptive immunity within the human population while sustaining replication. IMPORTANCEBecause the spike protein is strongly associated with certain virological properties of SARS-CoV-2, such as immune evasion and infectivity, most previous studies on SARS-CoV-2 variants have focused on spike protein mutations. However, the non-spike proteins also contribute to infectivity, as observed throughout the evolution of Omicron subvariants. In this study, we demonstrate a "trade-off" strategy in SARS-CoV-2 Omicron JN.1 in which the reduced infectivity caused by spike mutation is compensated by non-spike mutations. Our results provide insight into the evolutionary scenario of the emerging virus in the human population.

microbiology↗

bioRxiv2025

Spatial dynamics of the tumor microenvironment in emerging resistance to targeted therapy in EGFR-mutated NSCLC

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) provide therapeutic benefit in EGFR mutation-positive non-small cell lung cancer, but some individuals develop early resistance. We performed spatial transcriptomics analysis of pre- and posttreatment tumor samples from the same patients to explore the underlying mechanisms of such early resistance. The proportion and activation of fibroblasts increased in association with the development of early resistance, whereas a distinct tumor cell cluster showed activation of tumor necrosis factor- signaling via the NF-{kappa}B pathway even before treatment. Also in the early resistance sample, specific tumor cell clusters interacted with immune and stromal cells. Immature tertiary lymphoid structures (TLSs) were enriched in the early resistance sample, whereas mature TLSs were observed in the long-term response sample. These findings implicate tumor heterogeneity and an inflammatory tumor microenvironment in early EGFR-TKI resistance, providing insight into potential therapeutic strategies to improve treatment outcomes.

cancer biology↗

bioRxiv2024

Calcineurin inhibition deactivates pyruvate dehydrogenase and induces proximal tubule cell metabolic dysfunction, causing profibrotic phenotype

Calcineurin inhibitors (CNIs) are indispensable immunosuppressants for transplant recipients and patients with autoimmune diseases, but chronic use causes nephrotoxicity, including kidney fibrosis. Why inhibiting calcineurin, a serine/threonine phosphatase, causes kidney fibrosis remains unknown. We performed single-nucleus RNA sequencing of the kidney from a chronic CNI nephrotoxicity mouse model and found an increased proportion of injured proximal tubule cells, which exhibited altered expression of genes associated with oxidative phosphorylation, cellular senescence and fibrosis. In cultured primary human renal proximal tubule epithelial cells, CNIs caused phosphorylation (deactivation) of pyruvate dehydrogenase, impaired mitochondrial metabolism and senescence-associated phenotypes, all of which were ameliorated by pyruvate dehydrogenase activation. Finally, administration of dichloroacetic acid, a known activator of pyruvate dehydrogenase, in the chronic CNI nephrotoxicity mouse model mitigated kidney fibrosis and the associated transcriptional changes. Collectively, calcineurin inhibition deactivates pyruvate dehydrogenase and induces proximal tubule cell metabolic dysfunction, causing profibrotic phenotype.

molecular biology↗

bioRxiv2024

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in production of value-added products, bioremediation and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high affinity transport of nutrients, iron uptake, nitrogen metabolism and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment. IMPORTANCERhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments and some strains are found associated with plants and have plant growth promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

microbiology↗

bioRxiv2024

Cholesterol sulfate prevents maternal-fetal conflict by locally modulating immune reactivity

Although placental mammals are at high risk of maternal-fetal immune conflict, it is unclear how the semi-allogeneic fetus avoids rejection. Cholesterol sulfate (CS) is a bioactive metabolite that inhibits leukocyte migration and activation. This study investigated the roles and cells associated with CS in pregnant mice and humans. CS was sequentially produced by maternal-derived endometrial cells and fetal-derived placental trophoblasts before and after placentation. When mated with allogeneic males, CS-deficient mice showed increased fetal resorption rates under induced placental inflammation. This phenotype disappeared when the activity of the CS-producing enzyme was restored in the placenta. Placental CS levels were reduced in patients with "villitis of unknown etiology." Thus, we uncovered the spatiotemporal control of CS production and its relevance to local immunosuppression during pregnancy.

immunology↗

bioRxiv2024

Two types of regeneration mechanism in acute liver injury

The liver has a strong regenerative capacity, but the mechanisms of liver regeneration are not well understood. Furthermore, many previous studies on liver regeneration have been conducted in partial hepatectomy models, which may differ from acute liver injury with inflammation and necrosis, as observed in many clinical cases. In this study, we conducted a single-cell RNA-seq analysis (scRNA-seq) of liver regeneration in mice treated with acetaminophen (APAP) using publicly available data. We discovered that two cell proliferation populations appeared simultaneously during a single regenerative process. The two populations differed significantly in terms of differentiation, localization, proliferation rate, and signal response. Furthermore, one of the populations was induced by contact with necrotic tissue and exhibited a higher proliferative capacity with a dedifferentiated feature. These findings can shed new light on liver regeneration and aid in the development of therapeutic strategies for liver failure.

pathology↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant

In middle-late 2023, a sublineage of SARS-CoV-2 Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. Here, we performed multiscale investigations to reveal virological features of newly emerging EG.5.1 variant. Our phylogenetic-epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T, are critical to the increased viral fitness. Experimental investigations addressing the growth kinetics, sensitivity to clinically available antivirals, fusogenicity and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 is comparable to that of XBB.1.5. However, the cryo-electron microscopy reveals the structural difference between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible at least in our experimental setup. Our multiscale investigations provide the knowledge for understanding of the evolution trait of newly emerging pathogenic viruses in the human population.

microbiology↗

bioRxiv2023

A purine salvage bottleneck leads to bacterial adenine cross-feeding

Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we fortuitously discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue growth of an Escherichia coli purine auxotroph. Here we found that an E. coli purine auxotroph can stably coexist with R. palustris due to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized by R. palustris under diverse growth conditions. Computational models suggested that adenine externalization occurs via passive diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that accumulation and externalization of adenine stems from an adenine salvage bottleneck at the enzyme encoded by apt. Ectopic expression of apt eliminated adenine externalization, supporting our hypothesis. A comparison of 49 R. palustris strains suggested that purine externalization is relatively common, with 15 of the strains exhibiting the trait. Purine externalization was correlated with the genomic orientation of apt orientation, but apt orientation alone could not explain adenine externalization in some strains. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.

microbiology↗

bioRxiv2023

Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection

Monitoring in vivo viral dynamics can improve our understanding of pathogenicity and tissue tropism. For positive-sense, single-stranded RNA viruses, several studies have attempted to monitor viral kinetics in vivo using reporter genomes. The application of such recombinant viruses can be limited by challenges in accommodating bioluminescent reporter genes in the viral genome. Conventional luminescence also exhibits relatively low tissue permeability and thus less sensitivity for visualization in vivo. Here we show that unlike NanoLuc bioluminescence, the improved method, termed AkaBLI, allows visualization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Syrian hamsters. By successfully incorporating a codon-optimized Akaluc luciferase gene into the SARS-CoV-2 genome, we visualized in vivo infection, including the tissue-specific differences associated with particular variants. Additionally, we could evaluate the efficacy of neutralizing antibodies and mRNA vaccination by monitoring changes in Akaluc signals. Overall, AkaBLI is an effective technology for monitoring viral dynamics in live animals.

microbiology↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 XBB.1.5 variant

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the F486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determined the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. The intrinsic pathogenicity of XBB.1.5 in hamsters is lower than that of XBB.1. Importantly, we found that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC expression. In vivo experiments using recombinant viruses revealed that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, these data suggest that the mutations in ORF8 and S could enhance spreading of XBB.1.5 in humans.

microbiology↗

bioRxiv2023

Upregulated Fcrl5 disrupts B cell anergy and causes autoimmunity

B cell anergy plays a critical role in maintaining self-tolerance by inhibiting autoreactive B cell activation to prevent autoimmune diseases. Here, we demonstrated that Fc receptor-like 5 (Fcrl5) upregulation contributes to autoimmune disease pathogenesis by disrupting B cell anergy. Fcrl5--a gene whose homologs are associated with human autoimmune diseases--is highly expressed in age/autoimmunity-associated B cells (ABCs), an autoreactive B cell subset. By generating B cell-specific Fcrl5 transgenic mice, we demonstrated that Fcrl5 overexpression in B cells caused systemic autoimmunity with age. Furthermore, Fcrl5 upregulation in B cells exacerbated the systemic lupus erythematosus-like disease model and increased the levels of ABCs and activated T cells. Mechanistically, an increase in Fcrl5 expression broke B cell anergy, activating autoreactive B cells in the presence of a self-antigen. Fcrl5 facilitated toll-like receptor signaling, reactivating anergic B cells. Thus, Fcrl5 is a potential regulator of B cell-mediated autoimmunity by regulating B cell anergy. This study provides important insights into the role of Fcrl5 in breaking B cell anergy and its effect on the pathogenesis of autoimmune diseases.

immunology↗

bioRxiv2023

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii

Sorghum (Sorghum bicolor) is a major food and bioenergy grass species cultivated worldwide. To promote more robust and sustainable growth of this important crop, we need a deeper understanding of the plant-microbe interactions between sorghum and soil microbial communities that benefit plant host resiliency and enhance nutrient acquisition. The release of specific metabolites from plant roots, or root exudation, drives these plant-microbe interactions, but the molecular pathways by which root exudates shape the sorghum rhizosphere microbiome require further elucidation. To investigate these complex interkingdom interactions in the sorghum rhizosphere, we developed a photoaffinity probe based on sorgoleone, a hydrophobic secondary metabolite and allelochemical produced in sorghum seedling root exudates. Here, we apply a new synthetic sorgoleone diazirine alkyne photoaffinity probe (SoDA-PAL) to the identification of sorgoleone-binding proteins in Acinetobacter pittii SO1, a potential plant growth promoting microbe derived from Sorghum bicolor rhizosphere soil. Competitive photoaffinity labeling of A. pittii whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins that were complementary to a previously identified gene cluster involved in sorgoleone catabolism. Proteins identified by SoDA-PAL included a select set of putative transporters, transcription regulators, and a subset of proteins with lipid and secondary metabolic activities. We confirm binding of SoDA-PAL to a putative hydrolase in the /{beta} fold family (OH685_09420) through structural bioinformatics and in-vitro recombinant protein analysis. This photoaffinity labeling approach using metabolite-based probes can be extended in the future to proteomic profiling of complex rhizosphere microbiomes to discover genes that can be leveraged to promote beneficial plant-microbe interactions. ImportanceHere we demonstrate a photoaffinity-based chemical probe modeled after sorgoleone, a known secondary metabolite released from the roots of sorghum, can be used to dissect complicated plant-microbe interactions. Applying this probe to the sorghum-associated bacterium Acinetobacter pittii identified diverse proteins that directly interact with sorgoleone. We show that probe labeling is dose-dependent and is sensitive to competition with purified sorgoleone, demonstrating the probe is selective for protein targets that directly interact with sorgoleone. By using the probe to broadly profile proteins that interact with sorgoleone, we identified bacterial catabolic pathways, unintuitive transcriptional regulation pathways, and vital exchange mechanisms involving transporters that may be involved in sorgoleone utilization and cellular response toward this plant metabolite. We envision that this workflow will expand our understanding of the sorghum root exudate interactome and elucidate the molecular mechanisms by which specific metabolites shape the sorghum rhizosphere microbiome.

biochemistry↗

bioRxiv2023

Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion

Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals and humans and is used for bioethanol production. Its root tips exude large amounts of a lipophilic benzoquinone called sorgoleone. Sorgoleone is an allelochemical that suppresses the growth of competing plant seedlings and is mineralized by microbes in soil. As an avenue to understand how sorghum and its root microbiome may be connected through root exudates, we identified the molecular determinants of microbial sorgoleone degradation and the distribution of this trait among microbes. We isolated and studied from sorghum-associated soils, three bacterial strains classified as Acinetobacter, Burkholderia, and Pseudomonas species that grow with sorgoleone as a sole carbon and energy source. The genomes of these strains were sequenced and subjected to transcriptomic and gene fitness analyses to identify candidate sorgoleone degradation genes. Follow up mutational analysis showed that sorgoleone catabolism is dependent on four contiguous genes that are conserved among the species we sequenced. Phylogenetic analysis of the sorgoleone degradation gene cluster showed that sorgoleone catabolism is enriched in sorghum-associated Streptomyces strains. The discovery of bacteria that grow on a compound like sorgoleone that is plant specific and not widely distributed in the environment, provides an opportunity to study how a plant exudate can enforce the development of a rhizosphere specific microbiome for the mutual benefit of plant and microbe. SignificanceThe grain crop sorghum exudes an herbicidal compound called sorgoleone from its root tips, which inhibits the growth of other plants. We isolated bacteria that grow on sorogleone and identified a cluster of bacterial genes required for sorogleone degradation that can be used as a biomarker for this trait. An approach to improve the production of crops in stressful conditions such as drought, is to encourage their association with plant growth promoting bacteria. Our discovery of sorgoleone degradation genes opens the door to engineering bacteria that receive benefit from sorghum in the form of a plant-specific growth substrate, and in return promote the growth of this crop.

microbiology↗