Biology subjects

Anderson, L. N.

Publications and source records attributed to Anderson, L. N..

7 recordsLinked to original sources

bioRxiv2026

Cyanophage CP12 Rewires Host Carbon Regulation through Interface Remodeling and Redox Buffering

Picocyanobacteria drive ocean carbon fixation, and cyanophages reshape host metabolism during infection. In cyanobacteria, the intrinsically disorder Calvin cycle protein 12 (CP12) assembles glyceraldehyde-3-phosphate dehydrogenase (GAP2) and phosphoribulokinase (PRK) into the inhibitory dark complex, yet how phage CP12 homologs modulate redox-sensitive partners remains unclear. Here, we examined viral CP12 across sequence, structure, and post-translational modification (PTM) complexities to resolve the mechanistic remodeling of dark-complex assembly and regulation. Protein-family analysis of CP12 homologs across diverse lineages showed that viral CP12 preserves interface-dominated positions while shifting partner-facing chemistry toward charged and geometry-modulating features. Matched molecular dynamics simulations (MD) of Prochlorococcus MED4 and cyanophage P-HM2 showed that phage CP12 preserves assembly while strengthening PRK-facing contacts and reducing GAP2-facing interface burial. MED4 redox proteomics identified coordinated cysteine oxidation across CP12 and GAP2 under light disturbance, guiding MD to explore thiol-PTM states. Conformational divergence increased with PTM load and localized mainly to GAP2 modifications. Thiol PTM at GAP2 imposed the largest CP12 binding-energy cost, which P-HM2 CP12 buffered, yielding smaller comparative binding-energy penalties than host CP12. These findings link sequence-driven chemistry to interface dynamics and redox PTM responsiveness to light, defining phage CP12 as a regulatory mimetic that may retune host carbon regulation during infection.

microbiology↗

bioRxiv2026

Extreme genome reduction selectively retains modular regulatory architecture in Prochlorococcus MED4: conserved transcriptional modules reveal core physiological regulatory programs

Prochlorococcus MED4 is a minimal photoautotroph whose extreme genome streamlining extends to its transcriptional regulatory architecture, yet it dominates high-light oligotrophic surface waters and drives marine carbon cycling. Despite ecological significance, MED4 remains genetically intractable, lacking molecular tools to characterize regulatory mechanisms and construct a transcriptome-wide regulatory map. To address this, we assembled an RNA-seq compendium of 253 samples, including 207 new samples capturing transcriptional responses across three classes of experiments: diverse environmental perturbations, a 24-hour circadian cycle, and phage infection. Using independent component analysis (ICA) applied to 247 quality-filtered samples, we identify 32 independently regulated gene set modules in MED4 (iModulons). By comparison, we previously identified 78 iModulons in the model cyanobacterium Synechococcus elongatus PCC 7942, revealing how dramatically genome reduction has simplified MED4s regulatory architecture. Of the 32 iModulons in MED4, 13 are conserved modules that correlate with experimentally validated transcriptional regulons in PCC 7942, identifying regulatory programs that resisted elimination under extreme selective pressure. These conserved modules reveal regulatory programs governing photosynthesis and light responses (RpaB), circadian rhythms (RpaA), and nutrient assimilation (NtcA, PhoB). Known regulator-specific DNA-binding motifs upstream of genes in conserved modules independently support their identification as regulatory targets. Notably, RpaA governs circadian rhythms through three temporally distinct modules in MED4 versus one in PCC 7942, and the RpaB photoprotection module similarly splits into two. This work uncovers the minimal regulatory core governing photosynthesis, circadian rhythms, and C/N/P metabolism in a globally critical but genetically intractable photoautotroph. This approach offers a generalizable framework for regulatory inference beyond model organisms. ImportanceThe minimal photoautotroph Prochlorococcus MED4 possesses only 28 transcriptional regulators, versus 150+ found in most cyanobacteria, reflecting a genome streamlined by billions of years of natural selection. This streamlining minimized metabolic costs, enabling MED4 to dominate nutrient-depleted oceans today. This raises a fundamental question: which regulatory programs did nature choose to keep? The answer matters, but MED4 cannot be studied by conventional genetics, placing its molecular machinery beyond direct experimental reach. Instead, we use large-scale computational methods to define groups of co-regulated genes in MED4. By comparing MED4 with a genetically tractable model cyanobacterium, we can distinguish which regulatory programs nature preserved from those it discarded. This work reveals the minimal regulatory architecture sufficient to sustain the smallest oxygenic photoautotroph on Earth. The principles uncovered here, distinguishing essential from dispensable regulatory programs in a naturally streamlined organism, inform the design of minimal photosynthetic platforms for biotechnology.

systems biology↗

bioRxiv2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET images as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the "dark complex," modulate metabolic flux at a conserved regulatory node of the Calvin-Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4. Significance StatementThis work advances 4D whole-cell modeling by presenting the first spatiotemporal simulation of a photosynthetic autotroph using the Lattice Microbes platform. Using Prochlorococcus marinus MED4, we show that subcellular spatial organization of organelles, diffusion constraints, and redox regulation collectively shape central carbon metabolism across orders of magnitude in space and time. Through a perturbation-based strategy that generates multi-omics data sets over time, we construct and validate a spatially and temporally resolved model of MED4, constrained by high-resolution (10 nm) cryo-electron tomography. Our results highlight the importance of localized biochemical reactions and redox-dependent post-translational modification of enzymes in regulating carbon fixation in a noisy environment under light disturbance. This study establishes a spatiotemporal, whole-cell physiology modeling framework as a transformative tool for uncovering multiscale regulatory responses to environmental gradients.

systems biology↗

bioRxiv2025

EcoKMER: One-stop shop for spatio-temporal metagenomic exploration using DataFed

Spatially distributed environmental sampling generates highly complex and multidimensional datasets illuminating key insights into microbial diversity, evolutionary-coevolutionary processes, and host-pathogen interactions. While these sampling methods generate high value datasets, dataset size, the dataset integration, visualization, analysis, and provenance tracking present significant bottlenecks to scientific discovery. To address this bottleneck, we developed EcoKMER, an R-Shiny front-end application designed to streamline metagenomic data accessibility and provide geospatial context to data in support of hypothesis-driven investigations into environmental sampling, supported by DataFed as its back-end data management platform. EcoKMER enables interactive visualization and filtering of harmonized metagenomic data and metadata using an interoperable approach, allowing users to extract spatially distributed sample-based metadata on top of environmental parameters such as geolocation, temperature, pH, for investigating ecological changes across time and space enhancing sample processing methods. As an example, we deployed this tool to track analysis of metagenomes from the organisms in the Salish Sea Estuary, consistent with existing community-accepted standards. Built on top of DataFed, a flexible and robust scientific data management system built for data lakehouse architectures, EcoKMER is positioned as a powerful tool to improve sampling strategy decision making, accelerate new insights for collaborative biological and environmental research, and fostering AI-ready analyses designed to enhance discovery and guidance for bioeconomic engineering. The published manuscript is available at https://www.osti.gov/biblio/3412938

bioinformatics↗

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↗

bioRxiv2021

Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. We observed that Fusarium sp. DS 682, a representative of common saprotrophic soil fungi, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces ([~]12 {micro}m) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral derived nutrient transport and unique K chemical moieties following fungal induced mineral weathering. Specific membrane transport proteins were expressed in the presence of minerals, including those involved in oxidative phosphorylation pathways and transmembrane transport of small molecular weight organic acids. This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment.

microbiology↗

bioRxiv2018

Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites

Chlamydia trachomatis is the most common bacterial sexually transmitted infection, responsible for millions of infections each year. Despite this high prevalence, the elucidation of the molecular mechanisms of Chlamydia pathogenesis has been difficult due to limitations in genetic tools and its intracellular developmental cycle. Within a host epithelial cell, chlamydiae replicate within a vacuole called the inclusion. Many Chlamydia-host interactions are thought to be mediated by the Inc family of type III secreted proteins that are anchored in the inclusion membrane, but their array of host targets are largely unknown. To investigate how the inclusion membrane proteome changes over the course of an infected cell, we have adapted the APEX system of proximity-dependent biotinylation. APEX is capable of specifically labeling proteins within a 20 nm radius in living cells. We transformed C. trachomatis to express the enzyme APEX fused to known inclusion membrane proteins, allowing biotinylation and pull-down of inclusion-associated proteins. Using quantitative mass spectrometry against APEX labeled samples, we identified over 400 proteins associated with the inclusion membrane at early, middle, and late stages of epithelial cell infection. This system was sensitive enough to detect inclusion interacting proteins early in the developmental cycle, at 8 hours post infection, a previously intractable time point. Mass spectrometry analysis revealed a novel, early association between C. trachomatis inclusions and endoplasmic reticulum exit sites (ERES), functional regions of the ER where COPII-coated vesicles originate. Pharmacological and genetic disruption of ERES function severely restricted early chlamydial growth and the development of infectious progeny. APEX is therefore a powerful in situ approach for identifying critical protein interactions on the membranes of pathogen-containing vacuoles. Furthermore, the data derived from proteomic mapping of Chlamydia inclusions has illuminated an important functional role for ERES in promoting chlamydial developmental growth.

microbiology↗