Search NASA⌕ Search

SEARCH · Search NASA

Results for “BIOSYNTHESIS”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as “Candidatus Synoicihabitans palmerolidicus.” The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗
DOE OSTI2023

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

ABSTRACT Polyolefins derived from plastic wastes are recalcitrant for biological upcycling. However, chemical depolymerization of polyolefins can generate depolymerized plastic (DP) oil, comprising of a complex mixture of saturated, unsaturated, even, and odd hydrocarbons suitable for biological conversion. While DP oil contains a rich carbon and energy source, it is inhibitory to cells. Understanding and harnessing robust metabolic capabilities of microorganisms to upcycle the hydrocarbons in DP oil, both naturally and unnaturally occurring, into high-value chemicals are limited. Here, we discovered that an oleaginous yeast, Yarrowia lipolytica, undergoing short-term adaptation to DP oil robustly utilized a wide range of hydrocarbons for cell growth and production of citric acid and neutral lipids. When growing on hydrocarbons, Y. lipolytica partitioned into planktonic and oil-bound cells with each exhibiting distinct proteomes and amino acid distributions invested in establishing these proteomes. Significant proteome reallocation toward energy and lipid metabolism, belonging to 2 of the 23 Eukaryotic Orthologous Groups classes C and I, enabled robust growth of Y. lipolytica on hydrocarbons, with n-hexadecane as the preferential substrate. This investment was even higher for growth on DP oil where classes C and I were ranked one and two, respectively, and many associated proteins and pathways were expressed and upregulated including the hydrocarbon degradation pathway, Krebs cycle, glyoxylate shunt and, unexpectedly, propionate metabolism. However, a reduction in proteome allocation for protein biosynthesis, at the expense of the observed increase toward energy and lipid metabolisms, might have caused the inhibitory effect of DP oil on cell growth. IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.

1-alkenes↗
DOE OSTI2025

Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation

ABSTRACT Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host,Mtbfaces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions,Mtbcan enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. DormantMtbposes a major challenge to curing infections and eradicating TB globally. We subjectedMtbmc 2 6020 (ΔlysAand ΔpanCD), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancyin vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia inMtb. IMPORTANCE Tuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogenMycobacterium tuberculosis(Mtb).Mtbexcels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes thatMtbundergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.

Microbiology↗
DOE OSTI2026

Biosynth Pipeline v1.0

BioPKS Pipeline is a computational pipeline for retrosynthetic design of small molecule biosynthesis pathways (e.g. retrobiosynthesis). It combines capabilities by interfacing with existing retrobiosynthesis tools- RetroTide (developed at LBNL) and DORAnet to create pathways that combine multiple biosynthesis approaches- both megasynthase assembly line enzymes and single step enzymes.

Backman, Tyler [Lawrence Berkeley National Laborat↗
DOE OSTI2020

Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production

Biofuels and value-added biochemicals derived from renewable biomass via biochemical conversion have attracted considerable attention to meet global sustainable energy and environmental goals. Isobutanol is a four-carbon alcohol with many advantages that make it attractive as a fossil-fuel alternative. Zymomonas mobilis is a highly efficient, anaerobic, ethanologenic bacterium making it a promising industrial platform for use in a biorefinery. In this study, the effect of isobutanol on Z. mobilis was investigated, and various isobutanol-producing recombinant strains were constructed. The results showed that the Z. mobilis parental strain was able to grow in the presence of isobutanol below 12 g/L while concentrations greater than 16 g/L inhibited cell growth. Integration of the heterologous gene encoding 2-ketoisovalerate decarboxylase such as kdcA from Lactococcus lactis is required for isobutanol production in Z. mobilis. Moreover, isobutanol production increased from nearly zero to 100-150 mg/L in recombinant strains containing the kdcA gene driven by the tetracycline-inducible promoter Ptet. In addition, we determined that overexpression of a heterologous als gene and two native genes (ilvC and ilvD) involved in valine metabolism in a recombinant Z. mobilis strain expressing kdcA can divert pyruvate from ethanol production to isobutanol biosynthesis. This engineering improved isobutanol production to above 1 g/L. Finally, recombinant strains containing both a synthetic operon, als-ilvC-ilvD, driven by Ptet and the kdcA gene driven by the constitutive strong promoter, Pgap, were determined to greatly enhance isobutanol production with a maximum titer about 4.0 g/L. Finally, isobutanol production was negatively affected by aeration with more isobutanol being produced in more poorly aerated flasks. This study demonstrated that overexpression of kdcA in combination with a synthetic heterologous operon, als-ilvC-ilvD, is crucial for diverting pyruvate from ethanol production for enhanced isobutanol biosynthesis. Moreover, this study also provides a strategy for harnessing the valine metabolic pathway for future production of other pyruvate-derived biochemicals in Z. mobilis.

09 BIOMASS FUELS↗
DOE OSTI2026

Data for Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5-Aminolevulinic Acid Production

Biological production of 5‐aminolevulinic acid (5‐ALA) has received growing attentionover theyears.However, thereis the tradeoff between 5‐ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5‐ALA. To address this limitation, we engineered an acid‐tolerant yeast, Issatchenkia orientalis SD108, for 5‐ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5‐ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5‐ALA was improved from 28mg/L to 120‐, 150‐, and 300mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5‐ALA to 510mg/L, a 13‐fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid‐tolerant I. orientalis SD108ΔPDC has a high potential for 5‐ALA production at a large scale in the future.

Bioproducts↗
DOE OSTI2026

Data for High Yield Production of 3-Hydroxypropionic Acid Using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Bioproducts↗
DOE OSTI2020

Modeling and Manipulating Phenylpropanoid Pathway Flux for Bioenergy

We have made important strides toward our project goals over the past five years. First, we developed and published a novel isotopic feeding system to investigate metabolic fluxes of the lignin biosynthesis. Next, we have developed and published a kinetic model of the phenylpropanoid pathway. As an extension of that work, we developed a multilayer kinetic model of lignin biosynthesis. Next we conducted a systematic transcriptome and metabolome analysis for phenylpropanoid metabolism. Finally, we have identified three strategies that enhance the accumulation of 2-phenylethanol in plants.

09 BIOMASS FUELS↗
DOE OSTI2021

Developing Cost Effective Biological Removal Technology for Selenium and Nitrate from Flue Gas Desulfurization Wastewater from an Existing Power Facility

Funding from this project supported new research in environmental biotechnology at WVSU Energy and Environmental Science Institute (WVSUEESI) to develop biological treatment techniques for FGD wastewater using photosynthetic organisms algae and plants. We tested the possibility of using algae and plants in treating FGD wastewater. Results suggested that algae and plants could able to perform normal photosynthesis under low concentrations of selenium. However, higher concentrations of selenium are lethal on photosynthesis. The total protein data indicated that FGD wastewater induced the accumulation of complete proteins in the duckweeds compared to control plants. It appears that nitrate, nitrates, and other compounds in FGD wastewater promote total protein accumulation. The FGD wastewater treatment has triggered Triacylglycerols (TAG) and carbohydrate accumulation in duckweed. We studied the differential gene expression using RNA-Sequencing data. Gene expression analysis revealed that glycolysis, fatty acid, triacylglycerol biosynthesis, and starch degradation were up-regulated; on the contrary, gluconeogenesis, photosynthesis, and starch biosynthesis genes were down-regulated by FGD wastewater treatment. We confirmed the expression of some of these genes using q-RT PCR analysis. We demonstrated that when FGD gypsum was blended with the coal mine soil to grow the bioenergy crop, Camelina, it could grow and produce seed. Moreover, Camelina is a non-edible oilseed crop and has heavy metal sequestering properties, making it the right reclamation choice. Besides, this project provided the opportunity for WVSU undergraduates to integrate hands-on research and education. Funding from this grant helped us to enhance student hands-on experience in water quality and environmental science and participation in STEM research and education.

09 BIOMASS FUELS↗
DOE OSTI2023

Light Energy Transduction in Green Sulfur Bacteria

Green sulfur bacteria (GSB) are exquisitely adapted for growth at extraordinarily low light intensities. They are important primary producers of biomass in many anoxic environments, and they contribute significantly to the biogeochemical cycling of carbon, nitrogen, and sulfur on Earth. Green bacteria more generally share the property of using chlorosomes for light-harvesting, and these unusual organelles have many unique features. These include the presence of a monolayer lipid-protein envelope, self-assembling bacteriochlorophylls (BChl) in which pigment-pigment interactions predominate, and the presence of redox components ([2Fe-2S] ferredoxins and quinones) that play a role in regulating excitation energy transfer to the type-1 homodimeric reaction centers. The reaction centers of GSB are related to Photosystem I of cyanobacteria and higher plants but also exhibit several unique structural and functional features. The long-term objectives of this research program are to understand the structure, functions, and biogenesis of the chlorosomes, reaction centers, and electron transport chains that carry out the photochemical transduction of light energy into chemical energy in the model green sulfur bacterium, Chlorobaculum (formerly Chlorobium) tepidum. Over a period of 26 years, we characterized chlorosomes in detail. We identified the proteins in the chlorosome envelopes of diverse organisms, identified the nearest neighbors of those proteins, and characterized the chlorosomes of mutant strains lacking one to five of these proteins. After the genome sequence of Cba. tepidum became available, we identified all genes encoding enzymes for BChl a , BChl c/d/e/ƒ , and Chl a biosynthesis Cba. tepidum . We additionally identified all genes encoding enzymes for carotenoid biosynthesis. By constructing a bchQRU mutant strain that produces [Et, Me]-BChl d , together with collaborators who are specialists in solid-state NMR and cryo-electron microscopy, we solved the structure of the BChls in chlorosomes. Using similar methods and chlorosomes containing [Et, Me]-BChl c , we then showed that alternative structures were possible using the same syn-anti BChl dimer. The structures were refined by introducing spectroscopic data from single-chlorosome measurements. Over the course of this project, we sequenced the genomes of approximately twenty GSB strains, which provided important information for comparative analyses. Through analyses of metagenomic data from Mushroom and Octopus Springs in Yellowstone National Park, we identified a novel chlorophototroph belonging to the phylum Acidobacteriota. We successfully isolated an axenic culture of this organism. We characterized the photosynthetic apparatus of this bacterium, named Chloracidobacterium thermophilum, in significant detail, in particular its type-1, homodimeric reaction centers. Surprisingly, these reaction centers contain three types of Chls, BChl a , Chl a , and Zn-BChl a' . We showed that a dimer of Zn-BChl a' is the primary donor and Chl a the primary acceptor of electrons in this reaction center by using advanced spectroscopic techniques. We isolated eight additional strains of Chloracidobacterium spp. from Mushroom Spring and Rupite hot springs in Bulgaria. Comparative genomes showed that these represent three species, Cab. thermophilum , Cab. aggregatum , and Cab. validum . By applying comparative genomics, genetic, biochemical biophysical and physiological approaches to study green bacteria, we produced a wealth of new information about the remarkable light-harvesting and energy transduction capabilities of these poorly characterized microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Investigation of encapsulin nanocompartment systems as ascaffold for biomaterials synthesis in Rhodococcus species (DOE ECRP Annual Report 2023)

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., CdS nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology (Final Technical Report)

Fatty acids can be produced biosynthetically in microbes and these compounds can serve as precursors to biodiesels and other high value oleochemicals. However, progress on engineering fatty acid biosynthesis, and biofuel synthesis more generally, has been hindered by current quantification methods that are either indirect or not amenable to high-throughput or single-cell resolution screening. In this project, we assembled an interdisciplinary team with complimentary expertise in synthetic biology and microscopy, metabolic engineering, and chemical imaging to address these challenges. We used chemical imaging to directly measure lipid biosynthesis in Escherichia coli engineered to produce fatty acids, obtaining detailed single-cell resolution measurements. We deployed stimulated Raman scattering (SRS) microscopy in concert with multiplexed genome engineering and gene circuit design strategies from synthetic biology to optimize production of fatty acids. These results provided novel insight into cell-to-cell heterogeneity present in biofuel production strains. In addition, we introduced new chemical imaging methods which are label-free and do not require fluorescent reporters. These efforts were complemented by other studied developing foundational tools for regulation and control, which offer excellent potential for advancing researchers’ ability to rapidly design, build, and test strains for enhanced biofuel synthesis.

09 BIOMASS FUELS↗
DOE OSTI2024

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcusspecies. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., CdS nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species (Annual Report 2025)

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., alkene, inorganic nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Symbiosis Under Stress: How Arbuscular Mycorrhizal Fungi and Sorghum Metabolism Shift Under Drought

As drought becomes more prevalent across the globe, causing billions of dollars in agricultural loss, the need to maintain crop health and productivity grows increasingly important. Out of the most important cereal crops, sorghum shows the greatest drought tolerance, and plant-microbiome interactions at the root region play a crucial role in this. A key microbial player is arbuscular mycorrhizal fungi (AMF), which deliver water and nutrients to plants in exchange for nutrients they cannot produce. Using sorghum as a model plant, we combine mass-spectrometry based proteomics and metabolomics to examine metabolic interactions between sorghum roots and AMF under drought stress. With AMF, sorghum downregulated lipid-related biological processes involving fatty acid biosynthesis and metabolism. Similarly, amino acid biosynthesis pathways were also suppressed; however, metabolite analysis revealed increased amino acid abundance related to the phenylpropanoid pathway. AMF also enhanced the upregulation of drought-protective osmolytes, such as mannitol and sorbitol, suggesting their key role in mediating sorghum’s response to drought stress. AMF hyphal biomass also had an increased abundance of key osmoprotectant amino acids, indicating similar mechanisms of drought tolerance between sorghum and AMF. Metabolomic evidence also suggested that carbohydrate exchange between sorghum and AMF shifted under stress, indicating an altered exudation pattern likely driven by drought response. Our results demonstrate the molecular mechanisms through which AMF modulate sorghum metabolism under drought conditions, highlighting their promising role in improving crop resilience. By identifying the molecular targets that can improve drought tolerance, we can begin engineering drought resistant agricultural biosystems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species (Annual Report 2025)

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., alkene, inorganic nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine and Deep Learning: Artificial Intelligence Application in Biotic and Abiotic Stress Management in Plants

Biotic and abiotic stresses significantly affect plant fitness, resulting in a serious loss in food production. Biotic and abiotic stresses predominantly affect metabolite biosynthesis, gene and protein expression, and genome variations. However, light doses of stress result in the production of positive attributes in crops, like tolerance to stress and biosynthesis of metabolites, called hormesis. Advancement in artificial intelligence (AI) has enabled the development of high-throughput gadgets such as high-resolution imagery sensors and robotic aerial vehicles, i.e., satellites and unmanned aerial vehicles (UAV), to overcome biotic and abiotic stresses. These High throughput (HTP) gadgets produce accurate but big amounts of data. Significant datasets such as transportable array for remotely sensed agriculture and phenotyping reference platform (TERRA-REF) have been developed to forecast abiotic stresses and early detection of biotic stresses. For accurately measuring the model plant stress, tools like Deep Learning (DL) and Machine Learning (ML) have enabled early detection of desirable traits in a large population of breeding material and mitigate plant stresses. In this review, advanced applications of ML and DL in plant biotic and abiotic stress management have been summarized.

59 BASIC BIOLOGICAL SCIENCES↗