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DOE OSTI2022

Data for Metabolic Engineering of Oleaginous Yeast Rhodotorula toruloides for Overproduction of Triacetic Acid Lactone

The plant-sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2-pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl-CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP-citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl-CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12-ACL1-ACC1 using fed-batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl-CoA-derived polyketides from low-cost carbon sources.

Conversion↗

DOE OSTI2025

Data for Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

photosynthesis↗

DOE OSTI2022

Reversible domain closure modulates GlnBP ligand binding affinity

Glutamine binding protein (GlnBP) is an Escherichia Coli periplasmic binding protein, which binds and carries glutamine to the inner membrane ATP-binding cassette (ABC) transporter. GlnBP binds the ligand with affinity around 0.1μM measured by isothermal titration calorimetry (ITC) and ligand binding stabilizes protein structure shown by its increase in thermodynamic stability. However, the molecular determinant of GlnBP ligand binding is not known. Electrostatic and hydrophobic interaction between GlnBP and glutamine are critical factors. We propose that the freedome of closure movement is also vital for ligand binding. In order to approve this hypothesis, we generate a series of mutants with different linker length that has different magnitude of domain closure. Mutants show different ligand binding affinity, which indicates that the propensity of domain closure determines the ligand binding affinity. Ligand binding triggers gradual ensemble conformational change. Structural changes upon ligand binding are monitored by combination of small angle x-ray scattering (SAXS) and NMR spectroscopy. Detailed structure characterization of GlnBP contributes to a better understanding of ligand binding and provides the structural basis for biosensor design.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T . pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T . pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T . pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T . pallidum , and we propose that the protein be referred to henceforth as TpPta.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗

DOE OSTI2024

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca 2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Evaluation of an in vitro three-dimensional HepaRG spheroid model for genotoxicity testing using the high-throughput CometChip platform

Three-dimensional (3D) culture systems are increasingly being used for genotoxicity studies due to improved cell-to-cell interactions and tissue-like structures that are limited or lacking in 2D cultures. The present study optimized a 3D culture system using metabolically competent HepaRG cells for in vitro genotoxicity testing. 3D HepaRG spheroids, formed in 96- or 384-well ultra-low attachment plates, were exposed to various concentrations of 34 test articles, including 8 direct-acting and 11 indirect-acting genotoxicants/carcinogens as well as 15 compounds that show different genotoxic responses in vitro and in vivo. DNA damage was evaluated using the high-throughput CometChip assay with concurrent cytotoxicity assessment by the ATP assay in both 2D and 3D cultures. 3D HepaRG spheroids maintained a stable phenotype for up to 30 days with higher levels of albumin secretion, cytochrome P450 gene expression, and enzyme activities compared to 2D cultures. 3D spheroids also demonstrated a higher sensitivity than 2D cultures for detecting both direct- and indirect-acting genotoxicants/carcinogens, indicating a better prediction of in vivo genotoxicity responses. When DNA damage dose-response data were quantified using PROAST software, 3D spheroids generally had lower or similar benchmark dose values compared to 2D HepaRG cells and were more comparable with primary human hepatocytes. These results demonstrate that 3D models can be adapted to the CometChip technology for high-throughput genotoxicity testing and that 3D HepaRG spheroids may be used as a reliable and pragmatic in vitro approach to better support the hazard identification and risk assessment of potential human genotoxic carcinogens.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Impaired cardiac glycolysis and glycogen depletion are linked to poor myocardial outcomes in juvenile male swine with metabolic syndrome and ischemia

Abstract Obesity continues to rise in the juveniles and obese children are more likely to develop metabolic syndrome (MetS) and related cardiovascular disease. Unfortunately, effective prevention and long‐term treatment options remain limited. We determined the juvenile cardiac response to MetS in a swine model. Juvenile male swine were fed either an obesogenic diet, to induce MetS, or a lean diet, as a control (LD). Myocardial ischemia was induced with surgically placed ameroid constrictor on the left circumflex artery. Physiological data were recorded and at 22 weeks of age the animals underwent a terminal harvest procedure and myocardial tissue was extracted for total metabolic and proteomic LC/MS–MS, RNA‐seq analysis, and data underwent nonnegative matrix factorization for metabolic signatures. Significantly altered in MetS versus. LD were the glycolysis‐related metabolites and enzymes. In MetS compared with LD Glycogen synthase 1 (GYS1)‐glycogen phosphorylases (PYGM/PYGL) expression disbalance resulted in a loss of myocardial glycogen. Our findings are consistent with the concept that transcriptionally driven myocardial changes in glycogen and glucose metabolism‐related enzymes lead to a deficiency of their metabolite products in MetS. This abnormal energy metabolism provides insight into the pathogenesis of the juvenile heart in MetS. This study reveals that MetS and ischemia diminishes ATP availability in the myocardium via altering the glucose‐G6P‐pyruvate axis at the level of metabolites and gene expression of related enzymes. The observed severe glycogen depletion in MetS coincides with disbalance in expression of GYS1 and both PYGM and PYGL. This altered energy substrate metabolism is a potential target of pharmacological agents for improving juvenile myocardial function in MetS and ischemia.

Broadwin, Mark↗

DOE OSTI2024

Laboratory time series moisture manipulative experiment from sediment across the contiguous US: time series aerobic respiration and geochemistry (v2)

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration across the contiguous United States (CONUS). The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS CONUS-Scale Model-Sample Study (CM). This study was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. The data package associated with the CM study is available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689. CM sampling began in April 2022 and ended in October 2023. This study uses subsamples from a subset of CM samples collected between June 2022 and June 2023. The original field samples were labeled as CM_###. Subsequent subsamples for this study were labeled as EC_###. The labels from the field samples and the EC subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EC_001 is a subsample from CM_001). See the critical details section below for more details on sample naming. This data package was originally published in August 2024. It was updated in February 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate this data package, see this infographic from the River Corridor SFA https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) adenosine triphosphate (ATP); (4) percent carbon and nitrogen; (5) effect size; (6) iron (II); (7) gravimetric moisture; (8) respiration rates and raw dissolved oxygen values; (9) specific conductance; (10) pH; (11) temperature; (12) a summary containing median values of each data type for each treatment (wet and dry); (13) methods codes; (14) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla FTICR-MS data. This folder contains three subfolders, one containing the sediment .xml data files, one containing the sediment CoreMS output files, the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Productivity and bioproduct formation in phototropic knock/out mutants in micro algae

Phototropin is a blue light receptor, which mediates a variety of blue-light elicited physiological processes in plants and algae. In higher plants these processes include phototropism, chloroplast movement and stomatal opening. In the green alga Chlamydomonas reinhardtii, phototropin plays a vital role in progression of the sexual life cycle and in the control of the eye spot size and light sensitivity. Phototropin is also involved in blue-light mediated changes in the synthesis of chlorophylls, carotenoids, chlorophyll binding proteins. We compared the transcriptome of phototropin knock out (PHOT KO) mutant and wild-type parent to analyze differences in gene expression in high light grown cultures (500 μmol photons m⁻²s⁻¹). Our results indicate the up-regulation of genes involved in photosynthetic electron transport chain, carbon fixation pathway, starch, lipid, and cell cycle control genes. With respect to photosynthetic electron transport genes, genes encoding proteins of the cytochrome b6f and ATP synthase complex were up regulated potentially facilitating proton-coupled electron transfer. In addition genes involved in limiting steps in the Calvin cycle Ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO), Sidoheptulose 1,7 biophosphatase (SBPase), Glyceraldehyde-3-phosphate dehydrogenase (3PGDH) and that mediate cell-cycle control (CDK) were also up regulated along with starch synthase and fatty acid biosynthesis genes involved in starch and lipid synthesis. In addition, transmission electron micrographs show increased accumulation of starch granules in PHOT mutant compared to wild type, which is consistent with the higher expression of starch synthase genes. Collectively, the altered patterns of gene expression in the PHOT mutants were associated with a two-fold increase in growth and biomass accumulation compared to wild type when grown in environmental photobioreactors (Phenometrics) that simulate a pond environment. In conclusion, our studies suggest that phototropin may be a master gene regulator that suppresses rapid cell growth and promotes gametogenesis and sexual recombination in wild type strains.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Where Have All of the Electrons Gone? Understanding the Role of Alternative Electron Flow and O 2 Reduction in Balancing Cellular Redox (Final Technical Report)

An informed understanding of the fundamentals of light-driven electron transfer reactions in photoautotrophic organisms is necessary to enable improved photosynthetic efficiencies for the production of renewable fuels and novel biomaterials. To obtain high photosynthetic yields, light energy must be efficiently coupled to the fixation of CO 2 . Sub-optimal environmental conditions and metabolic routing (caused by blocks in biosynthetic routes) can severely impact the conversion of light energy to biomass and lead to reactive oxygen production, which in turn can cause cellular damage and productivity losses. Hence, plants, algae, and photosynthetic bacteria have evolved a network of alternative outlets to sustain the flow of photosynthetically derived-electrons. Our research was focused on the nature and integration of these outlets. The data obtained in this project will inform efforts to rationally engineer crop plants and algae to improve photosynthetic yields by enhancing electron transfer reactions to CO 2 reduction and targeted biomass accumulation. A major project research thrust was focused on identifying and quantifying the flow of photosynthetic reductant through electron transfer circuits that result in the light-dependent reduction of O 2 . New energy management strategies were identified that are used when normal carbon assimilation pathways are compromised due to nutrient deprivation, and/or by a reduction in starch synthesis/carbon storage, all conditions resulting in highly reduced intracellular redox pools. The green alga Chlamydomonas reinhardtii, and likely many other algae, have multiple O 2 -reducing pathways that play critical roles in maintaining cellular metabolic balance and scavenging electrons that could potentially cause cellular damage, which in some instances leads to reduced photosynthetic yields but increased fitness. We explored the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: (1) reduction of O 2 to H 2 O through Flavodiiron proteins (FLVs) and (2) Plastid Terminal Oxidases (PTOX), and (3) the synthesis of starch. Real-time measurements of O 2 exchange demonstrated that FLVs immediately engage during dark to light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified, for the first time, maximal FLV activity and its overall capacity to direct photosynthetic electrons towards O 2 reduction. However, when starch synthesis is compromised, a greater proportion of electrons is directed toward O 2 reduction through the FLVs, while PTOX, which is sensitive to the PQ pool redox state, is activated. This suggests, that starch synthesis has an important role in priming/regulating CBBC and electron transport. We also identified a biological ‘switch’ in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b 6 f complex when reductant and ATP generated by PET are in excess of the capacity of carbon metabolism to utilize these products; we specifically show a restriction at this switch when sta6 mutant cells, which cannot synthesize starch, are limited for nitrogen (growth inhibition) and subjected to a dark to light transition. This restriction causes diminished electron flow to PSI, which prevents PSI photodamage, and the plastid alternative oxidase (PTOX) becomes fully activated, serving as an electron valve that dissipates excitation energy absorbed by PSII, thereby lessening PSII photoinhibition. Furthermore, illumination of the cells following the dark acclimation gradually diminishes the restriction at the switch. Future engineering of these switches may allow more effective electron transfer to lipid (biofuel) pathways and diminish the number of electrons “wasted” in the reduction of O 2 to water. Lastly, we explored metabolic routing of electrons during algal fermentation and discovered multiple novel pathways that are activated when the preferred anoxic routes are blocked. These provide valuable products (e.g. lactate, glycerol) that can be used in broad portfolio of biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Energy Efficient Waste Heat Coupled Forward Osmosis for Effluent Water Management at Coal-Fired Power Plants

This project sought to evaluate the technical and economic viability of the Aquapod©, a transformational low energy (<200 kJ/kg water) waste heat coupled forward osmosis (FO) technology, to manage effluents, meet cooling water demands, and achieve water conservation in a coal-fired power plant environment. The Aquapod© process is innovative because it is heat-driven, avoids the evaporation of water, and uses no toxic chemicals such as ammonia or amines. The Aquapod© process accomplishes this using an aqueous two-phase system (ATPS) coupled FO process. The evaluation revealed that the Aquapod© process offers a pathway to exploit waste heat resources within a power plant to achieve flue-gas desulfurization (FGD) wastewater volume reduction and water recovery with minimal pretreatment. Water recovery of 80% from FGD wastewater was achieved with minimal pretreatment, exceeding the project target of 50%. The estimated electrical energy of 2.16 kWh/m 3 of water produced for the Aquapod© process met the project target of < 3.6 kWh/m 3 . The heat required for the process operation was approximately 186 kJ/kg of produced water, which was slightly lower than the project target of 200 kJ/kg. The estimated treatment cost for installing and operating the Aquapod© process in conjunction with a spray dryer evaporator to achieve zero-liquid discharge (ZLD) of the 100 gpm FGD wastewater was $13.24/m 3 over a 30-year lifetime. As a point of reference, this study’s host power plant currently incurs a cost of $3.70/m 3 – $8.87/m3 on a discharged volume basis to discharge its wastewater into the publicly owned treatment works (POTW) after physical-chemical treatment. Therefore, the Illinois power plant would incur an incremental cost increase of $4.37/m 3 – 9.54/m 3 to achieve ZLD using the Aquapod© and spray dryer combination. Ample opportunities exist to further lower the ZLD capital and operating costs in the next design iteration to attain pipe parity at the higher end of the site treatment costs.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2021

Engineering Forisome Scaffolds: Elucidating Spatial Self-Assembly Patterning of Bio-inorganic Complexes

Organisms can synthesize biomaterials incorporating an array of naturally occurring elements while overcoming challenges and insults. Although, it is known that most cellular biomaterials are synthesized in specialized cellular compartments, there are knowledge gaps about how organic/inorganic biomaterial synthesis is orchestrated inside cells. In addition, there is great potential in understanding how individual monomers can self-assembly into organized patterns to form responsive biomaterials. Forisomes are a natural responsive biomaterial found in legume plants that serve as a plug sieve element in the plant phloem that undergo anisotropic conformational changes by rapid (<1 s) ATP-independent from condensed spindle to plug-like form, triggered by the influx of Ca 2+ . Addressing principles of forisome synthesis and assembly will determine how biomaterials containing inorganic elements self-assemble and conduct chemical modification to produce biomaterials or undergo biomineralization. We employ transcription and translation (TXTL) using cell-free expression systems for forisome monomer expression, self-assembly, and pattern probing. We conducted experiments to precisely control forisome proteins synthesis of various monomers SEO1, SEO2, SEO3, and SEO4 to explore self- assembly. We demonstrate forisome self-assembly of the SEO monomers is possible and indicate unique monomer fluorescent labeling patterns that require additional analysis. We investigated locations and linkers for adding tetracysteine tag fluorophore probes to determine impacts of self-assembly and anisotropic conformational changes.

42 ENGINEERING↗

DOE OSTI2021

Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product (Final Report)

The goal is to achieve a comprehensive understanding of the nature, mechanism of function and biogenesis of c-type cytochromes and their oligomeric complexes. These cytochrome are ubiquitous heme proteins that are required for cellular bioenergetics, including photosynthesis (Ps) and respiration (Res), which are central to chemical energy (ATP) production by oxidative- and photophosphorylation. We contribute to the molecular characterization of individual and membrane-integral cytochromes as parts of Ps and Res electron transport (ET) pathways, using the facultative phototrophic bacteria of as excellent models for multidisciplinary investigations. Supported by this grant we discovered novel membrane-bound cytochromes and cyts c complexes that are important for Ps- and Res-ET. We worked out their biogenesis including maturation (covalent heme addition) and assembly of mature subunits into complexes. These involve fundamental process found virtually in all organisms and are fundamental processes with major significance to the “Photosynthetic Systems” program of DOE-BES, because the cytochromes are integral components of natural energy production systems. Elucidation of basic principles, and the knowledge gained by their study greatly impact on our ability to design, engineer, and create new natural, bio-hybrid, bio-inspired and artificial systems to better capture light, transduce and store its energy with improved efficacy and are of broad significance.

14 SOLAR ENERGY↗

DOE OSTI2023

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis (Final Report)

03 NATURAL GAS↗

DOE OSTI2024

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.

09 BIOMASS FUELS↗

DOE OSTI2021

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

cytochrome c oxidase↗

DOE OSTI2022

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Most transcriptomic studies of SARS-CoV-2 infection have focused on differentially expressed genes, which do not necessarily reveal the genes mediating the transcriptomic changes. In contrast, exploiting curated biological network, our PathExt tool identifies central genes from the differentially active paths mediating global transcriptomic response. Here we apply PathExt to multiple cell line infection models of SARS-CoV-2 and other viruses, as well as to COVID-19 patient-derived PBMCs. The central genes mediating SARS-CoV-2 response in cell lines were uniquely enriched for ATP metabolic process, G1/S transition, leukocyte activation and migration. In contrast, PBMC response reveals dysregulated cell-cycle processes. In PBMC, the most frequently central genes are associated with COVID-19 severity. Importantly, relative to differential genes, PathExt-identified genes show greater concordance with several benchmark anti-COVID-19 target gene sets. We propose six novel anti-SARS-CoV-2 targets ADCY2, ADSL, OCRL, TIAM1, PBK, and BUB1, and potential drugs targeting these genes, such as Bemcentinib, Phthalocyanine, and Conivaptan.

59 BASIC BIOLOGICAL SCIENCES↗