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DOE OSTI2025

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa, the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated the expression of genes encoding phosphatases, nucleases, and a phosphate transporter and directly repressed genes associated with the ribosome. Additionally, NUC-1 indirectly activated the expression of an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly repressed the expression of genes involved in phosphate acquisition and liberation after an extended period of phosphate starvation. Additionally, NUC-3 directly repressed the expression of the cyclin-dependent kinase inhibitor nuc-2. Thus, through the combination of NUC-3 direct repression of genes in the phosphate starvation response and nuc-2, an activator of the phosphate starvation response, NUC-3 serves to act as a brake on the phosphate starvation response after an extended period of phosphate starvation. This braking mechanism could reduce transcription, a phosphate-intensive process, under conditions of extended phosphate limitation.IMPORTANCEFungi have evolved regulatory networks to respond to available nutrients. Phosphate is often a limiting nutrient for fungi that is critical for many cellular functions, including nucleic acid and phospholipid biosynthesis, cell signaling, and energy metabolism. The fungal response to phosphate limitation is important in interactions with plants and animals. We investigated the global transcriptional response to phosphate starvation and the role of a major transcriptional regulator, NUC-1, in the model filamentous fungus Neurospora crassa. Our data show that NUC-1 is a bifunctional transcription factor that directly activates phosphate acquisition genes, while directly repressing genes associated with phosphate-intensive processes. NUC-1 indirectly regulates an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly represses phosphate acquisition genes and nuc-2, an activator of the phosphate starvation response, during extended periods of phosphate starvation. Thus, NUC-3 acts as a brake on the phosphate starvation response to reduce phosphate-intensive activities, like transcriptional activation, when phosphate starvation persists.

DNA affinity purification sequencing↗

DOE OSTI2021

Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana

The R2R3-MYB transcription factor MYB46 functions as a master switch for secondary cell wall biosynthesis, ensuring the exquisite expression of the secondary wall biosynthetic genes in the tissues where secondary walls are critical for growth and development. At the same time, suppression of its function is needed when/where formation of secondary walls is not desirable. Little is known about how this opposing control of secondary cell wall formation is achieved. We used both transient and transgenic expression of MYB46 and mitogen-activated protein kinase 6 (MPK6) to investigate the molecular mechanism of the post-translational regulation of MYB46. We show that MYB46 is phosphorylated by MPK6, leading to site specific phosphorylation-dependent degradation of MYB46 by the ubiquitin-mediated proteasome pathway. In addition, the MPK6-mediated MYB46 phosphorylation was found to regulate in planta secondary wall forming function of MYB46. Furthermore, we provide experimental evidences that MYB83, a paralog of MYB46, is not regulated by MPK6. The coupling of MPK signaling to MYB46 function provides insights into the tissue- and/or condition-specific activity of MYB46 for secondary wall biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans

During meiotic prophase, the essential events of homolog pairing, synapsis, and recombination are coordinated with meiotic progression to promote fidelity and prevent aneuploidy. The conserved AAA+ ATPase PCH-2 coordinates these events to guarantee crossover assurance and accurate chromosome segregation. How PCH-2 accomplishes this coordination is poorly understood. Here, we provide evidence that PCH-2 decelerates pairing, synapsis and recombination in C. elegans by remodeling meiotic HORMADs. We propose that PCH-2 converts the closed versions of these proteins, which drive these meiotic prophase events, to unbuckled conformations, destabilizing interhomolog interactions and delaying meiotic progression. Further, we find that PCH-2 distributes this regulation among three essential meiotic HORMADs in C. elegans: PCH-2 acts through HTP-3 to regulate pairing and synapsis, HIM-3 to promote crossover assurance, and HTP-1 to control meiotic progression. In addition to identifying a molecular mechanism for how PCH-2 regulates interhomolog interactions, our results provide a possible explanation for the expansion of the meiotic HORMAD family as a conserved evolutionary feature of meiosis. Taken together, our work demonstrates that PCH-2’s remodeling of meiotic HORMADs has functional consequences for the rate and fidelity of homolog pairing, synapsis, recombination and meiotic progression, ensuring accurate meiotic chromosome segregation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Optimizing Mu2e Spill Regulation System Algorithms

A slow extraction system is being developed for the Fermilab’s Delivery Ring to deliver protons to the Mu2e experiment. During the extraction, the beam on target experiences small intensity variations owing to many factors. Various adaptive learning algorithms will be employed for beam regulation to achieve the required spill quality. We discuss here preliminary results of the slow and fast regulation algorithms validation through the computer simulations before their implementation in the FPGA. Particle tracking with sextupole resonance was used to determine the fine shape of the spill profile. Fast semi-analytical simulation schemes and Machine Learning models were used to optimize the fast regulation loop.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Voluntary Renewable Energy Procurement Programs in Regulated Utility Markets

Multinational corporations are increasingly purchasing renewable energy (RE) to fulfill international commitments, reduce supply chain emissions, limit environmental impact, and secure stable and affordable electricity. The potential scale of global corporate RE purchasing has been estimated to be nearly 100 GW and growing; however, many markets still lack supportive enabling environments for corporations to access RE through on-site project development or private sector transactions. Even where allowed by law, on-site generation may be insufficient due to space and technical constraints, introducing additional challenges. Utility green pricing and utility green tariff programs backed by renewable energy certificates (RECs), referred to as utility green procurement programs (GPPs) in this report, offer powerful market-based solutions to utilities, regulators, and policymakers to provide corporate and other consumers with RE product options while generating revenue to support RE development. As RE markets expand around the globe, GPPs have proven to be effective mechanisms in market regimes, ranging from fully integrated state-owned utilities to broadly liberalized power markets. GPPs utilize RECs, which are a type of energy attribute certificate and closely resemble guarantees of origin, to track and ultimately monetize RE attributes that corporations and other buyers must procure to demonstrate progress against their RE commitments and make public claims of RE use. Time-tested and transparent REC accounting mechanisms provide market confidence, while at the same time offering flexibility to utilities, regulators, and customers for a range of applications. RECs are used in all types of electricity market structures, as indicated in Figure 1, but REC-based program designs and supporting components differ depending on the type of market. Liberalized markets allow for customers to contract directly with generators for electricity and RECs, while traditionally regulated markets with vertically integrated utility structures may have greater restrictions on generation asset ownership and electricity sales. RE markets can be further defined as being either mandatory or voluntary. Mandatory markets require suppliers to deliver specified amounts of RE to grid customers, such as under a renewable portfolio standard (RPS), while voluntary markets involve no legal mandates, but demand is driven by self-imposed customer goals.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Advancing Equity in Utility Regulation

Increasingly, states are recognizing equity as a goal of utility regulation, going beyond traditionally stated objectives to ensure that electricity systems are reliable, safe, and fairly priced. State initiatives are critical not only to address historical inequities, but to ensure equitable benefits and burdens in the transition to net-zero emissions by 2050. This report provides four perspectives on advancing equity in electric utility regulation, from representatives of energy justice and consumer organizations and a leading utility in this area. The authors provide recommendations related to regulatory issues such as stakeholder engagement, defining "public interest," intervenor funding, electricity infrastructure siting, access to distributed energy technologies, consumer protections, bill affordability programs, rate design, program design, and metrics to track and evaluate results of policies, regulations, and programs intended to deliver equitable outcomes.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Topics and Considerations for Developing State Geothermal Regulations

The intent of this document is to provide guidance to states for developing geothermal regulations that would be inclusive of all geothermal technologies (e.g., conventional and non-conventional power production and direct-use applications) with applicability in all states. As part of this project, the NREL project team reviewed and catalogued existing state and federal geothermal regulations, compiled best practices from geothermal and other extractive industries, and established a Geothermal Regulatory Stakeholder Working Group (SWG) to advise and review the geothermal regulatory guidance. The SWG met approximately monthly over the course of one year to review and discuss specific topics as relevant to this geothermal regulatory guidance. This report is broken into five main sections, which were identified in coordination with the SWG as the main topics for inclusion. Within these sections, a list of considerations within each category were identified and, in some cases, relevant examples from existing state and federal geothermal regulations are included to further illustrate the proposed considerations. This report includes the following topics: geothermal resource definition; leasing process; exploration approval process; drilling/wellfield development approval process; and underground injection control process.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

County Land-Use Regulations for Solar Energy Development in Colorado

We present a survey of county-level policies on ground-mounted solar development across Colorado, including both solar-specific ordinances as well as general land-use code that might be applicable in counties without solar-specific policies. This report provides an accessible reference for stakeholders interested in identifying counties with particular regulations or in analyzing the diversity of regulations across Colorado. We defined a set of search criteria to find information on solar definitions and classifications, permitting processes, and use-specific requirements in each of Colorado's 64 counties. With those criteria, we reviewed relevant ordinances, land-use code, and comprehensive and master plans. If any uncertainties were identified, we contacted county officials for clarification. The findings are categorized and mapped to illustrate the distribution of key policies adopted across Colorado's counties on the following topics: solar definitions, solar siting policy documentation, categorization of PV systems for permitting, 1041 permitting, solar on agricultural land, panel height restrictions, fencing requirements, vegetation management, visual impacts, decommissioning plans, and financial assurance for decommissioning. Additionally, we identify and discuss policies that might impact the deployment of agrivoltaics, a dual land use combining both agriculture and solar on the same land, which might not fit neatly in existing zoning definitions and solar-specific regulations.

14 SOLAR ENERGY↗

DOE OSTI2024

Process Safety Standards and Regulations

The list of standards, best practice, and regulations below are intended to give insight into what resources are available for developing a chemical control regime as well as information on what regulations other countries have used to implement such a regime. This list is not intended to be all inclusive and other regulations and standards related to controlling hazardous chemicals exist and should be consulted.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Bridging the Gap on Data and Analysis for Distribution System Planning: Information That Utilities Can Provide Regulators, State Energy Offices and Other Stakeholders

Electric utilities conduct planning annually to ensure their distribution system meets technical standards, policies, and regulations; addresses forecasted grid conditions; satisfies customer needs; and advances utility priorities. The plan identifies grid deficiencies, analyzes potential solutions, and prioritizes capital investments and other expenditures. About 20 U.S. states and jurisdictions require regulated utilities to file some type of distribution system plan with the public utility commission for review. Requirements for sharing distribution system data and analyses vary widely, from few specific requirements to a detailed list of information that must be provided. While utilities conduct extensive analysis to develop distribution system plans, in most jurisdictions regulators and stakeholders do not know what data are available and how the utility uses the data in planning and investing. This report aims to bridge the gap by increasing understanding of the types of data and analyses utilities employ to develop distribution system plans and how the information affects their decision-making. The report describes information that states and stakeholders can ask for related to 11 data categories: -Forecasting loads and distributed energy resources (DERs) -Scenario analysis -Worst-performing circuits -Asset management strategy -Hosting capacity analysis -Value of DERs -Grid needs assessment -Cost-effectiveness framework for investments -Distribution system investment strategy and implementation -Geotargeted programs -Non-wires alternatives procurements.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Basis for Dose and Reactor Safety Design Criteria for Army Regulation AR 50–7 and DA Pamphlet

This report describes the basis used to develop the radiological dose acceptance and design criteria contained in the draft updates to Army Regulation 50–7 (AR 50–7) Army Reactor Program and its accompanying draft Department of the Army (DA) Pamphlet (PAM), Army Reactor Program Procedures. These criteria will apply to Army nuclear reactors that fall under AR 50–7 and its accompanying DA PAM and ensure alignment with the overall objectives of the Army Reactor Program. The development basis for the radiological dose and design criteria supports a modern, technology-neutral, risk-informed, and performance-based approach to Army regulation of reactors and the demonstration of “adequate protection of the public.” To establish these criteria that support the Army’s unique operational requirements, multiple well-known and well-established standards and their supporting documentation were reviewed to ensure consistency with existing regulatory safety levels, including guidance from U.S. and international sources. These include the U.S. Nuclear Regulatory Commission’s (NRC’s) regulations and policy, the Canadian Nuclear Safety Commission’s (CNSC’s) regulatory documents, the International Atomic Energy Agency’s (IAEA’s) safety standards, as well as industry input that is tailored specifically to advanced microreactors. This report walks through the key definitions and associated references used for these criteria, which are outlined in Section 2.0. Based on these definitions, the dose acceptance criteria were established for various receptors for routine reactor operations (Section 3.2), design basis accidents (Section 3.3), and beyond design basis accidents (Section 3.4). Comparisons of multiple national and international dose limits are provided in these sections. Lastly, Section 4.0 outlines the reactor safety design criteria contained in the draft DA PAM and their associated bases.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

The multifaceted role of c-di-AMP signaling in the regulation of Porphyromonas gingivalis lipopolysaccharide structure and function

This study unveils the intricate functional association between cyclic di-3’,5’-adenylic acid (c-di-AMP) signaling, cellular bioenergetics, and the regulation of lipopolysaccharide (LPS) profile in Porphyromonas gingivalis, a Gram-negative obligate anaerobe considered as a keystone pathogen involved in the pathogenesis of chronic periodontitis. Previous research has identified variations in P. gingivalis LPS profile as a major virulence factor, yet the underlying mechanism of its modulation has remained elusive. We employed a comprehensive methodological approach, combining two mutants exhibiting varying levels of c-di-AMP compared to the wild type, alongside an optimized analytical methodology that combines conventional mass spectrometry techniques with a novel approach known as FLAT n . We demonstrate that c-di-AMP acts as a metabolic nexus, connecting bioenergetic status to nuanced shifts in fatty acid and glycosyl profiles within P. gingivalis LPS. Notably, the predicted regulator gene cdaR, serving as a potent regulator of c-di-AMP synthesis, was found essential for producing N-acetylgalactosamine and an unidentified glycolipid class associated with the LPS profile. The multifaceted roles of c-di-AMP in bacterial physiology are underscored, emphasizing its significance in orchestrating adaptive responses to stimuli. Furthermore, our findings illuminate the significance of LPS variations and c-di-AMP signaling in determining the biological activities and immunostimulatory potential of P. gingivalis LPS, promoting a pathoadaptive strategy. The study expands the understanding of c-di-AMP pathways in Gram-negative species, laying a foundation for future investigations into the mechanisms governing variations in LPS structure at the molecular level and their implications for host-pathogen interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The Role of Sugar Signaling in Regulating Plant Fatty Acid Synthesis

Photosynthates such as glucose, sucrose, and some of their derivatives play dual roles as metabolic intermediates and signaling molecules that influence plant cell metabolism. Such sugars provide substrates for de novo fatty acid (FA) biosynthesis. However, compared with the well-defined examples of sugar signaling in starch and anthocyanin synthesis, until recently relatively little was known about the role of signaling in regulating FA and lipid biosynthesis. Recent research progress shows that trehalose 6-phosphate and 2-oxoglutarate (2-OG) play direct signaling roles in the regulation of FA biosynthesis by modulating transcription factor stability and enzymatic activities involved in FA biosynthesis. Specifically, mechanistic links between sucrose non-fermenting−1–related protein kinase 1 (SnRK1)–mediated trehalose 6-phosphate (T6P) sensing and its regulation by phosphorylation of WRI1 stability, diacylglycerol acyltransferase 1 (DGAT1) enzyme activity, and of 2-OG–mediated relief of inhibition of acetyl-CoA carboxylase (ACCase) activity by protein PII are exemplified in detail in this review.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in Pogostemon cablin . In this study, the full-length cDNA of the FPP synthase gene from P. cablin ( PcFPPS ) was cloned and characterized. The expressions of PcFPPS are different among different tissues (highly in P. cablin flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal FPPS deletion mutation in yeast CC25. Transient overexpression of PcFPPS in P. cablin leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of PcFPPS in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of PcFPPS can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of PcWRKY44 in P. cablin upregulated the expression levels of PcFPPS and patchoulol synthase gene ( PcPTS ), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the PcFPPS and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.

Wang, Xiaobing↗

DOE OSTI2023

Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development

Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum’s resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm 2 ) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11 ) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1 ) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.

09 BIOMASS FUELS↗

DOE OSTI2023

An approach to learn regulation to maximize growth and entropy production rates in metabolism

Elucidating cell regulation remains a challenging task due to the complexity of metabolism and the difficulty of experimental measurements. Here we present a method for prediction of cell regulation to maximize cell growth rate while maintaining the solvent capacity of the cell. Prediction is formulated as an optimization problem using a thermodynamic framework that can leverage experimental data. We develop a formulation and variable initialization procedure that allows for computing solutions of the optimization with an interior point method. The approach is applied to photoheterotrophic growth of Rhodospirilium rubrum using ethanol as a carbon source, which has applications to biosynthesis of ethylene production. Growth is captured as the rate of synthesis of amino acids into proteins, and synthesis of nucleotide triphoshaptes into RNA and DNA. The method predicts regulation that produces a high rate of protein and RNA synthesis while DNA synthesis is reduced close to zero in agreement with production of DNA being turned off for much of the cell cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

GmMPK6 Positively Regulates Salt Tolerance through Induction of GmRbohI1 in Soybean

Salt stress is a critical environmental stress that impairs plant growth and development, especially in crop productivity; therefore, understanding the salt response in plants is the basis for their development of salt tolerance. Under salinity, soybean mitogen-activated protein kinase 6 (GmMPK6) is activated and positively regulates reactive oxygen species (ROS) generation. However, it is not yet elucidated how GmMPK6 regulates ROS generation and its role in salt tolerance. Here, we show that GmMPK6, solely activated in NaCl treatment, and gene expression of GmRbohI1 was not only reduced by MPK inhibitor SB202190 in NaCl treatment, but also increased in a GMKK1-expressing protoplast. Furthermore, SB202190 and the NADPH-oxidase inhibitor, diphenyleneiodonium chloride, increased susceptibility to salt stress. The expression of GmRD19A was induced by NaCl treatment, but this expression was compromised by SB202190. Consequently, we revealed that GmMPK6 induces ROS generation through the transcriptional regulation of GmRbohI1 and increases salt tolerance in soybean.

59 BASIC BIOLOGICAL SCIENCES↗