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DOE OSTI2025

RNAi and genome editing of sugarcane: Progress and prospects

SUMMARY Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan‐genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or Agrobacterium ‐mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture‐free technologies, such as spray‐induced gene silencing, virus‐induced gene silencing, or virus‐induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.

Brant, Eleanor [Agronomy Department, Plant Molecul↗

DOE OSTI2022

Mass transfer coefficients, kL, and air-CO2 ingassing rates in 3.4 m2 and 1-acre raceway ponds.

The US DOE 2016 Billion Ton Update (Langholtz 2016) projected that CO2 in flue-gas from power plants or similar sources would limit U.S. algal biofuel potential to under 5 billion gallons gasoline equivalent (gge) per year, due to lack of sufficient land, water and other requirements near such flue gas sources. 2nd generation carbon capture technologies are proposed to overcome this constraint (Davis 2017), and could expand this resource potential nearly 10-fold, assuming CO2 costs near the future, 2025 DOE NETL, goal of $40/metric ton CO2. An alternative pathway is the direct uptake of air CO2 into the algal ponds through an increase in the air-CO2 transfer rate resulting from the reaction of CO2 with hydroxide ions. However, such a ‘chemical enhancement’ in mass transfer depends on a high pH in the culture, and, by extension, the ability of microalgae to maintain high rates of carbon assimilation under such conditions. Abiotic experiments characterized the air-CO2 mass-transfer rate in 1-acre and 3.4 m2 raceway ponds as a function of pH, with rates approaching 10 g C/m2-day at pH 12 in the brackish water tested, equivalent to a biomass productivity potential of near 20 g AFDW/m2-day (@ 0.47 g C/g AFDW). The mass transfer rate was found to be nearly independent of the mass-transfer coefficient, indicating that at turbulence levels achievable in typical raceway ponds, the system is reaction rate, rather than diffusion limited. In biotic trials with an unknown green microalga, biomass productivity in ponds receiving CO2 from only direct surface air-CO2 exchange averaged 5 +/- 0.5 g AFDW/m2-day in August - September central California conditions, about half-that of experimental controls fertilized with supplemental CO2. pH in the air-only treatment reached a maximum of 10.5, supporting a model predicted air-CO2 ingassing rate between 2-3 g C/m2-day, consistent with the observed biomass carbon assimilation rate. Results suggest that unique alkaliphilic strains are required if reliant on direct in-pond air-CO2 transfer for algal inorganic carbon supply, and that reaching an economically viable biomass productivity will require strains that thrive at pH 11 and above.

09 BIOMASS FUELS↗

DOE OSTI2024

ATCCfinder - Download and Search the ATCC Genome Portal

Much strain-specific sequence data exists in research conducted before the deployment of large sequencing repositories, making it challenging to identify and validate the identity of strains used in these studies through bioinformatics and phenotyping. The American Type Culture Collection (ATCC) is an organization that sells a wide variety of microbes with strain-level taxonomy classification and associated sequenced reference genomes. Currently, ATCC does not provide a method for searching for sequence similarity between a query sequence and their database of reference genomes. Here I propose the software ATCCfinder, which utilizes ATCC application interface software (API) to generate query-able databases from ATCC Genome resources.

Koehler, Samuel↗

DOE OSTI2025

Evaluating the combined effects of light and water availability on the early growth and physiology of Tamarindus indica : Implications for restoration

Abstract Premise The tamarind tree (Tamarindus indica) is a species of significant cultural, economic, and ecological value, with a pantropical distribution. However, the tamarind is experiencing a decline in wild populations in its native range, but the reasons for its decline remain unknown. Methods We examined the critical early life‐history stages for tamarind establishment to understand how varying levels of light and water availability and watering frequency affect its regeneration. Through three greenhouse experiments, we assessed the impact of these resources on the germination, survival, growth, and physiological responses of tamarind seedlings and saplings. Results Water availability was critical for seed germination, but not light levels or pre‐germination treatments. Light was the primary limiting factor for seedling growth. Tamarinds in high light availability grew taller, had more biomass and larger diameter, but the effect of light was modulated by water availability, indicating that there was an interaction between both resources. Water and light affected specific leaf area and leaf dry matter content but not biomass allocation, root‐to‐shoot ratio, or stomatal conductance. Water availability influenced sapling growth, but watering frequency did not, indicating a resilience of tamarind saplings to changes in rainfall periodicity but a sensitivity to total rainfall amounts. Conclusions Our study underscores the importance of considering both light and water availability in tamarind restoration efforts and contribute to understanding plant responses and trade‐offs under different levels of critical resources. Our findings will inform conservation strategies to support the regeneration and long‐term survival ofTamarindus indicain its native habitats.

Plant Sciences↗

DOE OSTI2023

Talent Acquisition in Scientific and Engineering Disciplines: A Case Study of National Laboratory (TASED) [Thesis]

Identifying the hindrances to performing effective talent acquisition within the science, technology, engineering, and mathematics field is an important topic for technical hiring managers. Top candidates have multiple options during highly competitive market conditions requiring managers to look for unique solutions which diverge from competition. Prior to this study there has been very little research considering national laboratory research and development challenges from a technical hiring manager’s talent acquisition perspective. Utilizing a unique combination of national laboratory multi-organization survey, pilot study, Human Resource (HR) tracking data and trust based business strategy to enhance partnering this research finds hiring managers can leverage out of the box techniques to improve internal processes while developing industry support to target highly qualified individuals. This methodology could be utilized by technical hiring managers across federal national laboratory enterprise to effectively capture next generation staff and leadership talent who align with their organization professionally as well as social culture.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Sustaining On-going Risk Communication at the Riverton, Wyoming, Processing Site - 20310

An environmental risk assessment report has been completed to provide an updated assessment regarding current site conditions for the Riverton, Wyoming, Processing site. Argonne National Laboratory conducted the assessment in collaboration with the U.S Department of Energy (DOE) Office of Legacy Management (LM) and the Northern Arapaho Natural Resources Office (NANRO). The data quality objectives process conducted confirmed that data from plants growing on the Riverton site would be useful and would address an outstanding concern. Data available from site soil, groundwater, and surface water were also used in the assessment in conjunction with the new plant data. A plant survey was then conducted in 2018 to identify the plants at the Riverton site with known traditional Native American cultural uses for sampling and analysis. Laboratory analysis was conducted on the plant samples for the contaminants of concern. Samples were collected from plants growing on the groundwater plume area of the site, and the same was done for eight other areas not affected by the groundwater plume but still within the institutional control boundary. These eight areas served as reference areas for this study. This human health and ecological assessment update provide the quantitative risk information that was qualitatively addressed in a 1995 Risk Assessment Report on plants, livestock, and surface water exposures at the Riverton site [1]. The conditions at the Riverton site are protective of human health and the environment given the results of the update, in combination with past completed remedial action and ongoing monitoring activities and IC implementation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Comparative Study of Enhanced Geothermal System Supply Curves Across CONUS from Two Temperature Models Using the Renewable Energy Potential Model (reV)

Enhanced geothermal systems (EGS) have had recent breakthroughs within the geothermal sector. These breakthroughs are reflected in the National Renewable Energy Laboratory (NREL) 2024 Annual Technology Baseline and will result in updated EGS supply curves (i.e., the available resource capacity relative to cost). Our research uses NREL's Renewable Energy Potential (reV) model to compare EGS supply curves across the conterminous United States (CONUS) for two different temperature models: the Stanford temperature model (STM) and the Southern Methodist University temperature model (SMU). The reV model provides the levelized cost of energy (LCOE) at a consistent resolution across CONUS, taking into consideration transmission costs and constraints as well as technical exclusions pertaining to sensitive cultural, ecological, or infrastructure locations. In addition to a countrywide analysis of both models, we also conducted a regional analysis of Texas. We observed the STM had, on average, lower temperatures across different depths, resulting in slightly higher mean and median LCOEs as compared to the SMU temperature model at the same depths. In the regional analysis for Texas, however, when we compared only the common points between the two temperature models, the STM had lower median and mean LCOEs compared to SMU due to higher temperatures at depths greater than 5 km.

enhanced geothermal systems↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Resilience Lessons From the Southeast United States Woody Pellet Supply Chain Response to the COVID-19 Pandemic†

The Coronavirus Disease 2019 (COVID-19) instigated a pandemic that impacted economies, employment, and shipping worldwide. This paper reviews how one international supply chain performed and identifies lessons that may be helpful to improve future resilience. Economic and employment data through November 2020 are used to review the effects of COVID-19 on operations of the bioenergy supply chain in the southeastern United States (SE United States) that utilizes wood fiber to fabricate pellets. Conditions associated with the production of pellets in the SE United States changed with the outbreak of COVID-19. Federal and state government programs and classification of workers in this sector as “essential” during the pandemic helped maintain the woody pellet supply chain and other industries during a period of general shut down in 2020. The availability of personal protective equipment, long-term supply contracts, and established safety cultures are among the factors that enhance supply chain resilience while limited availability of skilled workers, inadequate stakeholder engagement, and dependence on external policies are among factors that reduce resilience. The analysis concludes with recommendations for the SE pellet supply chain, and other biomass supply chains, to improve their resilience to future disturbances. When best practices are implemented, SE United States biomass offers opportunities to contribute to post-pandemic economic recovery while incentivizing better forest resource management.

09 BIOMASS FUELS↗

DOE OSTI2022

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2021: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals of supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high-performance computing (HPC) needs; contributing to the community to build the next generation HPC workforce, and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2021 saw continued excellence in research supported by the OLCF’s leadership-class computing resources, including Summit (the nation’s most powerful supercomputer), the global scratch file system Alpine, the Scalable Protected Infrastructure (SPI), the Exploratory Visualization Environment for Research in Science and Technology (EVEREST), and the archival mass-storage resource High-Performance Storage System (HPSS). While maintaining access and exceptional user support for Summit, the OLCF continued to make progress on the installation and deployment of Frontier, which will be the nation’s first exascale system when it comes online at the start of CY 2023. Users have already begun running and optimizing scientific codes on Crusher, the OLCF test and development system equipped with Frontier’s architecture. Throughout the year, the OLCF maintained a strong culture of operational excellence, including risk management, workplace safety, and cybersecurity. The OLCF’s rigorous risk management strategy anticipated and mitigated risks, and at this time there are no high-priority operational risks. Similarly, ORNL and the OLCF were committed to operating under the US Department of Energy’s (DOE’s) safety regulations that ensure a safe workplace. Technical staff tracked and monitored existing threats and vulnerabilities within the OLCF while continually developing tools and practices to enhance operations without increasing the facility’s risk. CY 2021 was filled with outstanding results and accomplishments, including a very high rating from users on overall satisfaction for the eighth consecutive year; a tremendous number of node hours delivered to 1,671 researchers on Summit; and the successful delivery of the allocation split of roughly 60%, 20%, and 20% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director’s Discretionary (DD) programs, respectively (Section 2). COVID-19 research remained a focus in 2021, and the ALCC and DD programs allocated over 1 million Summit hours to the COVID-19 High Performance Computing Consortium. These accomplishments, coupled with the high utilization rates (i.e., overall and capability usage), represent the fulfillment of the promise of leadership class machines: efficient facilitation of leadership-class computational applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

A Novel Platform for Algal Biomass Production Using Cellulosic Mixotrophy (CeMix) (Final Technical Report)

This novel project, branded CeMIX for cellulosic mixotrophy, targets solutions for several technological barriers limiting the deployment of algae cultivation in sunny, arid regions (specifically the southwest United States). Opening up the region for algae cultivation could increase DOE’s resource assessments and biofuel potential for the U.S. Mixotrophic metabolism in support of liquid fuel production is completely dependent on the availability of waste organic carbon in order to avoid diversion of food resources for fuel production. The use of cellulosic sugar hydrolysate (CSH) produced via the NREL process provided a standardized carbon source for study of the underlying biochemistry and metabolic adjustments to mixotrophy. Mixotrophic metabolism uses both photosynthetic CO 2 fixation and sugar oxidation to improve biomass productivity and harvest yield. The project was high-risk, high-reward in the sense that adding organic carbon to algal cultivation is an invitation for rapid-growth, heterotrophic contaminants to overtake the culture and consume mineral nutrients needed for algal growth. To help evade this outcome the project focused on acidophilic red algae that require low pH conditions with 40-48°C optimal temperature profiles that define them as low-range thermophiles. This is the only project in the BETO portfolio to utilize extreme conditions of low pH and high operating temperatures to control pathogens and competitors in mass culture. The project yielded five major outcomes. 1) Harvest densities of 5-10 g ash-free dry weight are easily achieved, providing a 10-fold reduction in water required and dewatering demand. 2) Catabolic repression of photosynthesis in G. sulphuraria is conditionally repressed by low oxygen. 3) Mixotrophic growth on cellulosic hydrolysate consumes all C6 and C5 sugars concomitant with increases in floridean starch with little change in lipid content. Protein content can be manipulated between 35 and 54 wt% by varying the C:N molar ratio from 10:1 to 20:1, respectively. 4) Mixotrophic cultures with up to 50 mM total sugar are remarkably stable at pH 2.5 and daily average reactor temperatures of 40°C. 5) Capital costs for glass tubular photobioreactors are prohibitive for liquid fuel production using a hydrothermal liquefaction processing pathway. The economic outlook for covered raceway ponds is better with a project minimum fuel selling price at $3.32 dm 3 GE -1 .

09 BIOMASS FUELS↗

DOE OSTI2020

IMPLEMENTING CYBERSECURITY INTO AN EXISTING NATIONAL NUCLEAR NON-PROLIFERATION PROGRAMME – A CASE STUDY

Cyber threat profiling and risk mitigation is critical to any nuclear state organization and should be considered as part of any comprehensive nuclear security programme. Defining and evaluating the impact of the cyber threat to mission can be challenging. An existing national nuclear non-proliferation organization undertook an effort to incorporate computer security activities into its programme to address cyber risk. One of the primary goals of this endeavour was to develop a set of prioritised recommendations for organizational follow-through. The organization dedicated subject matter expert resources in the form of a cyber task force to support this goal. Opportunities were identified where computer security could be built into each programme including office-level strategies and tools. Of course, no new identified threat vector is easily considered and incorporated into existing programmes without impact. There are many obstacles to be overcome. Technically literate subject matter experts are difficult to find, management has comparatively less experience applying computer security into its programmes, and trying to change the culture to consider computer security risk at policy and programmatic levels takes time and management attention. As an outcome of this process, a roadmap for program integration was developed, including the establishment of a cyber support team. This paper will discuss the challenges and successes associated with establishing such a team.

Cyber Security, Nuclear, Non-proliferation↗

DOE OSTI2022

Controlled-Environment Agriculture and the Geography of Food, Energy and Water Resilience in the United States

USDA guidelines call for an increase in fruit and vegetable consumption in U.S. households to promote healthier diets. Access to fresh fruits and vegetables are especially lacking in food deserts and food swamps (characterized by a prevalence of food that is highly processed and lacking in nutritional value). Adoption of the recommended healthy diet, which more than doubles the consumption of fruits and vegetables, would have a wide variety of health benefits and would reduce the land footprint of U.S diets. However, adopting a healthy diet would increase phosphate and nitrogen impacts associated with fertilizers and pesticides and would significantly increase freshwater consumption and energy use because of the resource intensity of field cultivation of fruits and vegetables. The majority of these crops are grown in just a few states, including California and Arizona, which are increasingly impacted by climate change. In addition, rural communities are rapidly becoming food deserts, while food produced in these areas is transported long distances to market. In recent years, highly intensified controlled environment (CE) agricultural systems, (i.e., vertical farming) have been developed to provide fresh food closer to consumers. Fruits and vegetables, many of which are amenable to CE culture, occupy a uniquely impactful segment of the food supply-chain, including their value in improving nutrition for vulnerable communities. The objective of this work is to elucidate the location dependency of the energy and water impacts of adoption of distributed CE farming for an important portion of the food system.

controlled environment agriculture↗

DOE OSTI2022

Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions

Abstract The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.

09 BIOMASS FUELS↗

DOE OSTI2023

Development of a Geothermal Module in reV: Quantifying the Geothermal Potential while Accounting for the Geospatial Intersection of the Grid Infrastructure and Land Use Characteristics

The Renewable Energy Potential (reV) model is a geospatial platform for estimating technical potential and developing renewable energy supply curves, initially developed for wind and solar technologies. The model evaluates deployment constraints, considering land use, environmental, and cultural factors, and estimates the distance to existing grid features to connect future plants (Maclaurin et al., 2021). A pressing deficiency in the reV model, however, is representation of geothermal electricity generation technologies. To address this gap, we developed a novel geothermal generation module for reV that allows for representation and analysis at the same level of detail as other renewable technologies. This paper describes our process for evaluating data sources for the modeling, and presents five preliminary reV geothermal results. More specifically, we present two sets of resource data that represent upper and lower bounds for geothermal potential. We then present several sensitivity runs using the upper bound resource data; the results are encouraging that levelized cost of electricity (LCOE) can be reduced by optimizing the location and estimated capacity of the spatially diverse geothermal resource while considering the distance to existing grid infrastructure. Our preliminary supply curves and levelized cost of electricity (LCOE) results should be considered with care due to the highly uncertainty in geothermal resource potential data. We present median LCOE values for the conterminous U.S. for five scenarios: four hydrothermal (3.5km depth) and one EGS (4.5km depth). The capital and operating costs for each respective technology are modeled. We also compare results using two different resource data sources.

exclusions↗

DOE OSTI2024

Development of a Geothermal Module in reV: Quantifying the Geothermal Potential While Accounting for the Geospatial Intersection of the Grid Infrastructure and Land Use Characteristics: Preprint

exclusions↗

DOE OSTI2023

Renewable Energy Potential Model: Geothermal Supply Curves

The Renewable Energy Potential (reV) model is a geospatial platform for estimating technical potential and developing renewable energy supply curves, initially developed for wind and solar technologies. The model evaluates deployment constraints, considering land use, environmental, and cultural factors, and estimates the distance to existing grid features to connect future plants (Maclaurin et al., 2021). A pressing deficiency in the reV model, however, is representation of geothermal electricity generation technologies. To address this gap, we developed a novel geothermal generation module for reV that allows for representation and analysis at the same level of detail as other renewable technologies. The included paper describes our process for evaluating data sources for the modeling, and presents five preliminary reV geothermal results. More specifically, we present two sets of resource data that represent upper and lower bounds for geothermal potential. We then present several sensitivity runs using the upper bound resource data; the results are encouraging that levelized cost of electricity (LCOE) can be reduced by optimizing the location and estimated capacity of the spatially diverse geothermal resource while considering the distance to existing grid infrastructure. Our preliminary supply curves and levelized cost of electricity (LCOE) results provided here should be considered with care due to the high uncertainty in geothermal resource potential data. We present median LCOE values for the conterminous U.S. for three scenarios: two hydrothermal (3.5km depth, USGS heat flow & SMU temperatures respectively) and one EGS (4.5km depth, SMU temperatures). The capital and operating costs for each respective technology are modeled. We also compare results using two different resource data sources.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).

59 BASIC BIOLOGICAL SCIENCES↗