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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗
DOE OSTI2025

Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

ABSTRACT To combat the increasing levels of carbon dioxide (CO 2 ) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO 2 concentrations. A high-pH, high-alkalinity culture was designed for CO 2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO 3 ) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO 2 , respectively. Our data showed that 0.02 M NaHCO 3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO 3 formation conditions. At the 1 L scale, we reached 1.52 g L −1 biomass after 12 days and an extra 9.3% CO 2 was captured in the form of CaCO 3 precipitates. At the 500 L pilot scale, an extra 60% CO 2 was captured (Day 40) with a maximum CO 2 capture rate of 63.2 g m −2 day −1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO 3 for long-term CO 2 storage. IMPORTANCE Capturing carbon dioxide (CO 2 ) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO 2 through their natural photosynthetic pathways and are additionally able to convert CO 2 into a stable, recalcitrant form as calcium carbonate (CaCO 3 ). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO 2 captured as CaCO 3 at the 1 L scale and an extra 60% CO 2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO 2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO 3.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment. IMPORTANCE Rhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distinctiveness of genes contributing to growth of Pseudomonas syringae in diverse host plant species

A variety of traits are necessary for bacterial colonization of the interior of plant hosts, including well-studied virulence effectors as well as other phenotypes contributing to bacterial growth and survival within the apoplast. High-throughput methods such as transposon sequencing (TnSeq) are powerful tools to identify such genes in bacterial pathogens. However, there is little information as to the distinctiveness of traits required for bacterial colonization of different hosts. Here, we utilize randomly barcoded TnSeq (RB-TnSeq) to identify the genes that contribute to the ability of Pseudomonas syringae strain B728a to grow within common bean (Phaseolus vulgaris), lima bean (Phaseolus lunatus), and pepper (Capsicum annuum); species representing two different plant families. The magnitude of contribution of most genes to apoplastic fitness in each of the plant hosts was similar. However, 50 genes significantly differed in their fitness contributions to growth within these species. These genes encoded proteins in various functional categories including polysaccharide synthesis and transport, amino acid metabolism and transport, cofactor metabolism, and phytotoxin synthesis and transport. Six genes that encoded unannotated, hypothetical proteins also contributed differentially to growth in these hosts. The genetic repertoire of a relatively promiscuous pathogen such as P. syringae may thus be shaped, at least in part, by the conditional contribution of some fitness determinants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Global Soil Virus (GSV) Atlas

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset from 2,953 soils that comprises 616,935 uncultivated virus genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents the most extensive characterization of soil viral diversity to date and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Graham, Emily B↗
DOE OSTI2023

Transcription factors to improve resistance to environmental stress in plants

Plants, plant cells, and seeds are described herein that grow well and are resistant to environmental stresses such as drought and insects, where the plants have one or more mutations that reduce or eliminate the interaction of MYC transcription factors with the JAZ proteins. The plants can have an additional mutation that reduces or eliminates the function of the PHYB gene, and/or a heterologous PIF4 transgene or PIF4 expression cassette to improve the growth of the myc mutant plants. Methods of making and using such plants, plant cells, and seeds are also described.

Howe, Gregg A.↗
DOE OSTI2023

Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors

Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovery of genes that positively affect biomass and stress associated traits in poplar

Woody biomass serves as a renewable resource for various industries, including pulp and paper production, construction, biofuels, and electricity generation. However, the molecular mechanisms behind biomass traits are poorly understood, which significantly curtails the speed and efficiency of their improvement. We used activation tagging to discover genes that can positively affect tree biomass-associated traits. We generated and screened under greenhouse conditions a population of 2,700 independent activation tagging lines. A total of 761 lines, which had significantly and positively affected at least one biomass-associated trait, were discovered. The tag was positioned in the genome for forty lines which were affected in multiple traits and activation of proximal genes validated for a subset. For two lines we fully recapitulated the phenotype of the original lines through overexpression. Moreover, the overexpression led to more pronounced and additional improvements, not observed in the original lines. Importantly, the overexpression of a Fasciclin-like gene (PtaFLA10) and a Patatin-like gene (PtaPAT) was found to substantially improve biomass, with a 40% increase in dry-stem weight, and enhance drought tolerance, respectively. Additionally, PtaPAT overexpression increased cellulose content, which is crucial for biofuel production. Our work shows that the activation tagging approach applied even on a non-genome saturation scale in a poplar tree can be successfully used for the discovery of genes positively modify biomass productivity. Such dominant forward genetics approaches can aid in biotechnological manipulation of woody biomass traits and help unravel the functions and mechanisms of individual genes, gene families, and regulatory modules.

Plant Sciences↗
DOE OSTI2023

A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes

SUMMARY Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum , a drought and heat‐tolerant C4 species, requires a vast, large‐scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large‐scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)‐induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis ‐regulatory elements. A comparison of the distribution of mutations in the large‐scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS‐induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5′ UTR, gene body, and 3′‐UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the K a / K s value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB ( https://www.depts.ttu.edu/igcast/sorbmutdb.php ) and SorghumBase ( https://sorghumbase.org/ ). This current large‐scale sequence‐indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Emerging Role of Exosomal Long Non-coding RNAs in Spaceflight-Associated Risks in Astronauts

During spaceflight, astronauts are exposed to multiple unique environmental factors, particularly microgravity and ionizing radiation, that can cause a range of harmful health consequences. Over the past decades, increasing evidence demonstrates that the space environment can induce changes in gene expression and RNA processing. Long non-coding RNA (lncRNA) represent an emerging area of focus in molecular biology as they modulate chromatin structure and function, the transcription of neighboring genes, and affect RNA splicing, stability, and translation. They have been implicated in cancer development and associated with diverse cardiovascular conditions and associated risk factors. However, their role on astronauts’ health after spaceflight remains poorly understood. In this perspective article, we provide new insights into the potential role of exosomal lncRNA after spaceflight. We analyzed the transcriptional profile of exosomes isolated from peripheral blood plasma of three astronauts who flew on various Shuttle missions between 1998–2001 by RNA-sequencing. Computational analysis of the transcriptome of these exosomes identified 27 differentially expressed lncRNAs with a Log 2 fold change, with molecular, cellular, and clinical implications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MultiPhATE2: code for functional annotation and comparison of phage genomes

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Virioplankton assemblages from challenger deep, the deepest place in the oceans

Hadal ocean biosphere, that is, the deepest part of the world’s oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing↗
DOE OSTI2023

Prolonging genetic circuit stability through adaptive evolution of overlapping genes

Abstract The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or ‘entangled’ entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for >130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more ‘benign’ mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient

Abstract Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗