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

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improvement of eukaryotic protein predictions from soil metagenomes

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface

General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis , an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Detecting operons in bacterial genomes via visual representation learning

Contiguous genes in prokaryotes are often arranged into operons. Detecting operons plays a critical role in inferring gene functionality and regulatory networks. Human experts annotate operons by visually inspecting gene neighborhoods across pileups of related genomes. These visual representations capture the inter-genic distance, strand direction, gene size, functional relatedness, and gene neighborhood conservation, which are the most prominent operon features mentioned in the literature. By studying these features, an expert can then decide whether a genomic region is part of an operon. We propose a deep learning based method named Operon Hunter that uses visual representations of genomic fragments to make operon predictions. Using transfer learning and data augmentation techniques facilitates leveraging the powerful neural networks trained on image datasets by re-training them on a more limited dataset of extensively validated operons. Our method outperforms the previously reported state-of-the-art tools, especially when it comes to predicting full operons and their boundaries accurately. Furthermore, our approach makes it possible to visually identify the features influencing the network’s decisions to be subsequently cross-checked by human experts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms

Abstract Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation

Biological nitrogen fixation (BNF) is the reduction of N 2 into NH 3 in a group of prokaryotes by an extremely O 2 -sensitive protein complex called nitrogenase. Transfer of the BNF pathway directly into plants, rather than by association with microorganisms, could generate crops that are less dependent on synthetic nitrogen fertilizers and increase agricultural productivity and sustainability. In the laboratory, nitrogenase activity is commonly determined by measuring ethylene produced from the nitrogenase-dependent reduction of acetylene (ARA) using a gas chromatograph. The ARA is not well suited for analysis of large sample sets nor easily adapted to automated robotic determination of nitrogenase activities. Here, we show that a reduced sulfonated viologen derivative (S 2 V red ) assay can replace the ARA for simultaneous analysis of isolated nitrogenase proteins using a microplate reader. We used the S 2 V red to screen a library of NifH nitrogenase components targeted to mitochondria in yeast. Two NifH proteins presented properties of great interest for engineering of nitrogen fixation in plants, namely NifM independency, to reduce the number of genes to be transferred to the eukaryotic host; and O 2 resistance, to expand the half-life of NifH iron-sulfur cluster in a eukaryotic cell. This study established that NifH from Dehalococcoides ethenogenes did not require NifM for solubility, [Fe-S] cluster occupancy or functionality, and that NifH from Geobacter sulfurreducens was more resistant to O 2 exposure than the other NifH proteins tested. It demonstrates that nitrogenase components with specific biochemical properties such as a wider range of O 2 tolerance exist in Nature, and that their identification should be an area of focus for the engineering of nitrogen-fixing crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tropical lacustrine sediment microbial community response to an extreme El Niño event

Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015–2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi

Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Characterization of a widespread sugar phosphate-processing bacterial microcompartment

Many prokaryotes form Bacterial Microcompartments (BMCs) that encapsulate segments of specialized metabolic pathways to enhance catalysis. The various functions of metabolosomes, catabolic BMCs, are dictated by the signature enzyme that processes initial substrates of the confined pathway. The components and native functions of several metabolosomes have been experimentally characterized; however one of the most prevalent across all bacteria has yet to be studied. Sugar Phosphate Utilizing (SPU) BMC loci encode enzymes predicted to be involved in sugar phosphate metabolism. The SPU genetic loci are found in organisms occupying habitats ranging from soils to hot springs, highlighting the ubiquity of the SPU BMC. We bioinformatically characterized seven SPU subtypes, all which contain an enzyme unique to SPU BMCs, a deoxyribose 5-phosphate aldolase (DERA). Here, we define the fundamental characteristics of SPU BMCs and have expressed, purified, and characterized a set of SPU core enzymes. These include a protein-protein complex formed between a SPU BMC DERA and a predicted ribose 5-phosphate isomerase. Further, we show that the SPU BMC DERA is catalytically active and propose that it acts as the universal signature enzyme for the SPU BMC, with implications for fundamental understanding and biotechnological applications of SPU BMCs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Abstract Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Vik, Dean (ORCID:000000027546899X)↗
DOE OSTI2020

Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins

Abstract Copper (Cu) is an essential, but toxic, micronutrient for living organisms and cells have developed sophisticated response mechanisms towards both the lack and the excess of Cu in their environments. In this study, we achieved a global view of Cu-responsive changes in the prokaryotic model organism Rhodobacter capsulatus using label-free quantitative differential proteomics. Semi-aerobically grown cells under heterotrophic conditions in minimal medium (∼0.3 μM Cu) were compared with cells supplemented with either 5 μM Cu or with 5 mM of the Cu-chelator bathocuproine sulfonate. Mass spectrometry based bottom-up proteomics of unfractionated cell lysates identified 2430 of the 3632 putative proteins encoded by the genome, producing a robust proteome dataset for R. capsulatus. Use of biological and technical replicates for each growth condition yielded high reproducibility and reliable quantification for 1926 of the identified proteins. Comparison of cells grown under Cu-excess or Cu-depleted conditions to those grown under minimal Cu-sufficient conditions revealed that 75 proteins exhibited statistically significant (p < 0.05) abundance changes, ranging from 2- to 300-fold. A subset of the highly Cu-responsive proteins was orthogonally probed using molecular genetics, validating that several of them were indeed involved in cellular Cu homeostasis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized -- but only from archaeal methanogens that are anaerobic, O 2 -sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O 2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O 2 -sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A structural framework for unidirectional transport by a bacterial ABC exporter

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis of active virus–host interactions between individual populations, we focused on the critical biogeochemical process of methane (CH 4 ) oxidation and followed the transfer of carbon from hosts to their associated viruses in situ. Analysis of 13 C-enriched metagenomic DNA demonstrated that CH 4 -derived carbon is transferred into viral biomass via both primary and secondary utilizers of CH 4 and suggests viral predation is an important mechanism for releasing CH 4 -derived organic carbon into the soil matrix.

Lee, Sungeun↗