Search NASA⌕ Search

SEARCH · Search NASA

Results for “Stringent response”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the ΔprmA mutant in Escherichia coli revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the ΔprmA mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Triggering the stringent response enhances synthetic methanol utilization in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, i.e. the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here in this paper, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. By activating the stringent/stress response via ppGpp overproduction, or DksA and RpoS overexpression, we demonstrate improved biosynthesis of proteinogenic amino acids via endogenous upregulation of amino acid synthesis pathway genes. Thus, we were able to achieve biosynthesis of several limiting amino acids from methanol-derived carbon, in contrast to the control methylotrophic E. coli strain. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via stringent/stress response activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2022

Expression and structure of the Chlamydia trachomatis DksA ortholog

Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksA Ct ) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksA Ct in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksA Ct is similar to the DksA ortholog of Escherichia coli (DksA Ec ), DksA Ct did not functionally complement DksA Ec . Transcription of dksA Ct is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksA Ct and the correlation between dksA Ct and nrdR expression is consistent with a role for DksA Ct in the C. trachomatis developmental cycle.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1979

On the Performance of the Martin Digital Filter for High- and Low-pass Applications

A nonrecursive numerical filter is described in which the weighting sequence is optimized by minimizing the excursion from the ideal rectangular filter in a least squares sense over the entire domain of normalized frequency. Additional corrections to the weights in order to reduce overshoot oscillations (Gibbs phenomenon) and to insure unity gain at zero frequency for the low pass filter are incorporated. The filter is characterized by a zero phase shift for all frequencies (due to a symmetric weighting sequence), a finite memory and stability, and it may readily be transformed to a high pass filter. Equations for the filter weights and the frequency response function are presented, and applications to high and low pass filtering are examined. A discussion of optimization of high pass filter parameters for a rather stringent response requirement is given in an application to the removal of aircraft low frequency oscillations superimposed on remotely sensed ocean surface profiles. Several frequency response functions are displayed, both in normalized frequency space and in period space. A comparison of the performance of the Martin filter with some other commonly used low pass digital filters is provided in an application to oceanographic data.

Mcclain, C. R.↗
NASA NTRS2024

Substrate Matters: Ionic Silver Alters Lettuce Growth, Nutrient Uptake, and Root Microbiome in a Hydroponics System

Ionic silver (Ag+) is being investigated as a residual biocide for use in NASA spacecraft potable water systems on future crewed missions. This water will be used to irrigate future spaceflight crop production systems. We have evaluated the impact of three concentrations (31 ppb, 125 ppb, and 500 ppb) of ionic silver biocide solutions on lettuce in an arcillite (calcinated clay particle substrate) and hydroponic (substrate-less) growth setup after 28 days. Lettuce plant growth was reduced in the hydroponic samples treated with 31 ppb silver and severely stunted for samples treated at 125 ppb and 500 ppb silver. No growth defects were observed in arcillite-grown lettuce. Silver was detectable in the hydroponic-grown lettuce leaves at each concentration but was not detected in the arcillite-grown lettuce leaves. Specifically, when 125 ppb silver water was applied to a hydroponics tray, Ag+ was detected at an average amount of 7 μg/g (dry weight) in lettuce leaves. The increase in Ag+ corresponded with a decrease in several essential elements in the lettuce tissue (Ca, K, P, S). In the arcillite growth setup, silver did not impact the plant root zone microbiome in terms of alpha diversity and relative abundance between treatments and control. However, with increasing silver concentration, the alpha diversity increased in lettuce root samples and in the water from the hydroponics tray samples. The genera in the hydroponic root and water samples were similar across the silver concentrations but displayed different relative abundances. This suggests that ionic silver was acting as a selective pressure for the microbes that colonize the hydroponic water. The surviving microbes likely utilized exudates from the stunted plant roots as a carbon source. Analysis of the root-associated microbiomes in response to silver showed enrichment of metagenomic pathways associated with alternate carbon source utilization, fatty-acid synthesis, and the ppGpp (guanosine 3′-diphosphate 5′-diphosphate) stringent response global regulatory system that operates under conditions of environmental stress. Nutrient solutions containing Ag+ in concentrations greater than 31 ppb in hydroponic systems lacking cation-exchange capacity can severely impact crop production due to stunting of plant growth.

lettuce↗
DOE OSTI2025

CRISPRt data studying the physiological role of an Acinetobacter-specific sigma factor

Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS."

Peters, Jason M. [GLBRC - University of Wisconsin]↗
DOE OSTI2025

Physiological roles of an Acinetobacter -specific σ factor

ABSTRACT The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF “SigAb”; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, “SabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, “ aabA ” and “ aabB ,” have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb , aabA , and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii . IMPORTANCE Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter -specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Bacon, Emily E. (ORCID:0000000180907689)↗
DOE OSTI2025

Bacteria export alarmone synthetases that produce (p)ppApp and (p)ppGpp

Guanosine penta- and tetraphosphate [(p)ppGpp] and their adenosine analogs [(p)ppApp] are bacterial second messengers known as alarmones. Members of the RelA-SpoT homolog (RSH) family synthesize (p)ppGpp to mediate the stringent response during nutrient starvation, whereas (p)ppApp synthetases have been identified as bactericidal toxins in diverse contexts including type VI secretion systems, toxin-antitoxin modules, and phages. Although alarmone synthesis has traditionally been viewed as a cytoplasmic process, early studies in Streptomyces suggested the existence of secreted alarmone synthetases. Here, we identify SaEAS, an exported alarmone synthetase (EAS) from Streptomyces albidoflavus, as the long-mysterious source of extracellular alarmone synthetase activity in Streptomyces. SaEAS produces both (p)ppGpp and (p)ppApp at rates exceeding 100,000 molecules per minute and has kinetic properties adapted to low substrate environments. A broader bioinformatic survey reveals ~600 EASs linked to a range of specialized bacterial secretion systems. Characterization of two additional EASs, VpEAS from Vibrio parahaemolyticus and AaEAS from Amycolatopsis azurea, shows that both produce (p)ppGpp exclusively and inhibit bacterial growth when localized to the cytoplasm. These findings challenge the longstanding view of (p)ppGpp as strictly pro-survival and unveil a diverse family of secreted RSH enzymes with potential roles in interbacterial antagonism and environmental signaling.

Ahmad, Shehryar↗
DOE OSTI2024

Vaccination induces broadly neutralizing antibody precursors to HIV gp41

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evaluation of the Performance and Exhaust Emissions of a 4 Cylinder CI Engine Operating With Dimethyl Ether (DME) and Propane Blends

In response to stringent emissions regulations and the need for higher efficiency engines, the utilization of DME and propane fuel blends in compression ignition (CI) engines has gained interest in the automotive industry. In this study, a range of DME-propane blends are explored in a CI combustion strategy at high injection pressures. A GT-Power model of a 2.2 L Hyundai CI engine was developed to facilitate evaluation of the impacts of variations of DME and propane blends at a light and medium engine speed-torque-load operating condition; specifically at 1500 rpm, 50 Nm and 2.84 bar brake mean effective pressure (BMEP); and 2000 rpm, 150 Nm, 8.53 bar BMEP speed-torque-load combination. Here, the GT-Power model was validated using Computational Fluid Dynamics (CFD) simulations. The results indicate that high diesel-like efficiencies can be achieved with a 100% DME mass substitution and up to 50% propane-DME blends could be implemented without a significant penalty on engine performance indicators. Significant brake specific nitrogen oxides (BSNOx) reductions were also observed along with reductions in carbon dioxide (CO2) and soot when leveraging these fuel blends.

computational fluid dynamics↗
NASA NTRS1988

Analysis of FDDI synchronous traffic delays

The Fiber Distributed Data Interface (FDDI) high-speed token-ring protocol provides support for two classes of service: synchronous, to support applications which require deterministic access to the channel, and asynchronous, to support applications which do not have such stringent response-time requirements. The purpose of this paper is to determine how to set ring parameters to support synchronous traffic most efficiently. Both theoretical results and results obtained from a simulation study are presented.

Johnson, Marjory J.↗
NASA NTRS1992

Control integration concept for hypersonic cruise-turn maneuvers

Piloting difficulties associated with conducting aircraft maneuvers in hypersonic flight are caused in part by the nonintuitive nature of the aircraft response and the stringent constraints anticipated on allowable angle of attack and dynamic pressure variations. An approach is documented that provides precise, coordinated maneuver control during excursions from a hypersonic cruise flight path and the necessary flight condition constraints. The approach is to achieve specified guidance commands by resolving altitude and cross range errors into a load factor and bank angle command by using a coordinate transformation that acts as an interface between outer and inner loop flight controls. This interface, referred to as a 'resolver', applies constraints on angle of attack and dynamic pressure perturbations while prioritizing altitude regulation over cross range. An unpiloted test simulation, in which the resolver was used to drive inner loop flight controls, produced time histories of responses to guidance commands and atmospheric disturbances at Mach numbers of 6, 10, 15, and 20. Angle of attack and throttle perturbation constraints, combined with high speed flight effects and the desire to maintain constant dynamic pressure, significantly impact the maneuver envelope for a hypersonic vehicle.

Raney, David L.↗
DOE OSTI2020

Tailoring a Global Iron Regulon to a Uropathogen

Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O 2 -dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O 2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Far-ultraviolet observations of the supernova remnant N49 using the Hopkins Ultraviolet Telescope

The Hopkins Ultraviolet Telescope has been used to obtain the first sub-Lyman-alpha spectrum of an extragalactic SNR, N49, in the LMC. Emission from O VI 1032, 1038 has been detected in this spectral region. The measured fluxes of C IV, semiforbidden O IV, and O VI and the upper limit on N V provide stringent limits on the shocks responsible for the bulk of the O VI production. O VI cannot originate in the shocks with velocities of 140 km/s or less because the postshock temperature is not high enough. The nonradiative main blast wave cannot account for the brightness of the observed O VI emission. The majority of the O VI must originate in an optically faint system of shocks with velocities of 190-270 km/s and preshock densities of 20-40 cu cm. The emission from such high-velocity shocks is dominated by O VI.

Vancura, Olaf↗
NASA NTRS1978

Evaluation of radiation interference in the Voyager Sun Sensor's cadmium sulfide detector

The simulation of radiation interference effects and the results of a radiation interference test on two Voyager Sun Sensor prototype detector assemblies are reported. The derivation of test levels and requirements are discussed and show that cobalt 60 gamma radiation is an effective and practical simulator of the ionization dose rate effects induced by high-energy electron flux incident on the spacecraft at a rate of 3.7 x 10 to the 8th e/sq cm-sec (10 rad(Si)/s) during closest approach to Jupiter. The test results provide information that is used to confirm an analytic correlation, and to predict satisfactory performance of a spacecraft sun sensing device having stringent angular resolution requirements. The measured detector response shows that at dose rates incident on the detector elements of 2 rad(Si)/sec, which is four times that expected during Jupiter encounter, the radiation-induced angle error is almost an order of magnitude less than that allowed by the acceptance criteria.

Clarke, T. C.↗
NASA NTRS1994

Performance results of cooperating expert systems in a distributed real-time monitoring system

There are numerous definitions for real-time systems, the most stringent of which involve guaranteeing correct system response within a domain-dependent or situationally defined period of time. For applications such as diagnosis, in which the time required to produce a solution can be non-deterministic, this requirement poses a unique set of challenges in dynamic modification of solution strategy that conforms with maximum possible latencies. However, another definition of real time is relevant in the case of monitoring systems where failure to supply a response in the proper (and often infinitesimal) amount of time allowed does not make the solution less useful (or, in the extreme example of a monitoring system responsible for detecting and deflecting enemy missiles, completely irrelevant). This more casual definition involves responding to data at the same rate at which it is produced, and is more appropriate for monitoring applications with softer real-time constraints, such as interplanetary exploration, which results in massive quantities of data transmitted at the speed of light for a number of hours before it even reaches the monitoring system. The latter definition of real time has been applied to the MARVEL system for automated monitoring and diagnosis of spacecraft telemetry. An early version of this system has been in continuous operational use since it was first deployed in 1989 for the Voyager encounter with Neptune. This system remained under incremental development until 1991 and has been under routine maintenance in operations since then, while continuing to serve as an artificial intelligence (AI) testbed in the laboratory. The system architecture has been designed to facilitate concurrent and cooperative processing by multiple diagnostic expert systems in a hierarchical organization. The diagnostic modules adhere to concepts of data-driven reasoning, constrained but complete nonoverlapping domains, metaknowledge of global consequences of anomalous data, hierarchical reporting of problems that extend beyond a single domain, and shared responsibility for problems that overlap domains. The system enables efficient diagnosis of complex system failures in real-time environments with high data volumes and moderate failure rates, as indicated by extensive performance measurements.

Schwuttke, U. M.↗