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28 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase

Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg 2+ -decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg 2+ ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of γ-phosphate from ATP to MVAPP, followed by the production of IPP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids

Per- and polyfluoroalkyl substances (PFASs), also known as forever chemicals, are global contaminants, but understanding of microbiota–PFAS interactions is limited. Here we show that bacteria covalently incorporate n:3 fluorotelomer carboxylates (FTCAs) into phosphatidylethanolamine and phosphatidylglycerol, two prominent components of bacterial lipid bilayers. Lipidomics of the soil bacterium Pseudomonas sp. strain 273 grown in the presence of 7:3 FTCA or 8:3 FTCA estimated that 7–12% of the bacterium’s glycerophospholipid pool contains the respective polyfluoroacyl chains. This covalent incorporation was observed in five other axenic bacterial cultures tested, including other Pseudomonas species, Escherichia coli and Enterococcus faecalis, albeit with lower incorporation percentages. Incorporation occurred over a broad concentration range, and n:3 FTCAs with varying chain length were covalently incorporated into membranes. Biotransformation of polyfluoroalkyl substances (also known as precursors) results in n:3 FTCA intermediates, which bacteria can covalently incorporate into their glycerophospholipid pools. We conclude that bacteria can form fluoromembranes when exposed to precursors and are a potential PFAS sink.

Xie, Yongchao [University of Tennessee, Knoxville ↗
DOE OSTI2021

Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

Abstract Background Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study’s aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds. Methods Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison. Results All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (–2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%–49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness. Conclusions The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.

Tedim, Ana P.↗
DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Probiotic Lactobacillus acidophilus Strain INMIA 9602 Er 317/402 Administration Reduces the Numbers of Candida albicans and Abundance of Enterobacteria in the Gut Microbiota of Familial Mediterranean Fever Patients

Intestinal microorganisms play a crucial role in health and disease. The disruption of host–microbiota homeostasis has been reported to occur not only during disease development but also as a result of medication. Familial Mediterranean fever (FMF) is an inflammatory genetic disease characterized by elevated systemic reactivity against the commensal gut microbiota and high levels of Candida albicans in the gut. This study’s major objective was to investigate the effects of commercial probiotic Narine on the relative abundance of gut bacteria (specifically, enterobacteria, lactobacilli, Staphylococcus aureus, and enterococci) of C. albicans carrier and non-carrier FMF patients in remission. Our main finding indicates that the probiotic reduces numbers of C. albicans and abundance of enterobacteria in male and female patients of C. albicans carriers and non-carriers. It has pivotal effect on Enterococcus faecalis: increase in male non-carriers and decrease in female ones regardless of C. albicans status. No effect was seen for Lactobacillus and S. aureus. Our data suggest that M694V/V726A pyrin inflammasome mutations leading to FMF disease may contribute to gender-specific differences in microbial community structure in FMF patients. The study’s secondary objective was to elucidate the gender-specific differences in the gut’s microbial community of FMF patients. The tendency was detected for higher counts of enterobacteria in female FMF subjects. However, the small number of patients of these groups preclude from conclusive statements, pointing at the need for additional investigations with appropriate for statistical analysis groups of subjects involved in the study.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Preflight and postflight microbiological results from 25 space shuttle crews

Clinical-microbiological investigations are an important aspect of the crew health stabilization program. To ensure that space crews have neither active nor latent infections, clinical specimens, including throat and nasal swabs and urine samples, are collected at 10 days (L-10) and 2days (L-2) before launch, and immediately after landing (L+0). All samples are examined for the presence of bacteria and fungi. In addition, fecal samples are collected at L-10 and examined for bacteria, fungi and parasites. This paper describes clinical-microbiological findings from 144 astronauts participating in 25 Space Shuttle missions spanning Space Transportation System (STS)-26 to STS-50. The spectrum of microbiological findings from the specimens included 25 bacterial and 11 fungal species. Among the bacteria isolated most frequently were Staphylococcus aureus, Enterobacter aerogenes, Enterococcus faecalis, Escherichia coli, Proteus mirabilis and Streptococcus agalactiae. Candida albicans was the most frequently isolated fungal pathogen.

Pierson, Duane L.↗
NASA NTRS2012

Nonhazardous Urine Pretreatment Method

A method combines solid phase acidification with two non-toxic biocides to prevent ammonia volatilization and microbial proliferation. The safe, non-oxidizing biocide combination consists of a quaternary amine and a food preservative. This combination has exhibited excellent stabilization of both acidified and unacidified urine. During pretreatment tests, composite urine collected from donors was challenged with a microorganism known to proliferate in urine, and then was processed using the nonhazardous urine pre-treatment method. The challenge microorganisms included Escherichia coli, a common gram-negative bacteria; Enterococcus faecalis, a ureolytic gram-positive bacteria; Candida albicans, a yeast commonly found in urine; and Aspergillus niger, a problematic mold that resists urine pre-treatment. Urine processed in this manner remained microbially stable for over 57 days. Such effective urine stabilization was achieved using non-toxic, non-oxidizing biocides at higher pH (3.6 to 5.8) than previous methods in use or projected for use aboard the International Space Station (ISS). ISS urine pretreatment methods employ strong oxidants including ozone and hexavalent chromium (Cr(VI)), a carcinogenic material, under very acidic conditions (pH = 1.8 to 2.4). The method described here offers a much more benign chemical environment than previous pretreatment methods, and will lower equivalent system mass (ESM) by reducing containment volume and mass, system complexity, and crew time needed to handle pre-treatment chemicals. The biocides, being non-oxidizing, minimize the potential for chemical reactions with urine constituents to produce volatile, airborne contaminants such as cyanogen chloride. Additionally, the biocides are active under significantly less acidic conditions than those used in the current system, thereby reducing the degree of required acidification. A simple flow-through solid phase acidification (SPA) bed is employed to overcome the natural buffering capacity of urine, and to lower the pH to levels that fix ammoniacal nitrogen in the non-volatile and highly water soluble NH4 + form. Citric acid, a highly soluble, solid tricarboxylic acid essential to cellular metabolism, and typically used as a food preservative, has also been shown to efficiently acidify urine in conjunction with non-oxidizing biocides to provide effective stabilization with respect to both microbial growth and ammonia volatilization.

Akse, James R.↗
DOE OSTI2018

Possible involvement of Enterococcus infection in the pathogenesis of chronic pancreatitis and cancer

Highlights: • We found some bacteria in pancreatic juice and tissue of pancreatic cancer. • We identified E. faecalis infection in pancreas with chronic pancreatitis. • Serum antibody titers against E. faecalis are increased in pancreatic diseases. • Addition of E. faecalis antigens increased expression of inflammatory cytokine. • E. faecalis might be a novel target for preventing chronic pancreatic diseases. (Aim) Bacterial infection underlies the pathogenesis of many human diseases, including acute and chronic inflammation. Here, we investigated a possible role for bacterial infection in the progression of chronic pancreatitis. (Materials and Methods) Pancreatic juice was obtained from patients with pancreatic cancer (n = 20) or duodenal cancer/bile duct cancer (n = 16) and subjected to PCR using universal primers for the bacterial 16S ribosomal RNA gene. Bacterial species were identified by PCR using bile samples from four pancreatic cancer patients. PCR products were subcloned into T-vectors, and the sequences were then analyzed. Immunohistochemical and serologic analyses for Enterococcus faecalis infection were performed on a large cohort of healthy volunteers and patients with chronic pancreatitis or pancreatic cancer and on mice with caerulein-induced chronic pancreatitis. The effect of E. faecalis antigens on cytokine secretion by pancreatic cancer cells was also investigated. (Results) We found that 29 of 36 pancreatic juice samples were positive for bacterial DNA. Enterococcus and Enterobacter species were detected primarily in bile, which is thought to be a pathway for bacterial infection of the pancreas. Enterococcus faecalis was also detected in pancreatic tissue from chronic pancreatitis and pancreatic cancer patients; antibodies to E. faecalis capsular polysaccharide were elevated in serum from chronic pancreatitis patients. Enterococcus-specific antibodies and pancreatic tissue–associated E. faecalis were detected in mice with caerulein-induced chronic pancreatitis. Addition of Enterococcus lipoteichoic acid and heat-killed bacteria induced expression of pro-fibrotic cytokines by pancreatic cancer cells in vitro. (Conclusion) Infection with E. faecalis may be involved in chronic pancreatitis progression, ultimately leading to development of pancreatic cancer.

60 APPLIED LIFE SCIENCES↗