Role of vitamin K2 in the organization and function of Staphylococcus aureua membranes

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus’ metabolic response to its environment.

Environmental perturbations (e.g., antibiotic stress, nutrient starvation, oxidative stress) induce systems-level perturbations of bacterial cells that vary depending on the growth environment. The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditions. Genome-scale models (GEMs) of metabolism represent a knowledge-based platform for the contextualization and integration of multi-omic measurements and can serve to offer valuable insights of system-level responses. This work provides the most up to date reconstruction effort integrating recent advances in the knowledge of S. aureus molecular biology with previous annotations resulting in the first quantitatively and qualitatively validated S. aureus GEM. GEM guided predictions obtained from model analysis provided insights into the effects of medium composition on metabolic flux distribution and gene essentiality. The model can also serve as a platform to guide network reconstructions for other Staphylococci as well as direct hypothesis generation following the integration of omics data sets, including transcriptomics, proteomics, metabolomics, and multi-strain genomic data.

Aminonaphthoquinone induces oxidative stress inStaphylococcus aureus

The biological activity of 5-amino-8-hydroxy-1,4-naphthoquinone (ANQ) on Staphylococcus aureus was investigated in comparison with the unsubstituted 1,4-naphthoquinone (NQ). Complete inhibition of microbial growth was observed with ANQ and NQ at 50 and 10 µg/mL, respectively. The antibacterial effect of naphthoquinones decreased in the presence of sodium ascorbate, but the superoxide scavenger 4,5-dihydroxy-1,3-benzene-disulfonic acid (Tiron) was able to protect S. aureus only from the harmful effect of ANQ. Naphthoquinones blocked oxygen uptake and induced cyanide-insensitive oxygen consumption. When combining rotenone or salicylhydroxamic acid with ANQ or NQ, a slight decrease in respiratory activity was observed. Assays in the presence of naphthoquinones induced an increase of lipid peroxidation in S. aureus, as determined by thiobarbituric acid reactive substances. These results showed that 1,4-naphthoquinones effectively act as electron acceptors and induce an increase in reactive oxygen species that are toxic to S. aureus cells.

Phenotype microarray profiling of Staphylococcus aureus menD and hemB mutants with the small-colony-variant phenotype

Standard biochemical tests have revealed that hemin and menadione auxotrophic Staphylococcus aureus small-colony variants (SCVs) exhibit multiple phenotypic changes. To provide a more complete analysis of the SCV phenotype, two genetically defined mutants with a stable SCV phenotype were comprehensively tested. These mutants, generated via mutations in menD or hemB that yielded menadione and hemin auxotrophs, were subjected to phenotype microarray (PM) analysis of over 1,500 phenotypes (including utilization of different carbon, nitrogen, phosphate, and sulfur sources; growth stimulation or inhibition by amino acids and other nutrients, osmolytes, and metabolic inhibitors; and susceptibility to antibiotics). Compared to parent strain COL, the hemB mutant was defective in utilization of a variety of carbon sources, including Krebs cycle intermediates and compounds that ultimately generate ATP via electron transport. The phenotype of the menD mutant was similar to that of the hemB mutant, but the defects in carbon metabolism were more pronounced than those seen with the hemB mutant. In both mutant strains, hexose phosphates and other carbohydrates that provide ATP in the absence of electron transport stimulated growth. Other phenotypes of SCV mutants, such as hypersensitivity to sodium selenite, sodium tellurite, and sodium nitrite, were also uncovered by the PM analysis. Key results of the PM analysis were confirmed in independent growth studies and by using Etest strips for susceptibility testing. PM technology is a new and efficient technology for assessing cellular phenotypes in S. aureus.

Fluorometric Determination of Adenosine Nucleotide Derivatives as Measures of the Microfouling, Detrital, and Sedimentary Microbial Biomass and Physiological Status

Adenosine, adenine, cyclic adenosine monophosphate (AMP), AMP, nicotinamide adenine dinucleotide, adenosine diphosphate, and adenosine triphosphate (ATP) were recovered quantitatively from aqueous portions of lipid extracts of microfouling, detrital, and sedimentary microbial communities. These could be detected quantitatively in the picomolar range by forming their 1-N 6 -etheno derivatives and analyzing by high-pressure liquid chromatography with fluorescence detection. Lipid extraction and subsequent analysis allowed the simultaneous measurement of the microbial community structure, total microbial biomass with the quantitative recovery of the adenine-containing cellular components, which were protected from enzymatic destruction. This extraction and fluorescent derivatization method showed equivalency with the luciferin-luciferase method for bacterial ATP measurements. Quick-freezing samples in the field with dry ice-acetone preserved the ATP and energy charge (a ratio of adenosine nucleotides) for analysis at remote laboratories. The metabolic lability of ATP in estuarine detrital and microfouling communities, as well as bacterial monocultures of constant biomass, showed ATP to be a precarious measure of biomass under some conditions. Combinations of adenosine and adenine nucleotides gave better correlations with microbial biomass measured as extractable lipid phosphate in the detrital and microfouling microbial communities than did ATP alone. Stresses such as anoxia or filtration are reflected in the rapid accumulation of intracellular adenosine and the excretion of adenosine and AMP into the surrounding milieu. Increases in AMP and adenosine may prove to be more sensitive indicators of metabolic status than the energy charge.

Muramic acid as a measure of microbial biomass in estuarine and marine samples

Muramic acid, a component of the muramyl peptide found only in the cell walls of bacteria and blue-green algae, furnishes a measure of detrital or sedimentary procaryotic biomass. A reproducible assay involving acid hydrolysis, preparative thin-layer chromatographic purification, and colorimetric analysis of lactate released from muramic acid by alkaline hydrolysis is described. Comparison of semitropical estuarine detritus, estuarine muds, and sediments from anaerobic Black Sea cores showed muramic acid levels of 100 to 700 microng/g (dry weight), 34 microng/g, and 1.5 to 14.9 microng/g, respectively. Enzymatic assays of lactate from muramic acid gave results 10- to 20-fold higher. Radioactive pulse-labeling studies showed that [14C]acetate is rapidly incorporated into muramic acid by the detrital microflora. Subsequent loss of 14C, accompanied by nearly constant levels of total muramic acid, indicated active metabolism in procaryotic cell walls.

Nitrate reductase activity in heme-deficient mutants of Staphylococcus aureus

Mutants H-14 and H-18 of Staphylococcus aureus require hemin for growth on glycerol and other nonfermentable substrates. H-14 also responds to delta-aminolevulinate. Heme-deficient cells grown in the presence of nitrate do not have lactate-nitrate reductase activity but gain this activity when incubated with hemin in buffer and glucose. Lactate-nitrate reductase activity is also restored to the membrane fraction from such cells by incubation with hemin and dithiothreitol; addition of adenosine 5'-triphosphate has no effect upon the restoration. Cells grown with nitrate in the absence of hemin have two to five times more reduced benzyl viologen-nitrate reductase activity than do those grown with hemin. The activity increases throughout the growth period in the absence of hemin, but with hemin present enzyme formation ceases before the end of growth. There was no evidence of enzyme destruction. The distribution of nitrate reductase activity between membrane and cytoplasm was similar in cells grown with and without hemin; 70 to 90% was in the cytoplasm. It is concluded that heme-deficient staphylococci form apo-cytochrome b, which readily combines in vitro with its prosthetic group to restore normal function. The avaliability of the heme prosthetic group influences the formation of nitrate reductase.

Isolation and description of a menaquinone mutant from Bacillus licheniformis

A menaquinone mutant (SG1) of Bacillus licheniformis has been isolated by selecting for colonies that are resistant to low levels of kanamycin (1.5 mug/ml) but sensitive to the same concentration of kanamycin in the presence of shikimate (25 mug/ml). The wild type (IU1) contained 0.38 +/- 0.02 nmol of menaquinone-7 (MK-7) per mg (dry weight) of cells when grown +/- shikimate, whereas SG1 had less than 0.01 nmol of MK-7 per mg (dry weight) of cells when grown in the presence of shikimate. SG1 had a generation time of 85 min, as compared to 24 min for IU1 grown +/- shikimate. SG1 doubled with a generation time of 28 min when grown in the presence of shikimate. IU1 consumed O2 at various rates depending on the stage of growth. A triphasic O2 consumption curve with maxima at mid-exponential phase, the transition from exponential to stationary phase, and early stationary phase was found for IU1 +/- shikimate and SG1 + shikimate. SG1 grown without shikimate consumed O2 at a low level (10 to 20% of IU1). Normal respiration could be restored to SG1 8.5 min after shikimate addition, whereas normal growth was not restored until 40 min after shikimate addition. Electron microscopic studies of SG1 and IU1 have indicated a morphological alteration in the mutant. SG1 is a dwarf cell as compared to IU1, when grown without shikimate. However, SG1 grown with shikimate became morphologically indistinguishable from IU1.

A study of the action of the cationic proteins from rabbit polymorphonuclear leucocytes on the staphylococcal cell membrane

The inhibitory effect of cationic proteins from rabbit polymorphonuclear leucocytes on the oxidation of NADH by staphylococcal membrane preparations is described. Both cyanide and haematin are shown to interfere with the inhibitory process, by different mechanisms. Other authors have shown that glucose repressed staphylococci are diverted to a fermentative mode of metabolism. These findings were confirmed by demonstrating that membrane preparations from staphylococci grown in the presence of glucose have diminished cytochrome and succinic dehydrogenase levels. From a comparison of the effect of the cationic proteins on NADH oxidation in membrane preparations from organisms grown normally and under conditions of glucose repression, and from knowledge of the different susceptibility to the cationic proteins of the two types of organisms, it is suggested that the cationic proteins exert their bactericidal action on staphylococci following an energy dependent binding to the membrane.