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PubMed1993

Characterization of the RNase P RNA of Sulfolobus acidocaldarius.

RNase P is the ribonucleoprotein enzyme that cleaves precursor sequences from the 5' ends of pre-tRNAs. In Bacteria, the RNA subunit is the catalytic moiety. Eucaryal and archaeal RNase P activities copurify with RNAs, which have not been shown to be catalytic. We report here the analysis of the RNase P RNA from the thermoacidophilic archaeon Sulfolobus acidocaldarius. The holoenzyme was highly purified, and extracted RNA was used to identify the RNase P RNA gene. The nucleotide sequence of the gene was determined, and a secondary structure is proposed. The RNA was not observed to be catalytic by itself, but it nevertheless is similar in sequence and structure to bacterial RNase P RNA. The marked similarity of the RNase P RNA from S. acidocaldarius and that from Haloferax volcanii, the other known archael RNase P RNA, supports the coherence of Archaea as a phylogenetic domain.

Archaea↗
PubMed1996

Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium.

A genetic system was developed to investigate the supercoil structure of bacterial chromosomes. New res-carrying transposons were derived from MudI1734 (MudJr1 and MudJr2) and Tn10 (Tn10dGn). The MudJr1 and MudJr2 elements each have a res site in opposite orientation so that when paired with a Tn10dGn element in the same chromosome, one MudJr res site will be ordered as a direct repeat. Deletion formation was studied in a nonessential region (approximately 100 kb) that extends from the his operon through the cob operon. Strains with a MudJr insertion in the cobT gene at the 5' end of the cob operon plus a Tn10dGn insertion positioned either clockwise or counterclockwise from cobT were exposed to a burst of RES protein. Following a pulse of resolvase expression, deletion formation was monitored by scoring the loss of the Lac+ phenotype or by loss of tetracycline resistance. In exponentially growing populations, deletion products appeared quickly in some cells (in 10 min) but also occurred more than an hour after RES induction. The frequency of deletion (y) diminished with increasing distance (x) between res sites. Results from 15 deletion intervals fit the exponential equation y = 120 . 10(-0.02x). We found that res sites can be plectonemically interwound over long distances ( > 100 kb) and that barriers to supercoil diffusion are placed stochastically within the 43- to 45-min region of the chromosome.

Cell Division↗
PubMed1965

Structure and composition of the Bacillus anthracis capsule.

Avakyan, A. A. (Academy of Medical Sciences, Moscow, USSR), L. N. Katz, K. N. Levina, and I. B. Pavlova. Structure and composition of the Bacillus anthracis capsule. J. Bacteriol. 90:1082-1095. 1965.-Observations by various methods of light microscopy (phase contrast, dark-field, and fluorescence) revealed the complex structure of the Bacillus anthracis capsule, which changes regularly during the growth cycle of the culture. Special cytological methods of staining the capsule made it possible to study its fine structure, which is not revealed by negative staining with India ink. For example, the capsule shows a membranelike outline, fine transverse lines, and interruptions and transverse septa traversing the entire capsule. By using cytochemical methods, it was found that the capsule has a stratified structure and that the various layers of the capsule differ as to the value of the isoelectric point, metachromatic ability, sensitivity to various enzymes, and, consequently, chemical composition. It was thus shown that the membranelike outline of the capsule consists of peptides and neutral mucopolysaccharides. The middle part of the capsule consists of a complex of substances of both polysaccharide and protein nature, and the inner part consists of acid mucopolysaccharides. Observation of the capsular forms of B. anthracis by means of an electron microscope revealed differences in the osmiophilia and submicroscopic structure of the membranelike outline and the middle and inner parts of the capsule. Immunochemical studies conducted by the fluorescent-antibody method revealed localization of antigens in different parts of the capsule, and made it possible to differentiate the capsular antigens according to their serum-staining ability and according of their relations to enzymes, i.e., their chemical composition. This paper concerns the possibility of studying the fine structure of bacterial capsules in fixed preparations, and the differences and similarities of the antigens of the capsule and cell wall of B. anthracis and of the related species, B. megaterium.

Bacillus anthracis↗
PubMed2004

Pig slurry reduces the survival of Ralstonia solanacearum biovar 2 in soil.

The effect of added pig slurry and solarization on the survival of Ralstonia solanacearum biovar 2 strain 1609 in soil was analysed in soil microcosms and field plots. In addition, the invasion of potato plants by R. solanacearum and the development of disease symptoms were determined, as measures of induced disease suppressiveness. In untreated soil, R. solanacearum showed slow population declines in both microcosms and the field from, initially, 10(6-)10(7) to 10(3)-10(4) CFU.(g dry soil)(-1) in about 9 weeks. The suppressiveness assays of these untreated soils after this period revealed that most of the plants that were used developed wilting symptoms and (or) contained the pathogen in their lower stem parts, as shown by immunofluorescence colony staining and PCR. The addition of pig slurry resulted in a significantly lower population size of R. solanacearum as well as reduced numbers of infected and (or) diseased plants in the soil suppressiveness tests. On the other hand, solarization of soil also decreased R. solanacearum survival but did not enhance soil suppressiveness as measured by development of disease symptoms and (or) plant invasion after 9 weeks. Combined soil solarization and pig slurry addition showed an additive effect of both treatments. Healthy-looking plants, primarily from soils treated with pig slurry and solarization, incidentally revealed the latent presence of R. solanacearum in the lower stem parts. The mechanism behind the enhanced population declines and disease suppressiveness induced by pig slurry is unclear but shifts in community profiles were clearly discernible by PCR - denaturing gradient gel electrophoresis 9 weeks after pig slurry addition in the field experiment, indicating induced changes in the bacterial community structure.

Animals↗
PubMed1990

Bacterial phospholipid hydrolysis enhances the destruction of Escherichia coli ingested by rabbit neutrophils. Role of cellular and extracellular phospholipases.

Escherichia coli ingested by PMN are promptly growth arrested but undergo limited destruction. We have studied bacterial phospholipid hydrolysis as a possible limiting factor in the disassembly of ingested E. coli, comparing the fates, during phagocytosis by rabbit peritoneal exudate PMN, of three isogenic strains, differing in their content of the pldA gene encoding the principal E. coli phospholipase A (PLA), i.e., pldA-, pldA+, pldA (the latter strain bearing the pldA gene in a multicopy plasmid resulting in a 20-fold increase in PLA content). Ingestion and growth inhibition (greater than 99% within 15 min) were the same for the three strains, but phospholipid degradation differed according to bacterial PLA content: pldA up to 60%, pldA+ up to 30%, and pldA- up to 20%. Since the pldA- strain has no activatable PLA, phospholipid degradation in this strain demonstrates the action of a PMN PLA. Added PLA2-rich ascitic fluid (AF) or purified AF PLA2 increased the rate and extent of degradation of the pldA- strain, provided the enzyme was added before ingestion was complete. 125I-AF-PLA2 binds to both E. coli and PMN and thus can enter the vacuole during phagocytosis. Although up to 50-fold more AF-PLA2 than the PLA2 content of the PMN could be loaded into the PMN in this way, degradation of pldA- E. coli did not exceed 30%. Increased phospholipid degradation had no effect on the degradation of bacterial macromolecules. In contrast, bacterial disassembly manifest as structural disorganization, release of bacterial protein derived material, and inhibition of protein synthesis were markedly enhanced when greater than 50% of prelabelled bacterial phospholipids were degraded. These findings reveal a link between envelope phospholipid degradation and overall bacterial destruction, suggesting therefore that factors limiting PLA action limit the destruction of E. coli ingested by PMN.

Animals↗
PubMed2003

Degradation of flavonoid aglycones by rabbit, rat and human fecal flora.

The degradation of thirteen flavonoid aglycones-wogonin, diosmetin, hesperetin, baicalein, morin, genistein, daidzein, quercetin, naringenin, luteolin, kaempferol, apigenin and neophellamuretin-were investigated in rabbit, rat and human fecal flora suspensions as well as in artificial intestinal juice, using high performance liquid chromatography. Separation were performed with a Cosmosil 5C(18)-AR II column by isocratic and gradient elution with 0.1% (v/v) phosphoric acid-acetonitrile as a mobile phase, and detected at 254 nm. The flow rate was 1.0 ml/min. 5,7-Dimethoxycoumarin was used as the internal standard. The result indicated that all flavonoid aglycones except baicalein, diosmetin and quercetin were quite stable in artificial intestinal juice, whereas all were degraded in rabbit, rat and human feces suspension. In rabbit feces, wogonin, diosmetin and hesperetin were less degraded, whereas neophellamuretin, apigenin, kaempferol, luteolin, and naringenin were the most extensively degraded. In rat feces, wogonin and diosmetin were least degraded, whereas kaempferol, quercetin, genistein, luteolin, naringenin and neophellamuretin were extensively degraded. As in human feces, wogonin, daidzein and diosmetin were less degraded, whereas morin, genistein, baicalein, and quercetin were extensively degraded. In conclusion, wogonin and diosmetin were among the less degraded ones for all three feces tested. The presence of a methoxy group on the A or B ring of the flavonoid seems to protect the structure from bacterial degradation.

Animals↗
PubMed1995

Cytochrome P450 proteins and potential utilization in biodegradation.

The cytochrome P450 enzymes are major catalysts involved in the oxidations of xenobiotic chemicals in microorganisms as well as higher animals and plants. Because of their functional roles, they offer potential in biodegradation technology. A number of microbial P450s have already been characterized and offer advantages in terms of their high catalytic rates and facile expression in microorganisms. One approach to extending the catalytic selectivity to more compounds in the environment is rational design. In three cases, the three-dimensional structures of bacterial cytochrome P450 enzymes are available and can be further understood through studies with molecular dynamics. Many mammalian cytochrome P450 enzymes have been studied extensively and have potential for biodegradation because of their broad catalytic selectivities (e.g., P450 2E1). Several advances have been made in the heterologous expression of these proteins in microorganisms. Improvements under development include electron transfer from flavodoxin and the use of cytochrome P450:NADPH-cytochrome P450 reductase fusion proteins. Random mutagenesis offers the potential of improving the catalytic activities of some of these proteins. Future challenges include the use of cytochrome P450 expression vectors in microorganisms capable of thriving in the environment; recent success in expression of vectors in Salmonella genotoxicity tester strains may be encouraging in this regard.

Bacteria↗
PubMed2025

Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants↗
PubMed2001

The rational design of vaccine adjuvants for mucosal and neonatal immunization.

There is an urgent requirement for neonatal vaccines that induce effective and long-lasting immune responses at the mucosal surfaces of the gut and respiratory tract. The delay in their development has been due in part to a lack of understanding of the mucosal and neonatal immune systems. This work reviews recent advances in the understanding of the cells and molecules that mediate immunity, describing the importance of different T helper populations in determining the success of vaccination strategies. These advances have allowed the rational design of novel vaccine adjuvants and delivery systems that can selectively induce immunity at different anatomical sites mediated by distinct T cell populations. Five functional classes of adjuvant are described. These exploit mechanisms which a) create an antigen depot, b) preserve antigen conformation, c) direct antigen to specific immune cells, d) induce mucosal responses and e) induce cytotoxic T cell responses. Comparisons are made between the chemical structures of bacterial toxins and non-toxic derivatives that retain adjuvanticity. The concept of DNA immunization is introduced and the advantages and disadvantages of this novel approach are discussed. The specific problems relating to neonatal immunization are explored with particular reference to the functional immaturity of the neonatal immune system and interference by maternal antibody. Finally, recent work suggesting that there is no intrinsic barrier to designing effective neonatal vaccines deliverable by the mucosal route is discussed.

Adjuvants, Immunologic↗
PubMed2000

Combined effects of hydrostatic pressure, temperature, and the addition of allyl isothiocyanate on inactivation of Escherichia coli.

Combined effects of hydrostatic pressure, temperature, and the addition of allyl isothiocyanate (AIT) on the inactivation of Escherichia coli, including type O157, were investigated. Inactivation to undetectable levels by hydrostatic pressure alone requires 400 to 600 MPa. E. coli growth was delayed with increasing of applied pressure and the AIT concentration added subsequently. The antibacterial effects of AIT vapor increased on JCM 1649 and IFO 3301 after pressurization. The bactericidal effects of pressurization with the addition of AIT at 4 degrees C or 40 degrees C were greater than at 20 degrees C, and all bacteria tested were effectively killed at 200 or 250 MPa with 10 to 80 microg/ml of AIT. We tried to apply the combined treatment to a food product "Asazuke" (low salt vegetables), and it was confirmed that E. coli inoculated into the product was inactivated the same as in the in vitro test. We also studied the inactivation mechanism behind pressurization with AIT from the relationship between pressure resistance and precultivation temperature, and it was suggested that destruction of membrane structure caused bacterial kill.

Animals↗
PubMed1979

[Immunostimulating and adjuvant activities of a low molecular weight lipopeptide].

From crude extracts of a Streptomyces strain exhibiting immunopotentiating effects, a tetrapeptide was isolated and its structure established as L Ala leads to D isoGlu leads to L, L Dap comes from Gly. This peptide was devoid of biological activity but its chemical coupling with lauric acid gave a substance endowed with adjuvant and immunostimulating properties. This substance and the corresponding synthetic lauroyltetrapeptide were as active in this respect as the muramyl-dipeptide, thus far considered as the minimal adjuvant-active structure of bacterial cell walls: the presence of a sugar moiety is therefore not a prerequisite for immunopotentiating activities.

Adjuvants, Immunologic↗