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PubMed2002

Predicted structure and phyletic distribution of the RNA-binding protein Hfq.

Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The predicted structure aligns with most major features of the Methanobacterium thermoautotrophicum LSm protein structure. Conserved residues in Hfq are positioned at the same structural locations responsible for subunit assembly and RNA interaction in Sm proteins. A highly conserved portion of Hfq assumes a structural fold similar to the Sm2 motif of Sm proteins. The evolution of the Hfq protein was explored by conducting a BLAST search of microbial genomes followed by phylogenetic analysis. Approximately half of the 140 complete or nearly complete genomes examined contain at least one gene coding for Hfq. The presence or absence of Hfq closely followed major bacterial clades. It is absent from high-level clades and present in the ancient Thermotogales-Aquificales clade and all proteobacteria except for those that have undergone major reduction in genome size. Residues at three positions in Hfq form signatures for the beta/gamma proteobacteria, alpha proteobacteria and low GC Gram-positive bacteria groups.

Amino Acid Sequence↗

PubMed1977

Preparation of specifically labeled C-(lignin)- and C-(cellulose)-lignocelluloses and their decomposition by the microflora of soil.

Microbial decomposition of lignocellulose in soil was studied using radioisotope techniques. Natural lignocelluloses containing C in either their lignin or cellulose (glucan) components were prepared by feeding plants l-[U-C]phenylalanine or d-[U-C]glucose, respectively, through their cut stems. Detailed chemical and chromatographic characterization of labeled lignocelluloses from three hardwood and three softwood species showed that those labeled by the [C]glucose incorporation method contained specifically labeled cellulosic components, whereas those labeled by the [C]phenylalanine incorporation method contained specifically labeled lignin components. Microbial degradation of these differentially labeled lignocelluloses was followed by monitoring CO(2) evolution from selected soil samples incubated with known amounts of radiolabeled lignocelluloses. The lignin components of the six woods were shown to be decomposed in soil 4 to 10 times more slowly than their cellulosic components. These rates of mineralization were comparable to the generalized patterns previously reported in the literature. The present technique, however, was thought to be simpler, more sensitive, and less prone to interference than methods previously available.

Journal Article↗

PubMed2006

Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes.

BACKGROUND: Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi. RESULTS: We identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase. These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2) from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2) of the slime mould Dictyostelium discoideum and four intein coding sequences are in RNA polymerase II genes (RPB2), one each from the green alga Chlamydomonas reinhardtii, the zygomycete fungus Spiromyces aspiralis and the chytrid fungi Batrachochytrium dendrobatidis and Coelomomyces stegomyiae. The remaining intein coding sequence is in a viral relic embedded within the genome of the oomycete Phytophthora ramorum. The Chlamydomonas and Dictyostelium inteins are the first nuclear-encoded inteins found outside of the fungi. These new inteins represent a unique dataset: they are found in homologous proteins that form a paralogous group. Although these paralogues diverged early in eukaryotic evolution, their sequences can be aligned over most of their length. The inteins are inserted at multiple distinct sites, each of which corresponds to a highly conserved region of RNA polymerase. This dataset supports earlier work suggesting that inteins preferentially occur in highly conserved regions of their host proteins. CONCLUSION: The identification of these new inteins increases the known host range of intein sequences in eukaryotes, and provides fresh insights into their origins and evolution. We conclude that inteins are ancient eukaryote elements once found widely among microbial eukaryotes. They persist as rarities in the genomes of a sporadic array of microorganisms, occupying highly conserved sites in diverse proteins.

Alleles↗

PubMed2004

Peripheral B lymphocyte tolerance.

This lecture discusses two interrelated topics, B cell tolerance in the peripheral immune system and BAFF. Using the 3-83 antibody transgenic mouse bred to mice carrying cognate antigen in the liver, we previously found that clonal elimination drastically reduced the precursor frequency of autoreactive cells. The consensus model to explain this tolerance is the 2-signal hypothesis, which proposes that in the absence of T cell help BCR stimulation is a negative signal for B cells. However, this model fails to explain how these same B cells can respond to T-independent type II (TI-2) antigens, raising the question of how they distinguish TI-2 antigens from multimeric self determinants. We propose that B cells use NK-like missing self recognition to provide the needed specificity, as foreign antigens are unlikely to carry self markers. The model has implications for the evolution of the immune system, B lymphocyte signaling, tissue specificity of autoimmunity, and microbial subversion of the immune system. Overexpression of the critical B cell survival cytokine BAFF/BLyS has been associated with autoimmunity. We have discovered a novel splice isoform that regulates BAFF activity and may play a role in limiting B cell activity. The novel form, called DBAFF, is able to heteromultimerize with normal BAFF and can suppress receptor binding and proteolytic release from the cell surface. Preliminary studies from transgenic mice overexpressing wild type or DBAFF are consistent with a possible regulatory role for DBAFF, raising the possibility that the relative expression levels of BAFF and DBAFF regulates tolerance.

Animals↗

PubMedDate not supplied

Ecosystem function in alluvial tailings after biosolids and lime addition.

Municipal biosolids and agricultural limestone were incorporated into the surface of alluvial highly acidic, metal-contaminated mine tailings in Leadville, CO, in 1998. Amended sites were seeded and a plant cover was subsequently established. A range of chemical and biological parameters were measured over time to determine if treatment was sufficient to restore ecosystem function. An uncontaminated upstream control (UUC), a contaminated vegetated area (CVA), and soils collected from the tailings deposits before amendment addition were used for comparison. Standard soil extracts showed decreases in extractable Pb, Zn, and Cd in the amended soils. Increased CO2 evolution, reduced N2O, and elevated NO3- in the amended tailings indicated an active microbial community. Levels of CO2 and NO3- were elevated in comparison with the CVA and UUC. Ryegrass (Lolium perenne L.) and earthworm (Eisenia foetida) survival and metal uptake values were similar in amended tailings to a laboratory control soil. Ryegrass and worms in unamended tailings died. Field plant diversity was lower in amended areas than in CVA or UUC, with a higher percentage of the vegetative cover consisting of grasses. Small mammal analysis showed a low potential for elevated body Cd and Pb in the amended tailings. A re-entrainment study using fathead minnows (Pimephales promelas) showed no danger for resuspended amended tailings, as survival of fish was similar to the laboratory control. Data suggest that ecosystem function has been restored to the amended tailings, but that these systems are not yet in equilibrium.

Animals↗

PubMedDate not supplied

[A method for determining the CO2 released by resting cells of microorganisms during the oxidation of hydrocarbons].

A method is proposed for determining the oxidation of hydrocarbon substrates by microorganisms. The method is based on measuring the evolution of CO2 into the medium when the substrate is oxidized by washed microbial cells adsorbed on a spongy surface and incubated in a closed space into which CO2-free air is passed.

Biodegradation, Environmental↗

PubMedDate not supplied

[Effect of hydrogen peroxide and hydrated ferric oxides on the metabolism of soil microflora].

The effect of hydrogen peroxide and the mineral limonite on the rate of microbial processes was studied in poor and rich soils. The dynamics of CO2 evolution can be registered upon addition of hydrogen peroxide to chernozem samples, which confirms the existence of metabolism of soil microorganisms. In experiments with desert soil, the evolution of O2 increases rather than that of CO2, which is probably due to an increase in the number of microorganisms producing catalase. Limonite stimulates the metabolic activity of microrganisms. The cultural and morphological properties of microflora are described, which are typical of soils incubated in the presence of limonite and hydrogen peroxide. This work supports the conclusion that, theoretically, the ground of Mars may contain microorganisms which have adapted, in the course of evolution, to high concentrations of hydrogen peroxide and hydrated iron oxides (of the limonite type) in the surrounding medium.

Bacteria↗

PubMedDate not supplied

[Microbial contamination of the bile and its effects on the course of the surgical wound after cholecystectomy].

From a series of 58 cholecystectomies for chronic cholecystitis or for asymptomatic cholelithiasis, the authors have retrieved: 1) gall microbial contamination in 15,5% of the samples under study; 2) a complicated evolution--according to criteria defined for this research--of the operative wounds in 37,5% of the cases with positive gall cultures, and in 11% when the gall was sterile. It is the authors' opinion that cholecystectomy shows an actual septic risk, even in a non-acute clinical stage.

Adult↗

PubMed2001

Antimicrobial susceptibility of staphylococci isolated from the faeces of wild turkeys (Meleagris gallopavo).

AIMS: The purpose of this study was to investigate the staphylococcal flora associated with wild turkey populations. METHODS AND RESULTS: Faecal samples obtained from 26 wild turkeys over a 16-month period were inoculated onto mannitol salt agar plates to select for staphylococci. Fifty-seven randomly chosen isolates were identified as Staphylococcus lentus and their susceptibility determined against clindamycin, chloramphenicol, ciprofloxacin, erythromycin, oxacillin, penicillin G, rifampin, tetracycline, trimethoprim-sulfamethoxazole, and vancomycin. Resistance was minimal as only 3 isolates showed resistance to clindamycin, 3 isolates were resistant to oxacillin, 3 isolates were resistant to penicillin G, and 1 isolate was resistant to erythromycin. Multiple antibiotic resistance was also minimal. CONCLUSIONS: S. lentus is the predominant staphylococcal species associated with wild turkey faeces and antibiotic resistance in these organisms is not problematic. SIGNIFICANCE AND IMPACT OF THE STUDY: S. lentus has been shown as a potential causative agent of inflammatory reactions in the respiratory tract. Due to increased numbers of wild turkeys and more frequent human exposure, surveys to monitor microbial populations are warranted.

Animals↗

PubMed1968