Nonstandard genetic codes and translation termination

Genetic code is not universal. Various nonstandard versions of the code are known for some mitochondrial, prokaryotic, and eukaryotic genomes. The most common deviation is stop codon reassignment; i.e., a stop codon is decoded as a sense codon rather than as a signal for translation termination. Class 1 release factors (RFs: prokaryotic RF1 and RF2 and eukaryotic eRF1) recognize the stop codons and induce hydrolysis of peptidyl-tRNA in the ribosome. The specificity of class 1 RFs changes in organisms with a nonstandard code. The rare amino acids selenocysteine and pyrrolysine utilize essentially different decoding strategies. The review considers several hypotheses of the origin of nonstandard genetic codes. A new hypothesis is advanced, assuming a change in the specificity of class 1 RFs as a starting point for stop codon reassignment.     

Production of phytoestrogen <Emphasis Type="Italic">S</Emphasis>-equol from daidzein in mixed culture of two anaerobic bacteria

An anaerobic incubation mixture of two bacterial strains Eggerthella sp. Julong 732 and Lactobacillus sp. Niu-O16, which have been known to transform dihydrodaidzein to S-equol and daidzein to dihydrodaidzein respectively, produced S-equol from daidzein through dihydrodaidzein. The biotransformation kinetics of daidzein by the mixed cultures showed that the production of S-equol from daidzein was significantly enhanced, as compared to the production of S-equol from dihydrodaidzein by Eggerthella sp. Julong 732 alone. The substrate daidzein in the mixed culture was almost completely converted to S-equol in 24 h of anaerobic incubation. The increased production of S-equol from daidzein by the mixed culture is likely related to the increased bacterial numbers of Eggerthella sp. Julong 732. In the mixture cultures, the growth of Eggerthella sp. Julong 732 was significantly increased while the growth of Lactobacillus sp. Niu-O16 was suppressed as compared to either the single culture of Eggerthella sp. Julong 732 or Lactobacillus sp. Niu-O16. This is the first report in which two metabolic pathways to produce S-equol from daidzein by a mixed culture of bacteria isolated from human and bovine intestinal environments were successfully linked under anaerobic conditions.     

The effects of different electron donors on anaerobic nitrogen transformations and denitrification processes in Lake Taihu sediments

Nitrogen transformations in anaerobic sediments and leachate in Lake Taihu were simulated in the laboratory. Ammonium, nitrate and nitrite were analyzed after incubation under anaerobic conditions. Different reductive states and pH values were obtained by using different electron donors, such as glucose, sucrose, potato starch and sodium acetate. Chemical nitrogen transformation mechanisms were discussed relative to physico-chemical properties of lake sediment. Results demonstrated that nitrogen transformations in anaerobic conditions supplemented with different electron donors varied, and supplementation with certain electron donors may enhance nitrogen removal from anaerobic sediments. Among the four electron donors studied, higher nitrogen removal efficiencies were observed with acetate and starch. Saccharides, such as glucose, sucrose and starch, stimulate nitrate reduction to nitrite, while acetate stimulates nitrate reduction to ammonium.     

The biodiversity and ecology of Antarctic lakes: models for evolution

Antarctic lakes are characterised by simplified, truncated food webs. The lakes range from freshwater to hypersaline with a continuum of physical and chemical conditions that offer a natural laboratory in which to study evolution. Molecular studies on Antarctic lake communities are still in their infancy, but there is clear evidence from some taxonomic groups, for example the Cyanobacteria, that there is endemicity. Moreover, many of the bacteria have considerable potential as sources of novel biochemicals such as low temperature enzymes and anti-freeze proteins. Among the eukaryotic organisms survival strategies have evolved, among which dependence on mixotrophy in phytoflagellates and some ciliates is common. There is also some evidence of evolution of new species of flagellate in the marine derived saline lakes of the Vestfold Hills. Recent work on viruses in polar lakes demonstrates high abundance and high rates of infection, implying that they may play an important role in genetic exchange in these extreme environments.     

Two-stage biological treatment of olive mill wastewater with whey as co-substrate

Olive mill wastewater (OMW) is a highly polluting wastewater, caused by a high organic load and phenol content. These characteristics suggest that it may be suitable for aerobic treatment and anaerobic bacterial digestion. Aerobic treatment coupled with anaerobic bacterial digestion may be economically feasible as the methane produced is a valuable energy source while simultaneously purifying the OMW. In an attempt to improve the overall performance of the process, the addition of a co-substrate such as whey to the aerobic treatment pre-treatment of OMW by the yeast Candida tropicalis was studied.The two-stage system operated satisfactorily up to an organic loading rate (OLR) of 3.0 kg COD L⁻¹ day⁻¹ with a biogas production rate of 1.25 L_biogas L_reactor⁻¹ day⁻¹ and a total COD reduction in excess of 93% (62% COD reduction in aerobic pretreatment and 83% COD reduction in anaerobic digestion). Fifty-four percent of the phenol was biodegraded during the aerobic treatment stage, and biogas with between 68% and 75% methane was produced during anaerobic digestion.     

Enzymatic pre-hydrolysis applied to the anaerobic treatment of effluents from poultry slaughterhouses

A pool of hydrolases with 21.4 U g⁻¹ lipase activity was produced through solid-state fermentation of the fungus Penicillium restrictum in waste from the Orbignya oleifera (babassu) oil processing industry. Enzymatic hydrolysis and anaerobic biodegradability tests were conducted on poultry slaughterhouse effluents with varying oil and grease contents (150–1200 mg l⁻¹) and solid enzymatic pool concentrations (0.1–1.0% w/v). Enhanced anaerobic treatment efficiency relative to raw effluent was achieved when a 0.1% concentration of enzymatic pool was used in the pre-hydrolysis stage with 1200 mg oil and grease l⁻¹ (chemical oxygen demand (COD) removal efficiency of 85% vs. 53% and biogas production of 175 ml vs. 37 ml after 4 d).     

反相高效液相色谱法测定厌氧菌有机酸代谢产物

建立反相高效液相色谱测定厌氧菌代谢发酵有机酸产物(乙酸、乳酸)的方法并用于测定乳酸菌代谢发酵产物中的含量。反相高效液相方法是一种简单、准确、灵敏的方法,可用于同时定量测定厌氧菌的有机酸代谢产物。     

Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis

The genome architecture of ciliates, including features such as nuclear dualism and large-scale genome rearrangements, impacts gene and genome evolution in these organisms. To better understand the structure of macronuclear chromosomes in ciliates with extensively processed chromosomes, a sample of complete macronuclear chromosomes was sequenced from three ciliate species: Metopus es (Class [Cl]: Armophorea), Nyctotherus ovalis (Cl: Armophorea), and Chilodonella uncinata (Cl: Phyllopharyngea). By cloning whole macronuclear chromosomes into a plasmid vector, we generated nine clones from each of M. es and C. uncinata, and 37 clones from N. ovalis. Analysis of these macronuclear chromosomes provides insight into the evolution of genome features such as chromosome content, gene structure, and genetic code. Phylogenetic patterns can be found in telomere structure and codon usage, which are both more similar in M. es and N. ovalis than C. uncinata. In addition, we provide evidence of lateral transfer of a bacterial endo-beta-mannanase gene onto a M. es chromosome and report the discovery of a 42-bp conserved sequence motif within N. ovalis untranslated regions.     

Electron donors for biological sulfate reduction

Biological sulfate reduction is widely used for treating sulfate-containing wastewaters from industries such as mining, tannery, pulp and paper, and textiles. In biological reduction, sulfate is converted to hydrogen sulfide as the end product. The process is, therefore, ideally suited for treating metal-containing wastewater from which heavy metals are simultaneously removed through the formation of metal sulfides. Metal sulfide precipitates are more stable than metal hydroxides that are sensitive to pH change. Theoretically, conversion of 1 mol of sulfate requires 0.67 mol of chemical oxygen demand or electron donors. Sulfate rich wastewaters are usually deficient in electron donors and require external addition of electron donors in order to achieve complete sulfate reduction. This paper reviews various electron donors employed in biological sulfate reduction. Widely used electron donors include hydrogen, methanol, ethanol, acetate, lactate, propionate, butyrate, sugar, and molasses. The selection criteria for suitable electron donors are discussed.