Genome analysis of DNA repair genes in the alpha proteobacterium <Emphasis Type="Italic">Caulobacter crescentus</Emphasis>

Background  

The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria.     

Location and Formation of Cellulases in Trichoderma viride

The location and formation of cellulases and β-glucosidase in the fungus Trichoderma viride were studied on different substrates. The cellulases were found to be cell-bound during active growth on cellulose, CMC, and cellobiose. On CMC, much CM-cellulase was found cell-free but sonication released cellulase from the washed mycelium. Analysis of the carbohydrates of the mycelial cell wall after hydrolysis revealed glucose, mannose, and galactose—the same carbohydrates as reported to be present in purified cellulase from the same organism. Glucose repressed the formation of both CM-cellulase and Avicelase and cellobiose apparently the formation of Avicelase. Relatively little CM-cellulase was formed on cellobiose but a straight line was obtained when a differential plot of CM-cellulase versus protein was made.     

Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin

An intronless gene encoding a protein of 592 amino acid residues with similarity to 70-kDa heat shock proteins (HSP70s) has been cloned and sequenced from the amitochondrial protist Encephalitozoon cuniculi (phylum Microsporidia). Southern blot analyses show the presence of a single gene copy located on chromosome XI. The encoded protein exhibits an N-terminal hydrophobic leader sequence and two motifs shared by proteobacterial and mitochondrially expressed HSP70 homologs. Phylogenetic analysis using maximum likelihood and evolutionary distances place the E. cuniculi sequence in the cluster of mitochondrially expressed HSP70s, with a higher evolutionary rate than those of homologous sequences. Similar results were obtained after cloning a fragment of the homologous gene in the closely related species E. hellem. The presence of a nuclear targeting signal-like sequence supports a role of the Encephalitozoon HSP70 as a molecular chaperone of nuclear proteins. No evidence for cytosolic or endoplasmic reticulum forms of HSP70 was obtained through PCR amplification. These data suggest that Encephalitozoon species have evolved from an ancestor bearing mitochondria, which is in disagreement with the postulated presymbiotic origin of Microsporidia. The specific role and intracellular localization of the mitochondrial HSP70-like protein remain to be elucidated.      

Atmospheric nitrogen deposition explains patterns of plant species loss

Atmospheric nitrogen (N) deposition across Europe increased substantially from the 1950s to the 1990s. Targeted surveys suggest a negative correlation between N deposition and species richness within quadrats in sensitive habitats. However, it remains unclear whether plant species losses at national recording scales are correlated with nitrogen deposition. We relate plant species losses before 1987 in Great Britain to reduced and oxidized N deposition, land use change and climate change. The mean Ellenberg fertility (N) indices of plant species lost in each 100 km² cell before 1987 was compared with those of species that were recorded between 1987 and 1999. In 45% of squares, indices of species lost were significantly lower than those for species present after 1986. For 17%, primarily upland, squares, the opposite effect was found. A generalized least squares regression model, with difference in the mean Ellenberg N index between samples as the dependent variable, showed that higher deposition of reduced N was significantly associated with selective loss of species with a lower index. Arable land use and change in arable land use also demonstrated this positive relationship. Rough grazing, change in rough grazing, change in pasture and change in annual precipitation showed negative effects. Difference in Ellenberg R index was highly correlated with difference in Ellenberg N and was negatively correlated with oxidized N deposition, suggesting that the lack of a significant effect of oxidized N deposition on Ellenberg N was because it had effects through both acidification and eutrophication, while the effect of reduced N deposition was primarily through eutrophication. Our results suggest that N deposition, along with land use and precipitation changes, has been a significant driver of local plant extinctions. With N deposition increasing in many parts of the world, local extinctions of plant species may be experienced in other regions.     

Studies on the binding site of the galactose-specific agglutinin PA-IL from Pseudomonas aeruginosa

The binding properties of Pseudomonas aeruginosa agglutinin-I (PA-IL) with glycoproteins (gps) and polysaccharides were studied by both the biotin/avidin-mediated microtiter plate lectin-binding assay and the inhibition of agglutinin-glycan interaction with sugar ligands. Among 36 glycans tested for binding, PA-IL reacted best with two glycoproteins containing Galalpha1-->4Gal determinants and a human blood group ABO precursor equivalent gp, but this lectin reacted weakly or not at all with A and H active gps or sialylated gps. Among the mammalian disaccharides tested by the inhibition assay, the human blood group Pkactive Galalpha1-->4Gal, was the best. It was 7.4-fold less active than melibiose (Galalpha1-->6Glc). PA-IL has a preference for the alpha-anomer in decreasing order as follows: Galalpha1-->6 >Galalpha1-->4 >Galalpha1-->3. Of the monosaccharides studied, the phenylbeta derivatives of Gal were much better inhibitors than the methylbeta derivative, while only an insignificant difference was found between the Galalpha anomer of methyl- and p -NO2-phenyl derivatives. From these results, it can be concluded that the combining size of the agglutinin is as large as a disaccharide of the alpha-anomer of Gal at nonreducing end and most complementary to Galalpha1-->6Glc. As for the combining site of PA-IL toward the beta-anomer, the size is assumed to be less than that of Gal; carbon-6 in the pyranose form is essential, and hydrophobic interaction is important for binding.