Novel protein engineering strategy for creating highly receptor-selective mutant TNFs

Tumor necrosis factor (TNF) plays important roles in host defense and in preventing tumor formation by acting via its receptors, TNFR1 and TNFR2, functions of which are less understood. To this end, we have been isolating TNF receptor-selective mutants using phage display technique. However, generation of a phage library with large repertoire (>10⁸) is impeded by the limited transformation efficiency of Escherichia coli. Therefore, it is currently difficult to create a mutant library containing amino acid substitutions in more than seven residues. To overcome this problem, here we have used two different TNF mutant libraries, each containing random substitutions at six selected amino acid residues, and utilized a gene shuffling method to construct a randomized mutant library containing substitutions at 12 different amino acid residues of TNF. Consequently, using this library, we identified TNF mutants with greater receptor-selectivity and enhanced receptor-specific bioactivity than the existing mutants.     

Invasion of weeping lovegrass reduces native food and habitat resource of Eusphingonotus japonicus (Saussure)

To examine the relative importance and interactions of trophic and non-trophic effects of plant invasions on herbivores, we investigated how the invasion of weeping lovegrass Eragrostis curvula impacted Eusphingonotus japonicus, a food generalist grasshopper endemic to gravelly floodplains with sparse vegetation in Japan. Field observations and laboratory experiments showed that the grasshopper fed mainly on herbs endemic to the gravelly floodplains, which were negatively impacted by the alien grass. The alien grass was not consumed as food. Field censuses also showed that the abundance of the grasshopper was positively correlated with the coverage of endemic herbs in a plot where weeping lovegrass was not dominant. Dominance of the grass (i.e., habitat modification for E. japonicus) negatively impacted the grasshopper and weakened the positive relationship between the grasshopper and endemic herbs. These results suggest that an understanding of the relationship between non-trophic and trophic effects is essential to predict the impacts of plant invasions on herbivores.     

Efficient degradation of rice straw in the reactors packed by carbon fiber textiles

We have reported for the first time that agricultural and cellulosic waste, i.e., rice straw was directly applied to methanogenic bioreactors containing carbon fiber textiles (CFT) as supporting material. Addition of CFT to the methanogenic bioreactors enhanced the conversion of dichromate chemical oxygen demand of the substrate to methane (41%) to a greater extent than bioreactors without CFT (9%). In addition, removal of rice straw as a suspended solid was increased from 31% (in bioreactors without CFT) to 57% (in those with CFT). Methanogenic 16S rRNA gene analysis showed that the abundance of acetoclastic methanogen, genus Methanosarcina, was about 11 times higher in bioreactors with CFT (suspended fraction plus retained fraction to CFT) than in bioreactors without CFT (suspended fraction), resulting in lower concentration of acetate in bioreactors with CFT (0.4 mM) than in those without CFT (29.7 mM). On the other hand, the abundance of hydrogenotrophic methanogen, genus Methanobacterium, in bioreactors with CFT was similar to those without CFT. Bacterial communities in bioreactors with CFT were different from those in bioreactors without CFT. Our results indicated that specific microbial community and cooperative relationships between microorganisms in reactors containing CFT facilitated efficient decomposition of rice straw and its conversion to methane.     

Metabolism of mono- and dichloro-dibenzo-p-dioxins by Phanerochaete chrysosporium cytochromes P450

The white-rot fungus Phanerochaete chrysosporium possesses biodegradative capabilities of polychlorinated dibenzo-p-dioxins (PCDDs). One hundred twenty yeast clones expressing individual P450s of P. chrysosporum (PcCYPs), generated in our previous efforts, were screened for transformation of dioxin, and 40 positive clones were obtained. Of these clones, six clones showed metabolism of 2-chloro-dibenzo-p-dioxin, and a microsomal PcCYP designated as PcCYP11a3 showed much higher activity than any other PcCYPs. The turnover numbers of hydroxylation activities of PcCYP11a3 toward 1-MCDD (58 min⁻¹) and 2-MCDD (13 min⁻¹) are more than 200 times higher than those of previously reported PcCYP65a2. In addition, PcCYP11a3 catalyzes hydroxylation of 2,3-dichloro-dibenzo-p-dioxin. To our best knowledge, PcCYP11a3 has the highest activity toward PCDDs among the known CYPs derived from microorganisms. Although PcCYP11a3 showed no detectable activity toward 2,7-dichloro-dibenzo-p-dioxin and 2,3,7-trichloro-dibenzo-p-dioxin, PcCYP11a3 is promising as a template whose activity would be enhanced by site-directed mutagenesis.     

Glucagon regulates intracellular distribution of adipose differentiation-related protein during triacylglycerol accumulation in the liver

Cellular lipid droplets (LD) are organelles involved in cellular lipid metabolism. When liver cellular components were fractionated using sucrose density gradient centrifugation, adipose differentiation-related protein (ADRP) was distributed in both the top and bottom fractions, which correspond to the LD and membranous fractions, respectively, in the mouse liver under normal feeding conditions. After overnight fasting, triacylglycerol and ADRP increased nearly 2.5-fold in the mouse liver, and a portion appeared in the intermediate-density LD (iLD) fractions. ADRP in the iLD fractions was also increased in a mouse nonalcoholic steatohepatitis model induced by methione/choline-deficient diet. When HuH-7 human hepatoma cells were incubated with oleic acid for 24 h, the amount of ADRP increased, and it was distributed in both the LD and membrane fractions. However, ADRP appeared in the iLD fractions upon treatment of HuH-7 cells with glucagon. This behavior of ADRP was cAMP-dependent, as the ADRP-positive iLD fractions were induced by dibutylyl cAMP and were blocked by protein kinase A inhibitors. A portion of ADRP colocalized microscopically with calnexin, which is present in the iLD fractions, by treatment of HuH-7 cells or human primary hepatocytes with oleic acid and glucagon, but not by treatment with oleic acid alone. Glucagon has a role in the reorganization of endoplasmic reticulum membranes to generate ADRP-associated lipid-poor particles in hepatic cells, which is related to LD formation during lipid storage.     

Bilirubin oxidase activity of Bacillus subtilis CotA

The spore coat protein CotA from Bacillus subtilis was previously identified as a laccase. We have now found that CotA also shows strong bilirubin oxidase activity and markedly higher affinity for bilirubin than conventional bilirubin oxidase. This is the first characterization of bilirubin oxidase activity in a bacterial protein.     

Temperature-regulated formation of mycelial mat-like biofilms by Legionella pneumophila

Fifty strains representing 38 species of the genus Legionella were examined for biofilm formation on glass, polystyrene, and polypropylene surfaces in static cultures at 25 degrees C, 37 degrees C, and 42 degrees C. Strains of Legionella pneumophila, the most common causative agent of Legionnaires' disease, were found to have the highest ability to form biofilms among the test strains. The quantity, rate of formation, and adherence stability of L. pneumophila biofilms showed considerable dependence on both temperature and surface material. Glass and polystyrene surfaces gave between two- to sevenfold-higher yields of biofilms at 37 degrees C or 42 degrees C than at 25 degrees C; conversely, polypropylene surface had between 2 to 16 times higher yields at 25 degrees C than at 37 degrees C or 42 degrees C. On glass surfaces, the biofilms were formed faster but attached less stably at 37 degrees C or 42 degrees C than at 25 degrees C. Both scanning electron microscopy and confocal laser scanning microscopy revealed that biofilms formed at 37 degrees C or 42 degrees C were mycelial mat like and were composed of filamentous cells, while at 25 degrees C, cells were rod shaped. Planktonic cells outside of biofilms or in shaken liquid cultures were rod shaped. Notably, the filamentous cells were found to be multinucleate and lacking septa, but a recA null mutant of L. pneumophila was unaffected in its temperature-regulated filamentation within biofilms. Our data also showed that filamentous cells were able to rapidly give rise to a large number of short rods in a fresh liquid culture at 37 degrees C. The possibility of this biofilm to represent a novel strategy by L. pneumophila to compete for proliferation among the environmental microbiota is discussed.