Improvement of L-lysine production by Methylophilus methylotrophus from methanol via the Entner-Doudoroff pathway, originating in Escherichia coli

To improve the amino acid production by metabolic engineering, eliminating the pathway bottleneck is known to be very effective. The metabolic response of Methylophilus methylotrophus upon the addition of glucose and of pyruvate was investigated in batch cultivation. We found that the supply of pyruvate is a bottleneck in L-lysine production in M. methylotrophus from methanol as carbon source. M. methylotrophus has a ribulose monophosphate (RuMP) pathway for methanol assimilation, and consequently synthesized fructose-6-phosphate is metabolized to pyruvate via the Entner-Doudoroff (ED) pathway, and the ED pathway is thought to be the main pathway for pyruvate supply. An L-lysine producer of M. methylotrophus with an enhanced ED pathway was constructed by the introduction of the E. coli edd-eda operon encoding the enzyme involving the ED pathway. In this strain, the overall enzymatic activity of ED pathway, which is estimated by measuring the activities of 6-phosphogluconate dehydrogenase plus 2-keto-3-deoxy-6-phosphogluconate aldolase, was about 20 times higher than in the parent. This strain produced 1.2 times more L-lysine than the parent producer. Perhaps, then, the supply of pyruvate was a bottleneck in L-lysine production in the L-lysine producer of M. methylotrophus.     

Enzymatic Kolbe-Schmitt reaction to form salicylic acid from phenol: Enzymatic characterization and gene identification of a novel enzyme, Trichosporon moniliiforme salicylic acid decarboxylase

Salicylic acid decarboxylase (Sdc) can produce salicylic acid from phenol; it was found in the yeast Trichosporon moniliiforme WU-0401 and was for the first time enzymatically characterized, with the sdc gene heterologously expressed. Sdc catalyzed both reactions: decarboxylation of salicylic acid to phenol and the carboxylation of phenol to form salicylic acid without any byproducts. Both reactions were detected without the addition of any cofactors and occurred even in the presence of oxygen, suggesting that this Sdc is reversible, nonoxidative, and oxygen insensitive. Therefore, it is readily applicable in the selective production of salicylic acid from phenol, the enzymatic Kolbe-Schmitt reaction. The deduced amino acid sequence of the gene, sdc, encoding Sdc comprises 350 amino acid residues corresponding to a 40-kDa protein. The recombinant Escherichia coli BL21(DE3) expressing sdc converted phenol to salicylic acid with a 27% (mol/mol) yield at 30 °C for 9 h.     

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

Background

Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes.

Results

Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences.

Conclusions

Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.     

Identification of a gene involved in plasmid structural instability in Corynebacterium glutamicum

Expression plasmids that facilitate production of bio-based products are susceptible to toxic effects that frequently affect plasmid structural stability in recombinant microbial cells. In order to enhance plasmid stability in recombinant Corynebacterium glutamicum, an expression plasmid containing genes of the Clostridium acetobutylicum butyryl-CoA synthesis operon with high structural instability within wild-type C. glutamicum was employed. From a total of 133 mutants exhibiting disruptions in 265 suspect genes, only cgR_0322-deficient mutant was able to maintain the expression plasmid intact. The mutant exhibited normal growth under standard laboratory conditions but its transformation efficiency was about one order of magnitude lower than that of wild-type strain. The cgR_0322 gene encodes an endonuclease that is active against single- as well as double-stranded DNA substrates in the presence of Mg²⁺. The cgR_0322-deficient strain should therefore facilitate the development of more robust C. glutamicum strains to be used as microbial production hosts.     

Active behavior and 1/f noise in shell-changing behavior of the hermit crabs.

Hermit crabs are known to carry a gastropod shell to prevent abdomen from injuring by predators and cannibalism. One can regard the shell as a boundary between inside and outside worlds for hermit crabs. We conducted an experiment in which hermit crabs without shells deal with artificial tubes. The situation without a shell requires a part of experimental setup to be regarded as inside by each hermit crab. We accept the distance of locomotion as the indication of the estimation process performed by an individual on parts of the experimental setup. As a result, behavioral hierarchy was found with respect to the way of constituting the boundary. At each level of hierarchy, active behavior produced 1/f noise in comparison with the passive one. It suggests that finding 1/f noise at each level of hierarchy may lead to a lower level of hierarchy in another situation.     

Identification of Tek/Tie2 binding partners. Binding to a multifunctional docking site mediates cell survival and migration.

The Tek/Tie2 receptor tyrosine kinase plays a pivotal role in vascular and hematopoietic development. To study the signal transduction pathways that are mediated by this receptor, we have used the yeast two-hybrid system to identify signaling molecules that associate with the phosphorylated Tek receptor. Using this approach, we demonstrate that five molecules, Grb2, Grb7, Grb14, Shp2, and the p85 subunit of phosphatidylinositol 3-kinase can interact with Tek in a phosphotyrosine-dependent manner through their SH2 domains. Mapping of the binding sites of these molecules on Tek reveals the presence of a multisubstrate docking site in the carboxyl tail of Tek (Tyr(1100)). Mutation of this site abrogates binding of Grb2 and Grb7 to Tek in vivo, and this site is required for tyrosine phosphorylation of Grb7 and p85 in vivo. Furthermore, stimulation of Tek-expressing cells with Angiopoietin-1 results in phosphorylation of both Tek and p85 and in activation of endothelial cell migration and survival pathways that are dependent in part on phosphatidylinositol 3-kinase. Taken together, these results demonstrate that Angiopoietin-1-induced signaling from the Tek receptor is mediated by a multifunctional docking site that is responsible for activation of both cell migration and cell survival pathways.     

Dual interaction producing both territorial and schooling behavior in fish

Fish schools are frequently observed without a leader and an explicit condition forming school. Several models of schooling have been proposed focusing on the influence of neighbors, and introducing probability distributions, while these models are based on the separation of schooling and territorial behavior. We frequently consider the duality of aggregation of animals, in which behavioral patterns involve both attraction and repulsion, antagonistic with each other. The idea of probability does not explain this duality that can provide both schooling and territorial behavior. From these biological facts, we have constructed a behavior model in which the influence of neighbors is formulated by the interface between the states of neighbors and a map of changes in these states. This interface uses a self-similar nowhere differentiable transition map which is temporally constructed, encompassing a crucial duality of repulsive and attractive forces hidden in the interaction among fishes. We tested it with computer simulations against the biological reality of schooling and territorial behavior. Due to the influence neighbors can have on duality, the same model can show both schooling behavior with a high degree of polarization and territorial behavior.     

Breast form changes resulting from a certain brassière

Eleven adult female subjects aged 22-39 years wore a certain brassière for 3 months while anthropometry and moiré fringe photographs on the anterior trunk were taken regularly once a week. After the 3 months, the brassière was not worn for another 3 months. Then the measurements and photogrammetry were repeated for comparison using superimposed moiré configurations. The results are summarized as follows. Regardless of slim or obese trunk, subjects with pendent breasts showed the highest degree of breast form "correction" from wearing the brassière. In all subjects, after 3 months of brassière constraint, the underbust circumference was smaller but the chest circumference became enlarged, the distance between the right and left nipples became wider, and the breasts tended to hang down. This change was more marked in obese subjects with pendent breasts. And when this type of subject wore a "well-fitted" brassière for a long time, her breast form became developed; that is, her breasts hung down more.     

Discovery of selective and nonpeptidic cathepsin S inhibitors

Nonpeptidic, selective, and potent cathepsin S inhibitors were derived from an in-house pyrrolopyrimidine cathepsin K inhibitor by modification of the P2 and P3 moieties. The pyrrolopyrimidine-based inhibitors show nanomolar inhibition of cathepsin S with over 100-fold selectivity against other cysteine proteases, including cathepsin K and L. Some of the inhibitors showed cellular activities in mouse splenocytes as well as oral bioavailabilities in rats.