Seeing is believing: engineering anthocyanin and carotenoid biosynthetic pathways

The biosynthetic pathways of flavonoids and carotenoids have been well established, and the biosynthetic genes have been mostly isolated. Metabolic engineering of their biosynthetic pathways has provided not only novel colored or health-beneficial plants but also excellent models to study the efficacy of such engineering. In order to achieve a specific color by accumulating a corresponding compound, it is necessary to upregulate the pathway leading to the compound and downregulate the competing pathway. The regulation of gene expression has to be optimized in a target crop as well.     

Core 2 GlcNAc modification and megalin ligand-binding activity

Megalin, a receptor-like transporter glycoprotein, is expressed on kidney proximal tubular cells and reabsorbs small-molecular-weight proteins from the glomerular filtrate. Here, we report that mouse megalins differently modified with core 2 beta6GlcNAc transferase had different kinetic properties to a fluorescence-labeled ligand, retinol-binding protein (RBP). BALB/c mice, a wild-type strain in terms of the expression of kidney-specific core 2 beta6GlcNAc transferase, express megalin carrying the core 2 extended Le(x) epitope, while DBA/2 mice, a mutant-strain of the core 2 beta6GlcNAc transferase, express megalin lacking the epitope. We purified these two types of megalin using lentil lectin chromatography and measured the ligand-binding activities of the megalins using Cy5-labeled RBP by applying gel permeation chromatography (GPC) and fluorescence correlation spectroscopy (FCS). The analysis by GPC indicated that the apparent V(max) of the interaction between Cy5-labeled RBP and the megalins of BALB/c and DBA/2 mice was 60 microM and 30 microM, respectively, and the apparent K(m) was 11 microM and 17 microM, respectively. Scatchard analysis demonstrated the presence of two binding sites. Linear regression analysis resulted in a two-binding-site model characterized by a high-affinity site (K(dBALB)=12.0 microM; K(dDBA)=20.9 microM) and a low-affinity site (K(dBALB)=36.2 microM; K(dDBA)=58.8 microM). FCS analysis exhibited quite different K(m) and V(max) values from those obtained by GPC, but similar K(m) values for the two types of megalin, and a lower V(max) value for DBA/2 megalin than BALB/c megalin. These results suggest that the core 2 GlcNAc extended glycan chains on megalin can change the ligand-binding affinity and capacity.     

The Shapley value of phylogenetic trees

Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space basis of M. Both depend on the split counts of the tree. Finally, we characterize the Shapley value on tree games by four axioms, a counterpart to Shapley’s original theorem on the larger class of cooperative games. We also include a brief discussion of the core of tree games. Research of Francis Edward Su was partially supported by NSF Grants DMS-0301129 and DMS-0701308.     

Lytic β-1,3 Glucanase from Arthrobacter: Pattern of Action

The action pattern of lytic β-1,3 glucanase (glucanase I) from Arthrobacter which liberates predominantly laminaripentaose from various β-glucans has been studied. The enzyme was not active on short linear laminaridextrins, but was active on an enzymatically synthesized, linear β-1,3 oligoglucan preparation. Any intactness of the glucose residues of the chain ends of a substrate did not seem to be necessary for the action of the enzyme. The results of determination of laminaripentaose during a relatively early phase of the reaction suggested that about half of the reducing power liberated in the medium might be explained by the formation of the sugar. It seems that the formation of laminaripentaose relates to the initial attack of glucanase 1 on β-1,3 glucan chains.     

Energy Transducing Roles of Antiporter-like Subunits in Escherichia coli NDH-1 with Main Focus on Subunit NuoN (ND2)

The proton-translocating NADH-quinone oxidoreductase (complex I/NDH-1) contains a peripheral and a membrane domain. Three antiporter-like subunits in the membrane domain, NuoL, NuoM, and NuoN (ND5, ND4 and ND2, respectively), are structurally similar. We analyzed the role of NuoN in Escherichia coli NDH-1. The lysine residue at position 395 in NuoN (_NLys³⁹⁵) is conserved in NuoL (_LLys³⁹⁹) but is replaced by glutamic acid (_MGlu⁴⁰⁷) in NuoM. Our mutation study on _NLys³⁹⁵ suggests that this residue participates in the proton translocation. Furthermore, we found that _MGlu⁴⁰⁷ is also essential and most likely interacts with conserved _LArg¹⁷⁵. Glutamic acids, _NGlu¹³³, _MGlu¹⁴⁴, and _LGlu¹⁴⁴, are corresponding residues. Unlike mutants of _MGlu¹⁴⁴ and _LGlu¹⁴⁴, mutation of _NGlu¹³³ scarcely affected the energy-transducing activities. However, a double mutant of _NGlu¹³³ and nearby _KGlu⁷² showed significant inhibition of these activities. This suggests that _NGlu¹³³ bears a functional role similar to _LGlu¹⁴⁴ and _MGlu¹⁴⁴ but its mutation can be partially compensated by the nearby carboxyl residue. Conserved prolines located at loops of discontinuous transmembrane helices of NuoL, NuoM, and NuoN were shown to play a similar role in the energy-transducing activity. It seems likely that NuoL, NuoM, and NuoN pump protons by a similar mechanism. Our data also revealed that _NLys¹⁵⁸ is one of the key interaction points with helix HL in NuoL. A truncation study indicated that the C-terminal amphipathic segments of _NTM14 interacts with the _Mβ sheet located on the opposite side of helix HL. Taken together, the mechanism of H⁺ translocation in NDH-1 is discussed.     

Partial Sequences of Large Subunit Ribosomal DNA of a New Yeast Species,Trichosporon domesticum and Related Species

We determined the partial sequences of large subunit rDNA of a new yeast species, Trichosporon domesticum, which was isolated from the house of a summer-type hypersensitivity pneumonitis patient. Phylogenetically, T. domesticum was positioned in the taxonomic group containing T. montevideense and T. brassicae, which indicated an identical serotype. A phylogenetic relationship among all species of the genus Trichosporon which belong to the basidiomycetous yeast is clarified.