Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates in α-aminoadipate aminotransferase from Thermus thermophilus

To clarify the mechanism for substrate recognition of α-aminoadipate aminotransferase (AAA-AT) from Thermus thermophilus, the crystal structure of AAA-AT complexed with N-(5′-phosphopyridoxyl)-l-glutamate (PPE) was determined at 1.67 Å resolution. The crystal structure revealed that PPE is recognized by amino acid residues the same as those seen in N-(5′-phosphopyridoxyl)-l-α-aminoadipate (PPA) recognition; however, to bind the γ-carboxyl group of Glu at a fixed position, the Cα atom of the Glu moiety moves 0.80 Å toward the γ-carboxyl group in the PPE complex. Markedly decreased activity for Asp can be explained by the shortness of the aspartyl side chain to be recognized by Arg23 and further dislocation of the Cα atom of bound Asp. Site-directed mutagenesis revealed that Arg23 has dual functions for reaction, (i) recognition of γ (δ)-carboxyl group of Glu (AAA) and (ii) rearrangement of α2 helix by changing the interacting partners to place the hydrophobic substrate at the suitable position.     

Water and salt movement in soil driven by crop roots: a controlled column study

Water deficit and salt accumulation in soil presents serious problems to crop production in semi-arid regions. These problems depend on the active transpiration stream and the selective absorption of ions by crop roots. In this study, a large sized soil column system was used to examine the dynamics of water and ion transport and salt accumulation in soil layers. Special reference was placed on the effects of the active and selective absorption by roots of different crops (i.e., corn plants, sunflower plants and no plants). The column system was equipped with on-line systems for the control of groundwater level. Soil water content sensors enabled time-course evaluations of the volumetric water content and hence upward flux of the groundwater in the soils at different depths. Furthermore, the distribution and accumulation of ions in soil layers, plant organs and xylem sap were analyzed using ion chromatography. In this column experiment, diurnal and longer term changes in water movement and ion accumulation in soil, affected by root absorption characteristics of plants, were evaluated quantitatively. The results demonstrated that the column system was applicable for the quantitative analysis of the effects of root absorption by different crops on water deficit and salinization in soils.     

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.     

A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells

Synthetic biology is an emerging field that aims at constructing artificial biological systems by combining engineering and molecular biology approaches. One of the most ambitious research line concerns the so-called semi-synthetic minimal cells, which are liposome-based system capable of synthesizing the lipids within the liposome surface. This goal can be reached by reconstituting membrane proteins within liposomes and allow them to synthesize lipids. This approach, that can be defined as biochemical, was already reported by us (Schmidli et al. J. Am. Chem. Soc. 113, 8127-8130, 1991). In more advanced models, however, a full reconstruction of the biochemical pathway requires (1) the synthesis of functional membrane enzymes inside liposomes, and (2) the local synthesis of lipids as catalyzed by the in situ synthesized enzymes. Here we show the synthesis and the activity - inside liposomes - of two membrane proteins involved in phospholipids biosynthesis pathway. The proteins, sn-glycerol-3-phosphate acyltransferase (GPAT) and lysophosphatidic acid acyltransferase (LPAAT), have been synthesized by using a totally reconstructed cell-free system (PURE system) encapsulated in liposomes. The activities of internally synthesized GPAT and LPAAT were confirmed by detecting the produced lysophosphatidic acid and phosphatidic acid, respectively. Through this procedure, we have implemented the first phase of a design aimed at synthesizing phospholipid membrane from liposome within from within — which corresponds to the autopoietic growth mechanism.     

Phosphorylation of Tyr-398 and Tyr-402 in Occludin Prevents Its Interaction with ZO-1 and Destabilizes Its Assembly at the Tight Junctions

Occludin is phosphorylated on tyrosine residues during the oxidative stress-induced disruption of tight junction, and in vitro phosphorylation of occludin by c-Src attenuates its binding to ZO-1. In the present study mass spectrometric analyses of C-terminal domain of occludin identified Tyr-379 and Tyr-383 in chicken occludin as the phosphorylation sites, which are located in a highly conserved sequence of occludin, YETDYTT; Tyr-398 and Tyr-402 are the corresponding residues in human occludin. Deletion of YETDYTT motif abolished the c-Src-mediated phosphorylation of occludin and the regulation of ZO-1 binding. Y398A and Y402A mutations in human occludin also abolished the c-Src-mediated phosphorylation and regulation of ZO-1 binding. Y398D/Y402D mutation resulted in a dramatic reduction in ZO-1 binding even in the absence of c-Src. Similar to wild type occludin, its Y398A/Y402A mutant was localized at the plasma membrane and cell-cell contact sites in Rat-1 cells. However, Y398D/Y402D mutants of occludin failed to localize at the cell-cell contacts. Calcium-induced reassembly of Y398D/Y402D mutant occludin in Madin-Darby canine kidney cells was significantly delayed compared with that of wild type occludin or its T398A/T402A mutant. Furthermore, expression of Y398D/Y402D mutant of occludin sensitized MDCK cells for hydrogen peroxide-induced barrier disruption. This study reveals a unique motif in the occludin sequence that is involved in the regulation of ZO-1 binding by reversible phosphorylation of specific Tyr residues.Epithelial tight junctions (TJs)² form a selective barrier to the diffusion of toxins, allergens, and pathogens from the external environment into the tissues in the gastrointestinal tract, lung, liver, and kidney (1). Disruption of TJs is associated with the gastrointestinal diseases such as inflammatory bowel disease, celiac disease, infectious enterocolitis, and colon cancer (2–4) as well as in diseases of lung and kidney (5, 6). Numerous inflammatory mediators such as tumor necrosis factor α, interferon γ, and oxidative stress (7–12) are known to disrupt the epithelial TJs and the barrier function. Several studies have indicated that hydrogen peroxide disrupts the TJs in intestinal epithelium by a tyrosine kinase-dependent mechanism (11, 12).Four types of integral proteins, occludin, claudins, junctional adhesion molecules, and tricellulin are associated with TJs. Occludin, claudins, and tricellulin are tetraspan proteins, and their extracellular domains interact with homotypic domains of the adjacent cells (1, 2, 13). The intracellular domains of these proteins interact with a variety of soluble proteins such as ZO-1, ZO-2, ZO-3, 7H6, cingulin, and symplekin (14–23); this protein complex interacts with the perijunctional actomyosin ring. The interactions among TJ proteins are essential for the assembly and the maintenance of TJs. Therefore, regulation of the interactions among TJ proteins may regulate the TJ integrity. A significant body of evidence indicates that numerous signaling molecules are associated with the TJs. Protein kinases and protein phosphatases such as protein kinase Cζ (PKCζ), PKCι/λ (24), c-Src (25), c-Yes (26, 27), mitogen-activated protein kinase (28), PP2A, and PP1 (29) interact with TJs, indicating that TJs are dynamically regulated by intracellular signal transduction involving protein phosphorylation. Additionally, other signaling molecules such as calcium (30), phosphatidylinositol 3-kinase (31), Rho (32), and Rac (33) are involved in the regulation of TJs.Occludin, a ∼65-kDa protein, has been well characterized to be assembled into the TJs. Although occludin knock-out mice showed the formation of intact TJs in different epithelia (34), numerous studies have emphasized that it plays an important role in the regulation of TJ integrity. Occludin spans the membrane four times to form two extracellular loops and one intracellular loop, and the N-terminal and C-terminal domains hang into the intracellular compartment (35–37). In epithelium with intact TJs, occludin is highly phosphorylated on Ser and Thr residues (38), whereas Tyr phosphorylation is undetectable. However, the disruption of TJs in Caco-2 cell monolayers by oxidative stress and acetaldehyde leads to Tyr phosphorylation of occludin; the tyrosine kinase inhibitors attenuate the disruption of TJs (39, 40). Furthermore, a previous in vitro study demonstrated that Tyr phosphorylation of the C-terminal domain of occludin leads to the loss of its interaction with ZO-1 and ZO-3 (25).In the present study we identified the Tyr residues in occludin that are phosphorylated by c-Src and determined their role in regulated interaction between occludin and ZO-1 and its assembly into the TJs. Results show that 1) Tyr-379 and Tyr-383 in chicken occludin and Tyr-398 and Tyr-402 in human occludin are the exclusive sites of phosphorylation by c-Src, and these Tyr residues are located in a highly conserved sequence of occludin, YET-DYTT, 2) deletion of YEDTYTT or point mutation of Tyr-398 and Tyr-402 in human occludin attenuates the phosphorylation-dependent regulation of ZO-1 binding, 3) Y398D/Y402D mutation of human occludin leads to loss of ZO-1 binding and prevents its translocation to the plasma membrane and cell-cell contact sites in Rat-1 cells, 4) Y398D/Y402D mutation of occludin delays its assembly into the intercellular junctions during the calcium-induced assembly of TJs, and 5) expression of Y398D/Y402D mutant occludin sensitizes cell monolayers for hydrogen peroxide-induced disruption of barrier function.     

Transforming Potential of Src Family Kinases Is Limited by the Cholesterol-Enriched Membrane Microdomain

The upregulation of Src family kinases (SFKs) has been implicated in cancer progression, but the molecular mechanisms regulating their transforming potentials remain unclear. Here we show that the transforming ability of all SFK members is suppressed by being distributed to the cholesterol-enriched membrane microdomain. All SFKs could induce cell transformation when overexpressed in C-terminal Src kinase (Csk)-deficient fibroblasts. However, their transforming abilities varied depending on their affinity for the microdomain. c-Src and Blk, with a weak affinity for the microdomain due to a single myristate modification at the N terminus, could efficiently induce cell transformation, whereas SFKs with both myristate and palmitate modifications were preferentially distributed to the microdomain and required higher doses of protein expression to induce transformation. In contrast, disruption of the microdomain by depleting cholesterol could induce a robust transformation in Csk-deficient fibroblasts in which only a limited amount of activated SFKs was expressed. Conversely, the addition of cholesterol or recruitment of activated SFKs to the microdomain via a transmembrane adaptor, Cbp/PAG1, efficiently suppressed SFK-induced cell transformation. These findings suggest that the membrane microdomain spatially limits the transforming potential of SFKs by sequestering them away from the transforming pathways.Src family kinases (SFKs) are membrane-associated, non-receptor protein tyrosine kinases involved in a variety of intracellular signaling pathways (5). SFKs are comprised of eight members in mammals: c-Src, Fyn, c-Yes, Lyn, Lck, Hck, c-Fgr and Blk. Among these, c-Src, Fyn, and c-Yes are ubiquitously expressed, whereas the others are relatively concentrated in hematopoietic cell lineages. The intracellular distribution of each SFK also varies depending on their unique N-terminal sequences and acyl modifications (5, 27). These distinctive features of SFKs suggest that each SFK member plays a unique role in particular tissues or cells. In contrast, it is also known that SFKs have redundant and pleiotropic functions in regulating critical cellular events, such as cell division, motility, adhesion, angiogenesis, and survival (26). In a variety of human cancers, protein levels and/or specific activities of c-Src and c-Yes are frequently upregulated (13, 35). Upregulation of Lyn, Lck, Hck, c-Fgr, or Blk is also observed in some leukemias and lymphomas (10, 16, 26). These observations imply a role for SFKs in cell transformation, tumorigenesis, and metastasis (31). However, because SFK genes are rarely mutated in human cancers (31), the mechanisms underlying their upregulation in these cancers remain unclear. Furthermore, the distinctive expression patterns and functional redundancy among SFK members have hampered concurrent analyses of their intrinsic transforming abilities and contribution to cancer progression.In normal cells, the kinase activity of SFKs is negatively regulated by the phosphorylation of its C-terminal regulatory Tyr residue by C-terminal Src kinase (Csk) (21, 22). The cytoplasmic Csk requires Csk-binding scaffold proteins to gain efficient access to membrane-bound SFKs. Previously, we identified a transmembrane adaptor protein, Cbp (also known as PAG1), as a specific Csk-binding protein. Cbp/PAG1 is exclusively localized to a membrane microdomain enriched by cholesterol and sphingolipids and plays a scaffolding role for Cbp/PAG1 in Csk-mediated negative regulation of SFKs (3, 15). We also reported that expression of Cbp/PAG1 is noticeably downregulated by c-Src transformation and in some human cancer cells and that reexpression of Cbp/PAG1 can suppress c-Src-induced transformation and tumorigenesis (23). In addition, we showed that Cbp/PAG1 suppressed c-Src function independently of Csk by directly sequestering activated c-Src in the membrane microdomain. These findings suggest a potential role for Cbp/PAG1 as a suppressor for c-Src-mediated cancer progression. However, whether Cbp/PAG1 would serve as a suppressor for other SFK members and whether other microdomain adaptors, such as LIME (4, 11), would also contribute to the suppression of SFK-mediated transformation have yet to be examined.The membrane microdomain has been regarded as a signaling platform that harbors various signaling molecules and positively transduces cell signaling evoked by activated receptors (29). This model has been best exemplified in immunoreceptor-mediated signaling (8). Moreover, it was reported that SFKs could function positively when bound to Cbp/PAG1 in the microdomain (30, 32). Such positive roles of the microdomain in cell signaling are apparently inconsistent with its suppressive role in Src-mediated transformation. However, this discrepancy rather raises the possibility that the membrane microdomain would function to segregate or protect the normal signaling pathway from the transforming pathways. To prove this hypothesis, more extensive analysis of the role of the membrane microdomain in controlling cell transformation remains to be performed (28).To elucidate the role of the membrane microdomain in regulating the functions of SFKs, we first compared the transforming abilities of all SFK members using Csk-deficient cells, a reconstitution system in which wild-type SFKs can induce cell transformation (24), and we evaluated the relevance of the membrane distribution of SFKs to their transforming activities. We then investigated the role of the microdomain by disrupting or enhancing its function using methyl-β-cyclodextrin (MβCD) and a microdomain-specific adaptor, Cbp/PAG1, respectively. Our results show that the membrane microdomain and Cbp/PAG1 spatially limit the oncogenic potential of SFKs by sequestering them away from the transforming pathways.     

Effect of the presence of empty sites on the evolution of cooperation by costly punishment in spatial games

Cooperation and spiteful behavior are still evolutionary puzzles. Costly punishment, for which the game payoff is the same as that of spiteful behavior, is one mechanism for promoting the evolution of cooperation. A spatially structured population facilitates the evolution of either cooperation or spite/punishment if cooperation is linked explicitly or implicitly with spite/punishment; a cooperator cooperates with another cooperator and punishes/spites the other type of player. Different updating rules in the evolutionary game produce different evolutionary outcomes: with one updating rule—the score-dependent viability model, in which a player dies with a probability inversely proportional to the game score and the resulting unoccupied site is colonized by one player chosen randomly—the evolution of spite/punishment is promoted more than with the other updating rule—the score-dependent fertility model, in which, after a player dies randomly, the site is colonized by a player with a higher game score. If the population has empty sites, spiteful players or punishers should have less chance to interact with others and then spite/punish others. Thus the presence of empty sites would affect the evolutionary dynamics of spite/punishment. Here, we investigated whether the presence of empty sites discourages the evolution of spite/punishment in both a lattice-structured population and a completely mixing population where players interact with others randomly, especially when the score-dependent viability model is adopted. In the lattice-structured population adopting this viability model, the presence of empty sites promoted the evolution of cooperation and did not reduce the effect of spite/punishment. In the completely mixing population, the presence of empty sites did not promote evolution of cooperation by punishment. The evolutionary dynamics of the score-dependent viability model with empty sites were close to those of the score-dependent fertility model.     

Local increase in trapezius muscle oxygenation during and after acupuncture

Purpose

This study aimed to compare the trapezius muscle blood volume and oxygenation in the stimulation region and in a distant region in the same muscle during acupuncture stimulation (AS). We hypothesized that AS provokes a localized increase in muscle blood volume and oxygenation in the stimulation region.

Methods

Two sets of near-infrared spectrometer (NIRS) probes, with 40-mm light-source detector spacing, were placed on the right trapezius muscle, with a 50-mm distance between the probes. Changes in muscle oxygenation (oxy-Hb) and blood volume (t-Hb) in stimulation and distant regions (50 mm away from the stimulation point) were measured using NIRS. Nine healthy acupuncture-experienced subjects were chosen as the experimental (AS) group, and 10 healthy acupuncture-experienced subjects were chosen for the control (no AS) group. Measurements began with a 3-min rest period, followed by "Jakutaku" (AS) for 2 min, and recovery after stimulation.

Results

There was a significant increase in oxy-Hb (60.7 μM at maximum) and t-Hb (48.1 μM at maximum) in the stimulation region compared to the distant region. In the stimulation region, a significant increase in oxy-Hb and t-Hb compared with the pre-stimulation level was first noted at 58.5 s and 13.5 s, respectively, after the onset of stimulation.

Conclusion

In conclusion, oxygenation and blood volume increased, indicating elevated blood flow to the small vessels, not in the distant region used in this study, but in the stimulation region of the trapezius muscle during and after a 2-min AS.