Mutational separation of two pathways for editing by a class I tRNA synthetase

Aminoacyl tRNA synthetases (aaRSs) catalyze the first step in protein biosynthesis, establishing a connection between codons and amino acids. To maintain accuracy, aaRSs have evolved a second active site that eliminates noncognate amino acids. Isoleucyl tRNA synthetase edits valine by two tRNA(Ile)-dependent pathways: hydrolysis of valyl adenylate (Val-AMP, pretransfer editing) and hydrolysis of mischarged Val-tRNA(Ile) (posttransfer editing). Not understood is how a single editing site processes two distinct substrates--an adenylate and an aminoacyl tRNA ester. We report here distinct mutations within the center for editing that alter adenylate but not aminoacyl ester hydrolysis, and vice versa. These results are consistent with a molecular model that shows that the single editing active site contains two valyl binding pockets, one specific for each substrate.     

Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.

BACKGROUND: The AU binding homolog of enoyl-CoA hydratase (AUH) is a bifunctional protein that has two distinct activities: AUH binds to RNA and weakly catalyzes the hydration of 2-trans-enoyl-coenzyme A (enoyl-CoA). AUH has no sequence similarity with other known RNA binding proteins, but it has considerable sequence similarity with enoyl-CoA hydratase. A segment of AUH, named the R peptide, binds to RNA. However, the mechanism of the RNA binding activity of AUH remains to be elucidated. RESULTS: We determined the crystal structure of human AUH at 2.2 A resolution. AUH adopts the typical fold of the enoyl-CoA hydratase/isomerase superfamily and forms a hexamer as a dimer of trimers. Interestingly, the surface of the AUH hexamer is positively charged, in striking contrast to the negatively charged surfaces of the other members of the superfamily. Furthermore, wide clefts are uniquely formed between the two trimers of AUH and are highly positively charged with the Lys residues in alpha helix H1, which is located on the edge of the cleft and contains the majority of the R peptide. A mutational analysis showed that the lysine residues in alpha helix H1 are essential to the RNA binding activity of AUH. CONCLUSIONS: Alpha helix H1 exposes a row of Lys residues on the solvent-accessible surface. These characteristic Lys residues are named the "lysine comb." The distances between these Lys residues are similar to those between the RNA phosphate groups, suggesting that the lysine comb may continuously bind to a single-stranded RNA. The clefts between the trimers may provide spaces sufficient to accommodate the RNA bases.     

Isolation and enzymological characterization of infected and uninfected cell protoplasts from root nodules of Glycine max

Infected and uninfected cell protoplasts were isolated from soybean ( Glycine max L. Merr. cv. Akisengoku) root nodules and purified by the use of nylon mesh filters and discontinuous Percoll gradients. Activities of the enzymes involved in carbon and nitrogen metabolism were measured in cytoplasmic fractions of purified protoplasts, as well as in the bacteroids isolated from infected cell protoplasts and in the cortical tissues after enzymatic digestion of the central zone of the nodules.
A high degree of purity of both infected and uninfected cells was demonstrated by microscopic observations and assays of β-hydroxybutyrate dehydrogenase (EC 1.1.1.30) and uricase (EC 1.7.3.3) activities and leghemoglobin contents.
As a whole, higher specific activities of enzymes of glycolysis were found in the cortical and uninfected cells than in the infected cells. The activities of glycolytic enzymes were extremely low in the bacteroids. Invertase (EC 3.2.1.26) was highly localized in the cortex. However, activity of sucrose synthase (EC 2.4.1.13) was highest in the cytosol of infected cells. Alcohol dehydrogenase (EC 1.1.1.1) and lactate dehydrogenase (EC 1.1.1.27) activities were much higher in uninfected than in infected cells. Specific activities of enzymes for nitrogen assimilation, that is, glutamine synthetase (EC 6.3.1.2), glutamate synthase (EC 1.4.1.14), aspartate (EC 2.6.1.1) and alanine (EC 2.6.1.2) aminotransferase were several-fold higher in uninfected cells than in the infected cells.
The results are discussed in relation to the possible cellular organization of carbon and nitrogen metabolism in soybean root nodules.     

The fibronectin-derived anti-adhesive peptide III14-2 suppresses adhesion and apoptosis of leukemic cell lines through down-regulation of protein-tyrosine phosphorylation.

We previously found that fibronectin (FN) has a cryptic functional site (YTIYVIAL, #1848-1855) opposing to cell adhesion to extracellular matrix (ECM). The present study demonstrates that the FN peptide containing this anti-adhesive site, termed peptide III14-2, affects programmed cell death (PCD) (apoptosis) as well as cell adhesion by down-regulating protein-tyrosine phosphorylation. Peptide III14-2 suppressed the integrin alpha5beta1-mediated adhesion of leukemic cell lines (K562 and HL60), and protein tyrosine phosphatase inhibitor, 1 microM phenylarsine oxide (PAO) blocked the anti-adhesive effect of peptide III14-2. These leukemic cells underwent PCD when exposed to PAO at the higher concentration (5 microM), as judged by nuclear and DNA fragmentations, and which was reversed by tyrosine kinase inhibitor, genistein. Peptide III14-2 suppressed the PAO-induced PCD, whereas a control peptide in which the anti-adhesive sequence YTIYVIAL is scrambled, was inactive. Western blotting showed that PAO stimulated the tyrosine phosphorylation of cellular proteins including focal adhesion kinase and that peptide III14-2 inhibited them, suggesting that protein-tyrosine phosphorylation represents a common early signal for the adhesion and PCD. The anti-adhesive site of FN molecule may play a crucial role also in a variety of cellular processes other than adhesion and PCD by down-regulating protein-tyrosine phosphorylation.     

A neural correlate of the processing of multi-second time intervals in primate prefrontal cortex

Several areas of the brain are known to participate in temporal processing. Neurons in the prefrontal cortex (PFC) are thought to contribute to perception of time intervals. However, it remains unclear whether the PFC itself can generate time intervals independently of external stimuli. Here we describe a group of PFC neurons in area 9 that became active when monkeys recognized a particular elapsed time within the range of 1-7 seconds. Another group of area 9 neurons became active only when subjects reproduced a specific interval without external cues. Both types of neurons were individually tuned to recognize or reproduce particular intervals. Moreover, the injection of muscimol, a GABA agonist, into this area bilaterally resulted in an increase in the error rate during time interval reproduction. These results suggest that area 9 may process multi-second intervals not only in perceptual recognition, but also in internal generation of time intervals.     

Stability versus neuronal specialization for STDP: long-tail weight distributions solve the dilemma

Spike-timing-dependent plasticity (STDP) modifies the weight (or strength) of synaptic connections between neurons and is considered to be crucial for generating network structure. It has been observed in physiology that, in addition to spike timing, the weight update also depends on the current value of the weight. The functional implications of this feature are still largely unclear. Additive STDP gives rise to strong competition among synapses, but due to the absence of weight dependence, it requires hard boundaries to secure the stability of weight dynamics. Multiplicative STDP with linear weight dependence for depression ensures stability, but it lacks sufficiently strong competition required to obtain a clear synaptic specialization. A solution to this stability-versus-function dilemma can be found with an intermediate parametrization between additive and multiplicative STDP. Here we propose a novel solution to the dilemma, named log-STDP, whose key feature is a sublinear weight dependence for depression. Due to its specific weight dependence, this new model can produce significantly broad weight distributions with no hard upper bound, similar to those recently observed in experiments. Log-STDP induces graded competition between synapses, such that synapses receiving stronger input correlations are pushed further in the tail of (very) large weights. Strong weights are functionally important to enhance the neuronal response to synchronous spike volleys. Depending on the input configuration, multiple groups of correlated synaptic inputs exhibit either winner-share-all or winner-take-all behavior. When the configuration of input correlations changes, individual synapses quickly and robustly readapt to represent the new configuration. We also demonstrate the advantages of log-STDP for generating a stable structure of strong weights in a recurrently connected network. These properties of log-STDP are compared with those of previous models. Through long-tail weight distributions, log-STDP achieves both stable dynamics for and robust competition of synapses, which are crucial for spike-based information processing.     

Tenascin-C-derived Peptide TNIIIA2 Highly Enhances Cell Survival and Platelet-derived Growth Factor (PDGF)-dependent Cell Proliferation through Potentiated and Sustained Activation of Integrin α5β1

Tenascin-C is an adhesion modulatory matrix protein that is highly expressed in tumors; however, its biochemical activity involved in tumorigenesis is not fully understood. On the other hand, increasing evidence indicates the importance of integrin α5β1 in cancer development. We previously demonstrated that tenascin-C harbors a functional site that can be released as a proadhesive peptide such as TNIIIA2. Peptide TNIIIA2 is capable of inducing activation of β1-integrins including α5β1 via syndecan-4. In this study the proadhesive effect of TNIIIA2 was characterized by potentiated and sustained activation of integrin α5β1. Based on this effect, TNIIIA2 rendered nontransformed fibroblasts (NIH3T3) resistant to serum deprivation-elicited anoikis through activation of the Akt/Bcl-2 pathway. Moreover, TNIIIA2 hyperstimulated PDGF-dependent proliferation of NIH3T3 by activating integrin α5β1. Tenascin-C, a parental protein of TNIIIA2, also stimulated PDGF-dependent proliferation, which was blocked by a matrix metalloproteinase-2/9 inhibitor and an anti-TNIIIA2 function-blocking antibody, suggesting proteolytic exposure of the proadhesive effect of TNIIIA2. Mechanistic analyses revealed that TNIIIA2 induced a lateral association of PDGF receptor β with the molecular complex of activated integrin α5β1 and syndecan-4 in the membrane microdomains enriched with cholesterol/caveolin-1, resulting in prolonged activation of PDGF receptor β and the subsequent Ras/mitogen-activated protein kinase pathway in a PDGF-dependent manner. Of note, TNIIIA2 induced continuous proliferation in NIH3T3 in an integrin α5β1-dependent manner even after they formed a confluent monolayer. Thus, it was proposed that tenascin-C might be involved in deregulated cell growth through potentiated and sustained activation of integrin α5β1 after exposure of the proadhesive effect of TNIIIA2.     

Generation of a new red fluorescent condensed hetero-aromatic compound: 7,20-dimethyl-7,20-dihydro-7,20-diaza-naphto[a]dibenzo[j,q]perylene.

A coupling reaction of 5-methylbenz[b]acridin-12(5H)-one (MBA) with Zn and TiCl(4) provided a red fluorescent (FL) compound, as opposed to 5,5'-dimethyl-12,12'-bibenzo[b]acridylidene (DMBBA), probably through photochemical cyclization and aromatization by dehydrogenation of the overcrowded intermediate DMBBA. The structure of the red FL compound was assigned to 7,20-dimethyl-7,20-dihydro-7,20-diaza-naphto[a]dibenzo[j,q]perylene (DANDBP) and the fluorescence efficiency for DANDBP was determined to be 0.23 +/- 0.01.     

Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex

Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.