Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms

The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA^Tyrs. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA^Tyr(GΨA). Structural information for TyrRS–tRNA^Tyr complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs–tRNA^Tyrs pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNA^Tyr recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNA^Tyr pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNA^Tyr. On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.     

Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus

Tyrosine kinase (TK) proteins play a central role in cellular behavior and development of animals. The expansion of this superfamily is regarded as a key event in the evolution of the complex signaling pathways and gene networks of metazoans and is a prominent example of how shuffling of protein modules may generate molecular novelties. Using the intron/exon structure within the TK domain (TK intron code) as a complementary tool for the assignment of orthology and paralogy, we identified and studied the 118 TK proteins of the amphioxus Branchiostoma floridae genome to elucidate TK gene family evolution in metazoans and chordates in particular. Unlike all characterized metazoans to date, amphioxus has members of all known widespread TK families, with not a single loss. Putting amphioxus TKs in an evolutionary context, including new data from the cnidarian Nematostella vectensis, the echinoderm Strongylocentrotus purpuratus, and the ascidian Ciona intestinalis, we suggest new evolutionary histories for different TK families and draw a new global picture of gene loss/gain in the different phyla. Surprisingly, our survey also detected an unprecedented expansion of a group of closely related TK families, including TIE, FGFR, PDGFR, and RET, due most probably to massive gene duplication and exon shuffling. Based on their highly similar intron/exon structure at the TK domain, we suggest that this group of TK families constitute a superfamily of TK proteins, which we termed EXpanding TK, after their seemingly unique propensity to gene duplication and exon shuffling, not only in amphioxus but also across all metazoan groups. Due to this extreme tendency to both retention and expansion of TK genes, amphioxus harbors the richest and most diverse TK repertoire among all metazoans studied so far, retaining most of the gene complement of its ancestors, but having evolved its own repertoire of genetic novelties.     

Evaluation of neurotoxicity of TIQ and MPTP and of parkinsonism-preventing effect of 1-MeTIQ by in vivo measurement of pre-synaptic dopamine transporters and post-synaptic dopamine D(2) receptors in the mouse striatum.

Parkinsonism-inducing neurotoxicity of 1,2,3,4-tetrahydroisoquinoline (TIQ), as contrasted to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), and parkinsonism-preventing effect of 1-methyl-1,2,3,4-tetrahydroisoquinoline (1-MeTIQ) have been investigated in mice by measuring their effects on the in vivo binding of radioligand to pre-synaptic dopamine transporters (DATs) or to dopamine D(2) receptors (D2R) in the striatum. A significant reduction of the ligand-DATs binding was found in the mice treated with MPTP, but not with TIQ, under the dosage inducing behavioral abnormality and loss of tyrosine hydroxylase-positive cells in the substantia nigra. A slight decrease in the ligand-DATs binding was observed in the mice given a larger dose of TIQ. Compensatory up-regulation in the post-synaptic D2Rs was found in the MPTP-treated mice. Pre-treatment with (S)-enantiomer, but not (R)-enantiomer, of 1-MeTIQ prevented the degeneration of DATs to some extent. We concluded that the TIQ-induced parkinsonism model is different from the MPTP-induced model as evaluated by the radioligand-DATs binding and that (S)-1-MeTIQ has a preventing effect for the degeneration of the DATs to a certain extent.     

Crystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity

Crystals have been obtained for a 2,3-dihydroxybiphenyl dioxygenase (conventionally called BphC) from a polychlorinated biphenyl (PCB)-degrader, Pseudomonas sp. strain KKS1O2. The crystals were grown using both ammonium sulfate and MPD as the precipitating agents. The crystals belonged to a tetragonal space group (I422) and diffracted to 2.5 Å. © 1995 Wiley-Liss, Inc.     

A Cytosolic Phospholipase A2 from Potato Tissues Appears to Be Patatin

Phospholipase (PL) A₂ is involved in signal transduction inthe resistance reaction that is induced in potato by inoculationof an incompatible race of Phytophthora infestans, the lateblight fungus, or by treatment with fungal elicitor hyphal wallcomponents (Kawakita et al. 1993). In this study, PLA₂ in thesoluble fraction from potato tuber was purified. The followingresults suggested that the enzyme was, in fact, patatin: (1)the molecular mass of the purified enzyme was 40 kDa, the sameas that of patatin; (2) the pI of the purified enzyme was approximately4.75, which corresponds to that of patatin; and (3) the amino-terminalamino acid sequence of the purified enzyme showed a high degreeof homology to that of patatin. Patatin is known as a storageprotein of the potato tuber and it has been shown to have esteraseactivity. However, other enzymatic activities and the function(s)of patatin are unknown. We investigated the PLA activities ofthe purified patatin. The PLA₂ activity of the patatin was muchhigher than the PLA₁ activity, even though the protein exhibitedboth activities. The PLA₂ activity of the enzyme was particularlyapparent when phosphatidylcholine with linoleic acid at thesn-2 position was used as substrate. Lower activity was observedwith phosphatidylcholine with palmitic acid, oleic acid andarachidonic acid at the sn-2 position. (Received October 5, 1995; Accepted February 9, 1996)     

Isocoumarins from Coriandrum sativum

Two new isocoumarins, coriandrone A and B, were isolated from the aerial parts of Coriandrum sativum together with two known isocoumarins, coriandrin and dihydrocoriandrin. Their structure were established by spectroscopic means and X-ray analysis.     

Total synthesis of a gene for octopus rhodopsin and its preliminary expression.

To carry out systematic structure-function studies of octopus rhodopsin, photoreceptor protein of octopus visual cells, by means of specific amino-acid replacements, we have totally synthesized a DNA duplex of 1,365 base pairs that encodes the entire octopus rhodopsin of 455 amino acids [Ovchinnikov et al. (1988) FEBS Lett. 232, 69-72] by introducing codons preferred in Escherichia coli. Total synthesis simplifies site-specific mutagenesis in all parts of the gene by replacement of short restriction fragments by their newly synthesized counterparts containing the required nucleotide alterations. Thirty unique restriction sites were introduced in the octopus rhodopsin gene, which was assembled on a plasmid in two steps. Five cartridge genes of 344, 296, 320, 212, and 317 base pairs capable of being expressed independently were first constructed by using 48 synthetic oligonucleotides ranging in size from 54 to 73 nucleotides. The entire gene was constructed by consecutive linkage of cartridge genes. These cartridge genes were designed to correspond to the transmembrane helical unit of octopus rhodopsin, resulting in easy construction of various chimeric rhodopsins. The nucleotide sequences were confirmed by sequencing the cartridges as well as the entire gene. These synthetic genes were cloned into an expression vector carrying the trp promoter of E. coli, and were preliminarily expressed in vitro and in vivo.     

Oriented structure of pectic polysaccharides in pea epidermal cell walls

Polarized infrared absorption spectra of film specimens of theepidermal cell wall of the third internode of pea stems wererecorded before and after treatment with endopolygalacturonase(endo-PG) and endo-pectin lyase (endo-PL). The spectra showedthat the pectic polysaccharides solubilized with endo-PG wereessentially the same as those solubilized with endo-PL. Thedegree of esterification of the pectic polysaccharides was about20%, and their major sugar components were uronic acids (32.8%),arabinose (48.1%) and galactose (19.2%). The polarized infraredspectra showed that pectic polysaccharides have an orientedstructure in cell walls with their molecular chains orientedpreferentially parallel to the direction of cell elongation. ¹Present address: Research and Development, Kanzaki Paper Mfg.Co., Ltd., Amagasaki, Hyogo 660, Japan. ²Present address: Wakayama Research Laboratories, Kao Soap Co.,Ltd., Wakayama 640-91, Japan. (Received June 28, 1980; )