Functional dissection of the gamma-tubulin complex by suppressor analysis of gtb1 and alp4 mutations in Schizosaccharomyces pombe

In fission yeast, gamma-tubulin (encoded by the gtb1+ gene), Alp4 (Spc97/GCP2), and Alp6 (Spc98/GCP3) are essential components of the gamma-tubulin complex. We isolated gtb1 mutants as allele-specific suppressors of temperature-sensitive alp4 mutations. Mutation sites in gtb1 mutants and in several alp4 alleles were determined. The majority of substituted amino acids were mapped to a small area on the predicted surface of the gamma-tubulin molecule that might directly interact with the Alp4 protein. The cold sensitivity of gamma-tubulin mutants was almost completely suppressed by an alpha-tubulin mutation and partially suppressed by a low concentration of thiabendazole, a microtubule assembly inhibitor. Other gtb1 mutants had increased resistance to this drug. Gel-filtration and immunoprecipitation analyses suggested that the mutant gamma-tubulin formed an altered gamma-tubulin complex with increased stability compared to wild-type gamma-tubulin. In most gtb1 mutants, sexual development was impaired, and aberrant asci that contained an irregular spore shape and number were produced. In contrast, spore formation was not appreciably damaged in some alp4 and alp6 mutants, even at temperatures where vegetative proliferation was substantially defective. These results suggested that the function of the gamma-tubulin complex or the requirement of each component of the complex is differentially regulated between the vegetative and sexual phases of the life cycle in fission yeast. In addition, genetic data indicated intimate functional connections of gamma-tubulin with several kinesin-like proteins.     

pH-dependent fluorescence of uncharged benzothiazole-based dyes binding to DNA.

Uncharged benzothiazole-based dyes were synthesized, and their fluorescence properties were examined. These fluorescent dyes showed an intense fluorescence in aqueous solution in the presence of DNA. In addition, the fluorescence intensities were pH dependent, while those of the positively charged dyes were nearly independent of pH. The pH-dependent photophysical behavior suggests that interaction of protonated dyes with DNA results in high intensities of fluorescent emission.     

Sea urchin egg receptor for sperm: the oligosaccharide chains stabilize sperm binding

Sulfated O-linked oligosaccharides from the sea urchin egg receptorhave been shown to bind to acrosome-reacted sperm and to inhibitfertilization in a competitive bioassay. However, the inhibitoryactivity of these isolated chains was much lower than that ofa recombinant protein representing a portion of the extracellulardomain of the receptor. Because the isolated oligosaccharideslacked the potential polyvalency that they might have when linkedto the polypeptide backbone, in the current study we asked iftheir inhibitory activity could be increased by chemically couplingthem to a protein to form a neoglycoprotein. Using a recombinantfragment of the receptor we could not detect an oligosaccharidedependent increase in inhibitory activity with this neoglycoprotein,probably because of the much higher inhibitory activity of thepolypeptide backbone. Therefore, we examined the activity ofthe oligosaccharides coupled to a protein lacking the abilityto inhibit fertilization, namely, bovine serum albumin. A markedincrease in the inhibitory activity of the oligosaccharideswas observed with this neoglycoprotein. Finally, because inhibitionby the oligosaccharides and the polypeptide was measured inan end point assay, namely, inhibition of fertilization, wesought a more direct, kinetically sensitive way to measure theirproperties. Accordingly, an assay was devised (R.L.Stears andW.J.Lennarz, unpublished observations) involving measurementof sperm binding to beads that was dependent on the presenceof the receptor or its components. This assay revealed thatsperm binding to beads via the recombinant protein peaked at10 sec and then declined. In contrast, binding mediated by neoglycosylatedrecombinant protein reached a plateau. Thus, binding of spermto the oligosaccharides resulted in a more stable interactionthan that observed in binding to the polypeptide backbone. sperm binding sea urchin egg sperm binding oligosaccharide     

Aromatic C–H bond hydroxylation by P450 peroxygenases: a facile colorimetric assay for monooxygenation activities of enzymes based on Russig’s blue formation

Aromatic C–H bond hydroxylation of 1-methoxynaphthalene was efficiently catalyzed by the substrate misrecognition system of the hydrogen peroxide dependent cytochrome P450_BSβ (CYP152A1), which usually catalyzes hydroxylation of long-alkyl-chain fatty acids. Very importantly, the hydroxylation of 1-methoxynaphthalene can be monitored by a color change since the formation of 4-methoxy-1-naphthol was immediately followed by its further oxidation to yield Russig’s blue. Russig’s blue formation allows us to estimate the peroxygenation activity of enzymes without the use of high performance liquid chromatography, gas chromatography, and nuclear magnetic resonance measurements.     

Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions.

We performed random sequencing of cDNAs from nine biologically or industrially important cultures of the industrially valuable fungus Aspergillus oryzae to obtain expressed sequence tags (ESTs). Consequently, 21 446 raw ESTs were accumulated and subsequently assembled to 7589 non-redundant consensus sequences (contigs). Among all contigs, 5491 (72.4%) were derived from only a particular culture. These included 4735 (62.4%) singletons, i.e. lone ESTs overlapping with no others. These data showed that consideration of culture grown under various conditions as cDNA sources enabled efficient collection of ESTs. BLAST searches against the public databases showed that 2953 (38.9%) of the EST contigs showed significant similarities to deposited sequences with known functions, 793 (10.5%) were similar to hypothetical proteins, and the remaining 3843 (50.6%) showed no significant similarity to sequences in the databases. Culture-specific contigs were extracted on the basis of the EST frequency normalized by the total number for each culture condition. In addition, contig sequences were compared with sequence sets in eukaryotic orthologous groups (KOGs), and classified into the KOG functional categories.     

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO-FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO-FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO-FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO-FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution.     

The newly identified human nuclear protein NXP-2 possesses three distinct domains, the nuclear matrix-binding, RNA-binding, and coiled-coil domains

Using a monoclonal antibody that recognizes a nuclear matrix protein, we selected a cDNA clone from a lambdagt11 human placenta cDNA library. This cDNA encoded a 939-amino acid protein designated nuclear matrix protein NXP-2. Northern blot analysis indicated that NXP-2 was expressed in various tissues at different levels. Forcibly expressed green fluorescent protein-tagged NXP-2 as well as endogenous NXP-2 was localized in the nucleus and distributed to the nuclear matrix. NXP-2 was released from the nuclear matrix when RNase A was included in the buffer for nuclear matrix preparation. Mapping of functional domains was carried out using green fluorescent protein-tagged truncated mutants of NXP-2. The region of amino acids 326-353 was responsible for nuclear matrix binding and contained a cluster of hydrophobic amino acids that was similar to the nuclear matrix targeting signal of acute myeloleukemia protein. The central region (amino acids 500-591) was demonstrated to be required for RNA binding by Northwestern analysis, although NXP-2 lacked a known RNA binding motif. The region of amino acid residues 682-876 was predicted to have a coiled-coil structure. The RNA-binding, nuclear matrix-binding, and coiled-coil domains are structurally separated, suggesting that NXP-2 plays important roles in diverse nuclear functions, including RNA metabolism and maintenance of nuclear architecture.