Satoru Ohgiya

Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature

We performed genome-wide expression analysis to determine genetic responses in Saccharomyces cerevisiae to a low temperature environment using a cDNA microarray. Approximately 25% of the genes in the yeast genome were found to be involved in the response of yeast to low temperature. This finding of a large number of genes being involved in the response to low temperature enabled us to give a functional interpretation to the genetic responses to the stimulus. Functional and clustering analyses of temporal changes in gene expression revealed that global states of the expressions of up-regulated genes could be characterized as having three phases (the early, middle, and late phases). In each phase, genes related to rRNA synthesis, ribosomal proteins, or several stress responses are time-dependently up-regulated, respectively. Through these phases, yeast cells may improve reduced efficiency of translation and enhance cell protection mechanisms to survive under a low temperature condition. Furthermore, these time-dependent regulations of these genes would be controlled by the cAMP-protein kinase A pathway. The results of our study provide a global description of transcriptional response for adaptation to low temperature in yeast cells.

Isolation of clustered genes that are notably homologous to the eicosapentaenoic acid biosynthesis gene cluster from the docosahexaenoic acid-producing bacterium Vibrio marinus strain MP-1

A 40-kbp DNA fragment was isolated from the cosmid library of Vibrio marinus strain MP-1. Among the 22 putative open reading frames (ORFs) in this fragment, ORFs 8, 9, 10 and 11 had high homology with ORFs 5, 6, 7 and 8 of the eicosapentaenoic acid biosynthesis gene cluster, respectively. Then, we speculate that these ORFs are responsible for docosahexaenoic acid biosynthesis in this bacterium.

Isolation of a Pseudomonas species from fish intestine that produces a protease active at low temperature

A psychrotrophic bacterium producing a protease active at low temperatures was isolated from fish intestine and identified as a Pseudomonas species. Optimum growth and protease‐producing temperatures of this strain were 15°C and 10°C, respectively. The maximum temperature for proteolytic activity was 25°C, an unusually low temperature.

Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution.

Bacillus subtilis extracellular lipase (BsL) has an exceptionally low molecular weight (19.4 kDa) for a member of the lipase family. A crystallographic study was performed on BsL in order to design and produce mutant BsL that will be more suitable for industrial uses based on analysis of the three-dimensional structure. Recently, the crystal structure of BsL has been determined at 1.5 A resolution [van Pouderoyen et al. (2001). J. Mol. Biol. 309, 215–226]. In the present study, a new crystal form of BsL which provides diffraction data to higher resolution was obtained and its structure was determined at 1.3 A using the MAD method. It was found that the active-site residue Ser77 has alternate side-chain conformations . The Oγ atom of the first conformer forms a hydrogen bond to the N∊ atom of His155, a member of the catalytic triad. In contrast, the second conformer is constructed with a hydrogen bond to the side-chain atom of the adjacent His76. These two conformers presumably correspond to the active and inactive states, respectively. Similar alternate conformations in the catalytic serine residue have been observed in Fusarium solani cutinase determined at 1.0 A resolution and Penicillium purpurogenum acetylxylan esterase at 0.9 A resolution. In addition, a glycerol molecule, which was used as a cryoprotectant, is found to be located in the active site. On the basis of these results, a model for substrate binding in the reaction-intermediate state of BsL is proposed.

Total Biosynthesis of Diterpene Aphidicolin, a Specific Inhibitor of DNA Polymerase α: Heterologous Expression of Four Biosynthetic Genes in Aspergillus oryzae

Clustering of biosynthetic genes for producing fungal secondary metabolites, which frequently consist of less than ten genes, has been recognized with numerous genomes. The heterologous expression of whole genes in the clusters will therefore produce various types of natural products when using a suitable fungal host. We introduced the whole gene cluster for the biosynthesis of diterpene aphidicolin into the fungal quadruple auxotrophic host, Aspergillus oryzae, by using four different vectors (pTAex3, pPTRI, pUSA and pAdeA) which harbor a starch-inducible promoter/terminator to examine the expression conditions. The resulting quadruple transformant carrying the genes of geranylgeranyl diphosphate synthase PbGGS, terpene synthase PbACS, and two monooxygenases (PbP450-1 and PbP450-2) produced aphidicolin. The double and triple transformants also respectively produced aphidicolan-16β-ol and 3-deoxyaphidicolin. Alternative host Saccharomyces cerevisiae carrying the genes, PbGGS and PbACS, produced key intermediate aphidicolan-16β-ol. This is the first example of a total biosynthesis of terpenoids using fungal hosts.

A part of ice nucleation protein exhibits the ice-binding ability

We generated a recombinant 96‐residue polypeptide corresponding to a sequence Tyr176–Gly273 of ice nucleation protein from Pseudomonas syringae (denoted INP96). INP96 exhibited an ability to shape an ice crystal, whose morphology is highly similar to the hexagonal‐bipyramid generally identified for antifreeze protein. INP96 also showed a non‐linear, concentration‐dependent retardation of ice growth. Additionally, circular dichroism and NMR measurements suggested a local structural construction in INP96, which undergoes irreversible thermal denaturation. These data imply that a part of INP constructs a unique structure so as to interact with the ice crystal surfaces.

Evidence of Environmental and Vertical Transmission of Burkholderia Symbionts in the Oriental Chinch Bug, Cavelerius saccharivorus (Heteroptera: Blissidae)

ABSTRACT The vertical transmission of symbiotic microorganisms is omnipresent in insects, while the evolutionary process remains totally unclear. The oriental chinch bug, Cavelerius saccharivorus (Heteroptera: Blissidae), is a serious sugarcane pest, in which symbiotic bacteria densely populate the lumen of the numerous tubule-like midgut crypts that the chinch bug develops. Cloning and sequence analyses of the 16S rRNA genes revealed that the crypts were dominated by a specific group of bacteria belonging to the genus Burkholderia of the Betaproteobacteria. The Burkholderia sequences were distributed into three distinct clades: the Burkholderia cepacia complex (BCC), the plant-associated beneficial and environmental (PBE) group, and the stinkbug-associated beneficial and environmental group (SBE). Diagnostic PCR revealed that only one of the three groups of Burkholderia was present in ∼89% of the chinch bug field populations tested, while infections with multiple Burkholderia groups within one insect were observed in only ∼10%. Deep sequencing of the 16S rRNA gene confirmed that the Burkholderia bacteria specifically colonized the crypts and were dominated by one of three Burkholderia groups. The lack of phylogenetic congruence between the symbiont and the host population strongly suggested host-symbiont promiscuity, which is probably caused by environmental acquisition of the symbionts by some hosts. Meanwhile, inspections of eggs and hatchlings by diagnostic PCR and egg surface sterilization demonstrated that almost 30% of the hatchlings vertically acquire symbiotic Burkholderia via symbiont-contaminated egg surfaces. The mixed strategy of symbiont transmission found in the oriental chinch bug might be an intermediate stage in evolution from environmental acquisition to strict vertical transmission in insects.

Development of valuable yeast strains using a novel mutagenesis technique for the effective production of therapeutic glycoproteins

Yeast cells producing mammalian-type N-linked oligosaccharide show severe growth defects and the decreased protein productivity because of the disruption of yeast-specific glycosyltransferases. This decreased protein productivity in engineered yeast strains is an obstacle to the development of efficient glycoprotein production in yeast. For economic and effective synthesis of such therapeutic glycoproteins in yeast, the development of appropriate strains is highly desirable. We applied a novel mutagenesis technique that utilized the proofreading-deficient DNA polymerase delta variant encoded by the pol3-01 gene of Saccharomyces cerevisiae or the cdc6-1 gene of Schizosaccharomyces pombe to the engineered S. cerevisiae TIY20 strain and S. pombe KT97 strain, respectively. TIY20, which is deficient in the outer chain of mannan due to the disruption of three genes (och1Delta, mnn1 Delta, mnn4 Delta), and KT97, which is an och1 disruptant, are impractical as hosts for the production of therapeutic glycoproteins since they show a temperature-sensitive (ts) phenotype, a growth defect phenotype, and decreased protein productivity. We successfully isolated YAB mutants that alleviated the growth defect of the TIY20 strain. Surprisingly, these mutants generally secreted foreign proteins better than the wild-type strain. Furthermore, we successfully isolated YPAB mutants that alleviated the growth defect of the KT97 strain, too. The development of these new mutants by the combination of genetic engineering of yeast and this mutagenesis technique are major breakthroughs for the production of therapeutic glycoproteins in engineered yeast cells.

Molecular Cloning and Functional Analysis of Cynomolgus Monkey CYP1A2

Complementary DNA fragments encoding cynomolgus monkey CYP1A2 were amplified by the reverse transcriptase-polymerase chain reaction (RT-PCR) method from the liver total RNA of a 3-methylcholanthrene (3-MC)-treated cynomolgus monkey. The nucleotide sequence determined was 1630 bp long and contained an open reading frame for a polypeptide of 516 residues. The nucleotide and the deduced amino acid sequences of cynomolgus monkey CYP1A2 showed 95.1 and 92.8% identities to those of human CYP1A2, respectively. The level of CYP1A2 mRNA in the liver of untreated cynomolgus monkey was very low. Treatment with 3-MC increased it. Still, it was one-fortieth that of CYP1A1. Cynomolgus monkey CYP1A2 expressed in recombinant yeasts activated 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-3,8dimethylimidazo[4,5-flquinoxaline (MeIQx) at efficient rates in the umu mutagenicity test. This cytochrome P450 (CYP) also activated 2-amino-l-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), but less efficiently. These results indicate that cynomolgus monkeys have a functionally active CYPIA2 gene, but its expression level is very low in the liver of untreated cynomolgus monkeys.

Biotechnology of enzymes from cold-adapted microorganisms

One of the main goals in enzyme research is industrial application. Nowadays, we are surrounded by enzymes as well as chemicals produced by enzymes in our daily life. Since papain (EC 3.4.22.2) was used, probably as the first exogenous enzyme, to prevent the formation of chill hazes in beer,1 many enzymes isolated from various species have been developed for industrial use. These enzymes are used as biological catalysts in various industries such as detergent, food, chemical, textile, pharmaceutical, and paper industries. For instance, proteolytic enzymes are used for detergents; pharmaceutical agents; leather bating; enzymatic conversion of peptidyl substances; and food processing such as cheese production, meat tenderizing, dough conditioning in baking, and protein recovery from waste food materials.2 Most of the industrial enzymes have been isolated from mesophiles and thermophiles, since innumerable kinds of mesophiles are easily obtained from environmental sources, and enzymes obtained from thermophiles are suitable for industrial processes due to their thermostability. Heat-stable enzymes isolated from thermophiles also have an advantage in terms of storage stability, because they can be transported and stored at the ambient temperature. On the other hand, although many enzymes have also been isolated from cold-adapted microorganisms,3 psychrophiles and psychrotrophs, there have been few reports on the industrial use of such enzymes. It is reasonable to expect that cold-adapted microorganisms produce enzymes that are active even at a low temperature, i.e., “cold-active enzymes.” They would not only be more active at a low temperature than enzymes isolated from mesophiles and thermophiles but would also presumably have distinct characteristics.