Generation of Large Chromosomal Deletions in Koji Molds Aspergillus oryzae and Aspergillus sojae via a Loop-Out Recombination

We established a technique for efficiently generating large chromosomal deletions in the koji molds Aspergillus oryzae and A. sojae by using a ku70-deficient strain and a bidirectional marker. The approach allowed deletion of 200-kb and 100-kb sections of A. oryzae and A. sojae, respectively. The deleted regions contained putative aflatoxin biosynthetic gene clusters. The large genomic deletions generated by a loop-out deletion method (resolution-type recombination) enabled us to construct multiple deletions in the koji molds by marker recycling. No additional sequence remained in the resultant deletion strains, a feature of considerable value for breeding of food-grade microorganisms. Frequencies of chromosomal deletions tended to decrease in proportion to the length of the deletion range. Deletion efficiency was also affected by the location of the deleted region. Further, comparative genome hybridization analysis showed that no unintended deletion or chromosomal rearrangement occurred in the deletion strain. Strains with large deletions that were previously extremely laborious to construct in the wild-type ku70⁺ strain due to the low frequency of homologous recombination were efficiently obtained from Δku70 strains in this study. The technique described here may be broadly applicable for the genomic engineering and molecular breeding of filamentous fungi.     

Study of Homologous Recombination and Chromosomal Rearrangements inEscherichia coliStrains Carrying a Heterozygous Tandem Duplication

Heterozygous tandem duplications formed in conjugational matings in Escherichia coliprovides a convenient model system for studying the evolution of bacterial chromosome. Heterozygous duplications segregate various classes of haploid and diploid recombinants that appear as a result of unequal crossing over between sister chromosomes. In this work, an extended tandem duplication in the deooperon of E. colicarrying deoA deoB::Tn5/deoC deoD thr::Tn9alleles was examined. Recombination between homologous DNA repeats in the duplication was studied in strains carrying different combinations of recBC, sbcBC, recB::Tn10, recQ::Tn3and recF::Tn3mutations. The frequency of recombination between homologous DNA repeats was very high in all strains and did not decrease when the RecBCD and RecF recombinational pathways were simultaneously damaged in strains with the recB sbcBC recQ(or recF) genotype. It is assumed that unequal crossing over between direct DNA repeats in duplications may proceed through a particular pathway of adaptive recombination.     

Expression of SV40 Large T Antigen Stimulates Reversion of a Chromosomal Gene Duplication in Human Cells

Transformation of human cells is characterized by altered cell morphology, frequent karyotypic abnormalities, reduced dependence on growth factors and substrate, and rare “immortalization”—clonal acquisition of unlimited proliferative potential. We previously reported a marked increase in DNA rearrangements, arising between two duplicated segments in a transfected plasmid substrate, for five immortal human cell lines relative to three normal fibroblast strains [Finnet al.(1989)Mol. Cell. Biol.9, 4009–4017]. We have now assessed reversion of a 14-kilobase-pair duplication within the hypoxanthine phosphoribosyl transferase (HPRT) gene locus, in a fibroblast strain during its normal replicative lifespan and after stable transformation with SV40 large-T antigen. Revertants, selected under HPRT-dependent growth conditions immediately after purging preexistingHPRT⁺cells, were confirmed asHPRT⁺by hypoxanthine incorporation and 6-thioguanine sensitivity. Southern blot analyses indicate loss from most revertant clones of a restriction fragment representing the duplicatedHPRTregion, as predicted for homologous recombination between the 14-kilobase-pair repeats. Amplification of a subregion ofHPRTmRNA implicated deletion of duplicated exons in 93% of revertant colonies. Reversion toHPRT⁺was unaltered during the normalin vitrolifespan of these cells, but increased in 9 clones stably transformed with large-T antigen (mean = 3.8-fold; eachP< 10⁻⁵). Stimulation ofHPRT-reversion is abrogated in a variety of T-antigen mutants, and depends on continued induction of T antigen by glucocorticoid in two clones tested 10–30 doublings before replicative senescence. Since no immortal subclones arose from these clones, elevated reversion must precede immortalization. Increased DNA rearrangements, in cells expressing T-antigen, could facilitate the rare concurrence of multiple mutations necessary for immortalization.     

Study of RecA-Independent Homologous Recombination and a Chromosomal Rearrangement in the Escherichia coli Strain Carrying an Extended Heterozygous Tandem Duplication

A heterozygous tandem duplication in the Escherichia coli deo operon region deoAdeoB::Tn5/ deoCdeoDthr::Tn9 with the total length approximately 150 kb, which was obtained in the conjugational mating in the HfrH strain, was examined. By means of digestion with the NotI enzyme, pulsed-field gel electrophoresis, and the conjugational transfer of the duplication in the F^– strain, the chromosomal rearrangement, which occurred in the duplication region upon its stabilization in the bacterial genome, was studied. In a more stable strain, two new NotI sites were shown to appear in the chromosomal region located close to the duplication, which might have resulted from the transposition of the IS50 sequence from Tn5. The data were also obtained indicating the possibility of secondary transposition of the chromosomal segment between the two new NotI sites (approximately 30 kb) in the region located near the duplication. With the use of rec ⁺ and recA strains, two types of haploid and diploid segregants generated by the duplication were studied: DeoD⁺ (the deoD⁺ allele is not expressed in the original duplication due to the polar effect of the deoB::Tn5 insertion) and DeoC DeoD. The segregation of DeoD⁺ clones was shown to be RecA-dependent, whereas the DeoC DeoD segregants selected on the medium that contained thymine at a low concentration (i.e., under conditions of thymine starvation) appeared at a rather high frequency. However, the relative frequency of haploid clones, which have lost the duplication, strongly decreased in the recA genome among segregants of both types.     

全基因组与串联复制后白菜基因的保留

全基因组复制与串联复制是两种重要的基因扩增途径,在生物进化过程中普遍存在.这两种复制方式相互关系的研究在拟南芥中已经取得很多成果.白菜(Brassica rapa)属于十字花科(Brassicaceae)芸薹属(Brassca),是一类重要的经济作物,也是研究基因组多倍化和形态演化的模式植物.白菜基因组的测序与组装工作已经取得了重大成就,运用比较基因组学的方法,通过比较白菜与模式植物拟南芥,可以清晰鉴定白菜基因组经历的全基因组三倍化事件.同时,白菜与拟南芥同属于十字花科,有较近的起源关系和良好的基因组共线性关系.因此,拟南芥可以作为外群研究白菜全基因组三倍化以及串联重复之后基因的偏向性保留.结果发现,在白菜中存在物种特有的偏向性保留基因,即与环境刺激相关的基因和与激素相关的基因.     

Trehalase in conidia of Aspergillus oryzae

Horikoshi, Koki (The Institute of Physical and Chemical Research, Bunkyo-ku, Tokyo, Japan), and Yonosuke Ikeda. Trehalase in conidia of Aspergillus oryzae. J. Bacteriol. 91:1883-1887. 1966.-Trehalases (soluble trehalase and coat-bound trehalase) were found in the conidia of Aspergillus oryzae, and the total activity of the trehalases increased during the germination process. The soluble trehalase was purified by diethylaminoethyl-cellulose column chromatography; its optimal pH, Michaelis constant, and heat stability were studied. In vitro, the trehalases were competitively inhibited by d-mannitol, which was also contained in the conidia. Since the trehalose content in the conidia decreased at an early stage of germination, it was assumed that trehalase might begin to hydrolyze trehalose after the inhibitory effect of d-mannitol decreased.     

Lipase production of Aspergillus oryzae

Aspergillus oryzae produced a small amount of lipase (0.05–0.8 U/wet-g of solid medium) in solid cultures, in contrast to the larger amount (0.46 U/ml) in a shake-flask culture in a modified GYP medium containing 2% glucose, 1% yeast extract and 2% Polypepton. Optimum conditions of lipase production in the submerged culture of A. oryzae were determined in terms of pH, composition of medium, and temperature. In a shake-flask culture at 28°C, the maximum amount of lipase increased to 0.78 U/ml upon the addition of 3% soybean oil to the modified GYP medium. In a jar fermentor culture, 30 U/ml lipase activity was obtained after 72 h at 28°C under appropriate conditions. Lipase production was greatly influenced by the culture temperature, and the optimum temperature for lipase production was about 24°C with a narrow temperature range, which was 10 degrees lower than that for the growth. In the submerged cultures, two kinds of lipase at least exhibiting different substrate specificities were also suggested.     

Characterization of a neutral ceramidase orthologue from Aspergillus oryzae

Ceramide is an important molecule not only structurally but also regulationally as a modulator of various cellular events. Ceramidase (CDase) are classified into three different types (acid, alkaline, and neutral CDases). Neutral CDase could play an important role in the regulation of ceramide levels in the extracellular space. In this study, we describe the characterization of a neutral CDase orthologue from the filamentous fungus Aspergillus oryzae . The gene encoding the neutral CDase orthologue was cloned and overexpressed in A . oryzae . The purified recombinant enzyme was optimally active at pH 4.0–4.5 and 40 °C. The apparent K _m and V _max values of the enzyme for C12-NBD-ceramide were 3.32 μM and 0.085 μmol min⁻¹ mg⁻¹, respectively.     

Characterization of a novel lipolytic enzyme from Aspergillus oryzae

In this study, we report the characterization of a protein from Aspergillus oryzae, exhibiting sequence identity with paraben esterase from the genus Aspergillus. The coding region of 1,586 bp, including a 77-bp intron, encoded a protein of 502 amino acids. The gene without the signal peptide of 19 amino acids was cloned into a vector, pPICZαC, and expressed successfully in Pichia pastoris as an active extracellular protein. The purified recombinant protein had pH and temperature optima of 7.0–8.0 and 30 °C, respectively, and was stable at the pH range of 7.0–10.0 and up to 40 °C. The optimal substrate for hydrolysis by the purified recombinant protein, among a panel of α-naphthyl esters (C2–C16), was α-naphthyl butyrate (C4), with activity of 0.16 units/mg protein. The considerable hydrolytic activity of the purified recombinant enzyme toward tributyrin was determined. However, no paraben esterase activity was detected toward the ethyl, propyl, and butyl esters of 4-hydroxybenzoic acid. In addition, no activity was detected toward the methyl esters of ferulic, p-coumaric, caffeic, and sinapic acids that would indicate feruloyl esterase activity.     

On the safety of Aspergillus oryzae: a review

Conclusions Invasive growth or systemic infections by A. oryzae in healthy humans have never been reported. In a few cases, however, isolates identified as A. oryzae have been recovered from debilitated patients. A. oryzae has therefore low pathogenic potential but may, like many other harmless microorganisms, grow in human tissue under exceptional circumstances. Allergic diseases primarily caused by A. oryzae have been reported in few cases, but probably presuppose both a sensitivity to allergenic reactions and a massive exposure to conidia by inhalation. A. oryzae does not produce aflatoxins or any other cancerogenic metabolites. The absence of significant levels of mycotoxins in industrial products is regularly checked. We therefore consider A. oryzae an excellent host for the safe production of harmless products by recombinant strains.