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Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239.

Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y - DNA Res. (2011)

Bottom Line: Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae.Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae.The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Division, Kikkoman Corporation, 399 Noda, Noda City, Chiba 278-0037, Japan.

ABSTRACT
We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

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Analysis of transposons surrounding α-amylase genes in A. oryzae RIB40 and A. sojae NBRC4239. (A) Expected insertion site of A. oryzae Tao1 transposon. (B) Map of transposons surrounding A. oryzae and A. sojae α-amylase genes.
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DSR009F4: Analysis of transposons surrounding α-amylase genes in A. oryzae RIB40 and A. sojae NBRC4239. (A) Expected insertion site of A. oryzae Tao1 transposon. (B) Map of transposons surrounding A. oryzae and A. sojae α-amylase genes.

Mentions: We investigated transposons existing near the α-amylase genes in A. oryzae and A. sojae (Fig. 4A). We found that the ∼1.9-kb insertion sequence locating upstream the A. oryzae amy3 promoter is a transposon Tao1 (DDBJ/EMBL/GenBank accession number: AB021710.1). This transposon was flanked by inverted repeat sequences characteristic to ClassII DNA transposons (Fig. 4A).29 The Tao1 insertion site at the A. oryzae amy3 promoter region was found to correspond to the ‘TA’ sequence in the −533 to −532 region upstream the A. sojae amy3 promoter. This is consistent with that ClassII transposons tend to be preferentially integrated at a TA sequence, resulting in target site TA duplication on both flanking of the integrated transposon.29 The Tao1 is located at the further upstream of the amylase transcription factor AmyR recognition site30 and the CreA recognition sites31 involved in carbon catabolite repression (Fig. 4B). It is not clear whether Tao1 insertion affects the expression of the A. oryzae amy3 gene or not, and further study will be needed to clarify the effect of Tao1 insertion.Figure 4.


Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239.

Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y - DNA Res. (2011)

Analysis of transposons surrounding α-amylase genes in A. oryzae RIB40 and A. sojae NBRC4239. (A) Expected insertion site of A. oryzae Tao1 transposon. (B) Map of transposons surrounding A. oryzae and A. sojae α-amylase genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3111232&req=5

DSR009F4: Analysis of transposons surrounding α-amylase genes in A. oryzae RIB40 and A. sojae NBRC4239. (A) Expected insertion site of A. oryzae Tao1 transposon. (B) Map of transposons surrounding A. oryzae and A. sojae α-amylase genes.
Mentions: We investigated transposons existing near the α-amylase genes in A. oryzae and A. sojae (Fig. 4A). We found that the ∼1.9-kb insertion sequence locating upstream the A. oryzae amy3 promoter is a transposon Tao1 (DDBJ/EMBL/GenBank accession number: AB021710.1). This transposon was flanked by inverted repeat sequences characteristic to ClassII DNA transposons (Fig. 4A).29 The Tao1 insertion site at the A. oryzae amy3 promoter region was found to correspond to the ‘TA’ sequence in the −533 to −532 region upstream the A. sojae amy3 promoter. This is consistent with that ClassII transposons tend to be preferentially integrated at a TA sequence, resulting in target site TA duplication on both flanking of the integrated transposon.29 The Tao1 is located at the further upstream of the amylase transcription factor AmyR recognition site30 and the CreA recognition sites31 involved in carbon catabolite repression (Fig. 4B). It is not clear whether Tao1 insertion affects the expression of the A. oryzae amy3 gene or not, and further study will be needed to clarify the effect of Tao1 insertion.Figure 4.

Bottom Line: Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae.Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae.The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Division, Kikkoman Corporation, 399 Noda, Noda City, Chiba 278-0037, Japan.

ABSTRACT
We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

Show MeSH
Related in: MedlinePlus