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(Last modification:
02. September 2010)
Csy genes from Aspergillus oryzae
Wikipedia pages: in
English or
German.
They are small, unfortunately. There is a very nice review article on the
multiple uses and application of Koji mold (= Aspergillus
oryzae), including an interesting discussion of the history:
Machida et al., 2008.
This fungus is important because it is widely used in Japan's fermentation
industry (Koji mold), including soy sauce, sake, bean curd seasoning, and
vinegar production. Accordingly, the interest in its genome sequence was high,
and it was published already rather early (Machida
et al., 2005; Galagan et al.,
2005; Payne et al., 2006;
Kobayashi et al., 2007).
For our interests, it was important
that this fungus contained four type III PKS (Seshime
et al., 2005a). They were called CsyA, CsyB, CsyC, and CsyD. The name
abbreviation apparently is for chalcone
synthase, and
that is unfortunately symptomatic for the use of the terminology in this and
some other publications. Apparently any
sequence related to plant chalcone synthase (CHS) was considered as "functional
chalcone synthase" (used several times in the text), and that was and is misleading at
best. Even at that time it was already obvious that not all CHS-related proteins
actually have CHS functions. Unfortunately, the same loose use of identification
was applied in the "identification" of a phenylapropanoid pathway in this
organism (Seshime et al., 2005b):
sequence similarities were taken as evidence that bacteria and fungi do have the
enzymatic machinery for phenylpropanoid metabolism. Needless to say, this is
premature in absence of functional evidence. The same imprecise use of
terminology was used before for isomerases (Gensheimer
and Mushegian, 2004); one enzyme of the large protein family is the the
enzyme subsequent to the chalcone synthase reaction: it isomerizes the chalcone
to the flavanone.
Let's return to the Csy-family in
Aspergillus oryzae. The sequence analysis showed that CsyD is most likely a
non-functional protein: it has a large deletion just next to the active site
cysteine, and it also lacks the His and Asn residues which are essential for the
catalytic triad in type III PKS. The transcriptional analysis showed that CsyC
was not expressed under the conditions investigated.
Therefore CsyA and CsyB were of primary
interest in functional investigations, and these are described below. There
is so far no evidence whatsover that they have chalcone synthase activities.
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CsyA
(Yu et al., 2010)
The enzyme was overexpressed as
recombinant protein in E. coli, and the purified protein was investigated
with different possible CoA-ester. Most importantly,
CsyA was not a chalcone synthase
(CHS) because it had no activity at all with 4-coumaroyl-CoA, the starter
typical for these enzymes. It also showed no activity in the presence of only
malonyl-CoA, indicating that it required another starter CoA-ester. To make a
long story short: CsyA was identified as a pyrone synthase which
displayed broad substrate specificity toward fatty acyl-CoA starter units to
yield triketide and tetraketide pyrones. It synthesized triketide pyrones
from short chain starter units (C4-C8 CoAs), and both triketide and
tetraketide pyrones from longer fatty acyl starters (C10-C18 CoAs). It had no
activity with acetyl-CoA or propionyl-CoA, i.e. very small starters. It could not
synthesize resorcinols, i.e. could not carry out the aldol condensation typical
for STS-type cyclizations. Essentially the same products as detected in the
in vitro assays were also found in vivo.
There is actually no need to show a
figure of the reactions here, because the activities are pretty identical with
those of PKS18 and PKS11 from Mcyobacterium tuberculosis (more...),
and a type III PKS from Bacillus subtilis (more...).
Other type III PKS
with substrate preferences for long-chain
CoA-esters
in plants, bacteria, and fungi
-
-
-
-
Alkylresorcinols
and
long-chain pyrones in the bacterium Azotobacter vinelandii:
more...
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Alkylresorcinol
Streptomyces
griseus: more...
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Pyrone synthases in the bacteria
Mycobacterium tuberculosis and
Bacillus subtilis: more...
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CsyA and CsyB: type III
PKSs
in the fungus Aspergillus oryzae: more...
Update 02.
September: a totally different function for CsyA
Seshime et al., 2010b
This work turne out a rather surprising, unexpectet
result. In brief:
the authors expressed CsyA in a special A. oryzae
strain, under control of a strong promoter, and then analyzed the culture medium
(after three days of culture) for new compounds. Three new substances were
discovered, and the most dominant was analyzed in detail: it turned out to be
3,5-dihydroxbenzoic acid (DHBA). Feeding studies in fact indicated that four
acetyl residues went into its synthesis.
The figure below summarizes the model for the
biosynthesis of DHBA.
The model predicts acetyl-CoA as starter, three
condensations with malonyl-CoA, followed by aldol condensation to the resorcinol
ring system; it remains open whether the decarboxylation of orsellinic acid to
orcinol is also carried out by CsyA, or whether this is an independent step.
Other reactions are then proposed in the oxidation of the the methyl group the
carboxyl group of DHBA. It is a bit unfortunate that the analysis of the two
other compounds was not completed.
There was also modelling of the protein structure,
and the authors deduced that the active site cavity CsyA can accept only
short-chain acyl starters, for the formation of tetraketides.
I admit that I have rarely seen so contradictory results for
the same protein.
And I do not see an easy interpretation for that.
Seshime et al. end their publication with the comment "that proper expression
system is required for functional analysis of PKSs, even in the relatively small
type III PKS". Yes, indeed, I always would support that opinion. However,
in this case one would be tempted to ask whether the correlation of a gene and a
product formation in vivo, and some modelling of a possible protein
structure are really unequivocal evidence that this gene codes for the PKS in
its biosynthesis. Especially, and the authors apparently knew that publication,
if another group came with the purified recombinant protein to quite different
conclusions (see above, Yu et al., 2010). In this
context it seems also noteworthy that Yu et al. did in vivo
studies with the E. coli cells expressing CsyA, with the result that they
just about found the same pyrones from fatty acids as in vitro. This
shows that the Yu et al. results with the purified recombinant protein are not
just in vitro artifacts.
It will be interesting to see whether and how these
contradictory results can be reconciled.
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CsyB
(Seshime
et al., 2010a)
|
This
turned out to be interesting. The approach used overexpression of the csyB gene under the control of
the [alpha]-amylase
promoter in A. oryzae., i.e. in a fungus, and it was then
analyzed whether new secondary products could be identified. Actually,
there were some, and the most abundant was
3-(3-acetyl-4-hydroxy-2-oxo-2H-pyran-6-yl)propanoic acid, named
csypyrone B1. |
According to Seshime et al. (2010a) |
Configuration according to Song et al. (2006) |
Seshime et al. (2010) present a model
for the biosynthesis that involves CsyB reactions with two different starter
substrates, followed by a coupling of the two resultant molecules (see part
A in the
figure below). Note: the model allows succinyl-CoA or butyryl-CoA as starter. The use of butyryl-CoA would require a later oxidation of the terminal
methyl to a carboxyl group. However, that does not matter for the point discussed
below.
The proposal predicts an ordered sequence of condensations of malonyl-CoA with
two different substrates, but there is no precedent for that with type III PKS,
to the best of my knowledge. That of course does not exclude this possibility.
The authors point out a "similarity" of Csypyrone B1 with germicidin A
(see above), and they
cite that as an example for a biosynthesis using variable CoA-esters in one reaction sequence
by a type III PKS. However, even in the graphical abstract those authors pointed
out that the first condensation is carried out by FabH, and that the type III
PKS performs only one condensation (more...,
see also Song
et al., 2006).
I myself would tend to favor another
model of the biosynthesis; it is shown in part
B of the figure below. It
involves succinyl-CoA (or butyryl-CoA, not shown here) as starter CoA-ester, two
condensation reactions with malonyl-CoA, and then ring closure to the triketide
pyrone. In this model, the acetyl group of Csypyrone B1 would be added by a
tailoring enzyme, an acetyltransferase. This follows in its basic aspects the
biosynthesis of 2,4-diacetylphloroglucinol (more...),
except that a pyrone, not the phloroglucinol, would be the substrate for the
acetylation. It will be interesting to see what the real reaction sequence is.
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References
-
Yu, D., Zeng,
J., Chen, D., Zhan, J., 2010. Characterization and reconstitution of
a new fungal type III polyketide synthase from Aspergillus oryzae.
Enzyme and Microbial Technology 46, 575-580.
A putative type III polyketide synthase (PKS) gene, csyA, was cloned
from Aspergillus oryzae. It was ligated into pET28a and expressed in
Escherichia coli BL21-CodonPlus (DE3)-RIL. CsyA was identified as a
pyrone synthase which has displayed broad substrate specificity toward fatty
acyl-CoA starter units to yield triketide and tetraketide pyrones. It
synthesizes triketide pyrones by adding two units of malonyl-CoA to the
short chain starter units (C4-C8 CoAs), while yields both triketide and
tetraketide pyrones from longer fatty acyl starters (C10-C18 CoAs). A series
of fatty acyl N-acetylcysteamine thioesters (SNACs) (C5-C9) including
odd-numbered fatty acyl starters were synthesized, all of which can be
accepted by CsyA as the starter units to synthesize pyrones, indicating that
this enzyme has broad substrate specificity toward fatty acyl starters and
can be used to synthesize some unnatural pyrones. The optimal temperature
and pH for CsyA are 55o C and 7.5, respectively. Under the
optimal enzymatic conditions, CsyA exhibits high activity toward C6 and C7
starter units, and the kcat/Km values for hexanoyl- and heptanoyl-SNAC are
291.21 and 1615.58 s-1M-1, respectively. In addition
to its in vitro activity, CsyA can also take fatty acid biosynthetic
intermediates to synthesize a series of fatty acyl-primed pyrones in E.
coli cells.
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Seshime,
Y., Juvvadi, P. R., Kitamoto, K., Ebizuka, Y., Nonaka, T., Fujii, I.,
2010b. Aspergillus oryzae type III polyketide synthase CsyA is
involved in the biosynthesis of 3,5-dihydroxybenzoic acid. Bioorganic and
Medicinal Chemistry Letters 20, 4785-4788.
As a novel superfamily of type III polyketide synthases in microbes, four
genes csyA, csyB, csyC, and csyD, were found in the genome of Aspergillus
oryzae, an industrially important filamentous fungus. In order to
analyze their functions, we carried out the overexpression of csyA under the
control of a-amylase
promoter in A. oryzae and identified 3,5-dihydroxybenzoic acid (DHBA)
as the major product. Feeding experiments using 13C-labeled
acetates confirmed that the acetate labeling pattern of DHBA coincided with
that of orcinol derived from orsellinic acid, a polyketide formed by the
condensation and cyclization of four acetate units. Further oxidation of
methyl group of orcinol by the host fungus could lead to the production of
DHBA. Comparative molecular modeling of CsyA with the crystal structure of
Neurospora crassa 2'-oxoalkylresorcylic acid synthase indicated that CsyA
cavity size can only accept short-chain acyl starter and tetraketide
formation. Thus, CsyA is considered to be a tetraketide
alkyl-resorcinol/resorcylic acid synthase.
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Seshime,
Y., Juvvadi, P. R., Kitamoto, K., Ebizuka, Y., Fujii, I., 2010a.
Identification of csypyrone B1 as the novel product of Aspergillus oryzae
type III polyketide synthase CsyB. Bioorganic & Medicinal Chemistry 18,
4542-4546.
As a novel superfamily of type III polyketide synthases (PKSs) in microbes,
four genes, csyA, csyB, csyC, and csyD, were found in the genome of
Aspergillus oryzae, an industrially important filamentous fungus.
Although orthologs of csyA, csyC, and csyD genes are present in a closely
related species, Aspergillus flavus, csyB gene is unique to A.
oryzae. To identify its function, we carried out overexpression of
csyB gene under the control of [alpha]-amylase promoter in A. oryzae.
3-(3-Acetyl-4-hydroxy-2-oxo-2H-pyran-6-yl)propanoic acid, named csypyrone
B1, was identified as a CsyB product. Feeding experiments of 13C-labeled
acetate indicated that five acetate units were incorporated into csypyrone
B1. Two possible mechanisms are proposed for the biosynthesis of cycpyrone
B1: (1) condensation of succinyl-CoA with three acetyl/malonyl-CoAs, and the
following pyrone ring cyclization; (2) condensation of butyryl-CoA with
three acetyl/malonyl-CoAs, and the following pyrone ring cyclization and
side-chain oxidation.
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Seshime,
Y., Juvvadi, P. R., Fujii, I., Kitamoto, K., 2005a. Discovery of a novel superfamily of type III polyketide synthases in Aspergillus oryzae.
Biochemical and Biophysical Research Communications 331, 253-260.
Identification of genes encoding type III polyketide synthase (PKS)
superfamily members in the industrially useful filamentous fungus,
Aspergillus oryzae, revealed that their distribution is not specific to
plants or bacteria. Among other Aspergilli (Aspergillus nidulans and
Aspergillus fumigatus), A. oryzae was unique in possessing
four chalcone synthase (CHS)-like genes (CsyA, CsyB, CsyC, and CsyD).
Expression of CsyA, CsyB, and CsyD genes was confirmed by RT-PCR.
Comparative genome analyses revealed single putative type III PKS in Neurospora crassa and
Fusarium graminearum, two each in Magnaporthe grisea and Podospora anserina, and three in
Phenarocheate chrysosporium, with a phylogenic distinction from bacteria
and plants. Conservation of catalytic residues in the CHSs across species
implicated enzymatically active nature of these newly discovered homologs.
Accession numbers:
CsyA
(AB206758), protein =
BAD97390;
CsyB
(AB206759), protein =
BAD97391
CsyC
(AB206760), protein =
BAD97392
CsyD
(AB206761), protein =
BAD97394
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Machida, M., Yamada, O., Gomi, K., 2008. Genomics
of Aspergillus oryzae: learning from the history of Koji mold and
exploration of its future. DNA Research 15, 173-183.
At a time when the notion of microorganisms
did not exist, our ancestors empirically established methods for the
production of various fermentation foods: miso (bean curd seasoning) and
shoyu (soy sauce), both of which have been widely used and are essential for
Japanese cooking, and sake, a magical alcoholic drink consumed at a variety
of ritual occasions, are typical examples. A filamentous fungus,
Aspergillus oryzae, is the key organism in the production of all these
traditional foods, and its solid-state cultivation (SSC) has been confirmed
to be the secret for the high productivity of secretory hydrolases vital for
the fermentation process. Indeed, our genome comparison and transcriptome
analysis uncovered mechanisms for effective degradation of raw materials in
SSC: the extracellular hydrolase genes that have been found only in the
A. oryzae genome but not in A. fumigatus are highly induced
during SSC but not in liquid cultivation. Also, the temperature reduction
process empirically adopted in the traditional soy-sauce fermentation
processes has been found to be important to keep strong expression of the
A. oryzae-specific extracellular hydrolases. One of the prominent
potentials of A. oryzae is that it has been successfully applied to
effective degradation of biodegradable plastic. Both cutinase, responsible
for the degradation of plastic, and hydrophobin, which recruits cutinase on
the hydrophobic surface to enhance degradation, have been discovered in
A. oryzae. Genomic analysis in concert with traditional knowledge and
technology will continue to be powerful tools in the future exploration of
A. oryzae.
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Song, L., Barona-Gomez, F., Corre, C., Xiang, L.,
Udwary, D. W., Austin, M. B., Noel, J. P., Moore, B. S., Challis, G. L. ,
2006. Type III polyketide synthase ß-ketoacyl-ACP starter unit and
ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces
coelicolor genome mining. Journal of the American Chemical Society 128,
14754-14755.
Polyketide synthases (PKSs) are involved in
the biosynthesis of many important natural products. In bacteria, type III
PKSs typically catalyze iterative decarboxylation and condensation reactions
of malonyl-CoA building blocks in the biosynthesis of polyhydroxyaromatic
products. Here it is shown that Gcs, a type III PKS encoded by the
sco7221 ORF of the bacterium Streptomyces coelicolor, is required
for biosynthesis of the germicidin family of
3,6-dialkyl-4-hydroxypyran-2-one natural products. Evidence consistent with
Gcs-catalyzed elongation of specific ß-ketoacyl- ACP products of the fatty
acid synthase FabH with ethyl- or methylmalonyl-CoA in the biosynthesis of
germicidins is presented. Selectivity for ß-ketoacyl-ACP starter units and
ethylmalonyl-CoA as an extender unit is unprecedented for type III PKSs,
suggesting these enzymes may be capable of utilizing a far wider range of
starter and extender units for natural product assembly than believed until
now.
more...
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Seshime, Y., Juvvadi, P. R., Fujii, I., Kitamoto,
K., 2005b. Genomic evidences for the existence of a phenylpropanoid
metabolic pathway in Aspergillus oryzae. Biochemical and Biophysical
Research Communications 337, 747-751.
Plants interact with their environment by
producing a diverse array of secondary metabolites. A majority of these
compounds are phenylpropanoids and flavonoids which are valued for their
medicinal and agricultural properties. The phenylpropanoid biosynthesis
pathway proceeds with the basic C6-C3 carbon skeleton of phenylalanine, and
involves a wide range of enzymes viz., phenylalanine ammonia lyase,
coumarate hydroxylase, coumarate ligase, chalcone synthase, chalcone
reductase and chalcone isomerase. Recently, bacteria have also been shown to
contain homodimeric polyketide synthases belonging to the plant chalcone
synthase superfamily linking the capabilities of plants and bacteria in the
biosynthesis of flavonoids. We report here the presence of genes encoding
the core enzymes of the phenylpropanoid pathway in an industrially useful
fungus, Aspergillus oryzae. Although the assignment of enzyme function must
be confirmed by further biochemical evidences, this work has allowed us to
anticipate the phenylpropanoid metabolism profile in a filamentous fungus
for the first time and paves way for research on identifying novel fungal
flavonoid-like metabolites.
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Kobayashi, T., Abe, K., Asai, K., Gomi, K.,
Juvvadi, P. R., Kato, M., Kitamoto, K., Takeuchi, M., Machida, M. ,
2007. Genomics of Aspergillus oryzae. Bioscience, Biotechnology
and Biochemistry 71, 646-670.
The genome sequence of Aspergillus oryzae, a fungus used in the
production of the traditional Japanese fermentation foods sake (rice wine),
shoyu (soy sauce), and miso (soybean paste), has revealed prominent features
in its gene composition as compared to those of Saccharomyces cerevisiae
and Neurospora crassa. The A. oryzae genome is extremely
enriched with genes involved in biomass degradation, primary and secondary
metabolism, transcriptional regulation, and cell signaling. Even compared to
the related species A. nidulans and A. fumigatus, an abundance of metabolic
genes is apparent, with acquisition of more than 6 Mb of sequence in the A.
oryzae lineage, interspersed throughout the A. oryzae genome. Besides the
various already established merits of A. oryzae for industrial uses, the
genome sequence and the abundance of metabolic genes should significantly
accelerate the biotechnological use of A. oryzae in industry.
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Payne, G. A., Nierman, W. C., Wortman, J. R.,
Pritchard, B. L., Brown, D., Dean, R. A., Bhatnagar, D., Cleveland, T. E.,
Machida, M., Yu, J., 2006. Whole genome
comparison of Aspergillus flavus and A. oryzae. Medical
Mycology 44, 9-11.
Aspergillus flavus is a plant and animal pathogen that also produces
the potent carcinogen aflatoxin. Aspergillus oryzae is a closely
related species that has been used for centuries in the food fermentation
industry and is Generally Regarded As Safe (GRAS). Whole genome sequences
for these two fungi are now complete, providing us with the opportunity to
examine any genomic differences that may explain the different ecological
niches of these two fungi, and perhaps to identify pathogenicity factors in
A. flavus. These two fungi are very similar in genome size and number
of predicted genes. The estimated genome size (36.8 Mb) and predicted number
of genes (12 197) for A. flavus is similar to that of A. oryzae
(36.7 Mb and 12 079, respectively). These two fungi have significantly
larger genomes than Aspergillus nidulans (30.1) and Aspergillus
fumigatus (29.4). The A. flavus and A. oryzae genomes are
enriched in genes for secondary metabolism, but do not differ greatly from
one another in the predicted number of polyketide synthases, nonribosomal
peptide synthases or the number of genes coding for cytochrome P450 enzymes.
A micro-scale analysis of the two fungi did show differences in DNA
correspondence between the two species and in the number of transposable
elements. Each species has approximately 350 unique genes. The high degree
of sequence similarity between the two fungi suggests that they may be
ecotypes of the same species and that A. oryzae has resulted from the
domestication of A. flavus.
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Galagan, J. E., Calvo, S. E., Cuomo, C., Ma, L.
J., Wortman, J. R., Batzoglou, S., Lee, S. I., Basturkmen, M., Spevak, C.
C., Clutterbuck, J., Kapitonov, V., Jurka, J., Scazzocchio, C., Farman, M.,
Butler, J., Purcell, S., Harris, S., Braus, G. H., Draht, O., Busch, S.,
D'Enfert, C., Bouchier, C., Goldman, G. H., Bell-Pedersen, D.,
Griffiths-Jones, S., Doonan, J. H., Yu, J., Vienken, K., Pain, A., Freitag,
M., Selker, E. U., Archer, D. B., Penalva, M. A., Oakley, B. R., Momany, M.,
Tanaka, T., Kumagai, T., Asai, K., Machida, M., Nierman, W. C., Denning, D.
W., Caddick, M., Hynes, M., Paoletti, M., Fischer, R., Miller, B., Dyer, P.,
Sachs, M. S., Osmani, S. A., Birren, B. W. ,
2005. Sequencing of Aspergillus nidulans and comparative analysis
with A. fumigatus and A. oryzae. Nature 438, 1105-1115.
The aspergilli comprise a diverse group of filamentous fungi spanning over
200 million years of evolution. Here we report the genome sequence of the
model organism Aspergillus nidulans, and a comparative study with
Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae,
used in the production of sake, miso and soy sauce. Our analysis of genome
structure provided a quantitative evaluation of forces driving long-term
eukaryotic genome evolution. It also led to an experimentally validated
model of mating-type locus evolution, suggesting the potential for sexual
reproduction in A. fumigatus and A. oryzae. Our analysis of sequence
conservation revealed over 5,000 non-coding regions actively conserved
across all three species. Within these regions, we identified potential
functional elements including a previously uncharacterized TPP riboswitch
and motifs suggesting regulation in filamentous fungi by Puf family genes.
We further obtained comparative and experimental evidence indicating
widespread translational regulation by upstream open reading frames. These
results enhance our understanding of these widely studied fungi as well as
provide new insight into eukaryotic genome evolution and gene regulation.
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Machida, M., Asai, K., Sano, M., Tanaka, T.,
Kumagai, T., Terai, G., Kusumoto, K., Arima, T., Akita, O., Kashiwagi, Y.,
Abe, K., Gomi, K., Horiuchi, H., Kitamoto, K., Kobayashi, T., Takeuchi, M.,
Denning, D. W., Galagan, J. E., Nierman, W. C., Yu, J., Archer, D. B.,
Bennett, J. W., Bhatnagar, D., Cleveland, T. E., Fedorova, N. D., Gotoh, O.,
Horikawa, H., Hosoyama, A., Ichinomiya, M., Igarashi, R., Iwashita, K.,
Juvvadi, P. R., Kato, M., Kato, Y., Kin, T., Kokubun, A., Maeda, H., Maeyama,
N., Maruyama, J., Nagasaki, H., Nakajima, T., Oda, K., Okada, K., Paulsen,
I., Sakamoto, K., Sawano, T., Takahashi, M., Takase, K., Terabayashi, Y.,
Wortman, J. R., Yamada, O., Yamagata, Y., Anazawa, H., Hata, Y., Koide, Y.,
Komori, T., Koyama, Y., Minetoki, T., Suharnan, S., Tanaka, A., Isono, K.,
Kuhara, S., Ogasawara, N., Kikuchi, H.,
2005. Genome sequencing and analysis of Aspergillus oryzae. Nature
438, 1157-1161.
The genome of Aspergillus oryzae, a fungus important for the
production of traditional fermented foods and beverages in Japan, has been
sequenced. The ability to secrete large amounts of proteins and the
development of a transformation system have facilitated the use of A. oryzae
in modern biotechnology. Although both A. oryzae and Aspergillus flavus
belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike
A. flavus, does not produce aflatoxin, and its long history
of use in the food industry has proved its safety. Here we show that the
37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded
by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and
Aspergillus fumigatus. Comparison of the three aspergilli species revealed
the presence of syntenic blocks and A. oryzae-specific blocks (lacking
synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the
genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched
for genes involved in metabolism, particularly those for the synthesis of
secondary metabolites. Specific expansion of genes for secretory hydrolytic
enzymes, amino acid metabolism and amino acid/sugar uptake transporters
supports the idea that A. oryzae is an ideal microorganism for
fermentation.
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Gensheimer, M., Mushegian, A., 2004.
Chalcone isomerase family and fold: no longer unique to plants. Protein
Science 13, 540-544.
Chalcone isomerase, an enzyme in the isoflavonoid pathway in plants,
catalyzes the cyclization of chalcone into (2S)-naringenin. Chalcone
isomerase sequence family and three-dimensional fold appeared to be unique
to plants and has been proposed as a plant-specific gene marker. Using
sensitive methods of sequence comparison and fold recognition, we have
identified genes homologous to chalcone isomerase in all completely
sequenced fungi, in slime molds, and in many gammaproteobacteria. The
residues directly involved in the enzyme's catalytic function are among the
best conserved across species, indicating that the newly discovered homologs
are enzymatically active. At the same time, fungal and bacterial species
that have chalcone isomerase-like genes tend to lack the orthologs of the
upstream enzyme chalcone synthase, suggesting a novel variation of the
pathway in these species.
(Notes: i) the authors do not seem to understand the difference between
flavonoids and isoflavonoids, ii) the indiscriminate use of "chalcone
synthase" for any sequence in the type III PKS family is at best misleading:
it ignores that the family contains proteins with widely divergent
activities, and not only chalcone synthases. This was well-known already in
2004!).
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