Alternative Epimerization in C7N-Aminocyclitol Biosynthesis Is Catalyzed by ValD, A Large Protein of the Vicinal Oxygen Chelate Superfamily

Article abstract of DOI:10.1016/j.chembiol.2009.04.006

Gene valD, encodes a large vicinal oxygen chelate (VOC) superfamily protein, has been identified in the validamycin biosynthetic gene cluster. Inactivation of valD significantly reduced validamycin A production, which was fully restored with the full-leng

Full text of DOI:10.1016/j.chembiol.2009.04.006

Chemistry & Biology
Article
Alternative Epimerization in C7N-Aminocyclitol
Biosynthesis Is Catalyzed by ValD, A Large Protein
of the Vicinal Oxygen Chelate Superfamily
1,
1
Hui Xu,1,2,3 Yirong Zhang,1,3 Jongtae Yang,2 Taifo Mahmud,2, Linquan Bai, and Zixin Deng
*
*
1Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
2Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA
3These authors contributed equally to this paper
*Correspondence: Taifo.Mahmud@oregonstate.edu (T.M.), bailq@sjtu.edu.cn (L.B.)
DOI 10.1016/j.chembiol.2009.04.006
SUMMARY
Mahmud et al., 1999; Naganawa et al., 2002; Wu et al., 2007).
By comparing the stereochemistry of the final cyclitol moiety
Gene valD, encodes a large vicinal oxygen chelate and the first intermediate 2-epi-5-epi-valiolone, an epimerization
reaction is found to be required at the C-2 position in at least four
out of the five abovementioned C7N-aminocyclitols.
(VOC) superfamily protein, has been identified in the
validamycin biosynthetic gene cluster. Inactivation of
valD significantly reduced validamycin A production,
which was fully restored with the full-length valD and
partially restored with either N-terminal or C-terminal
half by complementation. Heterologously expressed
ValD catalyzed the epimerization of 2-epi-5-epi-
Recently, the biosynthetic gene clusters of acarbose, valida-
mycin, salbostatin, and cetoniacytone A have been cloned and
sequenced (Choi et al., 2008; Singh et al., 2006; Stratmann
et al., 1999; Wu et al., 2007; Yu et al., 2005). In the first isolated
acarbose biosynthetic gene cluster from Actinoplanes sp. SE50/
110, the AcbO protein was found to have no similarity with any
valiolone to 5-epi-valiolone. This metalloenzyme is a
homodimer with a metal ion-binding ratio of 0.73
mol/mole protein toward Fe2+, Mn2+, Ni2+, and Zn2+.
known proteins in the database and was initially predicted to
be an epimerase (Zhang et al., 2002). After phosphorylation of
2-epi-5-epi-valiolone by AcbM, subsequent conversion of
Individual and combined site-directed mutations of 2-epi-5-epi-valiolone 7-phosphate to 5-epi-valiolone 7-phosphate
catalyzed by AcbO unambiguously established its role as the
first epimerase involved in C7N-aminocyclitol biosynthesis
(Zhang et al., 2003). Moreover, SalO from the salbostatin bio-
eight putative active site residues revealed that the
N-terminal H44/E107 and the C-terminal H315/E366
are more critical for the activity than the internal
H130, E183, H229, and E291. Our data have estab-
lished ValD as one of the largest proteins of the VOC
superfamily, catalyzing an alternative epimerization
for C7N-aminocyclitol biosynthesis.
synthetic gene cluster in S. albus ATCC 21838 showed a 61%
identity with AcbO, and was proposed to be responsible for the
epimerization of 2-epi-5-epi-valiolone 7-phosphate to 5-epi-
valiolone 7-phosphate in salbostatin biosynthesis (Choi et al.,
2008).
However, so far no AcbO homolog has been found in the
biosynthetic gene clusters of validamycin and cetoniacytone
INTRODUCTION
A (accession number EF120454) (Bai et al., 2006). Moreover,
2-epi-5-epi-valiolone was significantly incorporated into valida-
The C7N-aminocyclitol family of natural products, exemplified mycin but not able to be phosphorylated by the required kinase
by the a-glucosidase inhibitor acarbose, the trehalase inhibitors ValC for validamycin biosynthesis (Dong et al., 2001; Minagawa
validamycin and salbostatin, the antitumor cetoniacytone A, and et al., 2007), suggesting a direct conversion of unmodified
the antibacterial agent pyralomicin 1a, are increasingly gaining 2-epi-5-epi-valiolone to 5-epi-valiolone, catalyzed possibly by a
recognition due to their significant clinical and agricultural uses different epimerization reaction. In silico analysis of genes within
(Figure 1) (Mahmud, 2003). Validamycin A is produced industri- the validamycin cluster revealed a gene (valD), located down-
ally using developed strains of Streptomyces hygroscopicus stream of the kinase gene valC, that encodes a protein similar
var. limoneus or S. hygroscopicus subsp. jinggangensis 5008, to members of the VOC superfamily (Bai et al., 2006). The VOC
and is widely used in Asia as a crop protectant (Iwasa et al., superfamily includes a set of structurally related proteins that
1970; Xia and Jiao, 1986). Structurally, it consists of the unsatu- are able to catalyze a large range of divalent metal-ion-depen-
rated aminocyclitol unit valienamine, the saturated aminocyclitol dent reactions. Members of this family include the glyoxalases I
unit validamine, and glucose. Through feeding experiments with (GLO) (Cameron et al., 1997), the extradiol dioxygenases (DHBD)
synthesized precursors and/or in vitro enzymatic catalysis, it has (Eltis and Bolin, 1996), the bleomycin resistance proteins (Dumas
been established that the valienamine biosynthesis is initiated et al., 1994), the fosfomycin resistance proteins (Pakhomova
by the conversion of sedoheptulose 7-phosphate to 2-epi-5-epi- et al., 2004), and the methylmalonyl-CoA epimerases (MMCE)
valiolone, which undergoes further different modifications to involved in the epimerization of (2S)-methylmalonyl-CoA to its
give final diverse products (Choi et al., 2008; Dong et al., 2001; (2R)-stereoisomer (Leadlay, 1981).
Chemistry & Biology 16, 567–576, May 29, 2009 ª2009 Elsevier Ltd All rights reserved 567

Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Figure 1. Chemical Structures of Bioactive
C7N-Aminocyclitols
The shared valienamine moiety or its analogs is
boxed.
Enzymatic Epimerization of 2-epi-
5-epi-Valiolone to 5-epi-Valiolone
by Heterologously Expressed ValD
To explore the exact biochemical func-
tion of ValD, the gene was amplified by
PCR and cloned into expression vector
pRSET B and introduced into E. coli
BL21(DE3)pLysS. Expression of ValD
was induced by IPTG to give a 51.8 kDa
soluble His6-tagged protein, which was
then purified on a BD TALONꢀ affinity
column.
In this article, we report the requirement of ValD for validamy-
cin biosynthesis through in vivo inactivation and complementa-
tion, and provide evidence that ValD is a large protein of the VOC
superfamily with a novel catalytic activity responsible for the
conversion of 2-epi-5-epi-valiolone to 5-epi-valiolone.
Characterization of ValD was carried out using the coupled
reactions of ValA and ValD with sedoheptulose 7-phosphate as
substrate. ValA is a 2-epi-5-epi-valiolone synthase that catalyzes
the conversion of sedoheptulose 7-phosphate to 2-epi-5-epi-
valiolone (Yu et al., 2005). The reaction was carried out for 3–6 hr
in the presence of NAD+ and Co2+, and the product was checked
by thin-layer chromatography (TLC) (Figure 3A). The results
clearly demonstrated that sedoheptulose 7-phosphate was
converted into 2-epi-5-epi-valiolone with ValA alone, and in the
presence of ValD, this product was further converted into 5-epi-
valiolone.
RESULTS
Inactivation of valD in S. hygroscopicus 5008 Drastically
Reduced the Production of Validoxylamine A
and Validamycin A
To further identify this conversion, a time-course 1H nuclear
magnetic resonance (NMR) experiment was conducted. How-
ever, as the activity of ValA requires NAD+ and Co2+ cofactor, a
direct 1H NMR experiment resulted in an unsatisfactory outcome
due to perturbation ofthe spectrum by cobalt. Therefore, 2-epi-5-
epi-valiolone was first enzymatically synthesized by a coupled
enzyme reaction using transketolase (EC 2.2.1.1) (Zhang et al.,
2002) and ValA. A decreased intensity of the proton signals
(Ha-6, Hb-6) of 2-epi-5-epi-valiolone and an increased intensity
of those of 5-epi-valiolone (H-4, H-6) were observed in the NMR
spectra, confirming the function of ValD as a 2-epi-5-epi-valio-
lone epimerase. In addition, the lack of H-2 signal of the product
indicates that the proton at this position has been replaced
by deuterium, which confirmed the epimerization occurs at the
C-2 position (Figure 3B).
To assess the role of valD in validamycin biosynthesis, a 1278 bp
internal DNA fragment, coding for 426 amino acids, was replaced
by the 1.4 kb aac(3)IV cassette. This was achieved by using a
pHZ1358-derived plasmid pJTU713, in which aac(3)IV was in-
serted between a 4.8 kb left flanking and a 1.7 kb right flanking
sequence of the 1278 bp DNA fragment to be replaced (Fig-
ure 2A). pJTU713 was introduced into wild-type S. hygroscopi-
cus 5008 through conjugation (Yu et al., 2005) and two thio-
strepton-sensitive apramycin-resistant derivatives (ZYR-4-1 and
ZYR-4-2) were obtained. Total DNA from these two strains and
from the wild-type 5008 was used as templates for polymerase
chain reaction (PCR) analysis using two primers, ValD-Det-F
and ValD-Det-R. The wild-type 5008 DNA gave a 1.6 kb PCR
product, whereas the mutants gave a 1.7 kb PCR product,
which confirmed that a 1278 bp DNA fragment internal to valD
has been replaced by the 1.4 kb aac(3)IV cassette (Figure 2B).
High-performance liquid chromatography (HPLC) analysis of Dimerization and Metal Ion Binding of ValD
the culture broths of ZYR-4-1 and ZYR-4-2 revealed that the In silico comparison and secondary structure analyses of ValD
production of validamycin A in the two valD mutants was drasti- revealed that the protein contains two metal-binding sites built
cally reduced to less than 5% of the wild-type production level, up from four babbb modules common to the VOC superfamily
indicating the important role of ValD in validamycin biosynthesis (Figure 4). Most members of the VOC superfamily exist as homo-
(Figure 2C).
dimers; each monomer contains two babbb modules that form
To further confirm that ValD is instrumental in validamycin a single metal-binding/active site (Bergdoll et al., 1998). Although
biosynthesis, the PCR-amplified valD gene was cloned down- each has a different metal preference, members of the VOC
stream of PermE* promoter and subsequently introduced into superfamily share almost identical metal-binding sites consisting
a valD mutant ZYR-4-1 by conjugation. HPLC analysis of the of four conserved residues, including the two Glu residues for
fermentation extracts from the resulting S. hygroscopicus ZYR-4 catalysis. Sequence comparisons of ValD with CetB, a homolo-
complemented with valD clearly demonstrated that validoxyl- gous protein from the cetoniacytone pathway (Wu et al., 2007),
amine A and validamycin A production was restored to about and MMCE from Propionibacterium shermanii showed that all
80% of that of the wild-type (Figure 2C).
of these proteins contain the conserved residues (Figure 4).
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Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Figure 2. Construction and Analysis of
valD-Inactivated Mutant Strains of S. hygro-
scopicus 5008
(A) Schematic representation for the replacement
of a 1278 bp fragment of valD with apramycin
resistance gene aac(3)IV. In shuttle plasmid
pJTU713, aac(3)IV was inserted between 4.80 kb
and 1.70 kb genomic fragments originally flanking
the deleted 1278 bp region. Although wild-type
5008 should give a 1.60 kb expected PCR-ampli-
fied product, mutant ZYR-4 should yield a 1.70 kb
product using a pair of primers (ValD-Det-F and
ValD-Det-R).
(B) Gel electrophoresis of PCR products of the
wild-type and the mutant strains.
(C) HPLC analysis of the wild-type (5008), the valD
mutant strain (ZYR-4), and the valD mutant strain
complemented with a plasmid harboring an intact
valD gene (ZYR-4/valD).Validamycin A and val-
idoxylamine A are indicated with filled arrows.
and zinc (0.12 mol) per mole of protein,
which suggests that ValD, similar to
MMCE and GLO, can bind a number of
different metal ions (Clugston et al.,
2004; Leadlay, 1981). However, the total
amount of metals was consistently about
0.73 mol/mole protein, suggesting that
the two putative metal binding sites in
ValD are not fully occupied by metal ions
and/or some of the protein present in its
apo-form. In addition, the Histag-free pro-
tein was treated with 0.5 mM EDTA for
20 min to remove the metal ion, and dia-
lyzed against metal ion-free buffer. Strong
binding between ValD and metal ions was observed with the
presence of iron (0.15 mol), manganese (0.22 mol), nickel (0.14
mol), and zinc (0.10 mol) per mole of protein by ICP-AES analysis
of the EDTA-treated Histag-free ValD. The EDTA treatment
slightly reduced the total amount of metals to 0.61 mol/mole pro-
tein mostly through the chelation of iron. In another metal ion
depletion attempt with 0.1 mM 1,10-phenanthroline, the treated
His6-tagged ValD still retained an epimerase activity when tested
using 2-epi-5-epi-valiolone as substrate.
Because the ValD primary sequence contains two repeating and
highly homologous glyoxalase-like units, both the N-terminal half
(G35-E194) and the C-terminal half (G220-A382) of the protein
were individually analyzed as a separate entry in the alignment.
Similar to ValD, several members of the VOC superfamily, e.g.,
large glyoxalases I from Saccharomyces cerevisiae (accession
number CAC16163) and large extradiol dioxygenase from Pseu-
domonas cepacia (accession number 1HAN_A), also have four
babbb modules. However, most of them, if not all, adopt a mono-
mer conformation. To find out whether ValD forms a monomer or
a dimer, the protein was purified and analyzed with a DynaPro The N-Terminal or C-Terminal Half of ValD Retained
dynamic light scattering instrument. The protein gave a radius Reduced Epimerization Activity
of 4.0 nm and the calculated molecular weight is 83.5 kDa based To investigate whether each individual half of ValD would inde-
on the standard curve, and 103 kDa based on the volume shape pendently have the same function as the full-length ValD, a
hydration model, both of which suggested that ValD forms complementation experiment was carried out through the intro-
a dimer. The result is consistent with that obtained from high- duction of plasmid pJTU946, a shuttle plasmid harboring the
performance gel filtration chromatography (see Figure S1 avail- recombinant N-terminal half of valD under the control of the
able online).
PermE* promoter, into ZYR-4 through conjugation. Validamycin
To investigate the metal ion cofactor of ValD, inductively production was partially restored ca. 20% of that of the wild-
coupled plasma atomic emission spectrometry (ICP-AES) was type. A similar complementation experiment with the C-terminal
used to analyze samples of freshly purified Histag-free ValD for half of ValD was also performed, resulting in ca. 20% of valida-
the presence of bound zinc, manganese, cobalt, nickel, iron, mycin production as well (Figure 5A). These results are consis-
magnesium, calcium, or copper. The results indicated the pres- tent with those of the in vitro enzymatic assays using recombi-
ence of iron (0.24 mol), manganese (0.22 mol), nickel (0.15 mol), nant N-terminal half and C-terminal half of ValD, showing that
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Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Figure 3. TLC and 1H NMR Analyses of ValD-Catalyzed Reactions
(A) TLC analysis of ValD-catalyzed reactions: lane 1, sedoheptulose 7-phosphate with 2-epi-5-epi-valiolone synthase ValA only; lane 2, sedoheptulose 7-phos-
phate with ValA and ValD; lane 3, sedoheptulose 7-phosphate with ValA and boiled ValD.
(B) 1H NMR analyses of ValD reaction. A solution of 2-epi-5-epi-valiolone in D2O was placed in a 5 mm NMR tube and the reaction was started by adding potas-
sium phosphate buffer (pH 7.4, 25 mM) and purified ValD to a final concentration of 0.018 mg/ml. After 1 hr, additional ValD was added into the reaction mixture to
a final concentration of 0.054 mg/ml protein. The geminal H-6a and H-6b of 2-epi-5-epi-valiolone appear as doublets, whereas those of 5-epi-valiolone appear as
a singlet. Asterisk (*) indicates the growing signal corresponding to the increased production of 5-epi-valiolone over the period of NMR measurement; x indicates
signals of impurities.
the truncated proteins have a significantly reduced capacity to sulting in double-site mutants H44N/H299N and E183A/E366A.
convert 2-epi-5-epi-valiolone to 5-epi-valiolone (data not shown). All mutants were individually cloned into the vector pPM927
It is noteworthy that the recombinant N-terminal and C-terminal and were introduced into ZYR-4 by conjugation. The production
halves of ValD expressed poorly in E. coli and appeared to be of validamycin A as a result of the complementation experiments
less stable than the full-length protein.
was analyzed by HPLC. Surprisingly, all of the four mutated ValD
proteins tested (H44N, E183A, H299N, and E366A) could restore
the validamycin production of ZYR-4 to a comparable level of the
wild-type, whereas the H44N/H299N and the E183A/E366A ValD
proteins were only able to restore low levels of validamycin
Investigation on the Involvement of Conserved Residues
in Validamycin Production and Epimerization through
Site-Directed Mutation
To investigate the effect of the conserved residues in ValD on its production (Figure 5B).
catalytic activity, a number of site-directed mutants of ValD were
Because results of the in vivo complementation experiments
generated, and their in vivo activities were initially analyzed by were inconclusive, we set out to characterize the in vitro cata-
complementation experiments. As shown in Figure 4, multiple lytic activity of the mutated ValD. In this experiment, all eight
sequence alignment of ValD and its homologs suggested that putative active site residues were individually altered—His was
H44, E107, H130, and E183 are the putative active site residues replaced by Asn and Glu was replaced by Ala—to give single-
in the N-terminal half, and H229, E291, H315, and E366 are residue mutants H44N, E107A, H130N, E183A, H229N, E291A,
the putative active site residues in the C-terminal half of ValD. H315N, and E366A. The mutants were produced as His6-tagged
Initially, only two His residues specific for metal ion binding proteins and their epimerase activity was tested using 2-epi-
and two Glu residues for catalysis were individually altered—H44 5-epi-valiolone as substrate. Because kinetic studies of these
and H229 were replaced by Asn and E183 and E366 were proteins were hampered by the lack of feasible analytical
replaced by Ala—to give single-residue mutants H44N, E183A, methods, we chose to monitor the relative catalytic activity of
1
H229N, and E366A. Also, combined mutations of H44N and the proteins using TLC and H NMR. The results, as monitored
H299N were performed to remove the two putative metal binding by TLC, indicated that the H130N, E183A, H229N, and E291A
residues, and combined mutations of E183A and E366A were proteins had a comparable epimerase activity to that of the
carried out to eliminate the two putative catalytic residues, re- wild-type, whereas the H44N, E107A, and E366A proteins had
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Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Figure 4. Amino Acid Alignments of the N-Terminal Half (G35-E194) and C-Terminal Half (G220-A382) of ValD with CetB and Methylmalonyl-
CoA Epimerase and Secondary Structure Predictions
Deduced amino acid sequences are from the following organisms: CetB (183 amino acids [aa]), Actinomyces sp. Lu 9419 (accession number EF120454); MMCE
(148 aa), Propionibacterium shermanii (accession number AAL57846). Based on the analysis of the three-dimensional structure of the MMCE from Propionibac-
terium shermanii, a functional attribution of the aa residues probably involved in metal-ion binding and/or catalysis is indicated as asterisks below the alignment.
In ValD mutants, conserved His residues are individually replaced with Asn, whereas conserved Glu residues are individually changed to Ala. The secondary
structure of ValD was predicted using Jpred, and b sheets are labeled as arrows and a-helix are labeled as coils above the alignment.
significantly reduced activities (Figure 5C). Mutation at H315 ap- DISCUSSION
peared to have a moderate effect on the epimerase activity.
Comparisons of the epimerase activity of H44N, E183A, Previously, valD had been considered to be a gene of unknown
H229N, and E366A by 1H NMR experiments (Figure 5D) con- function with no direct involvement in the biosynthesis of valida-
firmed that the H229N and the E183A single mutation proteins mycin. The encoded protein is similar to the glyoxalase/bleomy-
retain an epimerase activity comparable to the wild-type cin resistance proteins; however, no clear function of this protein
enzyme, whereas the H44N and the E366A proteins had signif- could be envisioned in the proposed validamycin pathway. In
icantly reduced activities, consistent with the TLC results. The addition, heterologous expression of a cassette harboring a
results suggested that four (the N-terminal residues H44 and selected number of the val genes, but without valD, in S. lividans
E107 and the C-terminal residues H315 and E366) of the eight 1326 resulted in the production of validamycin A, albeit in minute
putative active site residues in ValD might play more significant amounts and just detectable by mass spectrometry (Bai et al.,
roles in its catalytic activity, whereas the other four (the inner 2006). It was not until more recently that the wide distribution
residues H130, E183, H229, and E291) might contribute less of valD homologs in other C7-aminocyclitol/C7-cyclitol bio-
to its activity.
synthetic pathways, e.g., in the cetoniacytone and BE-40644
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Alternative Epimerization for C7N-Aminocyclitol
Figure 5. Catalytic Analysis of Mutated ValD
(A) HPLC analysis of validamycin production in the wild-type strain, the valD disruption mutant ZYR-4, and ZYR-4 complemented with the N-terminal half and the
C-terminal half of ValD.
(B) HPLC analysis of validamycin production in: (A) wild-type 5008; (B) valD disruption mutant ZYR-4; (C) ZYR-4 complemented with valD (H44N); (D) ZYR-4 com-
plemented with valD (E184A); (E) ZYR-4 complemented with valD (H229N); (F) ZYR-4 complemented with valD (E366A); (G) ZYR-4 complemented with valD
(H44N/H229N); (H) ZYR-4 complemented with valD (E184A/E366A). Peaks corresponding to validamycin A are indicated.
(C) Partial TLC of enzyme assays with single-residue mutated ValD after 30 min of incubations. Lane 1, 2-epi-5-epi-valiolone standard; lanes 2 – 9, reactions with
mutated proteins: H44N (2); E107A (3); H130N (4); E183A (5); H229N (6); E291A (7); H315N (8); E366A (9); 10, reaction with the wild-type ValD.
(D) Partial 1H NMR spectra of enzyme assays with a selected number of mutated ValD.
pathways, became obvious (Wu et al., 2007). Results of in silico valD inactivation still produce trace amounts of the antibiotic
comparisons of these clusters suggested that they might share (Figure 2). It is possible that the conversion of 2-epi-5-epi-valio-
the first two biochemical steps: cyclization of sedoheptulose lone into 5-epi-valiolone might slowly occur nonenzymatically,
7-phosphate and epimerization of the product to yield 5-epi- because trace amounts of 5-epi-valiolone were occasionally
valiolone, and the latter step might be catalyzed by the glyoxa- detected in purified 2-epi-5-epi-valiolone samples. This low level
lase/bleomycin resistance protein-like enzyme, such as ValD. nonenzymatic conversion could explain the production of a tiny
In this study, the involvement of ValD in validamycin biosynthesis amount of validamycin A detected by mass spectrometry in the
has been unambiguously demonstrated by gene inactivation heterologous experiments (without valD) in S. lividans 1326 (Bai
in S. hygroscopicus 5008. ValD was further confirmed to be a et al., 2006). Alternatively, a VOC homolog might be present in
2-epi-5-epi-valiolone epimerase by in vitro characterization of S. lividans that accounts for the epimerase activity and subse-
the recombinant protein, site-directed mutations, and comple- quent production of validamycin A.
mentation experiments.
ValD is related to members of the divalent metal-ion-depen-
Although ValD is directly involved in the biosynthesis of valida- dent VOC superfamily and shows its similarity to large GLOs and
mycin, mutant strains of S. hygroscopicus 5008 generated from DHBDs, which are commonly present as monomers. However,
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Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Figure 6. Proposed Biosynthetic Pathways to the Valienamine Moiety of C7N-Aminocyclitol Acarbose (Acb), Salbostatin (Sal), Validamycin A
(Val), and Cetoniacytone A (Cet)
ValD forms a dimer, making it one of the largest members of damycin A production. Even though other unknown factor(s)
the VOC superfamily known to date. Each monomer contains probably involved in this build-up, it can be explained by the
four modules that correspond to two metal-binding sites. Site- notion that even if some active site has been disrupted, the unaf-
directed mutagenesis of the individual putative active amino fected active sites might facilitate the production of validamycin
acid residues of ValD resulted in mutant proteins with various A, albeit slowly, during the course of several days of fermentation
degrees of epimerase activity; the site-directed mutations at to a comparable level of the wild-type production yield. However,
H44, E170, H315, and E366 reducedthe activity of theepimerase, when both putative active sites are disturbed, such as in the
whereas mutations at H130, E183, H229, and E291 did not seem H44N/H299N and E183A/E366A mutants, the productivity of
to affect the activity of the enzymes. Based on the four-module validamycin is severely compromised.
dimeric nature of ValD, the two monomers are probably arranged
In summary, most C7N-cyclitol-containing secondary metab-
in antiparallel. Moreover, the first two active residues H44 and olites are derived from a shunt pathway of the pentose phos-
E107 of one monomer might form a metal-binding site with the phate pathway involving a novel sugar phosphate cyclase (AcbC,
last two active H315 and E366 from the other monomer, creating CetA, SalQ, ValA, or their homologs), which mediates the cycli-
two active peripheral metal-binding sites within the dimer.
zation of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone
Therefore, the epimerization reaction catalyzed by ValD is pre- (Figure 6). In acarbose and salbostatin biosynthetic pathways,
dicted to take place via a metal ion complex, involving deproto- 2-epi-5-epi-valiolone is proven or suggested to be converted to
nation of 2-epi-5-epi-valiolone from one side of the complex by 5-epi-valiolone 7-phosphate through phosphorylation by AcbM
E107 or E366 to form an enolate intermediate, and reprotonation or SalL first and then through epimerization by AcbO or SalO
from the other side of the complex by E366 or E107 to give 5-epi- (Choi et al., 2008; Zhang et al., 2003). In validamycin biosyn-
valiolone (see Figure S2).
thesis, ValD establishes a branching point for valienamine bio-
Interestingly, in vivo complementation experiments with all synthesis through the alternative epimerization of 2-epi-5-epi-
single point mutation proteins resulted in full restoration of vali- valiolone to 5-epi-valiolone, which is probably shared by CetB
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Construction of pJTU713 for Targeted Replacement
in cetoniacytone A biosynthesis. With the identification of addi-
tional C7N-aminocyclitols and the cloning of their biosynthetic
gene clusters, further biosynthetic diversity for this class of
natural products is expected.
of a 1278 bp DNA Fragment Internal to valD
A 7.8 kb BclI fragment from pHZ2239 was cloned into the BamHI site of
pHZ1358 to generate pJTU712. Using the gel-purified 1384 bp EcoRI/HindIII
fragment from pIJ773 as template (Gust et al., 2003), a 1.4 kb disruption
cassette was obtained by PCR amplification with the primer pairs ValD-
PCR-F and ValD-PCR-R (Table S3). Amplification was performed with Taq
DNA polymerase in a 50 ml reaction with 100 ng template DNA, 10 mM dNTPs,
50 pmol each primer, and 5% DMSO in a thermocycler (BioRad). After initial
denaturation at 94ꢀC for 2 min, 10 cycles were performed with denaturation
at 94ꢀC for 45 s, annealing at 50ꢀC for 45 s, and extension at 72ꢀC for 90 s, fol-
lowed by 15 cycles with the annealing temperature increased to 55ꢀC. A last
elongation step was done at 72ꢀC for 5 min. This fragment was used to replace
the 1278 bp DNA internal to valD in pJTU712 using the l-Red-mediated
recombination. The resulting plasmid pJTU713 was used for targeted replace-
ment of a 1278 bp DNA fragment internal to valD with the 1.4 kb aac(3)IV
cassette in the wild-type strain 5008. The two oligonucleotide primers used
for valD mutant (ZYR-4) confirmation were ValD-Det-F and ValD-Det-R. PCR
amplification was performed with Taq DNA polymerase under similar condi-
tions. The PCR product was analyzed by gel electrophoresis and enzymatic
digestion.
SIGNIFICANCE
Well-studied biosynthetic mechanisms are crucial for in-
creasing the validamycin productivity and generating new
validamycin derivatives with better biological activities using
biosynthetic approaches. The data presented here provide
insights into the biosynthesis of validamycin, particularly
the catalytic function of ValD, which catalyzes the conver-
sion of free 2-epi-5-epi-valiolone to 5-epi-valiolone and
represents an alternative epimerization involved in C7N-
aminocyclitol biosynthesis. The dimeric ValD is one of the
largest proteins found in the VOC superfamily, and displays
a unique distribution of active site residues as revealed by
site-directed mutation. It also shows a strong binding
capacity toward several metal ions. Therefore in addition
to the requirement of cobalt by the cyclase ValA, the pres-
ence of metalloenzyme ValD suggests possible productivity
enhancement through metal ion optimization for validamy-
cin. The characterization of ValD also enriches the still
limited enzymatic toolbox for C7N-aminocyclitol biosynthetic
pathway engineering. Furthermore, degenerate primers
could be designed based on ValD/CetB and used for the
screening of more validamycin-type biosynthetic gene clus-
ters, whereas AcbO/SalO could be used for the screening of
acarbose-type biosynthetic gene clusters.
Construction of pJTU926 for the Complementation of ZYR-4
with Full-Length Recombinant valD
A 1.4 kb NdeI/EcoRI fragment from the expression plasmid harboring a full-
length valD was ligated to the NdeI/EcoRI-digested pJTU968 to give
pJTU925. Then the 1.7 kb MfeI/EcoRI fragment, containing PermE* promoter
and valD, was cleaved from pJTU925 and ligated into EcoRI-digested pPM927
to give pJTU926. The plasmid was introduced into ZYR-4 through conjugation
as previously described (Yu et al., 2005). The exconjugants were selected with
thiostrepton.
Construction of Recombinant N-Terminal Half of valD
and Complementation of ZYR-4
The N-terminal half of valD gene encoding amino acids 1–194 of ValD was
amplified by PCR with KOD-plus DNA polymerase using pJTU712 as template
and primers ValD-N-F and ValD-N-R. The PCR amplification was carried out
under the following conditions: initial denaturation at 94ꢀC for 5 min, then
10 cycles with denaturation at 94ꢀC for 1 min, annealing at 63ꢀC for 45 s,
and extension at 68ꢀC for 2 min, followed by 20 cycles with denaturation
at 94ꢀC for 45 s, annealing at 60ꢀC for 45 s, and extension at 68ꢀC for 2 min.
A last elongation step was performed at 68ꢀC for 5 min. The resultant PCR
product was purified, digested with BamHI and EcoRI, and ligated into
BamHI/EcoRI-digested pRSET B to generate pJTU942, which was sequenced
to validate the inserted DNA sequence. A 0.6 kb NdeI/EcoRI fragment from
pJTU942 harboring the N-terminal half of valD was ligated to the NdeI/EcoRI
digested pJTU968 to give pJTU944. Subsequently, the 0.9 kb MfeI/EcoRI frag-
ment was cleaved from pJTU944 and ligated into the EcoRI-digested pPM927
to give pJTU946. The plasmid was introduced into ZYR-4 through conjugation.
EXPERIMENTAL PROCEDURES
Bacterial Strains and Plasmids
Bacterial strains and plasmids used in this study are listed in Tables S1 and S2.
S. hygroscopicus 5008, the wild-type producer of validamycin, was used
for validamycin isolation, bioassay, and generation of mutant strains. E. coli
DH10B was used as cloning host, and E. coli BW25113 was used as the host
for l-Red-mediated recombination (Gust et al., 2003). pBlueScript KS(À) or
pMD-T vector (Takara) was used for cloning of PCR fragments. pHZ1358 (an
E. coli and Streptomyces shuttle vector) was used for gene replacement in
5008 (Sun et al., 2002). pJTU968 (a pRSET B derivative with PermE* promoter
and a polylinker) was used as a transitional vector. pPM927 was used for
mutant complementation (Smokvina et al., 1990).
Construction of Recombinant C-Terminal Half of ValD
and Complementation of ZYR-4
Reagents and General Procedures
The C-terminal half of valD encoding amino acids 220–451 was amplified by
PCR with KOD-plus DNA polymerase with pJTU712 as template and primers
ValD-C-F and ValD-C-R. The PCR amplification was carried under similar
conditions for that of the N-terminal half of valD. The PCR products were
digested with BamHI and EcoRI, and subsequently ligated into BamHI/EcoRI-
digested pRSET B to generate pJTU943. The plasmid was sequenced to
confirm the inserted DNA sequence. A 0.72 kb NdeI/EcoRI fragment from
pJTU943 harboring the C-terminal half of valD was ligated to the NdeI/
EcoRI-digested vector pJTU968 to give pJTU945. Then the 1.02 kb MfeI/
EcoRI fragment was cleaved from pJTU945 and ligated into the EcoRI-
digested pPM927 to give pJTU947, which was transferred into ZYR-4 through
conjugation.
Restriction enzymes, T4 DNA ligase, Taq polymerase, and KOD-plus poly-
merase were purchased from various companies (New England Biolabs,
Takara, MBI Fermentas, Toyobo, Shanghai Sangon). Synthesis of oligonucle-
otide primers and DNA sequencing of PCR products were performed by
Shanghai Sangon and Invitrogen Co., Ltd. Primers used are listed in Table
S3. Gel Recovery Kit (Tiangen) was used for DNA purification from agarose
gels. Stratagene QuikChange Site-Directed Mutagenesis Kit II XL was used
for site-directed mutagenesis. TSBY liquid medium (per liter: TSB 30 g, yeast
extract 10 g, sucrose 103 g [pH 7.2]) was used for growth of mycelia and isola-
tion of total DNA. SFM medium (2% agar, 2% mannitol, 2% soybean powder
[pH 7.2]) was used for sporulation and conjugation. ISP2 liquid medium (0.4%
yeast extract, 1% malt extract, 0.4% glucose [pH 7.3]) was used for the
fermentation of S. hygroscopicus 5008 and its derivatives. For Streptomyces,
apramycin and thiostrepton were used at 30 mg/ml and 25 mg/ml, respec-
tively, both in SFM agar and in liquid media. E. coli strains were cultured as
described elsewhere (Sambrook et al., 1989).
Site-Directed Mutagenesis of ValD
The desired mutations were introduced by using the QuikChange Site-
Directed Mutagenesis Kit II XL (Stratagene) according to the manufacturer’s
574 Chemistry & Biology 16, 567–576, May 29, 2009 ª2009 Elsevier Ltd All rights reserved

Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
instructions. The plasmid pValD (Table S2) was used as template and mutated
primers (Table S3) were used in the PCR to give individual mutants H44N,
E107A, H130N, E183A, H229N, E291A, H315N, and E366A. In order to
generate H44N/H229N ValD, a 0.93 kb SacI/EcoRI fragment from pJTU3252
with the H44N mutation was ligated to the SacI/EcoRI-digested plasmid
pJTU3250 with H229N mutation to give pJTU3262. Similarly, the E183A/
E366A ValD was constructed. A 0.78 kb NcoI/EcoRI fragment from pJTU3253
with E366A mutation was ligated to the NcoI/EcoRI-digested plasmid
pJTU3251 with E183A mutation to give pJTU3263. All single and double
mutant forms of valD were confirmed by DNA sequencing.
ion analysis, ValD was pretreated with 0.1 mM 1,10-phenanthroline and incu-
bated with 2-epi-5-epi-valiolone (5 mM). After 2 hr incubation, the protein was
precipitated by methanol (50 ml) and centrifuged at 12,000 rpm for 10 min. The
supernatant was collected and dried in vacuo. The product was analyzed
by TLC (SiO2, nBuOH/EtOH/H2O 9:7:4) and stained with cerium- and
molybdate-containing reagent.
Metal Ion Analysis of ValD Using Inductively Coupled Plasma Optical
Emission Spectrometry (ICP-OES)
Freshly purified His6-tagged ValD (4 mg) was digested with thrombin (4 U)
during dialysis against 20 mM Tris-HCl buffer (pH 7.5) overnight. The thrombin
was removed with Thrombin CleanCleave Kit (Sigma), and the Histag was then
removed by passing the protein solution through nickel column. The purified
Histag-free protein solution was split into two tubes, and one of them was
treated with 0.5 mM EDTA (pH 8.0) for 20 min. Both samples were subse-
quently dialyzed against 20 mM metal-ion-free Tris-HCl buffer (pH 7.5) prior
to the metal ion analysis by ICP-OES (Iris Advantage 1000, Thermo Electron)
with a charge injector device detector. The dialysis buffer was used as nega-
tive control. Metal-ion-free buffers were prepared by extraction with a CHCl3
solution of dithizone (0.02%, w/v).
Complementation of ZYR-4 with Single Site-Directed Mutants
of valD (H44N, E183A, H229N, or E366A)
The site-directed mutants of valD were cloned into the vector pPM927 in the
same way as the full-length valD and were introduced into ZYR-4 by conjuga-
tion. The exconjugants were selected with thiostrepton and confirmed by PCR
using the ValD-N-F and ValD-C-R as primers.
HPLC Analysis of Validamycin A
For HPLC analysis, the strains were cultured in 50 ml YMG liquid medium in
250 ml baffled flasks at 37ꢀC and 220 rpm for 6 days. The fermentation broth
was acidified with oxalic acid and applied to a Dowex 50W column (25 ml)
as previously reported (Dong et al., 2001). The extracts were loaded onto
Agilent ZORBAX SB-C18 column (5 mm, 4.6 3 250 mm) for HPLC analysis
(Waters 2690). The mobile phase (5 mM sodium phosphate buffer-methanol,
98:2, v/v) was applied with the flow rate of 0.6 ml/min at room temperature.
The eluate was monitored at 210 nm with Waters 996 photodiode array
detector and the data was analyzed with a Waters Millennium Chromatog-
raphy Manager.
Synthesis of 2-epi-5-epi-Valiolone and 5-epi-Valiolone
2-epi-5-epi-Valiolone was synthesized enzymatically in a coupled reaction
using transketolase (EC 2.2.1.1, Sigma) (Zhang et al., 2002) and ValA with
ribose 5-phosphate and hydroxypyruvate as the initial substrates. The enzyme
reaction was performed at 30ꢀC in a total volume of 30 ml containing 0.5 U
transketolase (Sigma), 9 mg purified ValA, 10 mM hydroxypyruvate (Sigma),
10 mM ribose 5-phosphate (Sigma), 0.5 mM thiamine pyrophosphate (Sigma),
1 mM NAD+, 1 mM MgCl2, 0.025 mM CoCl2, and 2 mM NaF (pH 7.6). The
reaction was monitored by TLC. The mixture was then applied to Vivaspin
15R concentrator (VIVASCIENCE) with a membrane of 10,000 MWCO HY
to remove the protein. The flow-through was lyophilized, dissolved in 1 ml of
ddH2O, and subjected to a Dowex 1 3 8 (Cl- form, Sigma) column chromatog-
raphy. The column was eluted with water and the fractions containing 2-epi-5-
epi-valiolone were pooled and lyophilized. 5-epi-Valiolone was synthesized
according to procedures reported previously (Mahmud et al., 2001).
Cloning and Heterologous Expression of Recombinant His6-Tagged
ValD, N-Terminal Half, and C-Terminal Half of ValD
The valD gene was amplified with Platinum Pfx DNA polymerase (Invitrogen)
using the cosmid clone 17F2 as template and primers valD-F and valD-R.
The natural start codon (GTG) was replaced with ATG to create an NdeI site
at the beginning of the gene. The PCR amplification was carried out in a ther-
mocycler (Eppendorf) under the following conditions: 30 cycles of 45 s at 94ꢀC,
45 s at 58ꢀC, and 90 s at 72ꢀC. The PCR products were digested with BamHI
and EcoRI, and subsequently ligated into BamHI/EcoRI-digested pRSET B
to generate pValD, which was verified by sequencing and introduced by
heat-pulse transformation into E. coli BL21 Gold(DE3)pLysS (Stratagene).
The transformants were grown in LBBS medium (50 ml) containing ampicillin
(100 mg/ml) and chloramphenicol (25 mg/ml) at 37ꢀC to an OD600 of 0.6. Iso-
propyl-b-D-thio-galactopyranoside (IPTG) was then added to a final concen-
tration of 0.4 mM and the incubation was continued at 25ꢀC for 24 hr. The cells
were harvested by centrifugation at 5000 rpm for 10 min and stored frozen at
À80ꢀC until further use.
Light Scattering Analysis of ValD
The protein was purified and analyzed by a DynaPro dynamic light scattering
instrument with Dynamics Version 4.0 software at a concentration of 4 mg/ml.
The detection was run at 4ꢀC for 30 scans.
1H NMR Analysis of ValD Reaction
A solution of 2-epi-5-epi-valiolone (1 mg) in D2O (0.4 ml) was placed in a 5 mm
NMR tube and the reaction was started by adding potassium phosphate buffer
(pH 7.4, 25 mM) and purified ValD solution. The reaction was carried out at
25ꢀC and 1H NMR measurements were performed under a water suppression
condition in 10 min intervals.
Preparation and Purification of His6-Tagged ValD, N-Terminal
Half and C-Terminal Half of ValD
Cells were thawed and resuspended in disruption buffer (50 mM NaH2PO4,
300 mM NaCl, 10 mM imidazole [pH 8.0]), the suspension was sonicated
three times for 15 s each, and cell debris was removed by centrifugation at
10,000 rpm for 7 min. The protein solution was applied to a BD TALONspinꢀ
column (BD Biosciences) and centrifuged at 3000 rpm for 1 min. The column
was washed with washing buffer (50 mM NaH2PO4, 300 mM NaCl [pH 8.0]),
twice, and washing buffer with 50 mM imidazole. The His6-tagged protein
was eluted with elution buffer (50 mM NaH2PO4, 300 mM NaCl, 500 mM imid-
azole [pH 8.0]) and dialyzed for 12 hr against 1 l dialysis buffer (31 mM K2HPO4/
KH2PO4 [pH 7.4] and 0.5 mM DTT). Protein concentration was measured by
the Bradford protein microassay with bovine serum albumin as standard.
SUPPLEMENTAL DATA
Supplemental Data include two figures and three tables and can be found with
this article online at http://www.cell.com/chemistry-biology/supplemental/
S1074-5521(09)00139-2.
ACKNOWLEDGMENTS
The authors thank Andrew P. Karplus, Patricia M. Flatt, and Xiumei Wu for
technical assistance and William Austin for metal ion analysis. Work at Oregon
State University was supported by a grant from the National Institutes of Health
(R01 AI061528). Work at Shanghai Jiao Tong University was supported by
grants from the 973 and 863 Programs of the Ministry of Science and Tech-
nology, the Natural Science Foundation of China, and Shanghai Leading
Academic Discipline Project B203. H.X. was in part supported by the
Exchange Program from China Scholarship Council. This article is dedicated
to H.G. Floss on the occasion of his 75th birthday.
Enzymatic Assays
Coupled-enzyme assays were carried out using protein solutions of ValA (Yu
et al., 2005) and ValD or mutated ValD (45 ml, 0.5 mg/ml) with sedoheptulose
7-phosphate (5 mM) as substrate in a 50 ml total volume containing 25 mM
potassium phosphate buffer (pH 7.4), CoCl2 (1 mM), NaF (2 mM), and NAD+
(1 mM). The reactions were carried out at 30ꢀC for 2 hr. For preliminary metal
Chemistry & Biology 16, 567–576, May 29, 2009 ª2009 Elsevier Ltd All rights reserved 575

Chemistry & Biology
Alternative Epimerization for C7N-Aminocyclitol
Received: November 18, 2008
Revised: March 4, 2009
Accepted: April 2, 2009
Published: May 28, 2009
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ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the anti-
fungal agent validamycin A. ChemBioChem 8, 632–641.
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