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Department of Chemistry, Department of Molecular Biosciences, Feinberg School of Medicine, Northwestern University,
Evanston, Illinois 60208, United States
Department of Genetics, Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of
Wisconsin, Madison, Wisconsin 53706, United States
*
S Supporting Information
Figure 1. Workow for an epigenetic approach to fungal natural product discovery. Following epigenetic perturbation by antagonism of histone
deacetylases (using either genetic or chemical inhibition), the extracellular metabolome is measured quantitatively using replicate LC-MS runs with
high mass accuracy. The results can be visualized in a volcano plot, where each point represents a metabolite that can potentially be annotated by
accurate mass and veried by MS2 fragmentation.
Figure 2. (A) Volcano-plot representation of global changes in the Aspergillus nidulans metabolome in response to reduced expression of rpdA.
Displayed in insets are the responses of several known metabolites. Each dot represents an individual compound (within 3 ppm in mass and 2
min in retention time), and the probability of that quantitative observation being statistically signicant is indicated by a p value on the y axis
(determined using the standard linear model within SIEVE software). Compounds observed on the right half of the plot are present at higher levels
in the rpdAKD samples. Compounds observed on the left-hand portion of the diagram are present at higher levels in the wildtype samples. Also
shown are representative liquid GMM growths of wildtype A. nidulans (left) and the rpdAKD strain (right). (B) Correlation of the quantitative
responses observed for all compounds that were >5 fold upregulated upon treatment with either 100 M SAHA (y axis) or rpdAKD (x axis).
the fellutamides, lipopeptide aldehydes that inhibit proteasome Northern blots of the xylP(p)::rpdA strain grown without
activity.22,23 xylose showed that the levels of the rpdA transcript were
RESULTS
Controllable Repression of an HDAC. We rst wanted to
reduced 14-fold relative to wildtype A. nidulans (Supporting
Information Figure 1b). Such growths where rpdA is knocked
down in expression are referred to as rpdAKD. The impact of
test the eects on the exported metabolome when the activity altered RpdA levels on the relative levels of >1100 molecular
of the HDAC RpdA was reduced. Since the complete deletion species in the exported metabolome were determined (Figure
of rpdA is lethal,24 we utilized a strain with the rpdA gene 2).
(AN4493) under the control of the xylose-inducible promoter Global Monitoring of the Exported Metabolome.
from Penicillium chrysogenum (xylP(p)).24 In this way, we Combining all strains analyzed, 1268 unique molecular species
generated a strain, RAAS58.4, where the expression of RpdA were detected by LC-MS. Mass spectrometric signals from
could be induced with the addition of xylose. Phenotypically, dierent isotope and adduct peaks were combined such that the
the uninduced xylP(p)::rpdA strain (grown without xylose) great majority of these species represent individual compounds
showed decreased radial growth, sparse hyphal structures, and produced by the fungus. The intact masses for these
poor conidiation and had increased pigment production compounds were used to search against a database containing
(Figure 2, insets at bottom). However, in the presence of the theoretical masses of 104 metabolites known to be
xylose, this strain appeared nearly identical to the wildtype produced by A. nidulans. When searching against this targeted
strain (Supporting Information Figure 1a). Analysis of database with a mass tolerance of 2 ppm, we putatively
B DOI: 10.1021/acschembio.5b00025
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identied 49 compounds. In order to verify all annotations We observed several general patterns in the comparison of
based on intact accurate mass, tandem mass spectra were extracts from wildtype and rpdAKD strains. For the 100 most
manually interrogated; 45 annotations were validated and are abundant compounds in the wildtype, their average expression
shown in Table 1. The ability of LC-MS/MS with accurate level decreased by 50% in the rpdAKD samples. However, the
mass (i.e., use of Fourier-transform mass spectrometry) to opposite general response was seen for the 100 least abundant
dereplicate fungal secondary metabolites has recently been compounds in the wildtype, whose average intensity increased
demonstrated.2528 However, annotated MS2 spectra (Support- >60-fold in rpdAKD. For the 100 compounds closest to the
ing Information Figures 28) are included to further validate median intensity in the wildtype, their average abundance
the ability of tandem MS with manual interpretation to increased >3-fold in rpdAKD. In addition to the general trends
condently identify known compounds. above, the levels of known compounds were more likely to be
Having dereplicated 45 known A. nidulans metabolites, we down-regulated in the rpdAKD samples than were unknowns
next turned to quantitative analysis of these and other (Supporting Information Figure 10). The reverse was also true:
metabolites in response to knockdown of rpdA. The results unknown compounds had a greater chance of being up-
from replicate analyses and ANOVA analysis of wildtype versus regulated by >10 fold in extracts of the rpdAKD strain
rpdAKD extracts are displayed using a volcano plot (Figure 2A). (Supporting Information Figure 10).
Chemical HDAC Inhibition Causes Expression and
Overall, reduced expression of rpdA led to a 4-fold increase in
Silencing of Many Secondary Metabolites. Similar to the
metabolite production of over 70% of all compounds identied
rpdAKD growths, the addition of chemical HDAC inhibitors,
in this study compared to wildtype; a greater than 10-fold
suberanilohydroxamic acid (SAHA), trichostatin A, or sodium
change was observed for over 60% of all compounds identied
butyrate, resulted in slower growth. Unlike the rpdAKD growths,
relative to wildtype. The compounds antibiotic 3127,29 F9775A pigmentation was unaltered relative to the wildtype growths.
and B,30 and alternariol31 were only seen at signicant levels in The levels of known metabolites were analyzed to study the
the rpdAKD samples. In contrast, several abundant and well eect of chemical HDAC inhibition. The levels of sterigmato-
studied compounds were present at reduced levels in the cystin and several emericellamides were reduced in all three
rpdAKD samples as compared to the wildtype. Production of chemical HDAC inhibition samples, consistent with observa-
sterigmatocystin, one of the most thoroughly characterized tions in the rpdAKD samples (Supporting Information Figure
mycotoxins,3234 was down-regulated by a factor of over 100 in 11). In particular, treatment with SAHA resulted in an up-
the rpdAKD strain compared to the wildtype (Figure 2A inset regulation of a large number of compounds also up-regulated in
and Supporting Information Figure 9). The compound 5- the rpdAKD samples. In SAHA-treated samples, 167 compounds
hydroxydihydro-sterigmatocystin was similarly down-regulated, were found to be present at levels >5 times higher than in
in this case by a factor of 25. A similar pattern was also wildtype A. nidulans. Of these, 141 were also up-regulated >5-
observed with the emericellamides, the arugosins, the fold in the rpdAKD samples (Figure 2B).
aspoquinolones, and the austinols (Supporting Information Inhibition of HDAC Activity Induces Production of the
Figure 9). Fellutamides. We identied dozens of compounds that do not
C DOI: 10.1021/acschembio.5b00025
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ACS Chemical Biology Articles
Figure 3. Selected ion chromatograms (SICs) of three fellutamides identied in this work. (A) Fellutamide B and (B) antibiotic 1656 G, are
fellutamides that were previously not known to be produced by A. nidulans, while (C) antibiotic 3127, is an analogue that was isolated from A.
nidulans strain 3127 from a 1991 Japanese Patent.38 Structural dierences between the three are highlighted in red. See Supporting Information
Figures 12 and 13 for verication of these fellutamides using tandem MS. Fold changes in expression are lower estimates obtained by taking the ratio
of MS signal intensities in samples of rpdAKD to wildtype A. nidulans; no background expression was detected in wildtype samples for antibiotics
1656 G and 3127 (panels B and C), whereas trace levels of fellutamide B were detectable in the wildtype (panel A).
dereplicate to known A. nidulans secondary metabolites and secondary metabolome. For example, treatment with the
that were produced at signicant levels only in the rpdAKD HDAC inhibitor SAHA led to the up-regulation of many
samples. Many of these were also up-regulated signicantly in compounds also up-regulated in the rpdAKD strain. Correlation
the chemical HDAC inhibitor-treated samples. On the basis of of all compounds >5 fold up-regulated in both SAHA-treated
intact accurate masses and similarities of fragmentation and the rpdAKD strain resulted in a roughly linear relationship
patterns, we found that A. nidulans is capable of making several (i.e., R2 of 0.7, Figure 2B). Activation of similar compounds at
of the lipopeptide aldehydes known as the fellutamides: comparable levels suggests that RpdA depletion and nonspecic
fellutamide B (92-fold up-regulated), antibiotic 1656-G (268- HDACi promote analogous states of hyperacetylation in bulk
fold up-regulated), and antibiotic 3127 (201-fold up-regulated) chromatin and even specic genomic loci.
(Figure 3). Inspection of the chromatographic retention and Intriguingly, another general pattern in the abundance
MS2 fragmentation of a synthetic fellutamide B standard35 changes of secondary metabolites in both the rpdAKD and
veries the identity of the endogenous compound (Supporting chemically HDAC-inhibited strains could be ascertained. Many
Information Figure 12) and strongly supports the annotations of the most abundant compounds present in wildtype/control
of the structurally related compounds identied as antibiotics extracts were reduced in HDACi samples, while many low
1656-G and 3127 (Supporting Information Figure 13). The abundance compounds were signicantly increased upon
fellutamides, originally isolated from Penicillium fellutanum,36 HDACi. A potential explanation for this phenomenon may
have also been isolated from other fungi including Aspergillus be that as additional secondary metabolism gene clusters are
versicolor,37 which is closely related to A. nidulans. Despite being activated upon the stress of HDACi, the building blocks
studied for decades, the ability of A. nidulans to produce the required for production of previously abundant compounds are
fellutamides has evaded detection until now. consumed by other, newly activated pathways.
DISCUSSION
The use of HDACi to induce expression of cryptic secondary
This study illustrates the importance in the choice of HDAC
to target: A. nidulans and most other lamentous fungi harbor
four classical HDACs, which potentially would result in distinct
metabolites has proven successful since evidence suggesting its metabolic proles upon selective inhibition. Here, the rpdA
potential started to be published.6 According to this strategy, gene was targeted because deletion of its homologue in
HDACi increases histone acetylation, causing large portions of Saccharomyces cerevisiae (rpd3) leads to the largest extent of
the fungal genome to become more euchromatic and global hyperacetylation, particularly on histones H3 and H4
transcriptionally active. This in turn leads to the expression of (unpublished results). From another study, the deletion of the
previously cryptic gene clusters and production of their nonessential HDAC, HdaA in A. nidulans, led to increases in
associated natural products. While this model has been two of the three secondary metabolites monitored (penicillin
supported by global transcriptomics,11,12 an assessment of the and sterigmatocystin) as determined by thin layer chromatog-
eects of HDACi on the secondary metabolome itself has been raphy.6 However, deletion of two other HDACs, HosB and
lacking until now. Quantitative monitoring of extracellular small HstA, did not aect levels of penicillin or sterigmatocystin.6
molecules following genetic or chemical HDACi revealed both Operationally, treatment with a chemical for nonspecic
up- and down-regulation in the levels of secondary metabolites. HDACi is more tractable for most laboratories than genetic
Upon implementation of a genetic approach targeting a manipulation of undomesticated fungal strains. Whether
specic HDAC, the rpdAKD strain of A nidulans displayed up- HDACi is superior to other stressors or perturbations of
regulation of diverse compounds such as alternariol, F9775-A fungi to coax production of new natural products is yet an open
and -B, three fellutamides, and 50 unknown metabolites. question. MS-based metabolomics with accurate mass for
Chemical HDACi was found to have analogous eects on the discovery of new secondary metabolites is becoming more
D DOI: 10.1021/acschembio.5b00025
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accessible, and its utility is demonstrated here with the rst formic acid (solvent B): time 0 min, 2% B; 35 min, 70% B; 54
unambiguous identication of the fellutamides as A. nidulans min, 98%B. The LC was placed in-line with a Q-Exactive mass
natural products. spectrometer for MS analysis. The instrument settings were as
CONCLUSION
Overall, these results provide a deeper view into the complex
follows: capillary temperature 250 C, sheath gas 8 (arbitrary
units), spray voltage 4.2 kV. Full MS spectra were acquired at
35 000 resolution for the mass range m/z 2001500 for all
regulatory mechanisms governing the production of secondary samples. Following each full MS scan, the top ve most intense
metabolites by large collections of hierarchically regulated ions were selected for a dependent MS2 scan. MS2 was
fungal genes. Rather than producing the expected global up- conducted using HCD with a normalized collisional energy of
regulation of secondary metabolism, reduction of RpdA activity 25. Each sample analyzed (e.g., wildtype, rpdAKD, and chemical
led to selective up-regulation in several compounds, such as HDACi) was prepared in biological triplicate, each of which
F9775-A and -B and three fellutamides. The discovery that the was run in technical duplicate.
fellutamides are biosynthesized by A. nidulans supports the use Informatics and Statistical Treatment of Data for
of HDAC inhibition for the discovery of cryptic secondary Quantitative Metabolomic Proling. SIEVE software
metabolites. In addition, RpdA perturbation led to down- version 2.0.178 was used for chromatographic alignment,
regulation in levels of several known metabolites: chiey
component detection, and relative quantication. Chromato-
sterigmatocystin and the emericellamides. The ability of
dierential mass spectrometry to detect and quantify such a graphic alignment was performed for all samples using an initial
large number of structurally diverse metabolites demonstrates tile size of 1000 frames. This led to alignment scores >0.95 for
its value as a tool for investigating fungal secondary metabolism all samples with a maximum time correction of 3.25 min.
and its regulation, particularly at an epigenetic level. Following alignment, component detection was performed
To date, many studies that use histone acetylation levels to using a mass tolerance of 10 ppm and a retention time window
coax secondary metabolites into expression have relied on levels of 3 min. A minimum intensity of 5 106 was selected as the
of gene transcripts as the measure of success for activation of threshold for dening a peak as a component. For each
secondary metabolism. While transcript levels do provide some component, a reconstructed ion chromatogram was created,
insight into gene-level regulation of secondary metabolism gene and the integrated intensity of the peak was calculated. The
clusters, the secondary metabolites themselves are the nal integrated intensities for a given component were averaged for
products of interest and are ultimately the entities responsible each condition. The resulting component ratios and p values
for biological activity. It follows that monitoring changes of the were calculated and plotted on a logarithmic scale to create a
secondary metabolome directly using high performance
volcano plot. This provides a visual representation of both the
quantitative mass spectrometry will provide a clear path to
relative expression level observed as well as the condence level
discovery of new compounds at a far faster rate than previously
possible. of that measurement for each metabolite.
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ASSOCIATED CONTENT
S Supporting Information
(10) Lee, I., Oh, J. H., Shwab, E. K., Dagenais, T. R., Andes, D., and
Keller, N. P. (2009) HdaA, a class 2 histone deacetylase of Aspergillus
fumigatus, affects germination and secondary metabolite production.
Figures display validation of genetic constructs and annotated
Fungal Genet. Biol. 46, 782790.
MS/MS spectra. This material is available free of charge via the (11) Lin, J. Q., Zhao, X. X., Zhi, Q. Q., Zhao, M., and He, Z. M.
Internet at http://pubs.acs.org.
F DOI: 10.1021/acschembio.5b00025
ACS Chem. Biol. XXXX, XXX, XXXXXX
ACS Chemical Biology Articles
G DOI: 10.1021/acschembio.5b00025
ACS Chem. Biol. XXXX, XXX, XXXXXX