REPORTS
such as insulin and nutrients. The direct regulation of CAD by S6K1 serves as a mechanism to
increase the pool of nucleotides available for the
RNA and DNA synthesis that accompanies cell
growth. In addition to protein and lipid synthesis,
pyrimidine synthesis represents another major
anabolic process that is responsive to changes in
cellular growth conditions through mTORC1
signaling.
References and Notes
1. M. Laplante, D. M. Sabatini, Cell 149, 274 (2012).
2. V. Iadevaia, Y. Huo, Z. Zhang, L. J. Foster, C. G. Proud,
Biochem. Soc. Trans. 40, 168 (2012).
3. T. Porstmann et al., Cell Metab. 8, 224 (2008).
4. K. Düvel et al., Mol. Cell 39, 171 (2010).
5. J. Huang, B. D. Manning, Biochem. J. 412, 179
(2008).
6. S. Menon, B. D. Manning, Oncogene 27, (Suppl 2),
S43 (2008).
7. A. Radu, V. Neubauer, T. Akagi, H. Hanafusa,
M. M. Georgescu, Mol. Cell. Biol. 23, 6139 (2003).
8. M. Mori, M. Tatibana, Methods Enzymol. 51, 111
(1978).
9. R. A. Williamson et al., Transplant. Proc. 28, 3088
(1996).
10. E. A. Carrey, D. G. Campbell, D. G. Hardie, EMBO J. 4,
3735 (1985).
11. P. P. Hsu et al., Science 332, 1317 (2011).
12. Y. Yu et al., Science 332, 1322 (2011).
13. H. Flotow, G. Thomas, J. Biol. Chem. 267, 3074
(1992).
Proteomic Mapping of Mitochondria
in Living Cells via Spatially
Restricted Enzymatic Tagging
Hyun-Woo Rhee,1*† Peng Zou,1* Namrata D. Udeshi,2 Jeffrey D. Martell,1 Vamsi K. Mootha,2,3,4
Steven A. Carr,2 Alice Y. Ting1,2‡
Microscopy and mass spectrometry (MS) are complementary techniques: The former provides
spatiotemporal information in living cells, but only for a handful of recombinant proteins at
a time, whereas the latter can detect thousands of endogenous proteins simultaneously, but only
in lysed samples. Here, we introduce technology that combines these strengths by offering
spatially and temporally resolved proteomic maps of endogenous proteins within living cells.
Our method relies on a genetically targetable peroxidase enzyme that biotinylates nearby proteins,
which are subsequently purified and identified by MS. We used this approach to identify
495 proteins within the human mitochondrial matrix, including 31 not previously linked to
mitochondria. The labeling was exceptionally specific and distinguished between inner membrane
proteins facing the matrix versus the intermembrane space (IMS). Several proteins previously
thought to reside in the IMS or outer membrane, including protoporphyrinogen oxidase,
were reassigned to the matrix by our proteomic data and confirmed by electron microscopy.
The specificity of peroxidase-mediated proteomic mapping in live cells, combined with its
ease of use, offers biologists a powerful tool for understanding the molecular composition of
living cells.
e sought to develop a method that
circumvents the limited specificity
and loss of material associated with
organelle purification in traditional mass spectrometry (MS)–based proteomics. Our approach
involves tagging the proteome of interest with
a chemical handle such as biotin while the cell
W
1328
is still alive, with all membranes, complexes,
and spatial relationships preserved. Thus, we
required a genetically targetable labeling enzyme that covalently tags its neighbors, but
not more distant proteins, in living cells. One
candidate is promiscuous biotin ligase (1–3),
but its labeling is extremely slow (requiring 24
15 MARCH 2013
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14. D. R. Alessi, F. B. Caudwell, M. Andjelkovic, B. A. Hemmings,
P. Cohen, FEBS Lett. 399, 333 (1996).
15. L. R. Pearce et al., Biochem. J. 431, 245 (2010).
16. C. C. Dibble, J. M. Asara, B. D. Manning, Mol. Cell. Biol.
29, 5657 (2009).
17. L. M. Graves et al., Nature 403, 328 (2000).
18. L. A. Musmanno, R. S. Jamison, R. S. Barnett, E. Buford,
J. N. Davidson, Somat. Cell Mol. Genet. 18, 309 (1992).
Acknowledgements: We thank M. Yuan and S. Breitkopf
for technical assistance with MS/MS and D. Patterson,
D. Kwiatkowski, and M. Zbinden for cell lines. This work was
supported in part by a grant from the LAM Foundation
(I.B.-S.); NIH grants F32-DK095508 (J.J.H.), P01-CA120964
(B.D.M. and J.M.A.), and R01-CA122617 (B.D.M.); Dana
Farber/Harvard Cancer Center grant P30-CA006516 (J.M.A.);
and a Sanofi Innovation Award (B.D.M.). I.B.-S. and J.J.H.
conceived and performed all experiments, analyzed all
experimental data, and prepared the manuscript. J.M.A.
performed and analyzed the MS/MS experiments. B.D.M.
directed the research, reviewed all experimental data, and
prepared the manuscript. All authors have reviewed the
manuscript and declare no competing financial interests.
Supplementary Materials
www.sciencemag.org/cgi/content/full/science.1228792/DC1
Materials and Methods
Figs. S1 to S7
Tables S1 to S4
References (19–23)
13 August 2012; accepted 25 January 2013
Published online 21 February 2013;
10.1126/science.1228792
hours) (fig. S1) (1, 2), and the proposed mechanism proceeds through a biotin-adenylate
ester, which has a half-life of minutes, implying a large labeling radius. Horseradish peroxidase (HRP)–catalyzed nitrene generation is
another possibility (4), but we were unable to
detect this labeling (fig. S2), and HRP is inactive when expressed in the mammalian cytosol (5).
We recently introduced engineered ascorbate
peroxidase (APEX) as a genetic tag for electron
microscopy (EM) (5). Unlike HRP, APEX is
active within all cellular compartments. In addition to catalyzing the H2O2-dependent polymerization of diaminobenzidine for EM contrast,
APEX also oxidizes numerous phenol derivatives to phenoxyl radicals. Such radicals are
short lived (<1 ms) (6, 7), have a small labeling radius (<20 nm) (8, 9), and can covalently
react with electron-rich amino acids such as
Tyr, Trp, His, and Cys (10–13). This chemistry forms the basis of tyramide signal amplification (14), but it has not been extended to
living cells.
1
Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. 2Broad Institute of
MIT and Harvard, Cambridge, MA 02142, USA. 3Department
of Molecular Biology, Massachusetts General Hospital, Boston,
MA 02115, USA. 4Department of Systems Biology, Harvard
Medical School, Boston, MA 02115, USA.
*These authors contributed equally to this work.
†Present address: Ulsan National Institute of Science and
Technology, Ulsan, Korea.
‡To whom correspondence should be addressed. E-mail:
[email protected]
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cell settings, insulin acutely stimulated an increase
in labeling of intermediates in pyrimidine synthesis in G9C cells expressing wild-type CAD,
and this was blocked by the S6K1 inhibitor (Fig.
4E and fig. S7, A and B). Although the synthesis
of N-carbamoyl-aspartate increased in response
to insulin in CAD-S1859A mutant–expressing
G9C cells, the labeling of pyrimidine intermediates downstream of CAD was not stimulated by
insulin, with these metabolites detected at amounts
similar to that in wild-type cells treated with the
S6K1 inhibitor (Fig. 4E). These data suggest that
the S6K1-mediated phosphorylation of S1859
enhances the in vivo dihydroorotase (E3) activity
of CAD, with additional points of regulation from
insulin and S6K1 possibly affecting upstream steps
in the pathway (fig. S7C). The cells expressing
CAD-S1859A were no longer acutely sensitive
to insulin for the stimulated incorporation of de
novo–synthesized pyrimidines into RNA and
DNA (fig. S7D).
This study demonstrates that mTORC1 serves
as a molecular link between growth signals and
acute control over pyrimidine synthesis. It is worth
emphasizing that mTORC1 and S6K1 are not
essential for de novo pyrimidine synthesis per se
but are required to increase flux through this pathway in response to growth-promoting signals,
To examine whether APEX could be employed for proteomic labeling (Fig. 1A), we targeted APEX to the mitochondrial matrix of
human embryonic kidney (HEK) cells and initiated labeling by adding biotin-phenol and 1 mM
H2O2 to the cell medium. Labeling was terminated
after 1 min by cell fixation or lysis. Imaging by
confocal microscopy (Fig. 1B) or stochastic optical reconstruction microscopy (STORM) (Fig.
1C) (15) showed that biotinylated proteins overlapped tightly with the mito-APEX construct.
Streptavidin blot analysis of cell lysates showed that
numerous endogenous proteins were biotinylated
in an APEX- and H2O2-dependent manner (Fig.
1D and fig. S3).
To test the generality of our approach, we also
analyzed other constructs that target APEX to
different cellular regions (figs. S4 and S5). Seven
different cytosol-facing APEX fusions gave distinct “fingerprints” in a streptavidin blot analysis,
suggesting that targeted APEX biotinylates only
a subset of cytosolic proteins, probably those in
its close vicinity. We performed additional experiments to characterize the small-molecule
specificity of APEX (fig. S2), the membrane permeability of the phenoxyl radical (fig. S6), and
the covalent adducts formed with amino acids
in vitro (fig. S7; see also supplementary materials and methods).
We used mitochondrial matrix-targeted APEX
to perform a proteomic experiment. Though
mitochondria have been extensively characterized by MS proteomics, all previous studies have
used mitochondrial purification, which is associated with sample loss and contamination. Consequently, the most comprehensive inventory of
mitochondrial proteins (16) integrates MS proteomic data with green fluorescent protein imaging and computational analysis. Furthermore,
proteome-scale maps of the matrix subcompartment in mammalian cells contain only a small
number of proteins (17), representing very low
coverage, probably because of the challenge of
enriching for this subcompartment.
Endogenous proteins biotinylated by mitoAPEX for 1 min in live HEK cells (as in Fig. 1)
were purified using streptavidin beads, digested
to peptides, and identified by tandem MS. We used
stable isotope labeling (18) of experimental and
control samples to distinguish between biotinylated
proteins and nonspecific binders (fig. S8). We
performed two independent replicates, each of
which produced a bimodal distribution of proteins
based on isotope ratio (fig. S8C). The high-ratio
distributions were strongly enriched for mitochondrial proteins, so we separated these hits and
intersected the results from both replicates to
obtain a list of 495 proteins (table S1), which we
call our “matrix proteome.” This list is expected
to contain both soluble matrix proteins and inner
mitochondrial membrane (IMM) proteins that
contact the matrix space.
Crossing our matrix proteome with earlier
literature revealed that it was highly enriched for
both mitochondrial and mitochondrial matrix
proteins (Fig. 2A). Ninety-four percent (464 proteins) had prior mitochondrial annotation, leaving
31 “mitochondrial orphans” without any previously known connection to mitochondria (table S2).
To further quantify the specificity of our matrix
proteome, we examined the components of the
electron-transport chain (Fig. 2C) and the TOM/
TIM/PAM protein-import pathway (Fig. 2D), because they are structurally and/or topologically
well characterized. In our matrix proteome, we
detected only those subunits with exposure to
the matrix space, illustrating the specificity and
membrane-impermeability of our tagging.
Fig. 1. Labeling the mito- A
B
OH
transfect
chondrial matrix proteome
biotin-phenol
with
in living cells. (A) Labeling
lyse cells
H2O2
mito-APEX
streptavidin beads
scheme. The APEX peroxidase
1 min
mass spectrometry
was genetically targeted to
the mitochondrial matrix
omit
via fusion to a 24–amino acid
omit H2O2
biotin-phenol
B
OH
B B
targeting peptide (5). Label- B
B
B
O
ing was initiated by the addition of biotin-phenol and neutravidin
endogenous proteins
H2O2 to live cells for 1 min.
(AF647)
Cells were then lysed, and
20 µm
biotinylated proteins were
recovered with streptavidinmito-APEX
C streptavidin
mito-APEX
coated beads, eluted, separated
(Cy3/Cy5)
merge
(anti-V5)
(anti-V5)
on a gel, and identified by MS.
+DIC
The peroxidase-generated phenoxyl radical is short-lived and
whole cell lysate
streptavidin bead-enriched
membrane-impermeant and, D
+
+
+
+
+
+
hence, covalently tags only mito-APEX: +
+
+
+
+
+
bead only
neighboring and not distant substrates: 1+ +2 3
500 nm
1
3
1
5
6
2
4
endogenous proteins. B, biotin.
230(B) Confocal fluorescence imaging of biotinylated proteins
100E
100 nm
100 nm
(stained with neutravidin) af80ter live labeling of HEK cells
60expressing mito-APEX as in
50(A). Controls were performed
40with either biotin-phenol or
30H2O2 omitted. DIC, differenmito-APEX
mito-APEX
kD
ponceau
coomassie
streptavidintial interference contrast. (C)
HRP
Superresolution STORM images showing streptavidin
and APEX (AF405/AF647) localization patterns at 22-nm resolution in U2OS trol lanes (2 and 3) of the streptavidin blot. (E) Electron microscopy of
cells. Samples were reacted as in (B). (D) Gel analysis of biotinylated mito- HEK cells expressing mito-APEX. EM contrast was generated by treating fixed
chondrial matrix proteins, before (lanes 1 to 3) and after (lanes 4 to 6) cells with H2O2 and diaminobenzidine. APEX catalyzes the polymerization of
streptavidin bead enrichment. Samples were labeled as in (B). Substrates diaminobenzidine into a local precipitate, which is subsequently stained with
are biotin-phenol and H2O2. Mammalian cells have four endogenously electron-dense OsO4 (5). Dark contrast is apparent in the mitochondrial matrix,
biotinylated proteins, three of which were observed in the negative con- but not the intermembrane space.
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15 MARCH 2013
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REPORTS
1329
REPORTS
31
17337
2
4
103
B 100%
2
4
13
3
D
4
32
60%
60%
40%
40%
20%
20%
1526
0%
human
464
matrix
289
mito
224
matrix
non-mito
mito
C
OMM
IMS
matrix
Complex I
(core subunits)
IMS
12
13 14 7,
10, 8
11 4
matrix
3
not detected
detected
15
2
not detected
detected
9 8
23
ii
iii
v
iv
10 13
50
H
D
C
C
G
F
G
F
A
16
TIM23
J
K
D I B
L
M
mtHsp70
PAM
MPP
F
ATP synthase
B I D
H G H
C
C
A J
E
18
Mge1
Complex IV
E+I
K
H
D
J
matrix 44
aminoacyl-tRNA synthetases
nucleoid-associated proteins
mitoribosomal proteins
tricarboxylic acid cycle enzymes
amino acid metabolism enzymes
not detected
detected
Complex III
C
L
J
F
A
E
M
K
c
a
b
F6
A
B
A
22
23 17
i
B
9
66
21
E+I
K
5
20
IMS
Complex II
D
6
16
i.
ii.
iii.
iv.
v.
mito specificity matrix specificity
567
40
0%
proteome proteome proteome proteome
TOM
20
cytosol
80%
80%
70
22
B
d
1
OSCP
Fig. 2. Specificity and depth of coverage of the mitochondrial matrix proteome.
(A) Analysis of specificity. The left two columns show the fraction of proteins
with prior mitochondrial annotation in the entire human proteome (column 1)
and in our matrix proteome (column 2). The right two columns show the
distribution of proteins with prior submitochondrial localization information,
for all mitochondrial proteins (column 3) and for our matrix proteome (column 4). See table S6 for details. (B) Analysis of depth of coverage. Five groups
of well-established mitochondrial matrix proteins (i to v) were crossed with our
proteomic list. For each group, 80 to 91% of proteins were detected in our
matrix proteome. See table S7 for details. (C) Analysis of labeling specificity
To analyze depth of coverage, we checked
our matrix proteome for well-established groups
of soluble matrix proteins (Fig. 2B). We detected
members of each group at a rate of 80 to 90%
and found nearly identical subsets of proteins in
each of the two replicates, suggesting that coverage was high, but for only ~85% of proteins.
The proteins we consistently did not detect were
not low-abundance proteins (fig. S8F), nor did
they lack surface-exposed tyrosine residues. We
hypothesize that these proteins were sterically
buried in macromolecular complexes, making
them inaccessible to the phenoxyl radical.
For a subset of proteins in our proteome, we
detected directly biotinylated peptides (fig. S9
and table S4). Tandem MS sequencing showed
that biotin-phenol was conjugated to tyrosine side
chains. In nearly all cases, the biotinylated tyrosine residue mapped to a surface-exposed site
on a soluble protein or a matrix-exposed site on
a transmembrane protein.
Our matrix proteome of 495 proteins provides a number of interesting insights. First, the
31 mitochondrial orphans may be newly discovered mitochondrial proteins. We selected and
1330
for protein complexes of the IMM. The subunits of complexes I to IV and F0-F1
adenosine triphosphate (ATP) synthase, for which structural information is
available, are illustrated. Subunits detected in our matrix proteome are
shaded red; those not detected are shaded gray. Note that because
structural information is not available for all 45 subunits of complex I, some
subunits that appear exposed here may not be exposed in the complete
complex. OSCP, oligomycin sensitivity conferral protein. (D) Same analysis
as in (C), for proteins of the TOM/TIM/PAM protein-import machinery that
span the OMM and IMM. All proteins depicted in (C) and (D) are listed,
with additional information, in table S8.
imaged six of these at random and found complete or partial mitochondrial localization for all
of them (fig. S10). Second, 240 proteins with
unknown submitochondrial localization can now
be assigned by our data to the matrix compartment (table S3). Third, we detected six proteins
previously assigned to the intermembrane space
(IMS) or outer mitochondrial membrane (OMM):
PPOX, CPOX, PNPT1, CHCHD3, COASY, and
SAMM50. To determine if our detection of these
proteins in the matrix was accurate, we performed
EM imaging, taking advantage of APEX’s additional functionality as an EM tag (5). APEX
fusions to five of the six proteins showed matrix
staining by EM (Fig. 3 and fig. S11). We were
unable to examine the final protein, SAMM50,
because APEX insertion at four different sites
abolished mitochondrial targeting.
The proteins PPOX and CPOX are particularly interesting in this group because they catalyze two of the later steps in heme biosynthesis
(Fig. 3A). Previous studies on purified mitochondria or mitoplasts treated with proteases or
membrane-impermeant inhibitors have localized
both enzymes to the IMS (19–22). Structural anal-
15 MARCH 2013
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SCIENCE
ysis and modeling have indicated that PPOX
docks to ferrochelatase (FECH), the final ironinserting enzyme of heme biosynthesis, through
the IMM (23) (Fig. 3F). This model is inconsistent with our EM data, because we found
that both the C terminus and amino acid 205 of
PPOX localize to the matrix (Fig. 3C). Our EM
data on CPOX, on the other hand, are consistent
with previous literature, because we found that
residue 70 localizes to the matrix (explaining the
detection of CPOX in our matrix proteome),
whereas the C terminus and residue 120 flanking
the active site localize to the IMS (Fig. 3D). Our
reassignment of PPOX from the IMS to the
matrix has implications for the nature of its interactions with CPOX and FECH and the mechanisms by which its substrates are transported across
the IMM.
We have developed a method for mapping
the proteomic composition of cellular organelles, using a genetically targetable peroxidase
that catalyzes the generation of short-lived, highly
reactive, and membrane-impermeant radicals in
live cells. With a temporal resolution of 1 min,
labeled proteins are harvested and identified by
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Downloaded from www.sciencemag.org on July 22, 2013
A 100%
REPORTS
A
B
matrix
IMS
E
PPOX1-205
Fe
FECH
(2.31)
1-70
1-120
CPOX
(1.91)
APEX
CPOX71-453
APEX70-CPOX
CPOX121-453
APEX120-CPOX
CPOX1-453
ALAD
HMBS
UROS
C
PPOX-APEX
APEX
APEX
CPOX
APEX205-PPOX
PPOX206-477
PPOX1-477
heme
PPOX
(2.49)
succinyl-CoA
ALAS1
(3.15)
APEX
CPOX-APEX
APEX
IMS
90
matrix 205
209
80
23
UROD
N
C
N
C
APEX205-PPOX
D
PPOX-APEX
APEX70-CPOX
110
APEX120-CPOX
PPOX
CPOX-APEX
PPOX
N
N
C
C
IMS
matrix
200 nm
200 nm
FECH
previous model
Fig. 3. Submitochondrial localization of the heme biosynthesis enzymes
CPOX and PPOX. (A) Model showing the submitochondrial localizations of the
eight core enzymes that catalyze heme biosynthesis, according to previous
literature (24). Four of these enzymes are detected in our matrix proteome
and are shown in red [with log2(heavy/light) ratios from replicate 1. CoA,
coenzyme A. Drawing adapted from (25). (B) Domain structures of PPOX and
CPOX fusions to APEX, imaged by EM in (C) and (D), respectively. Additional
EM images of PPOX-APEX are shown in fig. S11B. Scale bars in (C) and (D),
MS with the use of well-established techniques.
In addition to its simplicity, our method has no
noticeable toxicity, requires far less material than
conventional organellar proteomics, and takes
hours to implement rather than days (as for subcellular fractionation). Our initial demonstration
on the human mitochondrial matrix proteome
shows that specificity is exceptionally high because labeling is performed in living cells while
membranes and other structures are still intact.
Depth of coverage is also high for the majority
of proteins—most likely those that are sterically
accessible to the phenoxyl radical. Notably, our
method provides insight into the topology of
identified proteins. Finally, the same peroxidase,
APEX, can be used for both proteomic mapping
and EM visualization (5).
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Acknowledgments: We thank N. Watson (Whitehead
Institute Keck Microscopy Facility) and E. Vasile (Koch Institute
Microscopy Core Facility) for performing EM imaging,
H. B. Fraser for assistance with data analysis and manuscript
editing, C. Uttamapinant for picoyl azide-AF647, X. Zhuang
and her lab for advice on STORM, H. A. Dailey for advice on
CPOX and PPOX, and S. Calvo for assistance with data analysis.
Funding was provided by the NIH (grants DP1 OD003961 to
A.Y.T. and R01 GM077465 to V.K.M.), the Dreyfus Foundation
(A.Y.T.), the American Chemical Society (A.Y.T.), and the Broad
Institute of MIT and Harvard (S.A.C.). The authors have no
conflicting financial interests. A patent application relating to
the use of enzymes for proteomic mapping in live cells has been
filed by MIT. Proteomic data can be found in supplementary
tables S1 to S9. The authors will make the genetic constructs
used in this work widely available to the academic community
through Addgene (www.addgene.org/).
Downloaded from www.sciencemag.org on July 22, 2013
F
Supplementary Materials
www.sciencemag.org/cgi/content/full/science.1230593/DC1
Materials and Methods
Figs. S1 to S11
Tables S1 to S9
References (27–53)
24 September 2012; accepted 11 January 2013
Published online 31 January 2013;
10.1126/science.1230593
15 MARCH 2013
1331
Originally published 31 January 2013; corrected 14 March 2013
www.sciencemag.org/cgi/content/full/science.1230593/DC1
Supplementary Materials for
Proteomic Mapping of Mitochondria in Living Cells via SpatiallyRestricted Enzymatic Tagging
Hyun-Woo Rhee, Peng Zou, Namrata D. Udeshi, Jeffrey D. Martell, Vamsi K. Mootha,
Steven A. Carr, Alice Y. Ting*
*To whom correspondence should be addressed. E-mail: [email protected]
Published 31 January 2013 on Science Express
DOI: 10.1126/science.1230593
This PDF file includes:
Materials and Methods
Figs. S1 to S11
Full Reference List
Other Supplementary Material for this manuscript includes the following:
(available at www.sciencemag.org/cgi/content/full/science.1230593/DC1)
Tables S1 to S9 (in 2 Excel files)
Correction: In the main PDF, “Optimization of proteomic labeling conditions” was
separated into its own section, and a new method for “Localization of biotin-phenol
labeling sites” was added. In Table S4 (contained in an Excel file), biotinylated amino
acid residue numbers were added under the heading “Site Number.” Some abbreviations
were also spelled out for clarity.
Materials and Methods
Characterization of APEX-mediated biotinylation by fluorescence imaging (related to
Figs. 1B, S1, S2, S4, and S7)
HEK293T or COS7 cells were cultured in MEM supplemented with 10% fetal bovine
serum at 37 °C under 5% CO2. Cells were transfected with the APEX fusion construct of
interest using Lipofectamine 2000 (Invitrogen). Typically, 0.2 µg plasmid and 0.5 µL (for
COS7 cells) or 1.0 µL (for HEK293T cells) Lipofectamine in MEM (without serum) was
used for a 7×7 mm coverslip of cells 60-80% confluence. 4-6 hours after transfection, the
cell culture medium was changed back to MEM supplemented with 10% fetal bovine
serum. 18-24 hours after media change, biotin-phenol (final concentration Cf 500 µM)
was added in the cell culture media and the cells were incubated for 30 minutes at 37 °C.
Then H2O2 (Cf 1 mM) was added for 1 minute to initiate biotinylation. To halt the
reaction, the cells were washed three times with a “quencher solution” consisting of 10
mM sodium azide, 10 mM sodium ascorbate, and 5 mM Trolox in DPBS (Dulbecco’s
Phosphate Buffered Saline). Thereafter, the cells were fixed in 4% paraformaldehyde in
PBS at room temperature for 15 minutes. Cells were then washed three times with PBS
and permeabilized with pre-chilled methanol at -20 ºC for 5 minutes.
To detect biotinylated proteins, the fixed HEK293T or COS7 cells were stained
with 50 nM neutravidin-AF (AlexaFluor) or streptavidin-AF, after blocking overnight in
1% casein in PBS (“blocking buffer”) at 4 ºC. Neutravidin and streptavidin fluorophore
conjugates, which could be used interchangeably without a difference in performance,
were prepared by coupling neutravidin protein from Invitrogen or homemade streptavidin
protein (27) with AF647-NHS or AF568-NHS esters (Invitrogen) following the
manufacturer’s instructions.
To detect APEX expression, we also stained the cells with anti-Flag (Sigma;
1:300 dilution), anti-V5 (Invitrogen; 1:2000 dilution), or anti-myc (Millipore; 1:1000
dilution) mouse antibodies in blocking buffer for 1 hour at room temperature. Samples
were then washed 4 × 5 minutes with PBS and incubated with secondary goat antimouse-AF antibody (Invitrogen; 1:1000 dilution) in blocking buffer for 1 hour at room
temperature. Samples were washed 4 × 5 minutes with PBS, then maintained in DPBS at
room temperature for imaging.
Imaging was performed in confocal mode using a Zeiss AxioObserver.Z1
microscope equipped with a Yokogawa spinning disk confocal head and a Cascade II:512
camera. The confocal head contained a Quad-band notch dichroic mirror
(405/488/568/647 nm). Samples were excited by solid state 491 (~20 mW), 561 (~20
mW), or 640 nm (~5 mW) lasers. Images were acquired using Slidebook 5.0 software
(Intelligent Imaging Innovations), through a 63× oil-immersion objective for YFP/AF488
(528/38 emission filter), AF568 (617/73 emission filter), AF647 (700/75 emission filter),
and differential interference contrast (DIC) channels. Acquisition times ranged from 20 to
500 milliseconds. Imaging conditions and intensity scales were matched for each dataset
presented together.
In Fig. S1, mitochondria were stained by incubating cells with 500 nM
Mitotracker Deep Red (Invitrogen) in media for 30 minutes at 37 ºC, prior to cell
fixation.
Characterization of APEX-mediated biotinylation by streptavidin blotting of whole cell
lysate (related to Figs. 1D, S1, S3, and S5)
HEK293T cells transfected and labeled as above were washed 3 times with quencher
solution, then scraped and pelleted by centrifugation at 200 rpm for 5 minutes. The pellet
was stored at -80 °C, then lysed with RIPA lysis buffer (50 mM Tris, 150 mM NaCl,
0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, 1× protease cocktail (Sigma
Aldrich, catalog no. P8849), 1 mM PMSF (phenylmethylsulfonyl fluoride), 10 mM
sodium azide, 10 mM sodium ascorbate, and 5 mM Trolox) for 1 minute at 4 °C. The cell
pellet was resuspended by gentle pipetting. Lysates were clarified by centrifugation at
13,000 rpm for 10 minutes at 4 °C before separation on a 10% SDS-PAGE gel.
For blotting analysis, gels were transferred to nitrocellulose membrane, stained by
Ponceau S (10 minutes in 0.1% w/v Ponceau S in 5% acetic acid/water), and blocked
with “blot blocking buffer” (3% w/v BSA and 0.1% Tween-20 in Tris-buffered saline) at
4 °C overnight. The blots were immersed in 0.3 μg/mL streptavidin-HRP (Thermo
Scientific) at room temperature for 60 minutes, then rinsed with blot blocking buffer 4 ×
5 minutes before development with SuperSignal West Pico reagent (Thermo Scientific)
and imaging on an Alpha Innotech gel imaging system.
Electron microscopy of APEX fusions (related to Figs. 1E, 3, and S11)
HEK293T or COS7 cells were transfected with the APEX fusion construct of interest
using Lipofectamine as described above. Fixation was performed with 2% glutaraldehyde
in PBS as described previously (5). A solution of 3,3’-diaminobenzidine (DAB) was
overlaid, APEX-catalyzed polymerization was allowed to proceed for 5 - 25 minutes, and
DAB polymers were subsequently stained with OsO4 as described previously (5). Cells
were then rinsed 5 × 2 minutes in chilled distilled water and placed in chilled 2% aqueous
uranyl acetate (Electron Microscopy Sciences) for 1 hour. Cells were brought to room
temperature, washed in distilled water, then carefully scraped off the plastic, resuspended,
and centrifuged at 700 g for 1 minute to generate a cell pellet. The supernatant was
removed, and the pellet was dehydrated in a graded ethanol series (70%, 95%, 100%,
100%), for 10 minutes each time, then infiltrated in Eponate resin (Ted Pella) or
EMBED-812 (Electron Microscopy Sciences) using 1:1 (v/v) resin and anhydrous
ethanol for 1 hour, then 2:1 resin:ethanol overnight, then 100% resin for 2 hours. Finally,
the sample was transferred to fresh resin and polymerized at 60 °C for 48 hours.
Embedded cell pellets were cut with a diamond knife into 400 nm sections and imaged on
a FEI-Tecnai™ G² Spirit BioTWIN transmission electron microscope operated at 80 kV.
For the model presented in Fig. 3E, human PPOX (residues 1-477) and human
CPOX (residues 119-453) structures from PDB IDs 3NKS (26) and 2AEX (28) were
used. For the model in Fig. 3F, tobacco PPOX and human FECH structures from PDB
IDs 1SEZ (23) and 2QD1 (29) were used.
Two-color STORM super-resolution imaging (Fig. 1C)
U2OS cells were plated on Lab-Tek™ II Chambered Coverglass (Thermo Scientific) precoated with 10 μg/mL human fibronectin for 30 minutes. At 60-70% confluence, cells
were transfected with mito-APEX, labeled with biotin-phenol and H2O2, and fixed and
permeabilized as described above under “Characterization of APEX-mediated
biotinylation by fluorescence imaging.”
For two-color STORM, mito-APEX was detected by staining with mouse anti-V5
antibody (Invitrogen; 1:2000 dilution) in blocking buffer for 1 hour at room temperature.
Cells were then washed 4 × 5 minutes with PBS and incubated with donkey anti-mouseAF405/AF647 conjugate (1:2000 dilution). To detect biotinylated proteins, streptavidinCy3/Cy5 conjugate was added together with the secondary antibody, and the sample was
incubated in blocking buffer for 5 minutes at room temperature. The antibody conjugate
was prepared by coupling donkey anti-mouse antibody (Jackson Immunoresearch) with
AF405-NHS and AF647-NHS esters (Invitrogen). The streptavidin conjugate was
prepared by coupling homemade streptavidin protein (27) with Cy3-NHS and Cy5-NHS
esters (Invitrogen). Labeled cells were washed 4 × 5 minutes with PBS.
Stained samples were imaged in STORM imaging buffer (10% glucose (w/v), 50
mM Tris pH 8.2, 10 mM NaCl, 0.56 mg/mL glucose oxidase, 0.8 mg/mL catalase, and
7.7 mg/mL cysteamine). STORM images were acquired on a home-built setup
constructed on an Olympus IX-81 stand. A polychroic mirror (Di01-R405/488/561/635,
Semrock) was used to reflect lasers onto the sample. A 642 nm laser line operating at
maximum power (140 mW) was used to image AF647 and Cy5; 405 nm and 561 nm
laser lines were used alternately to activate fluorophore pairs, and their intensities (from
0.1 mW to ~10 mW) were adjusted during the course of imaging experiment to maintain
a steady level of fluorophore activation. Samples were illuminated by lasers in the
pseudo-TIRF mode, and images were collected on an EMCCD camera (Evolve,
Photometrics). Super-resolution images were typically reconstructed from more than
10,000 frames of localizations for each channel. Data were analyzed using Insight3
software from Xiaowei Zhuang (Harvard University).
Due to the use of overlapping reporter dyes (AF647 and Cy5) on the antibody and
the streptavidin, we performed controls to check the degree of cross-talk between the two
STORM channels. Control samples were prepared with only antibody labeling, or only
streptavidin labeling, and imaged under identical conditions. By measuring fluorophore
localization numbers we found that AF405/AF647 is activated by the 561 nm laser by
5.2% relative to activation by the 405 nm laser. Conversely, Cy3/Cy5 is activated by the
405 nm laser by 14.6% relative to activation by the 561 nm laser. These values represent
the cross-talk between streptavidin and anti-V5 channels in Fig. 1C.
Proteomic mapping of the mitochondrial matrix
We followed the experimental configuration shown in Fig. S8A. First, to metabolically
label the proteomes of HEK293T cultures with heavy or light isotopes of lysine and
arginine (18), we split early passage HEK293T cells on day 0 into two T25 flasks at 10–
15% confluence. One flask was cultured in light SILAC media: Dulbecco's Modified
Eagle’s Medium (DMEM) deficient in L-arginine and L-lysine (custom preparation from
Caisson Laboratories) that we supplemented with L-arginine (Arg0) and L-lysine (Lys0)
(Sigma-Aldrich) at concentrations of 84 mg/L and 146 mg/L, respectively, 10% dialyzed
fetal bovine serum (Sigma-Aldrich), penicillin, streptomycin, glutamine (Gibco), and 4.5
g/L glucose. The second flask was cultured in heavy SILAC media with the same
composition as above except Arg0 and Lys0 were replaced by L-arginine-13C6,15N4
(Arg10) and L-lysine-13C6,15N2 (Lys8) (Sigma Isotech). Every two days, before cells
reached confluency, the heavy and light SILAC cultures were split into fresh SILAC
heavy and light media, respectively. After three passages in T25 flasks, on day 6, light
and heavy SILAC cultures were expanded into T75 flasks at 20% confluence and
cultured for two more days. We prepared two T75 flasks (H1, H2) for heavy SILAC
cultures and three T75 flasks (L1, L2, L3) for light SILAC cultures.
On day 9, the H1, H2, L2, and L3 cultures containing 7-8 million cells each were
transfected with 15 µg mito-APEX plasmid using 75 µL Lipofectamine in 30 mL light or
heavy DMEM without serum or antibiotics. 4 hours after transfection, the media was
replaced with fresh light or heavy SILAC media, and the cells were incubated overnight.
On day 10, 18 hours after transfection, 500 µM biotin-phenol in 20 mL SILAC media
was added to the H1, H2, L1, and L3 cultures. Cells were incubated for 30 minutes at 37
°C before addition of H2O2 (final concentration Cf 1 mM) for 1 minute at room
temperature. Cells were then immediately quenched by aspirating off the biotinphenol/H2O2 solution and replacing with a “quencher solution” consisting of 10 mM
sodium azide, 10 mM sodium ascorbate, and 5 mM Trolox in 20 mL DPBS. Cells were
washed twice with the quencher solution and twice with DPBS to remove excess biotinphenol. For the L2 culture (negative control with biotin-phenol and H2O2 omitted), cells
were washed three times with DPBS. After the final wash, 7 mL of quencher solution
was added to each flask, and cells were collected by gentle pipetting followed by
centrifugation at 200 rpm for 5 minutes at room temperature. Supernatant was discarded,
and the cell pellet was stored at -80 °C.
Cell pellets were lysed by thawing on ice, then adding 300 µL of freshly-prepared
RIPA lysis buffer (50 mM Tris, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate,
1% Triton X-100, 1× protease cocktail (Sigma Aldrich, catalog no. P8849), 1 mM PMSF,
10 mM sodium azide, 10 mM sodium ascorbate, and 5 mM Trolox) and incubating for 5
minutes at 4 °C. Lysates were clarified by centrifugation at 13,000 rpm for 10 minutes at
4 °C. Protein concentration in the supernatant was measured using the Pierce 660 nm
Protein Assay kit, with bovine serum albumin as the reference standard.
Optimization of proteomic labeling conditions
The optimized proteomic labeling conditions described above were determined after
performing the following tests. To optimize the H2O2 concentration, we first decided to
restrict the H2O2 exposure time to 1 minute, to minimize cellular toxicity and maximize
the temporal resolution of our method. Given this temporal restriction, we found that
lowering the H2O2 concentration to <1 mM significantly reduced the biotinylation signal,
assessed by imaging. We suspect this is the case despite the low Km of APX for H2O2
(~20 µM (30)) and the high membrane permeability of H2O2 because endogenous
catalase activity in mammalian cells rapidly consumes exogenously added H2O2.
To optimize biotin-phenol delivery, we tested loading for 1 minute, 3 minutes, 10
minutes, and 30 minutes and found much stronger labeling with the 30 minute preincubation prior to H2O2 addition. This may be because the biotin-phenol probe has
limited membrane permeability. We also performed an empirical titration and found that
concentrations below 500 µM significantly reduced biotinylation signal, assessed by
imaging.
Finally, we found that it was critical to terminate the labeling after 1 minute with
a quencher solution containing radical quenchers and peroxidase inhibitor. With ordinary
cell lysis buffer, we observed biotinylation of outer mitochondrial membrane proteins
such as TOM20 by matrix-localized APEX, probably because peroxidase-mediated
labeling continues even after dissolution of mitochondrial membranes. Upon addition of
quenchers to the wash and lysis buffers, labeling of TOM20 and other contaminants was
eliminated.
Enrichment of biotinylated proteins with streptavidin beads
The supernatants from lysed SILAC cultures above were combined as shown in Fig.
S8A. H1 and L1 were mixed in a 1:1 ratio (by protein concentration) to give the
Replicate 1 sample, and H2 and L2 were mixed in a 1:1 ratio to give the Replicate 2
sample. In addition, L3 supernatant was spiked in at 5% (by protein concentration) to
each sample to facilitate quantitation of isotope ratios (to avoid infinite H/L values due to
absence of light peptides).
Streptavidin-coated magnetic beads (Pierce catalog no. 88817) were prepared by
washing twice with RIPA lysis buffer (formulation given above). 4 mg of total protein (at
4-5 mg/mL protein concentration) from each replicate sample was mixed with 500 µL of
streptavidin bead slurry. The suspensions were incubated at room temperature for 1 hour
with gentle rotation. Streptavidin beads were then washed with 2 × 1 mL RIPA lysis
buffer, once with 1 mL of 2M urea in 10 mM Tris-HCl pH 8.0, and again with 2 × 1 mL
RIPA lysis buffer. Biotinylated proteins were eluted by incubating the beads with 60 µL
1x NuPAGE LDS Sample Buffer (Invitrogen) supplemented with 20 mM DTT and 2 mM
biotin and heating to 95 °C for 5 minutes.
In-gel protein digestion and extraction
Biotinylated proteins eluted from magnetic streptavidin beads were separated on a
NuPAGE Novex Bis-Tris 4-12% gel run for 1 hour at 130V. The gel was stained
overnight with Coomassie G-250 (Invitrogen) and subsequently destained with water.
Lanes for each replicate were manually cut into 16 gel bands. Gel bands were destained
in 1:1 acetonitrile:100 mM ammonium bicarbonate pH 8.0 for several hours followed by
dehydration with acetonitrile. Dehydrated gel bands were swelled with 100 µL of 10 mM
DTT in 100 mM ammonium bicarbonate for one hour while shaking. The DTT solution
was subsequently removed and 100 µL of 55 mM iodoacetamide in 100 mM ammonium
bicarbonate was added to each gel band and allowed to react for 45 minutes in the dark.
The iodoacetamide solution was removed and bands were dehydrated with acetonitrile.
Approximately 10-50 µL of 20 ng/µL Sequencing Grade Trypsin (Promega) was added
to each sample and digestion was completed overnight with shaking at room temperature.
After the overnight digestion, excess trypsin solution was removed from each
sample and bands were incubated with 20 µL of extraction solution (60%
acetonitrile/0.1% TFA). The extraction solution was collected after 10 minutes and this
process was repeated two additional times. The final peptide extraction was completed by
incubating gel bands with 100% acetonitrile for 1-2 minutes. Extracted peptides were
dried to completeness in a vacuum concentrator, then reconstituted in 100 µL of 0.1%
formic acid and loaded onto C18 StageTips (31). The tips were washed twice with 50 µL
of 0.1% formic acid, and peptides were eluted with 50% acetonitrile/0.1% formic acid,
before drying in a vacuum concentrator.
Liquid chromatography-mass spectrometry
Dried peptides were reconstituted in 0.1% formic acid/3% acetonitrile and analyzed on a
Q Exactive mass spectrometer (Thermo Scientific) coupled online to an Easy-nLC 1000
UPLC (Proxeon). Online chromatographic separation was completed using a capillary
column (360 µm o.d. × 75 µm i.d.) with a 10 µm integrated emitter tip and self-packed
with 23 cm of 1.9 µm ReproSil-Pur C18-AQ resin (Dr. Maisch GmbH). The UPLC
mobile phase A was 0.1% formic acid/3% acetonitrile and the mobile phase B was 0.1%
formic acid/90% acetonitrile. A linear gradient flowing at 200 nL/min and starting at 6%
B and increasing to 30% B over 82 minutes was used to separate peptides with a total run
time of 120 minutes.
The Q Exactive mass spectrometer was operated in the data-dependent mode such
that after each MS1 scan, consecutive high energy collision dissociation MS2 scans were
recorded on the 12 most abundant precursors. The resolution used to acquire MS1 and
MS2 scans was 70,000 and 17,500, respectively. The MS1 advance gain control (AGC)
target was set to 3×106 ions and the maximum ion time was set to 10 msec. MS2 scans
were recorded with an AGC target of 5×104 ions with a maximum ion time of 120 msec,
isolation width of 2.5 m/z, normalized collision energy of 25, dynamic exclusion time of
20 sec, underfill ratio of 5.0%, and peptide match and isotope exclusion enabled.
Proteins and peptides were identified and quantified using the MaxQuant software
package (version 1.2.2.5) (32, 33). Data were searched against the UniProt human
database which contains 81,470 entries. A list of 248 common laboratory contaminants as
provided by the MaxQuant framework was also added to the database. A fixed
modification of carbamidomethylation of cysteine and variable modifications of Nterminal protein acetylation, oxidation of methionine, and biotin-phenol on tyrosine were
searched. The enzyme specificity was set to trypsin allowing cleavages N-terminal to
proline and a maximum of two missed cleavages was utilized for searching. The
maximum precursor ion charge state was set to 6. The precursor mass tolerance was set to
20 ppm for the first search where initial mass recalibration is completed and 6 ppm for
the main search. The MS/MS tolerance was set to 50 ppm and the top MS/MS peaks per
100 Da was set to 10. The peptide and protein false discovery rates were set to 0.01 and
the minimum peptide length was set to 6. Unmodified, N-terminally acetylated peptides,
and peptides with oxidized methionines were used for protein quantification.
Cut-off analysis to determine the mitochondrial matrix proteome (related to Fig. S8)
Protein information was obtained from the MaxQuant Protein Groups table and is
presented in Tables S1-S3. Proteins identified as reverse hits or contaminants were
removed from the dataset. For each replicate, only proteins identified by three or more
unique peptides with quantified SILAC ratios were retained for further analysis. Protein
SILAC ratios were calculated by MaxQuant as the median of all corresponding peptide
SILAC ratios (32, 33). Protein SILAC ratios from a given replicate were normalized such
that the median H/L value was 1.00.
Proteins identified in each replicate experiment were sorted into one of three
classes: (1) “mito” for those with previous mitochondrial annotation in MitoCarta (16),
the Gene Ontology Cell Component database, or literature; (2) “false-positive” for those
found in a hand-curated list of 2410 non-mitochondrial proteins (16); and (3) neither.
Separate histograms were prepared for class (1) and (2) proteins, binned by log2(H/L)
SILAC ratio, as in Fig. S8C. We calculated the false positive rate (FPR) as a function of
protein SILAC ratio using the equation:
The numerator is the conditional probability of finding a false positive protein in a
particular SILAC ratio range and is calculated as the number of false positive proteins
detected in that SILAC ratio range divided by the total number of false positive proteins
detected in the entire dataset. Likewise, the denominator is the conditional probability of
finding a known mitochondrial protein in a particular SILAC ratio range and is calculated
similarly. The FPR is the ratio of the two conditional probabilities, and is plotted in Fig.
S8D for Replicate 1.
We selected as our cut-off point for each replicate the SILAC ratio at which the
FPR reaches 0.1. All proteins above this cut-off are >10 times more likely to be
mitochondrial than non-mitochondrial. The cut-offs (in log2(H/L) units) for Replicates 1
and 2 were 1.05 and 1.25, respectively. This gave 527 enriched proteins for Replicate 1
and 579 enriched proteins for Replicate 2. We intersected these two lists to obtain the 495
proteins that we define as our mitochondrial matrix proteome.
Localization of biotin-phenol labeling sites
Biotin-phenol site information was obtained from the MaxQuant evidence table and is
presented in Table S4. Only modified peptides with a score >50 were retained for further
analysis. SILAC ratios of modified peptides were not used in this analysis. For a given
biotin-phenol-modified peptide, there can be multiple non-distinct peptides detected (due
to spread in liquid chromatography retention time and charge state); we present the
highest-scoring version across all non-distinct species in Table S4.
Synthesis of biotin substrates (related to Fig. S2)
Biotin conjugate 5 (biotin-XX-tyramide) was purchased from Invitrogen. Biotin
conjugate 8 (EZ-link photoactivatable biotin) was purchased from Pierce. The other
biotin conjugates were synthesized according to this general scheme:
All starting materials were purchased from Sigma Aldrich or Alfa Aesar except 3nitrotyramine (PIN Chemicals, UK). Biotin (100 mg) was dissolved in 2 mL DMSO
(dimethyl sulfoxide) at room temperature. Into this solution was slowly added 1.1
equivalents of HATU (2-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium
hexafluorophosphate) and 3.0 equivalents of DIPEA (N,N-diisopropylethylamine). The
mixture was stirred for 10 minutes at room temperature. Then 1.0 equivalent of the
primary amine was added slowly, and the reaction was incubated overnight at room
temperature with stirring. Products were purified by semi-preparative HPLC (Varian
Prostar model 210) using a C18 reverse phase column (Agilent Dynamax 250 × 21.4 mm,
microsorb 300-5 C18) with a 5% to 95% gradient of acetonitrile in water over 30
minutes. Biotin conjugates 1, 2, 3, 4, and 6 eluted at 18-20 minutes. Overall yields were
40-60%.
Biotin conjugate 7 was synthesized by hydrolysis of biotin conjugate 6. Ten
equivalents of NaOH were added to 100 mg of 6 in 1 mL methanol, and the mixture was
allowed to stir overnight at room temperature. Methanol was then removed in vacuo and
7 was purified by HPLC as described above.
MS characterization of purified probes on an Applied Biosystems Q-TRAP
instrument showed:
biotin conjugate 1: calculated for C18H26N3O3S [M+H]+: 364.1695; found: 364.3
biotin conjugate 2: calculated for C18H25N4O5S [M+H]+: 409.1546; found: 409.3
biotin conjugate 3: calculated for C18H26N3O4S [M+H]+: 380.1644; found: 380.4
biotin conjugate 4: calculated for C19H28N3O4S [M+H]+: 394.1801; found: 394.4
biotin conjugate 6: calculated for C20H28N3O5S [M+H]+: 422.1750; found: 422.2
biotin conjugate 7: calculated for C19H26N3O5S [M+H]+: 408.1593; found: 408.4
1
H-NMR for biotin conjugate 1 (500 MHz, d6-DMSO): δ 1.27 (2H, m), 1.42-1.61
(4H, m), 2.04 (2H, t, J = 7.5 Hz ), 2.57 (3H, m), 2.79 (1H, dd, J1 = 7.5 Hz, J2= 5 Hz),
3.05 (1H, dd, J1 = 6 Hz, J2= 2 Hz), 3.18 (2H, dd, J1= 6.5 Hz, J2= 6.5 Hz), 4.12 (1H, m),
4.30 (1H, m), 6.46 (1H, s), 6.56 (1H, s), 6.67 (2H, d, J = 8 Hz), 6.96 (2H, d, J = 8 Hz),
7.85 (1H, t, J = 5.5 Hz). 13C-NMR for biotin conjugate 1 (125 MHz, d6-DMSO): δ
25.502, 28.175, 28.358, 34.557, 35.396, 40.062, 55.625, 59.456, 61.283, 115.283,
129.618, 140.697, 155.921, 163.161, 172.288, 192.483.
Imaging assay to determine the membrane-permeability of the phenoxyl radical (Fig. S6)
HEK293T cells were transfected with W41AAPX targeted to either the cytosol (NES) or
inner leaflet of the plasma membrane (CAAX). 24 hours after transfection, cells were
incubated with 500 µM alkyne-phenol and 1 mM H2O2 for 1 minute at room temperature.
After washing cells three times with DPBS, click chemistry was performed on the cell
surface by incubating with 10 µM AF647-picolyl azide conjugate and a pre-formed
mixture of 200 µM CuSO4, 1 mM THPTA ligand, and 2.5 mM sodium ascorbate in
DPBS for 10 minutes at room temperature (34). Cells were quickly washed with DPBS
three times and immediately imaged live by confocal microscopy as described above.
For comparison, click chemistry was also performed on fixed and permeabilized
cells, in order to visualize the total population of alkyne-phenol-labeled molecules. For
this labeling, cells were first blocked after fixation using 1% bovine serum albumin + 1%
casein in PBS for 30 minutes at room temperature. Then cells were treated with 2.5 µM
AF647-picolyl azide conjugate and a pre-formed mixture of 1 mM CuSO4, 100 µM
TBTA ligand, and 2.5 mM sodium ascorbate in the same blocking buffer for 1 hour at
room temperature.
Gel filtration chromatography (Fig. S7B)
APEX and wtAPX were expressed in BL21-DE3 E. coli and purified by nickel affinity
chromatography as previously described (5). Protein concentrations were measured using
the BCA assay (Pierce). We found that purified APEX had an Abs405/Abs280 ratio > 2.0,
indicating high heme occupancy (5). Purified wtAPX had a lower ratio than this, so we
reconstituted the enzyme with purified heme as previously described (5) to obtain a final
Abs405/Abs280 ratio of 2.3. Gel filtration chromatography was performed on a Waters
HPLC system using a Superdex 75 10/300 column (GE Healthcare) as described
previously (5).
In vitro analysis of biotin-phenol reaction with purified amino acids (Fig. S7C)
Reactions were assembled as follows: 500 µM amino acid (all 20 were purchased from
Sigma), 500 µM biotin-phenol, 1 mM H2O2, and 10 nM HRP (Sigma catalog no. P6782)
in PBS pH 7.4. HRP was added last to initiate the reaction. After 10 minutes at room
temperature, reactions were quenched by addition of sodium azide (Cf 1 mM). Product
mixtures were analyzed by LC-MS. The LC was a Shimadzu UFLC-XR equipped with a
4.6 × 50 mm C18 column (Shimadzu catalog no. 220-91394-00) running a gradient of
5% to 95% acetonitrile in 0.1% trifluoroacetic acid/water over 20 minutes. The MS was
an Applied Biosystems Q-TRAP instrument.
Imaging analysis of mitochondrial orphans (Fig. S10)
Six mitochondrial orphan genes (TRMT61B, TRUB2, RPUSD3, PREPL, PNPO,
TRMT11) were obtained with C-terminal V5 tags in the pLX304 mammalian expression
vector from the Broad hORFeome library. COS7 cells were transfected with these
expression plasmids using Lipofectamine 2000. 24 hours later, cells were fixed and
stained with anti-V5 antibody as described above under “Characterization of APEXmediated biotinylation by fluorescence imaging”. To visualize mitochondria, cells were
also stained with rabbit anti-Tom20 antibody (Santa Cruz Biotechnology; 1:400 dilution)
in blocking buffer for 1 hour at room temperature, followed by secondary goat antirabbit-AF647 conjugate (Invitrogen; 1:1000 dilution) in blocking buffer for 1 hour at
room temperature. Labeled cells were washed 4 × 5 minutes with PBS before imaging.
Confocal microscopy was performed in the same way as described above.
To quantify the extent of mitochondrial localization for each of the orphan
proteins, the mitochondrial regions were first identified by automated image
segmentation of the anti-Tom20 (AF647) channel. These regions were examined visually
to ensure good overlap with the mitochondrial marker. The mean fluorescence intensity
of the orphan protein (AF568) channel was then calculated for both regions overlapping
with mitochondria (“mito”) and regions not overlapping with mitochondria (“non-mito”).
After subtracting background, the intensity ratios of “mito” over “non-mito” were
calculated. For each orphan protein, 3-5 fields of view each containing 1-3 cells were
analyzed in this way, and the mito/non-mito ratios were averaged.
Generation of cells stably expressing PPOX-APEX (related Fig. S11B).
HEK293T cells were transfected at ~70% confluence with PPOX-APEX (in pLX304)
and two lentiviral packaging plasmids (dR8.91 and pVSVG (16)) using Lipofectamine
2000. 48 hours after transfection, the cell culture media containing lentivirus was
collected and filtered through a 0.45 µm syringe filter. To a fresh HEK293T culture at
~70% confluence with ~200,000 cells was added 500 µL of the filtered lentiviruscontaining media. Two days after infection, cells were transferred to complete FBS media
containing 2 µg/mL blasticidin for selection. Infected cells were maintained in 2 µg/mL
blasticidin-containing media for 7 days (three passages), before replating for EM imaging.
Cloning and mutagenesis
A variety of strategies were used to clone the APEX fusion constructs. In some cases, we
PCR-amplified the APEX gene, digested with restriction enzymes, and ligated
directionally into similarly-cut vectors (e.g., pcDNA3, pDisplay, pEGFP, or pTRC). In
other cases, we used PCR overlap extension to fuse or insert the APEX gene to the gene
of interest. The resulting PCR product was digested with restriction enzymes and pasted
into cut vectors. This strategy was used to clone APEX120-CPOX, APEX70-CPOX,
APEX205-PPOX and APEX14-CHCHD3. Lastly, we used Gateway technology
(Invitrogen) to clone some constructs, such as PPOX-APEX.
In some APEX fusion constructs, a short linker was added between APEX and the
gene of interest. This was achieved by designing longer primers for PCR amplification of
the APEX gene. In all cases, the CMV promoter was used to drive expression in
mammalian cells. The pDisplay vector was used for constructs targeted to the secretory
pathway (e.g., ER lumen and cell surface); pDisplay contains an Igk chain signal
sequence and the transmembrane domain of the PDGF receptor (which is deleted for ER
lumen-targeted constructs). Occasionally, the pEGFP vector was used because it
originally contained the gene of interest (as in the case of actin-APEX). In all other cases,
pcDNA3 was used as a generic vector for expression of proteins targeted to the
mammalian cell cytosol or organelles other than the secretory pathway.
Point mutants were generated using standard QuikChange mutagenesis
(Stratagene). Primers 30-40 base pairs in length were designed to have melting
temperatures between 78-80 °C, with one or two mismatched base pairs.
We avoided using the HA epitope tag in this work because it is tyrosine-rich, and
hence likely to be damaged by the peroxidase/biotin-phenol reaction.
Genetic constructs
The two tables below summarize the plasmids used for peroxidase expression in
mammalian and bacterial cells. Human CPOX, PPOX, CHCHD3, Sam50, and COASY
genes were obtained from the Broad hORFeome library. Vimentin-APEX has been
described (5).
Mammalian expression plasmids
Name
Features
Promoter/
Vector
mito-APEX
NotI-mito-BamHI-V5APEX-Stop-XhoI
CMV/
pCDNA3
PPOX-APEX
NotI-PPOX-BamHI-V5APEX-Stop-XhoI
CMV/
pCDNA3
Variants
Details
Soybean APEX has 3 mutations
relative to wtAPX: K14D, W41F, and
E112K.
wtAPX gene from soybean was a gift
from Emma Raven (University of
Leicester).
mito matrix targeting sequence:
MLATRVFSLVGKRAISTSVCVRAH
(5)
V5: GKPIPNPLLGLDST
PPOX-APEX
for stable cells
attB1-PPOX-BamHI-V5APEX-Stop-attB2
CMV/
pLX304
APEX205-PPOX
NotI-PPOX(1-205)-NheI-V5APEX-AflII-10aa linkerPPOX(206-477)-Stop-XhoI
CMV/
pCDNA3
10aa linker: GGSGGSGGSR
CPOX-APEX
HindIII-CPOX-NotI-APEXFlag-Stop-AflII
CMV/
pCDNA3
Flag: DYKDDDDK
APEX120-CPOX
NotI-CPOX(1-120)-NheI-V5APEX-AflII-10aa linkerCPOX(121-453)-Stop-XhoI
CMV/
pCDNA3
10aa linker: GGSGGSGGSR
APEX70-CPOX
NotI-CPOX(1-70)-NheI-V5APEX-AflII-10aa linkerCPOX(71-453)-Stop-XhoI
CMV/
pCDNA3
10aa linker: GGSGGSGGSR
APEX-NES
NotI-Flag-APEX-NES-StopXhoI
CMV/
pCDNA3
IMS-APEX
NotI-LACTB(1-68)-BamHIV5-APEX-Stop-XhoI
CMV/
pCDNA3
LACTB(1-68):
MYRLLSSVTARAAATAGPAWDGG
RRGAHRRPGLPVLGLGWAGGLGL
GLGLALGAKLVVGLRGAVPIQS
(36).
The LACTB gene was a gift from
Timothy A. Brown and David A.
Clayton (HHMI Janelia Farm)
APEX-NLS
NotI-Flag-APEX-EcoRINLS-Stop-XhoI
CMV/
pCDNA3
NLS:
PKKKRKVDPKKKRKVDPKKKRKV
(37)
APEX-TM
EcoRI-ss-HA-ApaI-APEXSacII-myc-TM-Stop-NotI
CMV/
pDisplay
ss: Igk chain signal sequence in
pDisplay (Invitrogen).
HA: YPYDVPDYA
myc: EQKLISEEDL
TM: transmembrane domain of PDGF
receptor from pDisplay (Invitrogen)
APEX-KDEL
EcoRI-ss-BglII-APEX-V5KDEL-Stop-NotI
CMV/
pDisplay
KDEL: ER retention motif
C1(1-29)-APEX
HindIII-C1(1-29)-NotI-APEXV5-Stop-XhoI
CMV/
pCDNA3
C1(1-29):
MDPVVVLGLCLSCLLLLSLW
KQSYGGGKL (endoplasmic reticulum
membrane anchor (38))
Connexin43APEX
NotI-Cx43-12aa linkerBamHI-V5-APEX-StopXhoI
CMV/
pCDNA3
12aa linker: GSKGSGSTSGSG
Actin-APEX
NheI-Flag-APEX-4aa linkerXhoI-actin-Stop-BamHI
CMV/
pEGFP
APEX is derived from pea (5) rather
than soybean
4aa linker: SGLR
actin is human β-actin
W41F
NotI-Flag-W41FAPX-NESStop-XhoI
CMV/
pCDNA3
APX-NES
W41X
W41A
NES: LQLPPLERLTLD(35)
W41A
NotI-Flag-W41AAPX-EcoRICAAX-Stop-XhoI
CMV/
pCDNA3
CAAX:
RSKLNPPDESGPGCMSCKCVLS
(39)
HRP-TM
EcoRI-ss-HA-ApaI-HRPSacII-myc-TM-Stop-NotI
CMV/
pDisplay
The HRP gene was a gift from Frances
Arnold (Caltech)
HRP-KDEL
EcoRI-ss-BglII-HRP-V5KDEL-Stop-NotI
CMV/
pDisplay
PNPT1-APEX
NotI-PNPT1-BamHI-V5APEX-XhoI
CMV/
pCDNA3
The human PNPT1 gene was a gift
from Tsutomu Suzuki (University of
Tokyo)
APEX14CHCHD3
NotI-CHCHD3(1-14)-NheIV5-APEX-AflII-10aa linkerCHCHD3(15-227)-Stop-XhoI
CMV/
pCDNA3
10aa linker: GGSGGSGGSR
COASY-APEX
NotI-COASY-BamHI-V5APEX-Stop-XhoI
CMV/
pCDNA3
mito-pBirA
NotI-mito-BamHI-V5pBirA-Stop-XhoI
CMV/
pCDNA3
pBirA-KDEL
EcoRI-ss-BglII-pBirAKDEL-Stop-NotI
CMV/
pDisplay
pBirA-NLS
NotI-Flag-pBirA-EcoRINLS-Stop-XhoI
CMV/
pCDNA3
APX-CAAX
pBirA: R118G mutant of BirA
(promiscuous biotin ligase)
Bacterial expression plasmids
Name
Features
Promoter/Vector
His6-APEX
NcoI-His6-APEX-Stop-XbaI
lacO/pTRC99
His6-wtAPX
NcoI-His6-wtAPX-Stop-XbaI
lacO/pTRC99
Discussion of labeling radius
A future challenge lies in carefully defining the radius of peroxidase-catalyzed labeling
when it is not membrane-enclosed. An imaging readout following live cell labeling can
be misleading because biotinylated proteins can themselves diffuse during the 1 minute
labeling window. Previous EM studies on fixed cells suggest that the labeling radius of
the biotin phenoxyl radical can be as small as 20 nm (8, 9), and in the live cell context the
radius may be even smaller due to the presence of endogenous radical quenchers such as
glutathione. It should also be possible to modulate labeling radius using electron
withdrawing substituents or by co-application of radical scavengers to cells.
Supplementary Figures
Fig. S1. Comparison of promiscuous biotinylation by APEX and pBirA. (A)
Streptavidin blot analysis of whole cell lysate after live biotinylation by APEX or
promiscuous biotin ligase (pBirA = R118G BirA (3)) in three different HEK293T cell
compartments. The same samples were visualized by Ponceau stain on the left. APEX
labeling was performed for 1 minute (1m) with 500 µM biotin-phenol and 1 mM H2O2.
pBirA labeling was performed for 1 minute or 24 hours (24h) with 50 µM biotin, as
previously described (1). NLS = nuclear localization signal. KDEL = endoplasmic
reticulum retention sequence. mito = targeting sequence for the mitochondrial matrix.
pBirA-catalyzed biotinylation is undetectable after 1 minute in the nucleus and
mitochondrial matrix, and is very low in the lumen of the endoplasmic reticulum even
after 24 hours, in contrast to APEX-catalyzed biotinylation. (B) Imaging analysis of
biotinylation in the mitochondrial matrix. The top row shows 1 minute biotinylation by
mito-APEX, performed as in (A). In the bottom two rows, HEK293T cells were
transfected with mitochondrial matrix-localized pBirA. 24 hours after transfection, 50
μM biotin was added to the culture medium to permit promiscuous biotinylation. After 10
minutes or 1 hour, cells were fixed and stained with neutravidin to detect biotinylated
proteins and anti-V5 antibody (AF488 visualization) to detect pBirA expression.
Mitotracker Deep Red staining was also used to visualize mitochondria. The neutravidin
channel is shown at higher contrast in the rightmost column. The staining seen in rows 2
and 3 reflects endogenously biotinylated proteins (located in mitochondria (40)) because
the staining is equivalent between transfected (V5-positive) and untransfected cells. Thus
biotinylation of the mitochondrial matrix proteome by pBirA is insignificant after 1 hour,
whereas APEX-catalyzed biotinylation in the same compartment is strong after 1 minute.
Fig. S2. Reactivity of eight different biotin conjugates towards APX and HRP. Top:
Structures of biotin conjugates tested. These differ in electronic properties, linker length,
sterics, and charge. Aryl azide 8 was used in a previous study with HRP and proposed to
form a nitrene (4). Bottom: Imaging results with HEK293T cells expressing cytosolic
Flag-W41FAPX-NES (top row) or cell surface HRP-myc-TM (bottom row). NES = nuclear
export signal. TM = transmembrane domain of the PDGF receptor. For APX, labeling
was performed by incubating cells with 500 µM of the indicated biotin substrate for 30
minutes, then adding 1 mM H2O2 for 1 minute to initiate biotinylation. Cells were then
fixed and stained. For cell surface labeling with HRP, 100 μM of the indicated substrate
was added for 10 minutes, then 1 mM H2O2 was added for 1 minute to initiate labeling.
Cells were then fixed and stained. Anti-Flag/myc, streptavidin, and DIC images are
overlaid. Labeling was not detected with HRP-TM and probe 8, in contrast to a previous
report (4). The simplest conjugate, biotin-phenol 1, gave the strongest labeling of
intracellular proteins, so we used this probe for all peroxidase-mediated biotinylation
experiments in this work. Scale bars, 10 μm.
Fig. S3. APEX-catalyzed labeling requires addition of exogenous H2O2. HEK293T
cells expressing APEX in the mitochondrial matrix (lanes 4-6) or the intermembrane
space (IMS; lanes 7-9) were treated with biotin-phenol for 30 minutes and 1 mM H2O2
for 1 minute, as in the proteomic experiments, or with biotin-phenol alone for 30 minutes,
or with neither reagent. Cells were then quenched and lysed, and whole cell lysate was
analyzed by streptavidin-HRP blotting (two different exposures shown in middle and
right blots). Labeling of many endogenous proteins was observed in lanes 6 and 9. No
biotinylation above background was detected when biotin-phenol was added alone
without exogenous H2O2 (lanes 5 and 8), indicating that endogenous H2O2 is not
sufficient to start the reaction in either the matrix or the IMS. Untransfected HEK293T
cells are included for comparison in lanes 1-3. Arrowheads point to endogenously
biotinylated proteins (40).
Fig. S4. Imaging analysis of APEX- and HRP-catalyzed biotinylation in multiple
cellular compartments. (A) HEK293T cells were transfected with APEX or HRP
constructs targeted to various compartments. Labeling was performed with biotin-phenol
and H2O2 for 1 minute. Cells were then fixed and stained with streptavidin-AF568 to
visualize biotinylated proteins, and antibody to visualize Flag, V5, or myc tags on the
APEX/HRP enzymes. HRP-NES and mito-HRP constructs did not give detectable
streptavidin staining, as expected (data not shown). NLS = nuclear localization signal;
NES = nuclear export signal; mito = mitochondrial matrix signal; KDEL = endoplasmic
reticulum retention motif; TM = transmembrane helix of PDGF receptor. Specific
targeting sequences are given in the Materials & Methods. (B) Additional imaging
analysis of endogenous proteins biotinylated by mito-APEX and HRP-KDEL, with
respect to organelle markers. mito-GFP is GFP appended to a mitochondrial matrix signal.
ER-GFP is GFP targeted to the endoplasmic reticulum membrane via fusion to the first
29 amino acids of cytochrome P450 (38) (this plasmid was a gift from Erik Snapp, Albert
Einstein College of Medicine). COS7 cells were labeled and stained as in (A). Merged
images are shown in the right two columns. Tight overlap is observed between proteins
biotinylated by APEX/HRP and the respective organelle markers. All scale bars, 10 µm.
Fig. S5. Streptavidin blot analysis of APEX- and HRP-catalyzed biotinylation in
many cellular compartments. (A) The same constructs as in Fig. S4A were introduced
into HEK293T cells, which were labeled with biotin-phenol and H2O2 as in Fig. S4, then
lysed. Whole cell lysates were analyzed by 10% SDS-PAGE, with Ponceau S staining
(left) and streptavidin-HRP visualization of biotinylated proteins (right). Arrowheads
point to endogenously biotinylated proteins (40). (B) Same analysis as in (A), for fusion
constructs targeted to different regions of the cytosol. NES = nuclear export signal; IMS
= mitochondrial intermembrane space signal; C1(1-29) = endoplasmic reticulum membrane
anchor (APEX faces the cytosol) (38); CAAX = plasma membrane anchor (APEX faces
the cytosol); Cx43 = connexin 43. Note that the IMS freely exchanges components <5 kD
(including the biotin-phenoxyl radical) with the cytosol via porins in the outer
mitochondrial membrane (41). Pea APEX (5) instead of soybean APEX was used for the
vimentin and actin fusions. Soybean W41AAPX was used for the CAAX fusion. For each
of the organelle-targeted constructs in (A), and the cytosol-facing constructs in (B), a
unique “fingerprint” of biotinylated endogenous proteins is observed, illustrating the
spatial specificity of the labeling.
Fig. S6. Peroxidase-generated phenoxyl radicals do not cross the plasma membrane.
(A) Assay scheme. HEK293T cells were transfected with W41AAPX targeted to the
cytosol (NES) or inner leaflet of the plasma membrane (CAAX; green pacman). Labeling
was performed with alkyne-phenol and H2O2 for 1 minute. Thereafter click chemistry
was performed at the cell surface with membrane-impermeant AF647-picolyl azide (34).
Only if the phenoxyl radical crosses the plasma membrane will alkyne be present at the
cell surface and detectable by the AF647 reagent. Dimeric W41AAPX was used in this
experiment because it has higher activity in the mammalian cytosol than monomeric
APEX. (B) Images with W41AAPX-CAAX (left) and W41AAPX-NES (right). Nuclearlocalized YFP was a transfection marker. As a control (bottom rows labeled “total”), cells
were fixed and permeabilized prior to click chemistry to detect intracellular alkynephenol labeling. Insets show the same fields of view with 50-fold greater contrast.
Quantitation shows that the signal at the cell surface (top rows) represents <2% of the
total signal (bottom rows). The same results were obtained when we used biotin-phenol
instead of alkyne-phenol and detected labeling at the cell surface with membraneimpermeant streptavidin-AF568 (data not shown). The alkyne-phenol experiment is
shown here because it is more rigorous; detection of cell surface labeling by biotinphenol, especially near the lipid bilayer, could be impaired by the large size of
streptavidin.
Fig. S7. Peroxidase engineering and characterization of monomericity and amino
acid specificity in vitro. (A) The APEX construct previously introduced as a genetic tag
for electron microscopy was derived from pea ascorbate peroxidase (APX) (5). This
construct had three mutations relative to wild-type pea APX: two to make it monomeric
(K14D, E112K), and one to boost activity towards aromatic substrates (W41F). In this
work, we discovered that K14D and E112K had a more strongly monomerizing effect on
APX from soybean than from pea (both wild-type enzymes are constitutive dimers (42,
43)). We therefore switched to the soybean enzyme. In addition, we performed
comprehensive mutagenesis at the W41 active site residue to maximize intracellular
activity towards biotin-phenol. Confocal images are shown for HEK293T cells
expressing all possible W41x mutants (fused to nuclear export sequences, and on a
monomeric soybean APX background). After labeling for 1 minute with biotin-phenol
and H2O2, cells were fixed and stained with streptavidin-AF568 to detect biotinylated
proteins (red) and anti-Flag to detect peroxidase expression (green). The same experiment
with dimeric W41FAPX (soybean) is shown for comparison. Anti-Flag, streptavidin, and
DIC images are overlaid. From this experiment, we concluded that the W41F mutation
was best, and combined it with the monomerizing mutations to give soybean APEX
(K14D, W41F, E112K). Note that soybean-derived APEX was used for all EM and
proteomic labeling experiments in this work, except where indicated otherwise. Scale
bars, 10 μm. (B) Gel filtration chromatography was used to analyze the monomericity of
soybean-derived APEX, pea-derived APEX from our previous study (5), and wild-type
soybean APX (calculated molecular weight 29 kD). As expected (43), wild-type APX
runs as a dimer at all protein concentrations tested (250 nM–68 μM; apparent MW ~58
kD). Soybean APEX runs as a monomer (apparent MW ~30 kD), even at 270 μM, while
pea APEX runs as a monomer at lower concentrations but shows signs of dimerization at
higher concentrations, as previously observed (5). (C) HRP, biotin-phenol (BP), and
H2O2 were combined in 20 separate in vitro reactions with each of the amino acids (at
500 µM). Reactions were quenched after 10 minutes at room temperature and analyzed
by HPLC and MS. HRP was used because it has higher in vitro activity than APEX (5).
In all reactions, BP dimer was detected. In the reaction with tyrosine, a BP-tyrosine
adduct and tyrosine dimer with the masses and predicted structures shown were also
detected. Negative controls with HRP or H2O2 omitted eliminated the formation of these
products. In the reaction with cysteine, the amino acid was consumed but we did not
detect the expected cysteine-BP adduct or cysteine dimer. No reaction was detected for
the 18 other samples (apart from BP dimerization). We conclude that the reaction of BP
with tyrosine is the easiest to detect (see also Fig. S9), but reactions at other electron-rich
sidechains are also possible and have literature precedent (10-12). We note that based on
analysis of available protein structures, >90% of proteins are expected to have one or
more surface-exposed tyrosines 1 . Thus, even if phenoxyl radicals have a strong
preference for labeling at tyrosine, this specificity should not limit by much the potential
coverage of this technique.
1
. This value was calculated by determining the number of Tyr residues for each protein in the
human proteome, and applying the statistic that 80% of Tyr are surface-exposed (14). Hence, for
the 677 (3.3%) proteins with 1 Tyr, 80% of them will have a surface Tyr. For the 813 (4%)
proteins with 2 Tyr, 96% of them will have one or more surface Tyr, and so on.
Fig. S8. Determination of the mitochondrial matrix proteome. (A) Experimental setup.
We established “heavy” and “light” isotopically labeled HEK293T cell cultures using the
SILAC approach (18). Two replicate heavy SILAC cultures were labeled by pre-loading
biotin-phenol for 30 minutes, then adding 1 mM H2O2 for 1 minute to initiate
biotinylation. Two light SILAC cultures were processed in parallel as negative controls,
one with APEX omitted, and one with biotin-phenol and H2O2 omitted. After lysis, heavy
and light lysates were combined, enriched with streptavidin beads, eluted, separated by
gel, digested to peptides with trypsin, and analyzed by tandem MS. (B) Table showing
numbers of detected peptides, detected proteins, and enriched proteins for each replicate,
as well as the overlap between the two replicates. We required three or more unique
quantified peptides to consider a protein “detected”. (C) Distribution of SILAC ratios
(log2(H/L)) from the Replicate 1 experiment. The top panel shows “true positive”
analysis: the number of proteins within each SILAC ratio range (bin size 0.1) with prior
mitochondrial annotation. The bottom panel shows “false positive” analysis: the number
of proteins within each SILAC ratio range appearing in a hand-curated list of 2410 nonmitochondrial proteins (“false positive list”) (16). (D) False positive rate (FPR) as a
function of SILAC ratio. At a given SILAC ratio, the FPR measures the probability of
finding a false positive versus a true mitochondrial protein. We selected an FPR of 0.1 as
our cut-off point, i.e. 10 times more likely for a protein to be mitochondrial than a false
positive. Replicate 1 had 527 proteins above this cut-off, and Replicate 2 had 579
proteins. The overlap between these groups was 495 proteins, which we defined as our
matrix proteome (Table S1). (E) Correlation between SILAC ratios for Replicates 1 and 2.
R values are shown for all detected proteins, and for proteins in our matrix proteome
(proteins above and to the right of the dotted lines). (F) Correlation between SILAC ratio
(from Replicate 1) and protein abundance in human U2OS cells (44), for proteins in our
matrix proteome. The bottom strip, in red, shows protein copy number for matrix proteins
from Fig. 2B that were not detected in our matrix proteome.
Fig. S9. Mapping biotinylated peptides to transmembrane and soluble matrix
proteins. (A) Occurrence of surface-exposed tyrosines in soluble proteins with known
structure. (i) is from reference (45). (iii) is based on analysis of the 60 biotinylated
peptides we detect that map to soluble proteins with known structure (39 proteins). (ii) is
based on all the tyrosines (biotinylated or not, 401 in total) within these 39 proteins. The
criterion for “surface-exposed” is having >10 Å2 solvent-accessible area, as calculated by
PyMOL (45). This analysis shows that peroxidase-catalyzed biotinylation favors surface
exposed tyrosine sites on soluble proteins. Protein structures were obtained by searching
UniProt IDs in the Swiss Model Repository. Structures with >85% sequence homology to
our detected proteins were used for this analysis. (B) Protein structures showing the
positions of five of the biotinylated tyrosines (colored red, bp = biotin-phenol
modification) analyzed in (A). Non-labeled tyrosines within each protein are colored blue.
Sequences of detected biotinylated peptides are shown beneath each protein structure. (C)
Analysis of biotinylated peptides that map to transmembrane proteins with known or
predicted topologies (according to the UniProt database). Nearly all of the biotinylation
sites (14 out of 15) map to the matrix-exposed portion of these proteins. (D) Specific
examples from (C). Biotinylation sites are depicted by the red circle. Sequences of
detected biotinylated peptides are given underneath. (E) MS/MS spectrum recorded on
the SILAC heavy-labeled [M + 2H]2+ ion (m/z 1086.54) corresponding to the pyruvate
dehydrogenase E1β peptide VFLLGEEVAQbpYDGAYK shown in (B). The measured
precursor mass is within 1 p.p.m. of the calculated mass. Observed singly charged
fragment ions are labeled in the spectrum and indicate that Y63 is modified with biotinphenol. Details for all 167 biotinylated peptides are provided in Table S4.
Fig. S10. Fluorescence imaging shows mitochondrial localization of six
mitochondrial orphans. Six proteins selected at random from the 31 mitochondrial
orphans (Table S2) identified in our matrix proteome were V5-tagged and expressed in
COS7 cells. Protein localization was detected by anti-V5 staining (AF568). Mitochondria
were visualized by anti-Tom20 staining (AF647). The ratio of V5 signal intensity
overlapping with mitochondria versus not overlapping with mitochondria was quantified
(bottom). For reference, the mito/non-mito ratio was 5.4±2.0 for mito-APEX (a positive
control) and 1.4±0.16 for a cytosolic fluorescent protein (mCherry) fusion (a negative
control). Four of these six orphan proteins are related to tRNA editing: TRMT61B and
TRMT11 are tRNA methyltransferases, and TRUB2 and RPUSD3 are pseudouridylate
synthases. TRUB2 has a yeast homolog, PUS4, with mitochondrial annotation (46).
TRUB2 and RPUSD3 both have predicted mitochondrial targeting sequences. PREPL is
prolyl endopeptidase-like protein. Though annotated as a cytosolic protein, a previous
study found 35% of prolyl endopeptidase activity to be associated with crude
mitochondria (47). PNPO is pyridoxamine-phosphate oxidase, which catalyzes the last
and rate-determining step of vitamin B6 synthesis, thought to occur in the cytosol. PNPO
has a yeast homolog, PDX3, which was identified in an IMS proteomic study (48), but
not validated biochemically. Scale bars, 15 μm.
Fig. S11. Electron microscopy of APEX fusions to PNPT1, CHCHD3, COASY, and
PPOX. (A) PNPT1 and CHCHD3 were previously localized to the mitochondrial
intermembrane space (IMS) (49, 50), and COASY was previously localized to the outer
mitochondrial membrane (OMM) (51), yet we detected all three proteins in our
mitochondrial matrix proteome. APEX fusions to PNPT1 (C-terminal fusion) and
CHCHD3 (insertion between amino acids 14 and 15) gave mitochondrial matrix staining
by EM in HEK293T and COS7 cells, respectively. PNPT1 (polyribonucleotide
nucleotidyltransferase 1) is an RNA binding and processing protein. In addition to our
EM data which localizes the C-terminus to the matrix, we detected two PNPT1-derived
biotinylated peptides (Table S4) that indicate that Tyr302 and Tyr356 are both matrixexposed. CHCHD3 (coiled-coil-helix-coiled-coil-helix domain-containing protein 3)
plays a role in bridging the outer and inner mitochondrial membranes (52), so perhaps it
is not surprising that a portion of it (residue 14, according to our EM data) is matrixexposed. A C-terminal APEX fusion to COASY (bifunctional coenzyme A synthase) in
HEK293T cells gave matrix staining in some fields of view (top two images), and IMS
staining in other fields of view (bottom). (B) Same experiment as in Fig. 3C, except that
PPOX-APEX was stably rather than transiently expressed. These stable HEK293T cells
were prepared by lentiviral infection of the PPOX-APEX gene and selection in 2 µg/mL
blasticidin. All scale bars, 200 nm.
Supplementary Spreadsheet 1. Mitochondrial matrix proteome.
Table S1: Our mitochondrial matrix proteome (495 proteins), ranked from most enriched
to least enriched, according to log2(H/L) SILAC ratio from replicate 1. 93 additional
proteins below our cut-off point are also included but shaded grey.
Table S2: Mitochondrial orphans (31 proteins), ranked from most enriched to least
enriched.
Table S3: Mitochondrial matrix orphans (240 proteins), ranked from most enriched to
least enriched. These proteins have prior mitochondrial annotation but were not
previously known to be localized to the matrix.
Table S4: Biotinylated peptides detected (167 peptides derived from 103 proteins). The
peptides are grouped by protein and ranked by protein SILAC ratio.
Table S5: Column definitions.
Supplementary Spreadsheet 2. Analysis of protein groups and membrane complexes.
Table S6: Sub-mitochondrial localization of detected proteins. Related to Fig. 2A.
Table S7: Mitochondrial matrix protein groups detected. Related to Fig. 2B (analysis of
depth of coverage). Eight proteins in these groups that were not detected by RNA-Seq in
HEK293T cells (53) were not included in the analysis.
Table S8: Inner mitochondrial membrane protein complexes detected. Related to Figs.
2C-D.
Table S9: Column definitions.
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