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www.sciencemag.org/content/354/6311/aaf2786/suppl/DC1
Supplementary Materials for
Systems-level analysis of mechanisms regulating yeast metabolic flux Sean R. Hackett, Vito R. T. Zanotelli, Wenxin Xu, Jonathan Goya, Junyoung O. Park,
David H. Perlman, Patrick A. Gibney, David Botstein, John D. Storey, Joshua D. Rabinowitz*
*Corresponding author. Email: [email protected]
Published 28 October 2016, Science 354, aaf2786 (2016)
DOI: 10.1126/science.aaf2786
This PDF file includes:
Figs. S1 to S15 Tables S1 to S6 Captions for Tables S7 to S9 References
Other Supplementary Material for this manuscript includes the following: (available at www.sciencemag.org/content/354/6311/aaf2786/suppl/DC1)
Tables S7 to S9
http://www.sciencemag.org/content/%5bvol%5d/%5bissue%5d/%5bms.no.%5d/suppl/DC1 http://www.sciencemag.org/content/%5bvol%5d/%5bissue%5d/%5bms.no.%5d/suppl/DC1
Supplemental Tables
Pathway R ea
ct io
ns w
ith m
ea su
re d
en zy
m es
To ta
lp at
hw ay
re ac
tio ns
Fr ac
tio n
of re
ac tio
ns w
ith m
ea su
re d
en zy
m es
M ea
su re
d en
zy m
es
To ta
le nz
ym es
Fr ac
tio n
of m
ea su
re d
en zy
m es
Glycolysis / Gluconeogenesis 16 16 100% 17 18 94% Citrate cycle (TCA cycle) 12 12 100% 12 12 100% Biosynthesis of amino acids 73 83 88% 63 75 84% Purine metabolism 37 52 71% 28 41 68% Pyrimidine metabolism 27 39 69% 22 31 71% All reactions 346 524 66% 304 510 60%
Table S1: Proteomic coverage of enzymes in major metabolic pathways. For each pathway, we show both the fraction of reactions for which at least one isozyme was measured, as well as the total fraction of enzymes measured. Pathway annotations are based on KEGG.
58
# ye
as t
an no
ta tio
ns in
B R
E N
D A
# no
n- ye
as t
an no
ta tio
ns in
B R
E N
D A
R ea
ct io
ns R
eg ul
at or
C la
ss
A ce
to la
ct at
e Sy
nt ha
se (+
)A T
P 1
0 G
ol d
st an
da rd
A sp
ar ta
te K
in as
e (-
)T hr
eo ni
ne (u
ltr as
en si
tiv e)
7 34
G ol
d st
an da
rd G
lu ta
m at
e 5-
K in
as e
(- )P
ro lin
e 1
23 G
ol d
st an
da rd
H om
oc itr
at e
Sy nt
ha se
(- )L
ys in
e 8
18 G
ol d
st an
da rd
PR PP
A m
id ot
ra ns
fe ra
se (-
)A M
P 1
20 G
ol d
st an
da rd
A de
ny la
te K
in as
e (-
)A M
P 1
15 Pr
ev io
us ly
va lid
at ed
in ye
as t
C ys
ta th
io ni
ne B
et a-
Sy nt
ha se
(+ )S
A M
2 20
Pr ev
io us
ly va
lid at
ed in
ye as
t G
ua ny
la te
K in
as e
(- )G
M P
5 2
Pr ev
io us
ly va
lid at
ed in
ye as
t Tr
eh al
os e-
ph os
ph at
e Sy
nt ha
se (-
)I no
rg an
ic Ph
os ph
at e
4 4
Pr ev
io us
ly va
lid at
ed in
ye as
t O
rn ith
in e
C ar
ba m
oy ltr
an sf
er as
e (-
)A la
ni ne
0 4
B io
ch em
ic al
ly va
lid at
ed Py
ru va
te D
ec ar
bo xy
la se
(- )P
he ny
lp yr
uv at
e 0
2 B
io ch
em ic
al ly
va lid
at ed
Py ru
va te
K in
as e
(- )I
so ci
tr at
e 0
7 B
io ch
em ic
al ly
va lid
at ed
(c itr
at e)
A de
ny la
te K
in as
e (+
)T hr
eo ni
ne 0
1 N
ot te
st ed
A ld
ol as
e (-
)A M
P 0
7 N
ot te
st ed
A sp
ar ta
te C
ar ba
m oy
ltr an
sf er
as e
(+ )U
T P
0 2
N ot
te st
ed C
itr at
e to
C is
-a co
ni ta
te (-
)I so
ci tr
at e
0 2
N ot
te st
ed C
ys ta
th io
ni ne
G am
m a-
ly as
e (-
)A la
ni ne
0 2
N ot
te st
ed Fu
m ar
at e
(- )C
itr at
e 0
3 N
ot te
st ed
G lu
ta m
at e
D eh
yd ro
ge na
se (N
A D
P) (-
)Q ui
no lin
at e
0 4
N ot
te st
ed H
om oc
itr at
e Sy
nt ha
se (-
)Q ui
no lin
at e
1 0
N ot
te st
ed M
al ic
E nz
ym e
(N A
D )
(- )A
M P
0 4
N ot
te st
ed Ph
os ph
of ru
ct ok
in as
e (+
)F ru
ct os
e 1,
6- bi
sp ho
sp ha
te 0
8 N
ot te
st ed
Ph os
ph og
ly ce
ra te
D eh
yd ro
ge na
se (+
)M et
hi on
in e
0 1
N ot
te st
ed Ph
os ph
og ly
ce ra
te M
ut as
e (-
)3 -P
ho sp
ho gl
yc er
at e
1 2
N ot
te st
ed S7
P Ph
os ph
of ru
ct ok
in as
e (-
)P ho
sp ho
en ol
py ru
va te
0 29
N ot
te st
ed Tr
eh al
os e-
ph os
ph at
as e
(+ )F
6P 0
1 N
ot te
st ed
Tr eh
al os
e- ph
os ph
at as
e (+
)T re
ha lo
se 0
1 N
ot te
st ed
U T
P G
1P U
ri dy
ltr an
sf er
as e
(- )U
D P-
G lu
co se
0 11
N ot
te st
ed A
T P-
Ph os
ph or
ib os
yl tr
an sf
er as
e (-
)A M
P 0
4 B
io ch
em ic
al ly
in va
lid at
ed D
A H
P Sy
nt ha
se (-
)P E
P 0
2 B
io ch
em ic
al ly
in va
lid at
ed D
A H
P Sy
nt ha
se (-
)P he
ny lp
yr uv
at e
0 3
B io
ch em
ic al
ly in
va lid
at ed
G lu
co se
6- ph
os ph
at e
D eh
yd ro
ge na
se (-
)A M
P 0
3 B
io ch
em ic
al ly
in va
lid at
ed G
lu co
se 6-
ph os
ph at
e D
eh yd
ro ge
na se
(- )P
E P
0 3
B io
ch em
ic al
ly in
va lid
at ed
Ph os
ph og
lu co
na te
D eh
yd ro
ge na
se (+
)A sp
ar ta
te 0
1 B
io ch
em ic
al ly
in va
lid at
ed Py
ru va
te K
in as
e (-
)A M
P 0
7 B
io ch
em ic
al ly
in va
lid at
ed
Ta bl
e S2
: B
es t-
su pp
or te
d pr
ed ic
tio ns
of ph
ys io
lo gi
ca l
re gu
la to
rs of
ye as
t m
et ab
ol is
m ba
se d
on SI
M M
E R
(N =
35 ).
T he
12 re
gu la
to rs
lis te
d ab
ov e
th e
lin e
ha ve
be en
bi oc
he m
ic al
ly va
lid at
ed in
S. ce
re vi
si ae
.
59
1-by-1 testing of whether each metabolite as a regulator improves regulation-free model (based on fit only, no Bayesian analysis)
Does not improve Signi