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Affinity chromatography with an immobilized RNA enzyme

Abstract

M1 RNA, the catalytic subunit of Escherichia coli RNase P, has been covalently linked at its 3' terminus to agarose beads. Unlike M1 RNA, which is active in solution in the absence of the protein component (C5) of RNase P, the RNA linked to the beads is active only in the presence of C5 protein. Affinity chromatography of crude extracts of E. coli on a column prepared from the beads to which the RNA has been crosslinked results in the purification of C5 protein in a single step. The protein has been purified in this manner from cells that contain a plasmid, pINIIIR20, which includes the gene that codes for C5 protein. A 6-fold amplification of the expression of C5 protein is found in these cells after induction as compared to cells that do not harbor the plasmid.

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Affinity chromatography with an immobilized RNA enzyme

Author: Vioque Peña, Agustín; Altman, S.
Publisher: National Academy of Sciences
Year: 1986
Source: https://idus.us.es/bitstreams/45139b91-91f8-4e66-90b8-2e1b9c4b2215/download
P oc.
Na l.
Acad.
Sci.
USA
Vol.
83,
pp.
5904-5908,
Augus
1986
Biochemis y
A ini y
ch oma og aphy
wi h
an
immobilized
RNA
enzyme
(RNase
P/ca aly ic
RNA/ca aly ic
subuni
Ml
RNA/C5
p o ein)
AGUSTIN
VIOQUE
AND
SIDNEY
ALTMAN
Depa men
o
Biology,
Yale
Uni e si y,
New
Ha en,
CT
06520
Communica ed
by
Clemen
L.
Ma ke ,
May
5,
1986
ABSTRACT
Ml
RNA,
he
ca aly ic
subuni
o
Esche ichia
coli
RNase
P,
has
been
co alen ly
linked
a
i s
3'
e minus
o
aga ose
beads.
Unlike
Ml
RNA,
which
is
ac i e
in
solu ion
in
he
absence
o
he
p o ein
componen
(C5)
o
RNase
P,
he
RNA
linked
o
he
beads
is
ac i e
only
in
he
p esence
o
C5
p o ein.
A ini y
ch oma og aphy
o
c ude
ex ac s
o
E.
coli
on
a
column
p epa ed
om
he
beads
o
which
he
RNA
has
been
c osslinked
esul s
in
he
pu i ica ion
o
C5
p o ein
in
a
single
s ep.
The
p o ein
has
been
pu i ied
in
his
manne
om
cells
ha
con ain
a
plasmid,
pINIIIR20,
which
includes
he
gene
ha
codes
o
C5
p o ein.
A
6- old
ampli ica ion
o
he
exp ession
o
C5
p o ein
is
ound
in
hese
cells
a e
induc ion
as
compa ed
o
cells
ha
do
no
ha bo
he
plasmid.
A ini y
ch oma og aphy
has
been
used
o
pu i y
a
a ie y
o
biologically
impo an
molecules
such
as
enzymes,
co ac o s,
and
ho mone
ecep o s
(1,
2).
Immobilized
nucleic
acids
ha e
been
used
o
pu i y
o
iden i y
p o eins,
bo h
ca aly ic
and
nonca aly ic,
wi h
which
hey
in e ac .
Fo
example,
ibo-
somal
p o eins
ha
in e ac
wi h
5S and
5.8S
RNA
ha e
been
iden i ied
by
use
o
columns
made
wi h
hese
RNAs
(3-5).
We
now
epo
he
success ul
p epa a ion
o
a
column
made
wi h
an
immobilized
ca aly ic
RNA,
which
has
been
used
success ully
o
pu i y
he
p o ein
ha ,
oge he
wi h
he
RNA,
makes
up
Esche ichia
coli
RNase
P
in
i o.
RNase
P
is
he
enzyme
esponsible
o
ma u a ion
o
he
5'
e mini
o
RNA
p ecu so
molecules
in
i o
(6).
In
all
o ganisms
in es iga ed
hus
a ,
i
has
been
ound
ha
he
enzyme
is
composed
o
wo
kinds
o
subuni s,
one
o
which
is
RNA
and
one
o
which
is
p o ein,
and
bo h
o
which
a e
essen ial
o
ac i i y
in
i o
(7).
The
RNA
componen
(Ml
RNA)
o
E.
coli
RNase
P
and
o
some
o he
bac e ia
(8,
9)
can,
by
i sel ,
ca y
ou
he
ca aly ic
eac ion
unde
ce ain
condi ions
in
i o.
While
ample
quan i ies
o
hese
RNA
molecules
a e
a ailable,
s udies
o
he
holoenzyme
complex
om
E.
coli
ha e
been
hampe ed
by
he
di icul ies
in
he
pu i ica ion
o
su icien
quan i ies
o
he
pu e
p o ein
com-
ponen
(C5
p o ein)
o
biochemical
expe imen a ion.
The
gene
o
his
p o ein
( npA)
in
E.
coli
has
been
cloned
(10)
bu
does
no
o e exp ess
he
gene
p oduc
o
a
signi ican
deg ee.
We
ha e
inc eased
ou
yield
and
acili a ed
p epa a ion
o
C5
p o ein
by
using
a ini y
ch oma og aphy,
wi h
immobilized
Ml
RNA,
o
cell
ex ac s
p epa ed
om
E.
coli
cells
ha
ha bo
a
no el
subclone
o
he
cis on
and
con ain
he
npA
gene
adjacen
o
an
inducible,
s ong
p omo e .
In
addi ion
o
CS
p o ein
(M
13,700),
we
ha e
iden i ied
a
second
p o ein
(M
27,000)
ha
binds
s ongly
o
Ml
RNA.
METHODS
Bac e ial
S ains
and
Plasmids.
E.
coli
s ain
HB101
(F-,
hsdS20,
ecA13,
a a14,
p oAZ,
lacYI,
galk2,
psL20,
xyl-5,
m l-i,
supE44,
X-)
was
used
as
he
hos
cell
in
he
cloning
expe imen s.
E.
coli
s ain
MRE600
was
used
as
a
sou ce o
RNase
P.
Cells
we e
g own
in
he
ollowing
media
acco ding
o
he
equi ed
condi ions
o
each
expe imen :
LB
medium,
sup-
plemen ed
when
necessa y
wi h
ampicillin
(50
ug/ml);
M9
medium
supplemen ed
wi h
glucose
(2
mg/ml),
leucine
(50
pug/ml),
p oline
(100
gg/ml),
h eonine
(60
,.g/ml),
hiamine
(1
/ig/ml),
and,
when
necessa y,
ampicillin
(25
ug/ml).
Plasmids
pINIIIompAl
[gi
o
M.
Inouye
(11);
a
pBR322
de i a i e
ha
con ains
he
ipp
p omo e
and
he
inducible
lac
p omo e -ope a o
egion
ups eam
om
he
ompA
gene]
and
pFHC1008
[dona ed
by
F.
Hansen
(10)]
we e
used
in
he
cons uc ion
o
he
subclones.
Plasmid
pRR1,
ca ying
he
Ml
RNA
gene,
has
been
desc ibed
(12).
DNA
Manipula ions.
Plasmid
isola ion
and
ou ine
DNA
manipula ions
we e
pe o med
as
desc ibed
elsewhe e
(13).
Res ic ion
enzymes,
Klenow
agmen
o
E.
coli
DNA
polyme ase,
and
T4
DNA
ligase
we e
pu chased
om
New
England
Biolabs.
Cal
in es inal
phospha ase
was
pu chased
om
Boeh inge
Mannheim.
Pu i ica ion
o
Ml
RNA
and
RNase
P.
Ml
RNA
was
pu i ied
om
p epa a i e
polyac ylamide
gels
o
o al
RNA
om
E.
coli
HB101
ha
con ained
he
plasmid
pRR1
as
desc ibed
ea lie
(12).
Pa ially
pu i ied
RNase
P
was
ob ained
om
cellula
ex ac s
o
s ain
MRE600
a e
ch oma og aphy
on
DEAE-
Sephadex
and
p ecipi a ion
wi h
(NH4)2SO4
as
desc ibed
(14).
P epa a ion
o
P o ein
Labeled
wi h
35S.
Cells
we e
g own
o e nigh
in
M9
medium
a
370C,
washed
wice
wi h
M9
medium
om
which
sul a e
ions
we e
omi ed,
and
incuba ed
o
1
h
a
370C
in
he
sul a e- ee
medium.
[35S]Me hionine
(10
,uCi/ml;
1
Ci
=
37
GBq)
was
hen
added,
and
incuba ion
was
con inued
o
6
mo e
h .
Fo
s udies
o
he
induc ion
o
cells
ha
ca y
he
cons uc ed
pINIIIR20
exp ession
plas-
mid,
2
mM
isop opyl
3-D- hiogalac oside
(iP SGal)
was
added
a
he
same
ime
as
he
label.
Immobiliza ion
o
Ml
RNA.
P io
o
immobiliza ion,
an
aliquo
o
Ml
RNA
was
dephospho yla ed
and
labeled
a
he
5'
end
wi h
[y-32P]ATP
and
polynucleo ide
kinase
(P omega
Bio ec,
Madison,
WI)
as
desc ibed
(15).
The
labeled
RNA
(0.8
mg)
was
hen
oxidized
wi h
10
mM
sodium
pe ioda e
(16).
To
examine
he
e iciency
o
oxida ion,
he
abili y
o
he
pe ioda e- ea ed
Ml
RNA
o
ac
as
a
subs a e
in
an
RNA
ligase
condensa ion
wi h
cy idine
3',5'-[5'-32P]bisphospha e
was
es ed
(17).
We
concluded
ha
>95%
o
he
Ml
RNA
was
oxidized.
The
5'-end-labeled
and
oxidized
Ml
RNA
(0.8
mg;
4
x
106
cpm, Ce enko
adia ion)
was
coupled
o
0.5
ml
o
aga ose-
adipic
acid
dihyd azide
(P-L
Biochemicals)
as
desc ibed
(4),
washed
wi h
2
M
NaCl
un il
no
u he
adioac i i y
was
eleased,
and
packed
in
a
Pas eu
pipe e.
Abou
90%
o
he
RNA
was
ac ually
coupled
o
he
gel
as
es ima ed
om
he
adioac i i y
eco e ed
in
he
washes.
Abb e ia ions:
iP SGal,
isop opyl
/-D- hiogalac oside;
bp,
base
pai (s).
5904
The
publica ion
cos s
o
his
a icle
we e
de ayed
in
pa
by
page
cha ge
paymen .
This
a icle
mus
he e o e
be
he eby
ma ked
"ad e isemen "
in
acco dance
wi h
18
U.S.C.
§1734
solely
o
indica e
his
ac .
P oc.
Na l.
Acad.
Sci.
USA
83
(1986)
5905
Subcloning
o
he
npA
Gene
ha
Codes
o
C5
P o ein.
The
exp ession
plasmid
pINIIIR20
was
cons uc ed
o
inc ease
he
p oduc ion
o
C5
p o ein.
The
inducible
exp ession
ec o
pINIIIompA1
(11)
was
cu
a
he
unique
BamHI
si e,
and
he
s agge ed
ends
we e
illed
in
by
polyme iza ion
wi h
he
Klenow
agmen
o
E.
coli
polyme ase
I
and
dephospho yl-
a ed
wi h
cal
in es inal
phospha ase.
Plasmid
pFHC1008
(10),
which
con ains
pa
o
he
pmH
ope on
and
includes
he
comple e
sequence
o
pmH
( he
gene
o
ibosomal
p o ein
L34)
and
npA
( he
gene
o
C5
p o ein),
was
cu
a
he
unique
BssHII
and
A a
I
si es,
and
a
776-base-pai
(bp)
agmen
ha
con ained
he
pmH
and
npA
genes
was
pu i ied.
This
agmen
was
cu
wi h
Rsa
I
o
gi e
ou
agmen s
(538,
142,
67,
and
33
bp).
The
538-bp
agmen
con ained
mos
o
he
pmH
gene
and
he
comple e
npA
gene.
The
s agge ed
ends
we e
illed
wi h
he
Klenow
agmen ,
and
he
mix u e
o
agmen s
was
liga ed
o
he
linea ized
ec o
wi h
T4
DNA
ligase.
T ans o man s
we e
selec ed
by
ampicillin
esis ance,
and
hose
ca ying
he
538-bp
agmen
in
he
igh
o ien a ion
we e
iden i ied
by
es ic ion
analysis.
In
his
cons uc
he
pmH
gene
is
in
phase
wi h
he
coding
sequence
o
he
signal
pep ide
o
he
OmpA
p o ein
(11).
When
selec ion
o
ans o man s
was
ca ied
ou
in
LB
medium,
all
o
he
clones
ha
con ained
he
538-bp
agmen
had
he
agmen
inse ed
in
he
w ong
o ien a ion.
Howe e ,
when
selec ion
was
ca ied
ou
in
M9
medium,
he
igh
cons uc ion
was
ob ained.
This
esul
sugges s
ha
he
exp ession
o
he
ca boxyl- e minal-modi ied
L34
p o ein
does
no
pe mi
iabili y.
Leaky
induc ion
o
he
lac
gene
p omo e
by
chemical
con aminan s
in
LB
medium
(18)
is
a oided
in
minimal
medium.
No e
also
ha
E.
coli
s ain
HB101
ca ying
pINIIIR20
canno
g ow
in
he
p esence
o
2
mM
iP SGal.
Pu i ica ion
o
C5
P o ein.
Ex ac ion
o
RNAs.
The
RNAs
p esen
in
S30
ex ac s
o
in
RNase
P,
pa ially
pu i ied
a
leas
h ough
he
DEAE-Sephadex
s ep
(14),
we e
ex ac ed
wi h
LiCl/EDTA
by
he
me hod
o
Dijk
and
Li lechild
(19)
as
used
o
p epa a ion
o
ac i e
yeas
ibosomal
p o eins
(20).
(We
also
ha e
used
LiCl/EDTA
o
elu e
basic
p o eins
om
immobilized
RNA
as
is
desc ibed
below.)
One
olume
o
ex ac
was
mixed
wi h
2
olumes
o
10.5
M
LiCl,
and
EDTA
(pH
8.0,
adjus ed
wi h
NaOH)
was
added
o
a
concen a ion
o
10
mM.
The
mix
was
gen ly
agi a ed
o e nigh
a
4°C
and
cen i uged
a
100,000
x
g
o
10
h .
The
supe na an ,
con aining
he
p o eins,
was
dialyzed
agains
bu e
A
(50
mM
T is
HCl,
pH
7.4/10
mM
MgCl2/100
mM
NH4Cl/10
mM
2-me cap oe hanol).
A ini y
ch oma og aphy
on
immobilized
MI
RNA.
The
dialyzed
supe na an
om
he
p e ious
s ep
was
loaded
on
he
a ini y
column,
and
he
sample
was
eci cula ed
h ough
he
column
o e nigh
by
a
pe is al ic
pump.
The
column
was
hen
washed
and
elu ed
wi h
bu e
A
ha
con ained
di e en
concen a ions
o
NH4Cl
as
indica ed
in
he
legends
o
Figs.
2
and
3.
C5
p o ein
was
elu ed
in
he
inal
s ep
wi h
7
M
LiCl/10
mM
EDTA,
pH
8.0.
Elec opho esis
o
P o eins.
P o eins
we e
analyzed
on
0.1%
NaDodSO4/4
M
u ea/12.5%
ac ylamide
gels
by
he
me hod
o
Laemmli
(21).
To al
cellula
p o eins
we e
ana-
lyzed
om
a
cell
pelle
( om
0.5
ml
o
cul u e)
ha
was
boiled
o
3
min
in
loading
bu e
and
hen
loaded
di ec ly
on
he
gel.
O he
p o ein
ac ions
we e
p ecipi a ed
wi h
ichlo oace ic
acid
in
he
p esence
o
15
,ug
o
bo ine
se um
albumin,
when
necessa y,
be o e
boiling
in
loading
bu e
and
loading.
P o ein
concen a ions
we e
de e mined
by
he
me hod
o
Low y
e
al.
(22)
wi h
bo ine
se um
albumin
as
a
s anda d.
Assays
o
RNase
P
Ac i i y.
Recons i u ion
assays
we e
pe o med
by
he
di ec
mixing
me hod
(8)
in
50
mM
T is
HCl,
pH
7.4/10
mM
MgCl2/100
mM
NH4Cl.
PEG
(5%
w / ol)
was
added
whe e
indica ed.
Ml
RNA
ac i i y
was
assayed
in
50
mM
T is
HCl,
pH
7.4/100
mM
MgCl2/100
mM
NH4Cl/5%
PEG.
The
p ecu so
o
E.
coli
RNATY
was
used
as
subs a e
(23)
in
all
o
he
expe imen s
epo ed
he e.
All
incuba ions
we e
ca ied
ou
a
37°C
o
he
imes
indica ed.
The
eac ion
p oduc s
we e
analyzed
on
10%
(w / ol)
poly-
ac ylamide
gels
as
desc ibed
elsewhe e
(8),
and
he
amoun
o
p oduc
o med
was
es ima ed
by
scanning
densi ome y
o
au o adiog aphs.
When
immobilized
Ml
RNA
was
assayed,
i s
concen a ion
was
es ima ed
om
he
adioac i i y
o
i s
5'-end
label,
de e mined
by
scin illa ion
coun ing.
RESULTS
P ope ies
o
he
Ml
RNA
Column.
The
3'
e minus
o
Ml
RNA
can
be
al e ed
in
a ious
ways
wi h
li le
o
no
e ec
on
he
ca aly ic
ac i i y
o
he
RNA
(9,
24).
We
e i ied
(da a
no
shown)
ha
Ml
RNA
om
E.
coli,
oxidized
wi h
pe ioda e
o
c ea e
2'
and
3'
ke o
g oups,
has
simila
ac i i y
o
ha
o
in ac
Ml
RNA,
jus
as
Ma sh
and
Pace
(17)
ound
o
he
RNA
componen
o
Bacillus
sub ilis
RNase
P.
The
oxidized
Ml
RNA
was
coupled
h ough
a
dihyd azide
adipic
acid
space
o
aga ose
beads
as
desc ibed,
and
a
slu y
o
he
esul ing
ma e ial
was
es ed
o
RNase
P
ac i i y.
We
chose
he
pa icula
beads
and
space
o
educe
p oblems
o
s e ic
hind ance.
When
he
Ml
RNA-bead
complex
was
assayed
o
ac i i y
(Fig.
1),
he
ca aly ic
ac i i y
was
almos
ully
eco e ed
in
he
econs i u ion
assay
wi h
C5
p o ein
(lanes
5
and
6)
bu
was
almos
comple ely
los
when
es ed
unde
condi ions
whe e
he
ee
RNA
exhibi ed
ac i i y
by
i sel
(lanes
2
and
3).
No
ac i i y
was
obse ed
when
C5
p o ein
o
Ml
RNA
was
assayed
alone
in
bu e
con aining
10
mM
MgCl2.
Fu he mo e,
es ima es
o
ela i e
a es
o
clea age
we e
made
om
mo e
ex ensi e
kine ic
s udies
(da a
no
shown).
When
ee
and
immobilized
Ml
RNA
we e
assayed
in
he
p esence
o
C5
p o ein,
hey
had
abou
he
same
ac i i y.
Bu
abou
5%
o
he
expec ed
ac i i y
o
ee
Ml
RNA
was
eco e ed
when
he
slu y
o
immobilized
RNA
was
assayed
in
he
absence
o
C5
p o ein.
Howe e ,
when
he
slu y
was
analyzed
by
gel
elec opho esis,
abou
5%
o
he
RNA
an
as
ee
Ml
RNA
in
he
gel,
while
he
es
did
no
en e
he
gel.
F om
his
esul ,
we
in e
ha
a
small
amoun
o
Ml
RNA
was
leached
o
he
beads
and
could
accoun
o
he
ca aly ic
ac i i y
de ec ed
in
he
absence
o
p o ein.
Howe e ,
we
canno
ule
ou
he
possibili y
ha
his
small
amoun
o
1
2
3
5
-*
4
5
6
_
-p RNA-
IeRNAS
FIG.
1.
Compa ison
o
he
ac i i y
o
immobilized
Ml
RNA
wi h
ha
o
ee
oxidized
Ml
RNA.
Assays
we e
cam ed
ou
as
desc ibed
in
he
p esence
o
5%
PEG.
p RNA,
RNA,
and
5'
indica e
he
posi ions
o
he
subs a e
RNA
p ecu so
molecule
and
he
wo
clea age
p oduc s,
espec i ely.
Lanes:
1
and
4,
no
addi ion;
2,
10
ng
o
oxidized
Ml
RNA
assayed
o
15
min
in
bu e
ha
con ained
100
mM
MgCl2;
3,
10
ng
o
immobilized
Ml
RNA
assayed
as
in
lane
2;
5,
10
ng
o
oxidized
Ml
RNA
assayed
o
5
min
in
bu e
ha
con ained
10
mM
MgCl2
and
an
excess
o
pu i ied
C5
p o ein;
6,
10
ng
o
immobilized
Ml
RNA
assayed
as
in
lane
5.
Biochemis y:
Vioque
and
Al man
5906
Biochemis y:
Vioque
and
Al man
ac i i y
was,
in
ac ,
due
o
he
immobilized
RNA.
Analysis
o
he
slu y
a e
he
econs i u ion
assay
indica ed
ha
he
p esence
o
he
C5
p o ein
did
no
induce
he
elease
o
RNA
om
he
beads
(da a
no
shown).
The e o e,
he
ca aly ic
ac i i y
de ec ed
in
he
assay
in
he
p esence
o
C5
p o ein
was
due,
in
ac ,
o
he
coupled
RNA-bead
complex.
We
conclude
ha
immobiliza ion
o
he
3'
e minus
o
Ml
RNA
in e e es
wi h
a
c i ical
s ep
in
he
ac i a ion
o
he
enzyme,
in
he
absence
o
he
p o ein
co ac o .
Howe e ,
he
RNA
coupled
o
he
beads
appea s
o
e ain
he
desi ed
speci ici y
o
he
binding
o
C5
p o ein
so
ha
he
column
can
be
used
o
he
success ul
pu i ica ion
o
C5
p o ein.
To
analyze
he
condi ions
ha
allow
he
pu i ica ion
o
C5
p o ein
on
he
a ini y
column,
we
used
a
p o ein
mix u e
p epa ed
om
RNase
P
ha
had been
pa ially
pu i ied
h ough
he
DEAE-Sephadex
s ep
and
(NH4)2SO4
p ecipi a-
ion
as
desc ibed
by
S a k
e
al.
(14).
The
RNAs
p esen
in
his
p epa a ion
we e
ex ac ed
by
ea men
wi h
7
M
LiCl/10
mM
EDTA.
The
esul ing
p o ein
mix u e
was
essen ially
ee
o
RNA
(<1%,
as
de e mined
by
do ing
a
sample
on
aga ose
gel
ha
con ains
e hidium
b omide
and
isualizing
he
ma e ial
wi h
a
UV
ansillumina o ).
No
RNase
P
ac i i y
was
mani es ed
by
his
ma e ial
unless
exogenous
Ml
RNA
was
added.
The
C5
p o ein
in
he
p epa a ion
did
no
bind
o
DEAE-Sephadex
(da a
no
shown)
in
con as
o
he
holoenzyme,
which
does
bind
as
a
consequence
o
i s
RNA
con en .
These
esul s
con i med
ha
he
LiCI/EDTA
ex ac
was
ee
o
Ml
RNA,
and
he
C5
p o ein
con ained
in
i
was
s ill
ac i e
in
he
RNase
P
econs i u ion
assay.
Al hough
p o ein
ex ac s
o
B.
sub ilis
RNase
P
ha
ga e
RNase
P
ac i i y
in
he
econs i u ion
assay
ha e
been
made
using
ace ic
acid
o
emo e
RNA
(25),
his
me hod
has
no
yielded
p epa a ions
o
C5
p o ein
om
E.
coli
RNase
P
ha
a e
ac i e
in
econs i u ion
assays.
A
dialyzed
ex ac
o
RNase
P
om
which
he
RNA
had
been
emo ed
by
ea men
wi h
LiCl/EDTA
was
loaded
on
he
a ini y
column,
and
he
p o eins
ha
we e
elu ed
om
he
immobilized
RNA
a e
shown
in
Fig.
2.
The
posi ion
o
C5
p o ein
in
he
PAGE
analysis
o
he
elua es
is
shown
by
he
a ow
adjacen
o
lane
16.
(No e
ha
C5
p o ein
has
an
anomolous
elec opho e ic
mobili y.
I
mig a es
mo e
slowly
han
expec ed
om
i s
molecula
weigh .)
Op imized
condi-
ions
o
he
binding
o
his
p o ein
o
he
column
include
ecycling
o
he
load
sample
and
he
use
o
PEG
in
he
loading
bu e .
PEG
inc eases
binding
e iciency
by
enhancing
he
e ec i e
local
concen a ion
o
he
p o ein.
The
p o ein
composi ion
o
he
load
sample
and
he
low- h ough
ac ion
a e
shown
in
Fig.
2,
lanes
2
and
3.
The e
is
some
Msmea ing
o
hese
samples
because
o
he
p esence
o
PEG
in
he
bu e .
P o eins
in
subsequen
elua es
om
he
column
a e
shown
in
lanes
5-15.
Many
p o eins
we e
bound
o
he
column,
bu
mos
we e
elu ed
wi h
bu e
ha
con ained
0.37
M
NH4Cl
(lanes
5-8).
A
p o ein
o
appa en
M
27,000
bound
s ongly
o
he
column
bu
could
be
sepa a ed
om
CS
p o ein
by
elu ion
wi h
bu e
ha
con ained
0.7
M
NH4Cl
(lanes
11-13).
A e
his
elu ion,
only
C5
p o ein
emained
bound
o
he
column,
bu
i
could
be
elu ed
along
wi h
almos
all
ma e ial
ha
is
ac i e
in
he
RNase
P
econs i u ion
assay
by
7
M
LiCl/10
mM
EDTA
(lanes
14
and
15).
This
inal
elu ion
s ep
has
been
adap ed
success ully
om
he
me hod
used
o
sepa a e
ibosomal
p o eins
om
RNA
(19).
Each
ac ion
was
assayed
o
RNase
P
ac i i y
in
he
absence
and
p esence
o
Ml
RNA
in
bu e
ha
con ained
10
mM
MgCl2.
The
only
column
ac ion
exhibi ing
signi ican
ac i i y
in
he
p esence
o
added
Ml
RNA
was
he
one
co esponding
o
ha
seen
in
lane
14
o
Fig.
2
(LiCI/EDTA
wash).
The
p o ein
species
elu ed
om
he
column
ha
has
been
labeled
as
"C5
p o ein"
comig a es
wi h
ac i e
C5
p o ein
pu i ied
by
a
di e en
(and
less
e icien )
echnique
(8).
This
1
2 3
4
5
6
7
8 9
10
11
12
13
14
,5
16
i.
I
i
'a
..
.,
Al_
Fi2a
',.................
4.
4
9
FIG.
2.
Elec opho e ic
analysis
o
he
ac ions
elu ed
om
he
a ini y
column.
P o ein
ex ac ed
wi h
LiC1/EDTA
om
pa ially
pu i ied
RNase
P
(see
ex )
was
placed
in
bu e
A
ha
con ained
5%
PEG,
and
12
ml
(6
mg)
was
loaded
on
a
0.5-ml
column
con aining
700
,4g
o
bound
Ml
RNA.
The
sample
(lane
2)
was
eci cula ed
on
he
column
o
15
h
a
a
low
a e
o
6
ml/h .
The
low- h ough
ac ion
was
collec ed
(lane
3),
and
he
column
was
washed
in
succession
wi h
15
ml
o
bu e
A
ha
con ained
5%
PEG
(no
shown),
2
ml
o
bu e
A
(lane
4),
h ee
imes
wi h
0.6
ml
o
0.37
M
NH4Cl
in
bu e
A
(lanes
5-7),
h ee
imes
wi h
0.6
ml
o
0.5
M
NH4Cl
in
bu e
A
(lanes
8-10),
h ee
imes
wi h
0.6
ml
o
0.7
M
NH4Cl
in
bu e
A
(lanes
11-13),
and
wice
wi h
0.4
ml
o
7
M
LiCl/10
mM
EDTA
(lanes
14-15).
Lane
1
con ains
myoglobin
(M
17,200)
and
a
smalle
con aminan .
Lane
16
con ains
he
ollowing
molecula
weigh
ma ke s:
phospho ylase
B
(M
92,500),
bo ine
se um
albumin
(M
66,200),
o albumin
(M
45,000),
ca bonic
anhyd ase
(M
31,000),
soybean
ypsin
inhibi o
(M
21,500),
and
lysozyme
(M
14,400).
The
uppe mos
dense
band
in
lanes
2-15
is
he
bo ine
se um
albumin
used
as
ca ie
in
he
p epa a ion
o
he
sample.
Lanes
2
and
3
con ained
one- i h
as
much
sample
as
lanes
4-15.
The
a ow
nex
o
lane
16
indica es
he
posi ion
o
C5
p o ein.
The
gel
was
s ained
wi h
Coomassie
b illian
blue.
species,
elu ed
in
he
inal
s ep
(Fig.
2,
lane
14),
was
ac i e
in
he
econs i u ion
assay
o
RNase
P
ac i i y,
and
so
we
concluded
ha
i
is,
indeed,
C5
p o ein.
Howe e ,
a
species
wi h
simila
mobili y
in
he
gels,
was
elu ed
a
many
o
he
lowe
concen a ions
o
NH4Cl
bu
did
no
mani es
ac i i y
in
he
econs i u ion
assay
wi h
Ml
RNA.
The e
we e
many
basic
p o eins
in
addi ion
o
CS
p o ein
in
hese
elua es
ha
could
compe e
o
binding
si es
on
Ml
RNA.
I
is
also
possible
ha
he
C5
p o ein
in
hese
ac ions
was
i e e sibly
dena u ed.
We
ha e
no
eco e ed
ac i e
CS
p o ein
om
he
p o ein
elu ed
a
a
lowe
concen a ion
o
NH4Cl,
by
dialysis
agains
bu e
A,
o
by
ea men
o
hese
ac ions
wi h
LiCl/EDTA
p io
o
dialysis.
When
ac ions
ha
we e
elu ed
a
0.37
M
NH4Cl
we e
dialyzed
and
ecycled
h ough
he
column,
some
o
he
M
27,000
p o ein
and
he
appa en
C5
p o ein
we e
elu ed
a
highe
sal
concen a ions,
hough
mos
o
he
ma e ial
s ill
was
elu ed
a
0.37
M.
Vi ually
no
ac i e
CS
p o ein
was
eco e ed.
These
da a
indica e
ha
he
appa en
C5
p o ein
ha
was
elu ed
a
he
lowe
sal
con-
cen a ions
may
indeed
be
dena u ed
o
may
be
inhibi ed
in
he
econs i u ion
issay
by
he
concen a ions
o
o he
basic
p o eins,
including
he
M
27,000
p o ein,
which
a e
ela i ely
high
compa ed
o
hose
ound
in
c ude
ex ac s.
Twen y
g ams
o
E.
coli
yielded
abou
5.4
mg
o
LiCl
ex ac
and,
inally,
abou
5
,g
o
abou
15%
o
he
o al
C5
ac i e
p o ein
in
he
o iginal
7
M
LiCI/10
mM
EDTA
ex ac .
P oc.
Na l.
Acad
Sci.
USA
83
(1986)
P oc.
Na l.
Acad.
Sci.
USA
83
(1986)
5907
The
eco e y
o
ac i e
C5
p o ein
wi h
his
me hod
was
a
leas
h ee
imes
be e
han
ha
ob ained
by
p epa a i e
elec opho esis
o
he
same
amoun
o
s a ing
ma e ial
(14),
and
he
pu i ica ion
was
achie ed
in
less
han
hal
he
ime
needed
o
he
la e
me hod.
I
is
di icul
o
es ima e
accu a ely
he
ex en
o
eco e y
o
C5
p o ein
because
econs i u ed
RNase
P
ac i i y
depended
on
he
concen a-
ion
o
added
C5
p o ein
in
a
nonlinea
ashion
(unpublished
da a),
and
pu e
C5
p o ein
was
inac i a ed
on
dilu ion.
The
la e
p oblem
could
be
o e come,
in
pa ,
by
inclusion
o
PEG
in
he
dilu ion
bu e .
Thus,
ou
es ima es
o
o al
eco e ed
ac i i y
may
be
accu a e
only
wi hin
a
ac o
o
2.
I
one
assumes
ha
a
leas
one
C5
p o ein
molecule
can
bind
o
one
Ml
RNA
molecule,
he
capaci y
o
he
Ml
RNA
column
is
0.11
,ug
o
C5
p o ein
pe
Ag
o
Ml
RNA
a ailable
o
binding.
In
he
case
we
desc ibe,
he
heo e ical
capaci y
is
77
Ag
o
C5
p o ein.
The
only
limi a ion
in
scaling
up
his
p ocedu e
is
he
a ailabili y
o
Ml
RNA,
and
ha
is
no
longe
a
se ious
obs acle.
Ampli ica ion
o
C5
P o ein
in
Vi o.
To
enhance
he
yield
o
C5
p o ein
om
c ude
ex ac s
o
cells,
we
subcloned,
nex
o
a
s ong,
inducible
p omo e
in
pINIIlompAl,
he
gene
ha
codes
o
C5
p o ein
( npA)
and
he
adjacen
gene
ha
codes
o
he
ibosomal
p o ein
L34
( pmH)
om
pFHC1008.
C ude
ex ac s
we e
made
om
cells
ha
ha bo ed
he
new
ec o ,
pINIIIR20,
and om
he
pa en
cells
wi h
no
ec o .
These
ex ac s
we e
bo h
subjec ed
o
elec opho esis
o
analysis
o
he
p o ein
con en
and
also
we e
passed
o e
he
Ml
RNA
column.
The
p oduc ion
o
p o eins
in
cells
wi h
pINIIIR20,
a e
induc ion
wi h
iP SGal,
is
shown
in
Fig.
3,
lane
2.
Lane
1
shows
p o eins
om
an
ex ac
o
uninduced
cells.
No e
he
massi e
inc ease
in
he
p oduc ion
o
a
p o ein
ha
co e-
sponds
in
mobili y
o
L34,
he
gene
ha
is
adjacen
o
and
ups eam
om
npA,
he
gene
ha
codes
o
C5
p o ein.
The
uppe
a ow
in
lane
2
poin s
o
a
ain
mino
band,
unseen
in
1
23
A-I
0-
4
5
6
7
8
91011121314
45
31
-
21.5
-1
i.:
14.4
.-
$
FIG.
3.
Au o adiog am
o
he
elec opho e ic
analysis
o
p o eins
o
[5S]me hionine-labeled
E.
coli
s ain
HB101
ha
ca ies
pINIIIR20.
Lanes:
1,
uninduced
cells;
2,
cells
induced
wi h
2
mM
iP SGal;
3,
S30
ex ac
p epa ed
om
induced
cells;
4-14,
elu ion
pa e ns
om
he
immobilized
MI
RNA
column
o
he
S30
ex ac
shown
in
lane
3
a e
ex ac ion
o
RNAs
wi h
7
M
LiCl/10
mM
EDTA
(elu ion
was
done
as
in
Fig.
2,
bu
he
0.7
M
NH4Cl
washes
we e
omi ed);
4,
low- h ough
ac ion;
5,
bu e
A
con aining
5%
PEG
wash;
6,
bu e
A
wash;
7-9,
0.37
M
NH4Cl
washes;
10-12,
0.5
M
NH4Cl
washes;
13-14,7
M
LiCl/10
mM
EDTA
washes.
Gels
we e
d ied
and
exposed
o
24
h
(lanes
1-2),
1
wk
(lane
3),
o
4
wk
(lanes
4-14).
The
a ows
nex
o
lane
2
indica e
he
posi ions
o
he
L34
usion
p o ein
(lowe
a ow)
and
C5
p o ein
(uppe
a ow).
The
ha ch
ma ks
nex
o
lanes
2,
3,
and
4
show
he
posi ions
o
he
molecula
weigh
(X
10-3)
ma ke s
be ween
lanes
3
and
4.
The
a ow
nex
o
lane
14
indica es
he
posi ion
o
he
C5
p o ein.
No e
ha
ibosomal
p o ein
L34
is
no
p esen
in
he
p epa a ion
o
he
S30
ex ac
(lane
3)
om
he
o al
cell
p o ein
(lane
2).
he
uninduced
cells,
which
has
he
mobili y
o
C5
p o ein.
This
analysis
did
no
allow
us
o
es ima e
he
amoun
o
ampli ica ion
o
p oduc ion
o
C5
p o ein.
The e o e,
we
ea ed
he
c ude
ex ac
o
pINIIIR20
wi h
7
M
LiCl/10
mM
EDTA
o
emo e
RNA
and
used
he
esul ing
p o ein
in
econs i u ion
assays
o
RNase
P
ac i i y.
The
esul an
ac i i y
o
RNase
P
om
he
c ude
ex ac s
o
E.
coli
s ain
HB101
ha bo ing
plasmid
pINIIIR20
induced
wi h
iP SGal
is
abou
6- old
highe
han
he
ac i i y
in
he
ex ac
om
uninduced
cells.
We
p esumed,
he e o e,
ha
he
p oduc-
ion
o
C5
p o ein
in
he
induced
cells
is
a
leas
6- old
g ea e
han
in
uninduced
cells,
and
his
p esump ion
was
e i ied
by
expe imen s
wi h
adioac i ely
labeled
ex ac s.
When
an
S30
cell
ex ac ,
om
which
RNA
had
been
emo ed
wi h
7
M
LiCl/10
mM
EDTA
(Fig.
3,
lane
3),
o
induced
cells
ha bo ing
pINIIIR20
was
passed
o e
he
immobilized
Ml
RNA
column,
>80%
o
he
p o ein
ound
in
he
column
ac ion
elu ed
wi h
7
M
LiCl/10
mM
EDTA
(Fig.
3,
lane
13)
was
C5
p o ein,
as
judged
by
au o adiog aphy
o
ma e ial
labeled
wi h
35S.
The
yield
o
C5
p o ein
in
his
ac ion
is
4-
o
6- old
g ea e
han
ha
ound
in
ex ac s
o
uninduced
cells
as
de e mined
by
compa isons
o
he
eco -
e y
o
35S-labeled
C5
p o ein.
The
M
27,000
p o ein
was
no
appa en
in
he
ma e ial
elu ed
wi h
7
M
LiCl
om
he
column
ha
was
de i ed
om
he
induced
cells.
Ou
esul s
demon-
s a e
ha
i
is
possible
o
pu i y
a
e y
mino
p o ein
om
E.
coli
(abou
250
copies
pe
cell)
in
one
s ep
on
he
immobilized
Ml
RNA
column.
DISCUSSION
A ini y
ch oma og aphy
o
p o eins
on
immobilized
RNAs
has
been
used
as
an
analy ical
ool
o
de e mine
which
p o eins
in e ac
in
a
speci ic
manne
wi h
di e en
RNAs
(3-5).
We
ha e
used
his
me hod,
no
only
o
pu i y
p o eins
ha
bind
s ongly
o
Ml
RNA,
a
ca aly ic
mac omolecule,
bu
also
o
p epa e
hese
p o eins
in
amoun s
use ul
o
biochemical
expe imen a ion.
In
ac ,
we
ha e
been
able
o
pu i y
C5,
he
p o ein
componen
o
RNase
P,
in
a
single
ch oma og aphic
s ep
om
a
c ude
ex ac
o
E.
coli.
We
also
ha e
ound
ano he
p o ein
o
M
27,000
ha
binds
s ongly
o
Ml
RNA.
In
addi ion,
he
me hod
we
ha e
de eloped
allows
p o ein
pu i ica ion
o
be
achie ed
wi hou
he
use
o
dena u ing
agen s
such
as
NaDodSO4,
u ea,
o
ace ic
acid
o
o
lyophiliza ion.
Al hough
he
high
concen a ions
o
sal s
we
used
o
sepa a e
RNA
om
p o ein
in
he
ini ial
c ude
ex ac
and
in
he
column
elu ion
bu e s
in
gene al
will
a ec
he
e ia y
s uc u e
o
p o eins,
he
eco e ed
p o ein
is
in
a
"na i e"
s a e
(see
e .
19).
The
LiCl/EDTA
me hod
has
been
used
o
ex ac
yeas
ibosomal
p o eins
ha
a e
subsequen ly
able
o
econs i u e
unc ional
60S
yeas
ibo-
somal
subuni s
(20).
The
C5
p o ein
we
pu i ied
is
ac i e
in
he
econs i u ion
assay
o
RNase
P
ac i i y
and,
hus,
is
highly
sui able
o
u he
s udies
o
he
mechanism
o
ac ion
o
RNase
P.
A
p esen
we
do
no
know
i
he
M
27,000
p o ein
is
ela ed
o
he
unc ion
o
Ml
RNA
o
he
p ocessing
o
he
p ecu so
o
Ml
RNA
in
i o.
Al hough
he
size
o
he
M
27,000
p o ein
may
be
compa ible
wi h
ha
o
a
dime
o
C5
p o ein,
i
is
no
likely
ha
such
a
dime
su i es
boiling
in
NaDodSO4
o
elec opho esis
h ough
NaDodSO4
and
u ea,
bo h
p ocedu es
being
pa
o
ou
p o ocols.
In
addi ion,
he
M
27,000
p o ein
is
no
seen
in
he
inal
column
ac ions
o
35S-labeled
ex ac s
o
HB101
cells
ha
do
o
do
no
ha bo
pINIIIR20,
al hough
la ge
amoun s
o
C5
p o ein
a e
ob-
se ed.
This
obse a ion
indica es
ha
he
M
27,000
p o ein
lacks
me hionine
esidues
and,
he e o e,
is
un ela ed
o
C5
p o ein.
The
elu ion
om
he
a ini y
column
o
C5
p o ein
o e
a
wide
ange
o
sal
concen a ions
is
no
unexpec ed
because
Biochemis y:
Vioque
and
Al man
5908
Biochemis y:
Vioque
and
Al man
we
know
ha
Ml
RNA
can
exis
in
a
a ie y
o
con o ma-
ions,
some
o
which
may
p o ide
highe
speci ici y
o
binding
o
C5
p o ein
(and
M
27,000
p o ein)
han
o he s.
Howe e ,
he
amoun
o
ac i e
C5
p o ein
eco e ed
in
hese
ac ions
is
no
well
co ela ed
wi h
he
appa en
amoun
o
p o ein,
mos
o
he
ac i i y
being
eco e ed
in
he
inal
wash
wi h
7
M
LiCl/10
mM
EDTA.
A
his
poin
we
canno
say
o
ce ain
whe he
he
species
ha
comig a es
wi h
C5
p o ein
is
inac i e
o
modi ied
C5
p o ein,
which
binds
less
s ongly
o
Ml
RNA
han
does
na i e
C5
p o ein,
no
do
we
know
whe he
i s
ac i i y
is
simply
inhibi ed
by
he
p esence
o
basic
p o eins
ha
copu i y
wi h
i .
The
amoun
o
C5
p o ein
in
cellula
ex ac s
has
been
inc eased
by
subcloning
a
cis on
ha
con ains
he
gene
coding
o
his
p o ein
( npA)
om
he
plasmid
pFHC1008
o
a
si e
adjacen
o
an
inducible,
s ong
p omo e
in
he
plasmid
pINIIIompAl.
No mally,
npA
is
co ansc ibed
wi h
he
gene
o
ibosomal
p o ein
L34
( pmH)
and
wo
o he
p o eins
(10),
bu
no
signi ican
o e p oduc ion
o
he
npA
gene
p oduc
is
obse ed
in
cells
ha bo ing
pFHC1008,
al hough
L34
is
ampli ied
(10).
When
hese
wo
genes
a e
placed
adjacen
o
he
lpp
and
lac
p omo e s
in
pINIIIR20,
an
=6- old
ampli ica ion
o
C5
p o ein
is
obse ed,
as
judged
by
he
amoun
o
C5
eco e ed
a e
a ini y
ch oma og aphy.
Thus,
a
combina ion
o
he
no el
column
echnique
and
gene ic
enginee ing
has
led
o
a
signi ican
imp o emen
in
he
yield
and
e iciency
o
pu i ica ion
o
C5
p o ein.
In
cons uc ing
he
immobilized
RNA
column,
we
ook
ad an age
o
he
ac
ha
he
3'
e minus
o
Ml
RNA
can
be
al e ed
in
a ious
ways
wi hou
signi ican ly
diminishing
he
unc ion
o
he
molecule
(24).
Fu he mo e,
he
leng h
o
he
b idge
o
he
aga ose
beads
was
chosen
o
minimize
s e ic
p oblems
and,
hus,
we
an icipa ed
ha
he
immobilized
RNA
would
s ill
e ain
i s
ca aly ic
unc ion.
Howe e ,
ca aly ic
ac i i y
a
he
same
a e
as
shown
by
he
equi alen
amoun
o
ee
RNA
is
de ec ed
only
in
he
p esence
o
he
p o ein
co ac o .
This
esul
p omp s
he
specula ion
ha ,
o
he
RNA
o
unc ion
by
i sel ,
i
mus
ha e
some
deg ee
o
con o ma ional
lexibili y
a
i s
3'
e minus
ha
is
absen
when
i
is
co alen ly
linked
o
he
beads.
Con o ma ional
change,
such
as
dime iza ion
(26),
as
a
p elude
o
ca aly ic
unc ion
may
be
slowed
o
p e en ed
when
Ml
RNA
is
linked
o
he
beads.
Indeed,
some
immobilized
p o ein
enzymes
ha e
been
epo ed
o
unde go
con o ma ional
changes
10_-105
imes
mo e
slowly
han
do
he
ee
p o eins
(27).
Fo
he
immobilized
Ml
RNA
o
become
ac i e,
h ough
wha -
e e
con o ma ional
change
may
be
needed,
C5
p o ein
mus
be
p esen
as
an
essen ial
co ac o .
The
equi emen
o
a
p o ein
co ac o
in
his
eac ion
bea s
on
specula ion
ega d-
ing
ea ly
biochemical sys ems.
I
he
i s
enzymes
we e
composed
o
RNA
and
had
p ope ies
simila
o
hose
o
Ml
RNA,
immobiliza ion
on
he
in e io
o
p imi i e
cell
mem-
b anes
o
in
simple
o ganelles
would
ha e
c ea ed
immedia e
selec i e
p essu e
o
he
pa icipa ion
o
p o eins
in
enzy-
ma ic
eac ions.
The
p epa a ion
o
enzyma ically
ac i e
immobilized
RNA
may
also
be
o
p ac ical
signi icance
since
ca aly ically
ac i e
immobilized
p o eins
ha e
ound
wide-
sp ead
applica ions
(28).
Finally,
we
no e
ha
ac i e
RNase
P
can
be
econs i u ed
om
Ml
RNA
and
he
app op ia e
p o ein
componen s
om
HeLa
cells
(29)
and
B.
sub ilis
(8).
These
obse a ions
aise
he
possibili y
ha
he
a ini y-ch oma og aphy
p ocedu e
we
desc ibe
he e
may
be
use ul
in
pu i ying
he
p o ein
componen s
o
RNase
P
om
a
a ie y
o
o ganisms.
The
p ocedu e
also
may
be
adap ed
o
he
pu i ica ion
o
p o ein
co ac o s
ha
s imula e
o he
eac ions
known
o
be
ca alyzed
by
RNA
(30)
o
in
which
ibonucleop o eins
a e
in ima ely
in ol ed
(31).
We
hank
Donna
Wesolowski
o
pu i ying
Ml
RNA
and
ou
colleagues
o
aluable
ad ice
and
gi s
o
ma e ials.
A.V.
is
he
ecipien
o
a
long- e m
ellowship
om
he
Eu opean
Molecula
Biology
O ganiza ion.
This
wo k
was
suppo ed
by
g an s
om
he
Uni ed
S a es
Public
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and
he
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